Citrus Sinensis ID: 042225

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-----
Protein Sequence
MLKRRHPLSFGPLTEEDDLELRLGPRTVDSSHIAFQGRSINGIEDVPKVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQPPASI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccEEEEcccccccccccccccccHHHHHHHHHHHHcccccccccccccccccEEcccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHEccccccccccccccccccccccccccccccccHHHccccHHccccEEEccccccccEEccccccccEcccccHHHHHHHHHHHHHcccccHHHHHccHccccEEEcccccccccc
Coil and Loop (DISEMBL)
mlkrrhplsfgplteeddlelrlgprtvdsshiafqgrsingiedvpkvsndkekcrvcesrngmvVVGEVRFTCGICldtmkeesstkcghvfcKSCIVDAIrlqgrcptcrtrmsvRSIRRiffpqlqppasi
Flexible Loop (DISEMBL)
mlkrrhplsfgplteeddlelrlgprtvdsshiafqgrsingiedvpkvsndkekcrvcesrngmvvvgeVRFTCGICLDTMkeesstkcghVFCKSCIVdairlqgrcptcrtrmsvrsirriffpqlqppasi
Low Complexity Region (SEG)
MLKRRHPLSFGPLTEEDDLELRLGPRTVDSSHIAFQGRSINGIEDVPKVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQPPASI
Disordered region (IsUnstruct)
********************************IAFQG*SINGI**********EKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP********
Disordered Region (DISOPRED)
*************************************************************************TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI***********
Disordered Region (DISEMBL)
MLKRRHPLSFGPLTEEDDLELRLGPRTVDSSHIAFQGRSINGIEDVPKVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQPPASI
Disordered Region (DISPRO)
******PLSFGPLTEEDDLELRLG********************DVPKVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQP****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLKRRHPLSFGPLTEEDDLELRLGPRTVDSSHIAFQGRSINGIEDVPKVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQPPASI
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	135	2.2.26 [Sep-21-2011]
Q00940	295	Peroxisome biogenesis fac	N/A	no	0.318	0.145	0.465	6e-07
Q06554	1556	Uncharacterized ATP-depen	yes	no	0.4	0.034	0.370	1e-06
Q61510	634	E3 ubiquitin/ISG15 ligase	yes	no	0.377	0.080	0.426	1e-06
Q7YR34	539	Tripartite motif-containi	yes	no	0.414	0.103	0.372	2e-06
Q12899	539	Tripartite motif-containi	yes	no	0.414	0.103	0.372	2e-06
Q6LFN2	1103	RING finger protein PFF01	no	no	0.407	0.049	0.285	2e-06
Q8NHY2	731	E3 ubiquitin-protein liga	no	no	0.296	0.054	0.475	3e-06
Q9R1A8	733	E3 ubiquitin-protein liga	no	no	0.296	0.054	0.475	3e-06
Q62191	470	E3 ubiquitin-protein liga	no	no	0.362	0.104	0.48	3e-06
Q7YRV4	469	E3 ubiquitin-protein liga	no	no	0.362	0.104	0.44	3e-06

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

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 29/43 (67%)

Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRM 116
           TC +CL  MK+ S  +CGHVFC  C++D ++ +  CP CR +M
Sbjct: 244 TCMLCLSPMKDPSCGECGHVFCWKCVLDWVKERQECPLCRAKM 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 = 52.0 bits (123), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 20/54 (37%), Positives = 30/54 (55%)

Query: 73   FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF 126
             +C ICL  ++  +  KCGH FCKSCI+  +R   +CP 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|Q61510|TRI25_MOUSE E3 ubiquitin/ISG15 ligase TRIM25 OS=Mus musculus GN=Trim25 PE=2 SV=2

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/61 (42%), Positives = 33/61 (54%), Gaps = 10/61 (16%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG---RCPTCRTRMSVRSIRRIFFPQL 129
            +C +CL+  KE  +T CGH FC SC+ +   +QG   RCP CR    VR       PQL
Sbjct: 11  LSCSVCLELFKEPVTTPCGHNFCMSCLDETWVVQGPPYRCPQCRKVYQVR-------PQL 63

Query: 130 Q 130
           Q
Sbjct: 64  Q 64

Functions as an ubiquitin E3 ligase and as an ISG15 E3 ligase. Involved in innate immune defense against viruses by mediating ubiquitination of DDX58. Mediates 'Lys-63'-linked polyubiquitination of the DDX58 N-terminal CARD-like region which is crucial for triggering the cytosolic signal transduction that leads to the production of interferons in response to viral infection. Promotes ISGylation of 14-3-3 sigma (SFN), an adapter protein implicated in the regulation of a large spectrum signaling pathway. Mediates estrogen action in various target organs.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: n

EC: 3

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

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR---CPTCRTRMSVRSIRRIF 125
           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 = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR---CPTCRTRMSVRSIRRIF 125
           E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct: 11  EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDVRPISGSRPVCPLCKKPFKKENIRPVW 69

Homo sapiens (taxid: 9606)

>sp|Q6LFN2|ZNRF1_PLAF7 RING finger protein PFF0165c OS=Plasmodium falciparum (isolate 3D7) GN=PFF0165c PE=2 SV=1

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 72   RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIRRIFF 126
            R  C +C++  +     KCGH++C +CI + ++ + R CP C+     + +++IF 
Sbjct: 1047 RLICSVCMENFRNYIIIKCGHIYCNNCIFNNLKTRNRKCPQCKVPFDKKDLQKIFL 1102

Plasmodium falciparum (isolate 3D7) (taxid: 36329)

>sp|Q8NHY2|RFWD2_HUMAN E3 ubiquitin-protein ligase RFWD2 OS=Homo sapiens GN=RFWD2 PE=1 SV=1

 Score = 50.8 bits (120), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 19/40 (47%), Positives = 23/40 (57%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTC 112
           F C IC D ++E   TKCGH FC  CI  ++    RCP C
Sbjct: 134 FVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKC 173

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Involved in JUN ubiquitination and degradation. Directly involved in p53 (TP53) ubiquitination and degradation, thereby abolishing p53-dependent transcription and apoptosis. Ubiquitinates p53 independently of MDM2 or RCHY1. Probably mediates E3 ubiquitin ligase activity by functioning as the essential RING domain subunit of larger E3 complexes. In contrast, it does not constitute the catalytic RING subunit in the DCX DET1-COP1 complex that negatively regulates JUN, the ubiquitin ligase activity being mediated by RBX1.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9R1A8|RFWD2_MOUSE E3 ubiquitin-protein ligase RFWD2 OS=Mus musculus GN=Rfwd2 PE=1 SV=2

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 19/40 (47%), Positives = 23/40 (57%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTC 112
           F C IC D ++E   TKCGH FC  CI  ++    RCP C
Sbjct: 136 FVCPICFDMIEEAYMTKCGHSFCYKCIHQSLEDNNRCPKC 175

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Involved in JUN ubiquitination and degradation. Directly involved in p53 (TP53) ubiquitination and degradation, thereby abolishing p53-dependent transcription and apoptosis. Ubiquitinates p53 independently of MDM2 or RCHY1. Probably mediates E3 ubiquitin ligase activity by functioning as the essential RING domain subunit of larger E3 complexes. In contrast, it does not constitute the catalytic RING subunit in the DCX DET1-COP1 complex that negatively regulates JUN, the ubiquitin ligase activity being mediated by RBX1.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q62191|RO52_MOUSE E3 ubiquitin-protein ligase TRIM21 OS=Mus musculus GN=Trim21 PE=1 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSVRSIR 122
           TC ICLD M E  S +CGH FCK CI +  +  G  CP CR +  +R++R
Sbjct: 19  TCSICLDPMVEPMSIECGHCFCKECIFEVGKNGGSSCPECRQQFLLRNLR 68

E3 ubiquitin-protein ligase whose activity is dependent on E2 enzymes, UBE2D1, UBE2D2, UBE2E1 and UBE2E2. Forms a ubiquitin ligase complex in cooperation with the E2 UBE2D2 that is used not only for the ubiquitination of USP4 and IKBKB but also for its self-ubiquitination. Component of cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes such as SCF(SKP2)-like complexes. A TRIM21-containing SCF(SKP2)-like complex is shown to mediate ubiquitination of CDKN1B ('Thr-187' phosphorylated-form), thereby promoting its degradation by the proteasome. Monoubiquitinates IKBKB that will negatively regulates Tax-induced NF-kappa-B signaling. Negatively regulates IFN-beta production post-pathogen recognition by polyubiquitin-mediated degradation of IRF3. Mediates the ubiquitin-mediated proteasomal degradation of IgG1 heavy chain, which is linked to the VCP-mediated ER-associated degradation (ERAD) pathway. Promotes IRF8 ubiquitination, which enhanced the ability of IRF8 to stimulate cytokine genes transcription in macrophages. Plays a role in the regulation of the cell cycle progression. Enhances the decapping activity of DCP2. Exists as a ribonucleoprotein particle present in all mammalian cells studied and composed of a single polypeptide and one of four small RNA molecules. At least two isoforms are present in nucleated and red blood cells, and tissue specific differences in RO/SSA proteins have been identified. The common feature of these proteins is their ability to bind HY RNAs.2.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7YRV4|RO52_BOVIN E3 ubiquitin-protein ligase TRIM21 OS=Bos taurus GN=TRIM21 PE=2 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIR 122
           TC ICLD M E  S +CGH FC+ CI +  +  G  CP CR    ++++R
Sbjct: 15  TCSICLDPMVEPMSIECGHSFCQECISEVGKEGGSVCPVCRRHFLLQNLR 64

E3 ubiquitin-protein ligase whose activity is dependent on E2 enzymes, UBE2D1, UBE2D2, UBE2E1 and UBE2E2. Forms a ubiquitin ligase complex in cooperation with the E2 UBE2D2 that is used not only for the ubiquitination of USP4 and IKBKB but also for its self-ubiquitination. Component of cullin-RING-based SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes such as SCF(SKP2)-like complexes. A TRIM21-containing SCF(SKP2)-like complex is shown to mediate ubiquitination of CDKN1B ('Thr-187' phosphorylated-form), thereby promoting its degradation by the proteasome. Monoubiquitinates IKBKB that will negatively regulates Tax-induced NF-kappa-B signaling. Negatively regulates IFN-beta production post-pathogen recognition by polyubiquitin-mediated degradation of IRF3. Mediates the ubiquitin-mediated proteasomal degradation of IgG1 heavy chain, which is linked to the VCP-mediated ER-associated degradation (ERAD) pathway. Promotes IRF8 ubiquitination, which enhanced the ability of IRF8 to stimulate cytokine genes transcription in macrophages. Plays a role in the regulation of the cell cycle progression. Enhances the decapping activity of DCP2. Exists as a ribonucleoprotein particle present in all mammalian cells studied and composed of a single polypeptide and one of four small RNA molecules. At least two isoforms are present in nucleated and red blood cells, and tissue specific differences in RO/SSA proteins have been identified. The common feature of these proteins is their ability to bind HY RNAs.2.

Bos taurus (taxid: 9913)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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	135
116784892	231	unknown [Picea sitchensis] gi|224284637|	0.851	0.497	0.405	1e-19
116781725	203	unknown [Picea sitchensis]	0.422	0.280	0.578	5e-14
294462707	205	unknown [Picea sitchensis]	0.807	0.531	0.338	4e-13
224075260	242	predicted protein [Populus trichocarpa]	0.422	0.235	0.596	1e-12
217075410	242	unknown [Medicago truncatula] gi|3884945	0.407	0.227	0.563	3e-12
217070974	247	unknown [Medicago truncatula]	0.407	0.222	0.563	3e-12
224132232	213	predicted protein [Populus trichocarpa]	0.429	0.272	0.551	6e-12
224065401	209	predicted protein [Populus trichocarpa]	0.429	0.277	0.551	6e-12
15231414	182	RING/U-box domain-containing protein [Ar	0.444	0.329	0.516	7e-12
224053707	252	predicted protein [Populus trichocarpa]	0.407	0.218	0.563	7e-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 =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 58/143 (40%), Positives = 80/143 (55%), Gaps = 28/143 (19%)

Query: 12  PLTEEDDLELRLGPRTVDSSHIAF-------QGR--------------------SINGIE 44
           P+ +E+DLELRLGP    S+H+          GR                    S +G E
Sbjct: 86  PVIKEEDLELRLGPGGT-SAHVGVVHIPSLRNGRPERVRIQPVTIVPPIVPINISDDGEE 144

Query: 45  DVPKVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR 104
           +V K    ++      S N  V V EV+ TC IC+D+MKEE+ST CGH+FC+SCI+ AI+
Sbjct: 145 EVQKHVKKRKHGHPSNSNNLPVEVKEVKLTCAICMDSMKEETSTICGHIFCRSCIMSAIQ 204

Query: 105 LQGRCPTCRTRMSVRSIRRIFFP 127
            Q +CPTCR ++S+ +I RIF P
Sbjct: 205 FQKKCPTCRRKLSMANIHRIFLP 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 = 82.4 bits (202), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 33/57 (57%), Positives = 44/57 (77%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF 126
           EV+ TC IC+ TM+EE+ST CGH+FCK CI +AI L  RCPTCR ++++ 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|294462707|gb|ADE76898.1| unknown [Picea sitchensis]

 Score = 79.3 bits (194), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 43/127 (33%), Positives = 76/127 (59%), Gaps = 18/127 (14%)

Query: 17  DDLELRLGP----------RTVDSSHIAFQGRSINGIEDVPKVSNDKEKCR-----VCES 61
           +DLEL++GP          R++ + + + + R  +   D+  ++   ++C+     V + 
Sbjct: 76  EDLELQVGPAGTRMPLGRVRSLKNRNRSCE-RKTSSCRDLVDLTTSNDECQLNSSMVSKK 134

Query: 62  RNGMVVVG--EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR 119
           R   +  G  E++ +C IC+D MKEE++T CGHVFCK CIV AI +  +CP+CR +++++
Sbjct: 135 RKPALSTGVKEIKLSCAICMDKMKEETTTICGHVFCKKCIVRAIEVYKQCPSCRKKLTMK 194

Query: 120 SIRRIFF 126
           SI RI+ 
Sbjct: 195 SIHRIYI 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 = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/57 (59%), Positives = 41/57 (71%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQL 129
           F C IC+D MKE +STKCGHVFCKSCI  A+ +Q +CPTCR +   +SI RIF P  
Sbjct: 185 FCCPICMDEMKEATSTKCGHVFCKSCIEKALAVQKKCPTCRMKCIAKSIFRIFLPAF 241

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 = 76.6 bits (187), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 41/55 (74%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
           FTC IC+  M EE ST+CGH+FCKSCI  AI  Q +CPTCR +++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 = 76.3 bits (186), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 41/55 (74%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
           FTC IC+  M EE ST+CGH+FCKSCI  AI  Q +CPTCR +++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 = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 42/58 (72%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
           E  F C ICL  + EE STKCGH+FCK+CI DAI+ Q +CPTCR 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|224065401|ref|XP_002301799.1| predicted protein [Populus trichocarpa] gi|222843525|gb|EEE81072.1| predicted protein [Populus trichocarpa]

 Score = 75.5 bits (184), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 42/58 (72%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
           E  F C ICL  + EE STKCGH+FCK+CI DAI+ Q +CPTCR R++ + + R+F P
Sbjct: 149 EPTFNCPICLCPLVEEMSTKCGHIFCKACISDAIKRQAKCPTCRKRVTTKELIRVFLP 206

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 = 7e-12,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 44/60 (73%)

Query: 68  VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
           V E +F+C ICL    +E STKCGH+FCK CI +A+ LQ +CPTCR +++V+ + R+F P
Sbjct: 120 VEEPKFSCPICLCPFTQEVSTKCGHIFCKKCIKNALSLQAKCPTCRKKITVKDLIRVFLP 179

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 75.5 bits (184), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 41/55 (74%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
           F C IC+D ++E +STKCGHVFCK+CI  A+ +Q +CPTCR +   +SI RIF P
Sbjct: 195 FRCPICMDELQEATSTKCGHVFCKNCIKKALAVQKKCPTCRMKCRAKSIYRIFLP 249

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	135
TAIR|locus:2098505	182	AT3G07200 [Arabidopsis thalian	0.762	0.565	0.401	3.3e-15
TAIR|locus:505006682	203	AT5G48655 [Arabidopsis thalian	0.525	0.349	0.478	6.9e-15
FB|FBgn0037384	319	dgrn "degringolade" [Drosophil	0.414	0.175	0.448	7e-10
ZFIN|ZDB-GENE-030131-5243	336	rnf2 "ring finger protein 2" [	0.355	0.142	0.490	1.3e-08
UNIPROTKB|F1ND52	190	RNF4 "Uncharacterized protein"	0.385	0.273	0.423	2.6e-08
UNIPROTKB|F1NLH3	196	RNF4 "Uncharacterized protein"	0.385	0.265	0.423	2.6e-08
UNIPROTKB|G4NE71	448	MGG_00145 "Uncharacterized pro	0.407	0.122	0.418	4.8e-08
MGI|MGI:106657	470	Trim21 "tripartite motif-conta	0.362	0.104	0.48	6.6e-08
UNIPROTKB|A2AE50	122	TRIM26 "Tripartite motif-conta	0.414	0.459	0.372	6.8e-08
UNIPROTKB|A2AE51	159	TRIM26 "Tripartite motif-conta	0.414	0.352	0.372	6.8e-08

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

 Score = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 43/107 (40%), Positives = 61/107 (57%)

Query:    22 RLGPRTVDSSHIAFQGRSINGIEDVPKVSN-DKEKCRVCESRNGMVVVGEVRFTCGICLD 80
             R G + VD    A   RS     D   V + +  K R  +S+     V E +F+C ICL 
Sbjct:    76 RRGSQVVDVES-AGANRSTRRRSDQTSVDSVELNKPR--KSKAVAPPVEEPKFSCPICLC 132

Query:    81 TMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
                +E STKCGH+FCK CI +A+ LQ +CPTCR +++V+ + R+F P
Sbjct:   133 PFTQEVSTKCGHIFCKKCIKNALSLQAKCPTCRKKITVKDLIRVFLP 179

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 34/71 (47%), Positives = 45/71 (63%)

Query:    57 RVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRM 116
             RV  S+       E +FTC IC+    EE STKCGH+FCK CI  AI  QG+CPTCR ++
Sbjct:   130 RVSRSKAPAPPPEEPKFTCPICMCPFTEEMSTKCGHIFCKGCIKMAISRQGKCPTCRKKV 189

Query:   117 SVRSIRRIFFP 127
             + + + R+F P
Sbjct:   190 TAKELIRVFLP 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 = 147 (56.8 bits), Expect = 7.0e-10, P = 7.0e-10
 Identities = 26/58 (44%), Positives = 37/58 (63%)

Query:    70 EVRFTCGICLDTM--KEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF 125
             E  + C IC+D++  +E  STKCGHVFC+ CI  AIR   +CP 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

ZFIN|ZDB-GENE-030131-5243 rnf2 "ring finger protein 2" [Danio rerio (taxid:7955)]

 Score = 122 (48.0 bits), Expect = 1.3e-08, Sum P(2) = 1.3e-08
 Identities = 25/51 (49%), Positives = 33/51 (64%)

Query:    75 CGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGR-CPTCRTRM-SVRSIR 122
             C ICLD +K   +TK C H FC  CI+ A+R   + CPTCR ++ S RS+R
Sbjct:    51 CPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 101

GO:0008270 "zinc ion binding" evidence=IEA

GO:0033339 "pectoral fin development" evidence=IMP

GO:0003682 "chromatin binding" evidence=ISS

GO:0016604 "nuclear body" evidence=ISS

GO:0009948 "anterior/posterior axis specification" evidence=ISS

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0000278 "mitotic cell cycle" evidence=ISS

GO:0035102 "PRC1 complex" evidence=ISS

GO:0071339 "MLL1 complex" evidence=ISS

GO:0016874 "ligase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 25/59 (42%), Positives = 35/59 (59%)

Query:    74 TCGICLDTMKE--ES-----STKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF 125
             +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 = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 25/59 (42%), Positives = 35/59 (59%)

Query:    74 TCGICLDTMKE--ES-----STKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF 125
             +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 = 133 (51.9 bits), Expect = 4.8e-08, P = 4.8e-08
 Identities = 23/55 (41%), Positives = 35/55 (63%)

Query:    67 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSI 121
             + 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 = 132 (51.5 bits), Expect = 6.6e-08, P = 6.6e-08
 Identities = 24/50 (48%), Positives = 31/50 (62%)

Query:    74 TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIR 122
             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 = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 22/59 (37%), Positives = 32/59 (54%)

Query:    70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR---CPTCRTRMSVRSIRRIF 125
             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 = 123 (48.4 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 22/59 (37%), Positives = 32/59 (54%)

Query:    70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR---CPTCRTRMSVRSIRRIF 125
             E   TC ICLD +++  +  CGHVFC+SC  D   + G    CP C+      +IR ++
Sbjct:    11 EEEVTCSICLDYLRDPVTIDCGHVFCRSCTTDVRPISGSRPVCPLCKKPFKKENIRPVW 69

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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	135
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-08
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	5e-07
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	6e-07
COG5574	271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	7e-07
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	2e-05
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-05
smart00184	40	smart00184, RING, Ring finger	6e-05
COG5152	259	COG5152, COG5152, Uncharacterized conserved protei	7e-05
PLN03208	193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	2e-04
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	0.001
pfam13445	55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	0.001
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	0.003

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

 Score = 47.4 bits (113), Expect = 1e-08
 Identities = 17/46 (36%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 73  FTCGICLDTMKEESS---TKCGHVFCKSCIVDAIRLQGRCPTCRTR 115
             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 = 46.7 bits (111), Expect = 3e-08
 Identities = 19/44 (43%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 72  RFTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGRCPTCRT 114
              C ICLD +++    T CGHVFC+ CI+  ++ + +CP CRT
Sbjct: 2   ELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 46.9 bits (111), Expect = 5e-07
 Identities = 16/44 (36%), Positives = 19/44 (43%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCR 113
           +    C IC D       T C H FC  CI   +  Q +CP 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|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 = 43.2 bits (102), Expect = 6e-07
 Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 74  TCGICLDTMKEESST-KCGHVFCKSCIVDAIRL-QGRCPTCRT 114
            C ICL+  +E      CGHVFC+SCI   ++  +  CP CRT
Sbjct: 1   ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43

Length = 45

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

 Score = 46.0 bits (109), Expect = 7e-07
 Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 60  ESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ--GRCPTCRTRMS 117
             +NG+  +    + C +CL+  +  S T CGH+FC SC++ +   +    CP CR ++ 
Sbjct: 203 SKKNGLPFIPLADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262

Query: 118 VRSI 121
            + +
Sbjct: 263 PKKV 266

Length = 271

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

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 16/39 (41%), Positives = 18/39 (46%)

Query: 75  CGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCR 113
           C IC   +     T CGH FC  CI   +  Q  CP CR
Sbjct: 28  CRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

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

 Score = 39.0 bits (91), Expect = 2e-05
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 75  CGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGR-CPTC 112
           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|214546 smart00184, RING, Ring finger

 Score = 37.9 bits (88), Expect = 6e-05
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 75  CGICLDTMKEES-STKCGHVFCKSCIVDAIRLQG-RCPTC 112
           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

>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 = 7e-05
 Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 60  ESRNGMVVVG---EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRM 116
           E     V+ G   ++ F CGIC    +    T+CGH FC  C +   +    C  C    
Sbjct: 181 EYEEAPVISGPGEKIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240

Length = 259

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 16/78 (20%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCI----------------VDAIRLQGRCPTCRTRM 116
           F C ICLD +++   T CGH+FC  CI                 D  R   +CP C++ +
Sbjct: 19  FDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78

Query: 117 SVRSIRRIFFPQLQPPAS 134
           S  ++  I+    + P S
Sbjct: 79  SEATLVPIYGRGQKAPQS 96

Length = 193

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

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 11/63 (17%)

Query: 75  CGICLDTMKEESS--------TKCGHVFCKSCIVDAIRLQGRCPTCRTR-MSVRSIRRIF 125
           C IC++ + ++          + C HVFC  CI    + +  CP CRT  +SV   R  F
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVIKSR--F 234

Query: 126 FPQ 128
           F +
Sbjct: 235 FTK 237

Length = 238

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

 Score = 34.2 bits (79), Expect = 0.001
 Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 6/46 (13%)

Query: 72  RFTCGICLDTMKEES----STKCGHVFCKSCIVD--AIRLQGRCPT 111
            F C I  + M +E        CGHV+ +  +        + +CP 
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|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 33.9 bits (78), Expect = 0.003
 Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 13/53 (24%)

Query: 74  TCGICLDTMKEESST-------------KCGHVFCKSCIVDAIRLQGRCPTCR 113
            C IC +                     +CGH F   CI   ++ +  CP CR
Sbjct: 21  VCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	135
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.58
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.57
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.49
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.43
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.41
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.39
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.32
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.29
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.29
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.25
PHA02929	238	N1R/p28-like protein; Provisional	99.21
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	99.16
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.13
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	99.12
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	99.12
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	99.08
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.05
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	99.0
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	98.96
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.94
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.94
PF14634	44	zf-RING_5: zinc-RING finger domain	98.91
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.91
PHA02926	242	zinc finger-like protein; Provisional	98.89
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	98.81
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	98.8
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.71
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.69
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.66
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.66
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.59
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.48
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.44
COG5152	259	Uncharacterized conserved protein, contains RING a	98.41
KOG2660	331	consensus Locus-specific chromosome binding protei	98.26
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.22
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.17
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	98.08
KOG0297	391	consensus TNF receptor-associated factor [Signal t	98.06
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.03
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.0
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.91
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.9
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.89
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.82
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.82
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.73
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.73
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.71
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	97.69
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.68
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.66
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.63
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	97.55
PF04641	260	Rtf2: Rtf2 RING-finger	97.47
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.45
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.41
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.33
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.18
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.18
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	97.18
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.02
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.9
KOG4367	699	consensus Predicted Zn-finger protein [Function un	96.48
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	96.47
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.42
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	96.25
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.17
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.1
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.09
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.03
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	96.03
KOG4739	233	consensus Uncharacterized protein involved in syna	95.99
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	95.99
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.77
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.71
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.69
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.68
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.52
KOG4445	368	consensus Uncharacterized conserved protein, conta	95.34
KOG3002	299	consensus Zn finger protein [General function pred	95.09
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.95
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	94.79
PHA02825	162	LAP/PHD finger-like protein; Provisional	94.55
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	94.38
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	94.27
COG5109	396	Uncharacterized conserved protein, contains RING Z	94.27
PHA02862	156	5L protein; Provisional	94.26
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	94.15
PHA03096	284	p28-like protein; Provisional	93.76
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	93.4
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.88
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	92.86
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	92.76
KOG1940	276	consensus Zn-finger protein [General function pred	92.68
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	92.41
KOG3039	303	consensus Uncharacterized conserved protein [Funct	92.24
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	91.9
KOG3899	381	consensus Uncharacterized conserved protein [Funct	91.8
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	91.76
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	91.12
KOG3113	293	consensus Uncharacterized conserved protein [Funct	90.99
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	90.97
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	90.82
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	90.77
KOG0825	1134	consensus PHD Zn-finger protein [General function	86.84
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	86.62
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	86.39
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	85.34
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	85.13
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	84.68
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	84.17
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	83.74
KOG0289	506	consensus mRNA splicing factor [General function p	81.89
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	80.41

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

Probab=99.58  E-value=2.2e-15  Score=110.17  Aligned_cols=64  Identities=30%  Similarity=0.745  Sum_probs=57.9

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC---CCCccccccccccCceeecCCCCCCC
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVRSIRRIFFPQLQPP  132 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~~~~~~~~~~~  132 (135)
                      ....+.|.||++..++||++.|||.|||.||.+|+..+   +.||+|+..+..+.|+++|-++...+
T Consensus        44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG~~~~  110 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRGSKKP  110 (230)
T ss_pred             CCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccCCCCC
Confidence            45689999999999999999999999999999999843   56999999999999999999987544

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.57  E-value=3.9e-15  Score=106.94  Aligned_cols=64  Identities=31%  Similarity=0.729  Sum_probs=55.7

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc----------------CCCCccccccccccCceeecCCCCCCC
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL----------------QGRCPTCRTRMSVRSIRRIFFPQLQPP  132 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~----------------~~~CP~Cr~~~~~~~~~~~~~~~~~~~  132 (135)
                      ..+.+.|+||++.+.+|+.++|||.||+.||..|+..                ...||+||..+...+++++|..+...+
T Consensus        15 ~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygrg~~~~   94 (193)
T PLN03208         15 SGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGRGQKAP   94 (193)
T ss_pred             CCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeeccCCCCC
Confidence            4457889999999999999999999999999999752                247999999999999999998776443

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

Probab=99.49  E-value=1.4e-14  Score=102.16  Aligned_cols=58  Identities=47%  Similarity=1.075  Sum_probs=53.0

Q ss_pred             CCccceeeccccCccC--cEEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           69 GEVRFTCGICLDTMKE--ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~--p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      .+..+.|+||++.+.+  |+.+.|||+||+.||...++....||+|++.+..+++++|||
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            4467999999998886  466899999999999999999999999999999999999996

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

Probab=99.43  E-value=1.1e-13  Score=76.83  Aligned_cols=38  Identities=45%  Similarity=1.047  Sum_probs=30.7

Q ss_pred             eeccccCccCcEEcCCCCcccHHhHHHHHhcC----CCCccc
Q 042225           75 CGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ----GRCPTC  112 (135)
Q Consensus        75 C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~----~~CP~C  112 (135)
                      |+||+++|.+|++++|||+||..||.+|++..    ..||.|
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            89999999999999999999999999999844    368887

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

Probab=99.41  E-value=1.3e-13  Score=103.64  Aligned_cols=57  Identities=32%  Similarity=0.760  Sum_probs=52.0

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeec
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ......|.+|++...+|..++|||.||+.||.+|...+..||+||..+...+++-++
T Consensus       236 ~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi~Lr  292 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVICLR  292 (293)
T ss_pred             CCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcceeeec
Confidence            345688999999999999999999999999999999999999999999998887654

>smart00504 Ubox Modified RING finger domain

Probab=99.39  E-value=3.7e-13  Score=80.64  Aligned_cols=52  Identities=19%  Similarity=0.331  Sum_probs=48.9

Q ss_pred             ceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           73 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        73 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      +.|+||.+.+.+|+.++|||+||+.||..|++....||.|+..+..++++++
T Consensus         2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~   53 (63)
T smart00504        2 FLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPN   53 (63)
T ss_pred             cCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeC
Confidence            5799999999999999999999999999999988899999999988888876

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

>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=99.32  E-value=1.1e-12  Score=71.70  Aligned_cols=38  Identities=45%  Similarity=1.156  Sum_probs=33.8

Q ss_pred             eeccccCccCc-EEcCCCCcccHHhHHHHHhcCCCCccc
Q 042225           75 CGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGRCPTC  112 (135)
Q Consensus        75 C~IC~~~~~~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~C  112 (135)
                      |+||++.+.+| +.++|||.||+.|+.+|++....||+|
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 689999999999999999998899987

>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=99.29  E-value=2.2e-12  Score=74.19  Aligned_cols=46  Identities=28%  Similarity=0.857  Sum_probs=41.4

Q ss_pred             cceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCcccccccc
Q 042225           72 RFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      +..|.||++...+.+.++|||. ||..|+.+|++....||+||+++.
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            5679999999999999999999 999999999998899999999875

...

>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=99.29  E-value=1.1e-12  Score=73.40  Aligned_cols=40  Identities=40%  Similarity=1.013  Sum_probs=35.2

Q ss_pred             eeeccccCcc---CcEEcCCCCcccHHhHHHHHhcCCCCcccc
Q 042225           74 TCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQGRCPTCR  113 (135)
Q Consensus        74 ~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr  113 (135)
                      .|+||++.+.   ..+.++|||.||.+|+.+|++...+||+||
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            5999999885   357789999999999999999999999997

...

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.25  E-value=4.1e-12  Score=100.67  Aligned_cols=59  Identities=29%  Similarity=0.633  Sum_probs=51.6

Q ss_pred             CCCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeec
Q 042225           67 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        67 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ..+...+.|+||.+.+.+|+.++|||.||..|+..|+.....||+|+..+....+...+
T Consensus        21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~   79 (397)
T TIGR00599        21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNW   79 (397)
T ss_pred             cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccch
Confidence            34667889999999999999999999999999999999888899999998766665443

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.21  E-value=1.1e-11  Score=92.33  Aligned_cols=49  Identities=31%  Similarity=0.735  Sum_probs=42.0

Q ss_pred             CccceeeccccCccCc--------EEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           70 EVRFTCGICLDTMKEE--------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p--------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      ..+..|+||++.+.++        +.++|||.||..||.+|++...+||+||..+..
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            3467899999987653        456899999999999999999999999998873

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

Probab=99.16  E-value=2.7e-11  Score=75.00  Aligned_cols=55  Identities=22%  Similarity=0.280  Sum_probs=45.6

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHhc-CCCCccccccccccCceeec
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      +.+.|+|+.+++.+|+.+++||+|++.+|..|+.. ...||.++..+...++.+++
T Consensus         3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~   58 (73)
T PF04564_consen    3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNR   58 (73)
T ss_dssp             GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-H
T ss_pred             cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECH
Confidence            57899999999999999999999999999999998 78999999999998888763

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 ....

>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=99.13  E-value=4.3e-11  Score=65.80  Aligned_cols=38  Identities=34%  Similarity=0.998  Sum_probs=34.7

Q ss_pred             eeccccCccCcE-EcCCCCcccHHhHHHHHh--cCCCCccc
Q 042225           75 CGICLDTMKEES-STKCGHVFCKSCIVDAIR--LQGRCPTC  112 (135)
Q Consensus        75 C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~--~~~~CP~C  112 (135)
                      |+||++.+.+++ .++|||.||..|+.+|++  ....||.|
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            899999999998 899999999999999999  45679987

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 ....

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

Probab=99.12  E-value=3.3e-11  Score=96.83  Aligned_cols=63  Identities=29%  Similarity=0.753  Sum_probs=56.6

Q ss_pred             cceeeccccCccCcEEcCCCCcccHHhHHHHHhcC-----CCCccccccccccCceeecCCCCCCCCC
Q 042225           72 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-----GRCPTCRTRMSVRSIRRIFFPQLQPPAS  134 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-----~~CP~Cr~~~~~~~~~~~~~~~~~~~~~  134 (135)
                      +..||||++...-|..+.|||.||..||..++...     ..||+|+..+..++|.++++.+.|.+++
T Consensus       186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv~~e~~qkke~  253 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPVFIEDDQKKEE  253 (513)
T ss_pred             CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeeeeeccccccHH
Confidence            78899999999999999999999999999998844     4799999999999999999988776653

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

Probab=99.12  E-value=8.4e-12  Score=95.96  Aligned_cols=57  Identities=28%  Similarity=0.682  Sum_probs=52.3

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      .+...++|-||+++|..|+.++|+|+||..||..++..+..||.|+..+.+.+++..
T Consensus        19 ~lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n   75 (442)
T KOG0287|consen   19 TLDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNN   75 (442)
T ss_pred             hhHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhh
Confidence            456788999999999999999999999999999999999999999999998877654

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

Probab=99.08  E-value=5.6e-11  Score=88.64  Aligned_cols=52  Identities=31%  Similarity=0.783  Sum_probs=47.4

Q ss_pred             CccceeeccccCccCcEEcCCCCcccHHhHHH-HHhcCCC-CccccccccccCc
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVD-AIRLQGR-CPTCRTRMSVRSI  121 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~-~~~~~~~-CP~Cr~~~~~~~~  121 (135)
                      ..+++|.||++....|..++|||.||+.||.. |-+.+.. ||+||+.+..+++
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            56899999999999999999999999999999 8777765 9999999987777

>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=99.05  E-value=1.7e-10  Score=63.67  Aligned_cols=43  Identities=44%  Similarity=1.065  Sum_probs=36.7

Q ss_pred             eeeccccCccCcEEcC-CCCcccHHhHHHHHhc-CCCCccccccc
Q 042225           74 TCGICLDTMKEESSTK-CGHVFCKSCIVDAIRL-QGRCPTCRTRM  116 (135)
Q Consensus        74 ~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~  116 (135)
                      .|+||++.+.+++.+. |||.||..|+..|+.. ...||.|+..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            3899999997776665 9999999999999987 67899998753

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

Probab=99.00  E-value=1.2e-10  Score=88.13  Aligned_cols=55  Identities=31%  Similarity=0.632  Sum_probs=49.1

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCce
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~  122 (135)
                      .+...++|-||...+..|..++|||+||..||.+++..+..||+||.......++
T Consensus        21 ~LDs~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr   75 (391)
T COG5432          21 GLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLR   75 (391)
T ss_pred             cchhHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHhhhcc
Confidence            3556788999999999999999999999999999999999999999988765444

>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=98.96  E-value=5.8e-10  Score=69.01  Aligned_cols=40  Identities=33%  Similarity=0.906  Sum_probs=33.4

Q ss_pred             eeeccccCccCc-------------EEcCCCCcccHHhHHHHHhcCCCCcccc
Q 042225           74 TCGICLDTMKEE-------------SSTKCGHVFCKSCIVDAIRLQGRCPTCR  113 (135)
Q Consensus        74 ~C~IC~~~~~~p-------------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr  113 (135)
                      .|+||++.+.++             ....|||.||..||.+|++...+||+||
T Consensus        21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            399999988332             3458999999999999999999999997

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 ....

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

Probab=98.94  E-value=5.3e-10  Score=62.22  Aligned_cols=30  Identities=37%  Similarity=0.926  Sum_probs=21.4

Q ss_pred             eeccccCccC----cEEcCCCCcccHHhHHHHHhc
Q 042225           75 CGICLDTMKE----ESSTKCGHVFCKSCIVDAIRL  105 (135)
Q Consensus        75 C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~  105 (135)
                      |+||.+ +.+    |+.|+|||+||.+|+.++.+.
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 877    899999999999999999884

>smart00184 RING Ring finger

Probab=98.94  E-value=9.1e-10  Score=58.68  Aligned_cols=38  Identities=42%  Similarity=1.106  Sum_probs=34.2

Q ss_pred             eeccccCccCcEEcCCCCcccHHhHHHHHh-cCCCCccc
Q 042225           75 CGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGRCPTC  112 (135)
Q Consensus        75 C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~C  112 (135)
                      |+||++...+++.++|||.||..|+..|++ ....||.|
T Consensus         1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999988999999999999999999998 55679987

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)

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.91  E-value=9.2e-10  Score=61.56  Aligned_cols=41  Identities=34%  Similarity=0.976  Sum_probs=34.8

Q ss_pred             eeeccccCcc---CcEEcCCCCcccHHhHHHHHhcCCCCccccc
Q 042225           74 TCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQGRCPTCRT  114 (135)
Q Consensus        74 ~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~  114 (135)
                      .|++|++.+.   .+..++|||+||..|+..+......||+|++
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            3899999882   4678999999999999998856678999974

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

Probab=98.91  E-value=3.3e-10  Score=94.64  Aligned_cols=56  Identities=32%  Similarity=0.828  Sum_probs=51.5

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHh-cCCCCccccccccccCceeecC
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      .-+.|++|...+.+.+.+.|||.||..|+...+. .+..||.|...|..+|+.+||+
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            4678999999999999999999999999999887 4578999999999999999985

>PHA02926 zinc finger-like protein; Provisional

Probab=98.89  E-value=1e-09  Score=80.38  Aligned_cols=50  Identities=34%  Similarity=0.749  Sum_probs=39.8

Q ss_pred             CCccceeeccccCccC---------cEEcCCCCcccHHhHHHHHhcC------CCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKE---------ESSTKCGHVFCKSCIVDAIRLQ------GRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~---------p~~~~CgH~fc~~Ci~~~~~~~------~~CP~Cr~~~~~  118 (135)
                      .+.+..|+||++...+         ++..+|+|.||..||..|.+..      .+||.||..+..
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            4456789999997643         2456999999999999999843      459999998763

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

Probab=98.81  E-value=2.6e-09  Score=83.25  Aligned_cols=46  Identities=28%  Similarity=0.660  Sum_probs=39.6

Q ss_pred             ceeeccccCccCc---EEcCCCCcccHHhHHHHHhcCC-CCccccccccc
Q 042225           73 FTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSV  118 (135)
Q Consensus        73 ~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~  118 (135)
                      ..|+||++.|.+.   ..|||+|.||..||+.|+...+ .||+|+..+..
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            4899999999864   5689999999999999998764 59999987754

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

Probab=98.80  E-value=4e-09  Score=82.30  Aligned_cols=49  Identities=31%  Similarity=0.693  Sum_probs=42.3

Q ss_pred             CCccceeeccccCcc-C------------cEEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           69 GEVRFTCGICLDTMK-E------------ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~-~------------p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ..++..|.||++.+. .            |..++|||.+|.+|+..|+..+.+||.||.++.
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            457889999999743 2            367899999999999999999999999999854

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

Probab=98.71  E-value=2.6e-09  Score=63.73  Aligned_cols=53  Identities=40%  Similarity=0.868  Sum_probs=27.6

Q ss_pred             CccceeeccccCccCcEE-cCCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           70 EVRFTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      ++.++|++|.+.+.+|+. ..|.|.||..|+...+.  ..||+|..+.-..|++-+
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            346789999999999975 58999999999976444  459999999888877643

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.69  E-value=1.3e-08  Score=78.24  Aligned_cols=57  Identities=30%  Similarity=0.656  Sum_probs=44.2

Q ss_pred             cceeeccccC-ccCcE----EcCCCCcccHHhHHHHHh-cCCCCccccccccccCceeecCCC
Q 042225           72 RFTCGICLDT-MKEES----STKCGHVFCKSCIVDAIR-LQGRCPTCRTRMSVRSIRRIFFPQ  128 (135)
Q Consensus        72 ~~~C~IC~~~-~~~p~----~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~~~~~~~~  128 (135)
                      +..||+|... +.+|.    ..+|||.||.+|+...+. ....||.|+..+..+.+....|..
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            4679999983 33432    227999999999999765 446899999999998887776654

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).

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

Probab=98.66  E-value=1.9e-08  Score=76.68  Aligned_cols=46  Identities=26%  Similarity=0.735  Sum_probs=39.9

Q ss_pred             cceeeccccCccCc---EEcCCCCcccHHhHHHHHh-cCCCCcccccccc
Q 042225           72 RFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIR-LQGRCPTCRTRMS  117 (135)
Q Consensus        72 ~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~  117 (135)
                      ...|+||+..+.+.   +.+||.|.||..|+..|+. .+..||+||..+.
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP  372 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP  372 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence            36799999988743   6789999999999999998 6789999998875

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

Probab=98.66  E-value=1.3e-08  Score=84.31  Aligned_cols=52  Identities=33%  Similarity=0.659  Sum_probs=45.6

Q ss_pred             CccceeeccccCccC-----cEEcCCCCcccHHhHHHHHhcCCCCccccccccccCc
Q 042225           70 EVRFTCGICLDTMKE-----ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSI  121 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~  121 (135)
                      ..+..|.||.+.+..     +..++|||.||..|+..|++.+.+||.||..+.....
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~~  345 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDYVL  345 (543)
T ss_pred             hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhcccc
Confidence            347889999999998     7899999999999999999999999999996654443

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

Probab=98.59  E-value=1.5e-08  Score=75.91  Aligned_cols=47  Identities=36%  Similarity=0.853  Sum_probs=41.5

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRT  114 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~  114 (135)
                      ...+.+.|+||++.|.+|..++|||.||..|+..++.....||.||.
T Consensus         9 ~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            34567889999999999989999999999999999885568999993

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

Probab=98.48  E-value=1.7e-07  Score=59.23  Aligned_cols=48  Identities=31%  Similarity=0.715  Sum_probs=36.8

Q ss_pred             cceeeccccCccC------------c-EEcCCCCcccHHhHHHHHhc---CCCCcccccccccc
Q 042225           72 RFTCGICLDTMKE------------E-SSTKCGHVFCKSCIVDAIRL---QGRCPTCRTRMSVR  119 (135)
Q Consensus        72 ~~~C~IC~~~~~~------------p-~~~~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~~~  119 (135)
                      +..|.||...|..            | +.-.|+|.||..||.+|+..   +..||+||..+..+
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            5568888877662            2 22379999999999999995   35899999987643

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

Probab=98.44  E-value=1.1e-07  Score=75.74  Aligned_cols=58  Identities=24%  Similarity=0.572  Sum_probs=49.9

Q ss_pred             cCCCCcCCCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           61 SRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        61 ~~~~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      +.......+..++.|.||+..+.+|++++|||.||..||.+.+.....||.||..+..
T Consensus        73 ~~~s~~~~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   73 ALLSGPEEIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             hhhccCccccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            3344444567899999999999999999999999999999988888899999988864

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

Probab=98.41  E-value=1.6e-07  Score=67.80  Aligned_cols=47  Identities=30%  Similarity=0.784  Sum_probs=42.3

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      -.+.|.||...+..|+.+.|||.||..|..+-++....|-+|.+...
T Consensus       195 IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         195 IPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             CceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence            45789999999999999999999999999988888889999987654

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

Probab=98.26  E-value=2.1e-07  Score=71.69  Aligned_cols=52  Identities=31%  Similarity=0.673  Sum_probs=45.9

Q ss_pred             CCCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCcccccccccc
Q 042225           68 VGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR  119 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  119 (135)
                      .....+.|.+|..+|.+++++ .|-|+||++||..++.....||.|...+...
T Consensus        11 ~~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   11 ELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             hcccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            456788999999999998765 7999999999999999999999998887654

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

Probab=98.24  E-value=1e-06  Score=68.56  Aligned_cols=55  Identities=25%  Similarity=0.646  Sum_probs=46.9

Q ss_pred             CccceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      +....|.||+...++.+.+||.|. .|..|.+...-+...||+||.++..  +..++.
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~--ll~i~~  343 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE--LLEIYV  343 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHh--hheecc
Confidence            447789999999999999999997 8999999887778899999999864  555544

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

Probab=98.24  E-value=3.2e-07  Score=69.71  Aligned_cols=111  Identities=18%  Similarity=0.291  Sum_probs=70.3

Q ss_pred             CCcCCCCCCCCCccCCCcccccCCCcccCCCCccCCCCCcccccCCCCCCchhhhhhcccCCCCcCCCCccceeeccccC
Q 042225            2 LKRRHPLSFGPLTEEDDLELRLGPRTVDSSHIAFQGRSINGIEDVPKVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDT   81 (135)
Q Consensus         2 ~~~~~~~~~~p~~~~~d~e~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~   81 (135)
                      ++-...+.+.|.+-.+-.++.--.-+.|......+...-.+.........  ..   ............-.+.|-||..+
T Consensus       176 ~r~~~~~d~qpDicKdykeTgycg~gdSckFlh~r~DyK~GWqi~~e~d~--~k---e~~~~~~~D~~~~Pf~c~icr~~  250 (313)
T KOG1813|consen  176 TRAGERIDYQPDICKDYKETGYCGYGDSCKFLHDRSDYKAGWQIEFEWDS--AK---EKKRVKIEDIELLPFKCFICRKY  250 (313)
T ss_pred             hcccceeecCchhhhhhHhhCcccccchhhhhhhhhhccccceeehhhhc--cc---cccceecCCcccCCccccccccc
Confidence            44556677777777776666555555555555554443322221111111  11   11111122123345679999999


Q ss_pred             ccCcEEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           82 MKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        82 ~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      |.+||++.|||.||..|-..-++....|.+|.+...
T Consensus       251 f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  251 FYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             cccchhhcCCceeehhhhccccccCCcceecccccc
Confidence            999999999999999999888888889999977654

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

Probab=98.22  E-value=4.9e-07  Score=68.93  Aligned_cols=49  Identities=27%  Similarity=0.505  Sum_probs=43.0

Q ss_pred             ceeeccccCccCcEEcCCCCcccHHhHHHHHhcCC-CCccccccccccCc
Q 042225           73 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSVRSI  121 (135)
Q Consensus        73 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~  121 (135)
                      -.|+||+....-|+.+.|+|.||.-||....+..+ +|++||.++...-+
T Consensus         8 ~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i~   57 (324)
T KOG0824|consen    8 KECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTID   57 (324)
T ss_pred             CcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcchh
Confidence            45999999999999999999999999998887665 59999999986544

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

Probab=98.17  E-value=4.3e-07  Score=52.39  Aligned_cols=46  Identities=30%  Similarity=0.795  Sum_probs=40.2

Q ss_pred             cceeeccccCccCcEEcCCCCc-ccHHhHHHHHh-cCCCCcccccccc
Q 042225           72 RFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIR-LQGRCPTCRTRMS  117 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~-~~~~CP~Cr~~~~  117 (135)
                      +..|.||++...+.+...|||. .|..|-.+.++ ....||+||+++.
T Consensus         7 ~dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            3679999999999999999997 89999988777 5678999999876

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

Probab=98.11  E-value=2.7e-07  Score=71.68  Aligned_cols=50  Identities=38%  Similarity=0.879  Sum_probs=41.9

Q ss_pred             CCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhc-CCCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRL-QGRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~  118 (135)
                      +..++.|+||++.+...+++ .|+|.||..||..-++. ...||.||+.+..
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            34578899999999988766 69999999999877774 4689999998853

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

Probab=98.08  E-value=4.7e-06  Score=62.91  Aligned_cols=50  Identities=24%  Similarity=0.625  Sum_probs=42.0

Q ss_pred             CCCccceeeccccCccCcEEcC-CCCcccHHhHHHHHhc--CCCCcccccccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRL--QGRCPTCRTRMS  117 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~--~~~CP~Cr~~~~  117 (135)
                      ....+..|++|.+....|.+.. |||.||+.|+......  .++||.|..++.
T Consensus       235 ~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  235 TGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            3456788999999999998775 9999999999887763  479999987765

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

Probab=98.06  E-value=1.5e-06  Score=69.40  Aligned_cols=54  Identities=26%  Similarity=0.813  Sum_probs=47.6

Q ss_pred             CCccceeeccccCccCcEE-cCCCCcccHHhHHHHHhcCCCCccccccccccCce
Q 042225           69 GEVRFTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~  122 (135)
                      ..+++.|++|..++.+|+. +.|||.||..|+..|+.....||.|+..+......
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            5678999999999999998 49999999999999999988999998887655443

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

Probab=98.03  E-value=3.3e-06  Score=49.71  Aligned_cols=43  Identities=35%  Similarity=0.786  Sum_probs=30.0

Q ss_pred             CCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhc--CCCCcc
Q 042225           69 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRL--QGRCPT  111 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~--~~~CP~  111 (135)
                      ....+.|||....+.+|+.. .|||+|-+..|.+|++.  ...||+
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            34568899999999999874 89999999999999943  457998

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

Probab=98.00  E-value=1.7e-06  Score=65.19  Aligned_cols=55  Identities=20%  Similarity=0.509  Sum_probs=43.7

Q ss_pred             CccceeeccccCcc----------CcEEcCCCCcccHHhHHHHHh--cCCCCccccccccccCceee
Q 042225           70 EVRFTCGICLDTMK----------EESSTKCGHVFCKSCIVDAIR--LQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        70 ~~~~~C~IC~~~~~----------~p~~~~CgH~fc~~Ci~~~~~--~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      .++..|+||...+.          +...+.|+|.|+..||..|--  ++.+||.|++.+..+.++++
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmfsn  288 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMFSN  288 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhccC
Confidence            35667999987554          346789999999999999976  55689999999987766654

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

Probab=97.91  E-value=9.2e-06  Score=63.47  Aligned_cols=53  Identities=23%  Similarity=0.414  Sum_probs=47.7

Q ss_pred             CcCCCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           65 MVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        65 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ...+..++..|+||..-..+.+..||+|.-|+.||.+.+.+.+.|-.|+..+.
T Consensus       415 ~~lp~sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  415 KDLPDSEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             CCCCCcccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence            34456789999999999999999999999999999999999999999988776

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.90  E-value=1.3e-05  Score=59.84  Aligned_cols=57  Identities=25%  Similarity=0.363  Sum_probs=51.1

Q ss_pred             ccceeeccccCccCc----EEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeecCC
Q 042225           71 VRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      ..+.|++|.+.+.+.    +.-+|||+||+.|++..+...+-||+|.+++..++|+.+.--
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~LqrG  280 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQRG  280 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeeecc
Confidence            679999999999986    344899999999999999999999999999999999988543

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

Probab=97.89  E-value=2.3e-06  Score=52.41  Aligned_cols=48  Identities=27%  Similarity=0.684  Sum_probs=24.2

Q ss_pred             cceeeccccCcc-C---cEE----cCCCCcccHHhHHHHHhc---C--------CCCcccccccccc
Q 042225           72 RFTCGICLDTMK-E---ESS----TKCGHVFCKSCIVDAIRL---Q--------GRCPTCRTRMSVR  119 (135)
Q Consensus        72 ~~~C~IC~~~~~-~---p~~----~~CgH~fc~~Ci~~~~~~---~--------~~CP~Cr~~~~~~  119 (135)
                      +..|.||+..+. +   |..    ..|+..||..|+.+|+..   .        ..||.|+.++..+
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence            456999999765 2   211    269999999999999882   1        1499999988653

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

Probab=97.82  E-value=8.5e-06  Score=65.98  Aligned_cols=49  Identities=24%  Similarity=0.600  Sum_probs=38.5

Q ss_pred             CCccceeeccccCccC-----------------cEEcCCCCcccHHhHHHHHhc-CCCCcccccccc
Q 042225           69 GEVRFTCGICLDTMKE-----------------ESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMS  117 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~-----------------p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~  117 (135)
                      .+....|+||+....-                 -+.+||.|.|+..|+.+|+.. +..||+||.++.
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLP  634 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLP  634 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCC
Confidence            3455679999975531                 145699999999999999994 458999999875

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

Probab=97.82  E-value=9.8e-06  Score=63.88  Aligned_cols=58  Identities=22%  Similarity=0.643  Sum_probs=43.2

Q ss_pred             eeeccccCccCcEE---c-CCCCcccHHhHHHHHhcC---CCCccccccccccCce-eecCCCCCC
Q 042225           74 TCGICLDTMKEESS---T-KCGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVRSIR-RIFFPQLQP  131 (135)
Q Consensus        74 ~C~IC~~~~~~p~~---~-~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~-~~~~~~~~~  131 (135)
                      .|.||.+.+.+..-   + .|||+|+..|+..|+...   ..||.|+-.+..+.++ +++++.++.
T Consensus         6 ~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~N~~~~d~vvE   71 (465)
T KOG0827|consen    6 ECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVANPSTVDHVVE   71 (465)
T ss_pred             eeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeeechhhhhhhhc
Confidence            59999665543322   2 599999999999999843   5799999778777777 666665553

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

Probab=97.73  E-value=3.8e-06  Score=66.49  Aligned_cols=62  Identities=32%  Similarity=0.650  Sum_probs=50.2

Q ss_pred             cceeeccccCccCc-----EEcCCCCcccHHhHHHHHhc--CCCCccccccccccCceeecCCCCCCCC
Q 042225           72 RFTCGICLDTMKEE-----SSTKCGHVFCKSCIVDAIRL--QGRCPTCRTRMSVRSIRRIFFPQLQPPA  133 (135)
Q Consensus        72 ~~~C~IC~~~~~~p-----~~~~CgH~fc~~Ci~~~~~~--~~~CP~Cr~~~~~~~~~~~~~~~~~~~~  133 (135)
                      ...|+||++.+.-+     +.+.|||.|-..||+.|+.+  .+.||.|.....++++++.|--.+++.|
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~i~~e~alR~qa~d   72 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQIRPEYALRVQAMD   72 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHHHHHHHHHHHHHHh
Confidence            45799999988765     46789999999999999963  2479999998888999888766655543

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

Probab=97.73  E-value=2e-05  Score=61.85  Aligned_cols=55  Identities=31%  Similarity=0.730  Sum_probs=42.4

Q ss_pred             CCcCCCCccceeeccccCccCcE-----E---cCCCCcccHHhHHHHHh--c-----CCCCccccccccc
Q 042225           64 GMVVVGEVRFTCGICLDTMKEES-----S---TKCGHVFCKSCIVDAIR--L-----QGRCPTCRTRMSV  118 (135)
Q Consensus        64 ~~~~~~~~~~~C~IC~~~~~~p~-----~---~~CgH~fc~~Ci~~~~~--~-----~~~CP~Cr~~~~~  118 (135)
                      ........+..|.||++...+..     .   .+|.|.||..||..|..  +     .+.||.||.....
T Consensus       153 ~~a~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~  222 (344)
T KOG1039|consen  153 SFALQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSF  222 (344)
T ss_pred             ccCcCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccc
Confidence            33444567889999999777654     3   57999999999999984  3     3689999977653

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

Probab=97.71  E-value=1.6e-05  Score=63.05  Aligned_cols=53  Identities=28%  Similarity=0.586  Sum_probs=43.2

Q ss_pred             cceeeccccCccCcEEcCCCCcccHHhHHHHHhc--CCCCccccccccccCceee
Q 042225           72 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL--QGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~--~~~CP~Cr~~~~~~~~~~~  124 (135)
                      ...|.||-+--.+-..-+|||..|..|+..|...  ..+||.||..+....-+.+
T Consensus       369 FeLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vii  423 (563)
T KOG1785|consen  369 FELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVII  423 (563)
T ss_pred             HHHHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccceee
Confidence            4569999998877777799999999999999864  4689999999976544333

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

Probab=97.69  E-value=2.2e-05  Score=48.80  Aligned_cols=30  Identities=30%  Similarity=0.656  Sum_probs=27.5

Q ss_pred             CCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           89 KCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        89 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      -|.|.|+.+||.+|+..+..||++|+.+..
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            599999999999999999999999987754

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

Probab=97.68  E-value=1.5e-05  Score=61.08  Aligned_cols=42  Identities=33%  Similarity=0.870  Sum_probs=37.0

Q ss_pred             cceeeccccCccCcEEc-CCCCcccHHhHHHHHh-cCCCCcccc
Q 042225           72 RFTCGICLDTMKEESST-KCGHVFCKSCIVDAIR-LQGRCPTCR  113 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-~~~~CP~Cr  113 (135)
                      .+.|+.|..++.+|+.+ .|||.||..||...+. ..+.||.|.
T Consensus       274 ~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~  317 (427)
T COG5222         274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCS  317 (427)
T ss_pred             cccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCcc
Confidence            38999999999999988 6899999999987665 568999994

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

Probab=97.66  E-value=2.3e-05  Score=64.15  Aligned_cols=52  Identities=27%  Similarity=0.740  Sum_probs=44.6

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHh-----cCCCCcccccccccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR-----LQGRCPTCRTRMSVR  119 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~  119 (135)
                      .......|.+|.+.-.+++.+.|.|.||..|+.++..     ..-+||+|...++..
T Consensus       532 enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  532 ENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            4556788999999999999999999999999999877     235899998887653

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

Probab=97.63  E-value=2.1e-05  Score=60.83  Aligned_cols=58  Identities=29%  Similarity=0.573  Sum_probs=50.5

Q ss_pred             CccceeeccccCccCcEEcC-CCCcccHHhHHHHHhcCCCCccccccccccCceeecCC
Q 042225           70 EVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      .+...|++|.....+|..+. -|-+||+.|+..++.+.+.||+-..+....+++++|-+
T Consensus       298 ~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~v~~l~rl~~~  356 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPASVDHLIRLFNK  356 (357)
T ss_pred             CccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcchHHHHHHHhcC
Confidence            35677999999999997775 59999999999999999999999999988888877643

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

Probab=97.55  E-value=8.2e-05  Score=42.38  Aligned_cols=39  Identities=23%  Similarity=0.596  Sum_probs=30.7

Q ss_pred             eecccc--CccCcEEcCCC-----CcccHHhHHHHHhcC--CCCcccc
Q 042225           75 CGICLD--TMKEESSTKCG-----HVFCKSCIVDAIRLQ--GRCPTCR  113 (135)
Q Consensus        75 C~IC~~--~~~~p~~~~Cg-----H~fc~~Ci~~~~~~~--~~CP~Cr  113 (135)
                      |.||++  .-.++...||.     |.+|..|+.+|+..+  ..||+|+
T Consensus         2 CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        2 CRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             ccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            889997  33456778885     779999999999754  4899984

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

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.47  E-value=0.0002  Score=54.31  Aligned_cols=60  Identities=22%  Similarity=0.458  Sum_probs=48.8

Q ss_pred             CCCccceeeccccCccCc----EEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeecCCC
Q 042225           68 VGEVRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQ  128 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~  128 (135)
                      .....+.|||....|...    ...+|||+|+..++.+.- ....||+|..++...|++.|.-+.
T Consensus       109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Lnp~~  172 (260)
T PF04641_consen  109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLNPPE  172 (260)
T ss_pred             cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEecCCc
Confidence            356788999999999643    234999999999999873 456799999999999999886554

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

Probab=97.45  E-value=2.1e-05  Score=66.79  Aligned_cols=52  Identities=25%  Similarity=0.544  Sum_probs=42.1

Q ss_pred             ccceeeccccCccCc---EEcCCCCcccHHhHHHHHhcCCCCccccccccccCce
Q 042225           71 VRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~  122 (135)
                      ....|++|+..+.+.   ....|+|.||..|+..|-+...+||+||..|..-.+.
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V~  176 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKVL  176 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheeeee
Confidence            456788888777654   2347999999999999999999999999988765443

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

Probab=97.41  E-value=9e-05  Score=59.47  Aligned_cols=48  Identities=31%  Similarity=0.591  Sum_probs=38.9

Q ss_pred             CCCccceeeccccCccCc----EEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           68 VGEVRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ...+--+||||++.+...    +.+.|.|.|+-.|+..|..  .+||+||....
T Consensus       171 ~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~--~scpvcR~~q~  222 (493)
T KOG0804|consen  171 GLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD--SSCPVCRYCQS  222 (493)
T ss_pred             CcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc--CcChhhhhhcC
Confidence            345667899999988865    3568999999999999843  57999998665

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

Probab=97.33  E-value=0.00012  Score=47.65  Aligned_cols=28  Identities=25%  Similarity=0.567  Sum_probs=25.7

Q ss_pred             CCCCcccHHhHHHHHhcCCCCccccccc
Q 042225           89 KCGHVFCKSCIVDAIRLQGRCPTCRTRM  116 (135)
Q Consensus        89 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~  116 (135)
                      .|.|.|+..||.+|++....||+|.+.-
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            5999999999999999999999997654

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

Probab=97.18  E-value=0.00012  Score=63.58  Aligned_cols=50  Identities=20%  Similarity=0.581  Sum_probs=39.0

Q ss_pred             CCCccceeeccccCcc--C-----cEEcCCCCcccHHhHHHHHhcC--CCCcccccccc
Q 042225           68 VGEVRFTCGICLDTMK--E-----ESSTKCGHVFCKSCIVDAIRLQ--GRCPTCRTRMS  117 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~--~-----p~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~  117 (135)
                      ..+....|+||..++.  +     .....|.|.||..|+..|++..  .+||+||..+.
T Consensus      1465 ~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1465 KFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             hcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            3456778999998765  1     2334699999999999999954  58999997765

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

Probab=97.18  E-value=4.4e-05  Score=58.27  Aligned_cols=42  Identities=33%  Similarity=0.843  Sum_probs=36.5

Q ss_pred             cceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCcccccccc
Q 042225           72 RFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ...|.||++...+-+.|+|||. -|..|=.+    ...||+||+.+.
T Consensus       300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence            7889999999999999999996 79999754    348999998774

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

Probab=97.18  E-value=9.6e-05  Score=45.56  Aligned_cols=45  Identities=36%  Similarity=0.755  Sum_probs=33.1

Q ss_pred             eeeccccCccC------------cEEc-CCCCcccHHhHHHHHhc---CCCCccccccccc
Q 042225           74 TCGICLDTMKE------------ESST-KCGHVFCKSCIVDAIRL---QGRCPTCRTRMSV  118 (135)
Q Consensus        74 ~C~IC~~~~~~------------p~~~-~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~~  118 (135)
                      .|-||.-.|..            |.++ -|.|.|+..||.+|+..   +..||+||..+..
T Consensus        22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            57777666553            1222 49999999999999984   3579999987653

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.02  E-value=0.00046  Score=39.99  Aligned_cols=48  Identities=23%  Similarity=0.561  Sum_probs=37.7

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccC
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRS  120 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  120 (135)
                      ....|..|...-...+.++|||..|..|..-+  .-..||.|..++...+
T Consensus         6 ~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    6 PEQPCVFCGFVGTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             cceeEEEccccccccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence            34567888888788899999999999997543  3467999999887554

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

Probab=96.90  E-value=0.0008  Score=52.73  Aligned_cols=48  Identities=33%  Similarity=0.713  Sum_probs=37.0

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      .......|.||.+...+.+.++|||.-|  |..-... -..||+||..+..
T Consensus       301 ~~~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs~~-l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCSKH-LPQCPVCRQRIRL  348 (355)
T ss_pred             ccCCCCceEEecCCccceeeecCCcEEE--chHHHhh-CCCCchhHHHHHH
Confidence            3455677999999999999999999866  6654433 3459999987753

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

Probab=96.48  E-value=0.0012  Score=53.31  Aligned_cols=35  Identities=23%  Similarity=0.623  Sum_probs=31.6

Q ss_pred             CccceeeccccCccCcEEcCCCCcccHHhHHHHHh
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR  104 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~  104 (135)
                      ++++.|+||...|++|+.++|+|..|..|....+.
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            46788999999999999999999999999987654

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

Probab=96.47  E-value=0.0025  Score=50.57  Aligned_cols=56  Identities=20%  Similarity=0.466  Sum_probs=45.2

Q ss_pred             ccceeeccccCcc---CcEEcCCCCcccHHhHHHHHhcC---CCCccccccccccCceeecC
Q 042225           71 VRFTCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        71 ~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      ..+.|||=.+--.   .|+.+.|||+.++.-+.+..++.   +.||+|-......+..++||
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            5788998776444   37899999999999999988743   57999988777777777775

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

Probab=96.42  E-value=0.0034  Score=44.05  Aligned_cols=34  Identities=18%  Similarity=0.484  Sum_probs=26.2

Q ss_pred             ccceeeccccCccCcEEcC------------CCCcc-cHHhHHHHHh
Q 042225           71 VRFTCGICLDTMKEESSTK------------CGHVF-CKSCIVDAIR  104 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~------------CgH~f-c~~Ci~~~~~  104 (135)
                      ++..|+||++...++|.|-            |+..| +..|++++.+
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            3567999999999999884            44433 6789988766

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.

>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=96.25  E-value=0.003  Score=48.32  Aligned_cols=53  Identities=25%  Similarity=0.611  Sum_probs=39.5

Q ss_pred             eeecccc-CccCc----EEcCCCCcccHHhHHHHHh-cCCCCccccccccccCceeecC
Q 042225           74 TCGICLD-TMKEE----SSTKCGHVFCKSCIVDAIR-LQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        74 ~C~IC~~-~~~~p----~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      .|++|.. .+.+|    ..-+|||..|.+|+...+. ....||.|...+....++...|
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~nfr~q~f   60 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNNFRVQTF   60 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcccchhhc
Confidence            4889986 44454    2238999999999999887 4578999998887766654433

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

Probab=96.17  E-value=0.0034  Score=50.13  Aligned_cols=35  Identities=37%  Similarity=0.850  Sum_probs=29.6

Q ss_pred             CccceeeccccCccCc---EEcCCCCcccHHhHHHHHh
Q 042225           70 EVRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIR  104 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~  104 (135)
                      ...+.|.||++.....   +.++|+|.||+.|+..++.
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFT  219 (445)
T ss_pred             hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHH
Confidence            3578899999977653   5689999999999999877

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

Probab=96.10  E-value=0.0014  Score=55.78  Aligned_cols=50  Identities=32%  Similarity=0.788  Sum_probs=42.4

Q ss_pred             ceeeccccCccCcEEcCCCCcccHHhHHHHHhcC--CCCccccccccccCcee
Q 042225           73 FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ--GRCPTCRTRMSVRSIRR  123 (135)
Q Consensus        73 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~~~~  123 (135)
                      ..|.+|.+ ...++.+.|||.||..|+...+...  ..||.||..+...+++.
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 7788899999999999999887743  46999999887766654

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

Probab=96.09  E-value=0.003  Score=35.72  Aligned_cols=42  Identities=33%  Similarity=0.888  Sum_probs=20.9

Q ss_pred             eeccccCccCc--EEc--CCCCcccHHhHHHHHh-cCCCCccccccc
Q 042225           75 CGICLDTMKEE--SST--KCGHVFCKSCIVDAIR-LQGRCPTCRTRM  116 (135)
Q Consensus        75 C~IC~~~~~~p--~~~--~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~  116 (135)
                      |++|.+.+...  ...  +||+.+|..|+...+. ....||-||++.
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            67888877322  223  6899999999998886 467899999764

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

Probab=96.03  E-value=0.0081  Score=47.29  Aligned_cols=50  Identities=32%  Similarity=0.755  Sum_probs=41.6

Q ss_pred             CCCCccceeeccccCccCcEEcCCCCcccHHhHHHH--HhcCCCCccccccc
Q 042225           67 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDA--IRLQGRCPTCRTRM  116 (135)
Q Consensus        67 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~--~~~~~~CP~Cr~~~  116 (135)
                      ..+++...|.||.+-+.-...+||+|..|--|-.+.  +..++.|++||...
T Consensus        56 dtDEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          56 DTDEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            346678889999999998889999999999998654  44778999998653

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

Probab=96.03  E-value=0.0041  Score=47.74  Aligned_cols=45  Identities=29%  Similarity=0.679  Sum_probs=36.6

Q ss_pred             cceeeccccCccC------cEEcCCCCcccHHhHHHHHhcC-CCCccccccc
Q 042225           72 RFTCGICLDTMKE------ESSTKCGHVFCKSCIVDAIRLQ-GRCPTCRTRM  116 (135)
Q Consensus        72 ~~~C~IC~~~~~~------p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~  116 (135)
                      ...|-||.+.+..      |..+.|||.+|..|+...+.+. -.||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            3569999988873      5677899999999999877755 4689999984

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

Probab=95.99  E-value=0.0018  Score=48.25  Aligned_cols=48  Identities=25%  Similarity=0.732  Sum_probs=33.3

Q ss_pred             ceeeccccCcc-Cc-EEcCCCCcccHHhHHHHHhcCCCCccccccccccCce
Q 042225           73 FTCGICLDTMK-EE-SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        73 ~~C~IC~~~~~-~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~  122 (135)
                      +.|..|..-.. ++ ..+.|+|+||..|...-.  ...|++|++++....+-
T Consensus         4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~i~l~   53 (233)
T KOG4739|consen    4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRIIQLN   53 (233)
T ss_pred             EEeccccccCCCCceeeeechhhhhhhhcccCC--ccccccccceeeeeecc
Confidence            45777776444 33 457999999999985431  12799999998755443

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

Probab=95.99  E-value=0.0068  Score=41.39  Aligned_cols=50  Identities=30%  Similarity=0.731  Sum_probs=42.2

Q ss_pred             CccceeeccccCccCcEEcC----CCCcccHHhHHHHHhcC---CCCcccccccccc
Q 042225           70 EVRFTCGICLDTMKEESSTK----CGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVR  119 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~----CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~  119 (135)
                      ..-+.|.||.+...+...+.    ||-..|..|....++..   ..||+|+..+...
T Consensus        78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             CCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence            36789999999999888773    99999999999988854   4799999888654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.77  E-value=0.0078  Score=47.23  Aligned_cols=56  Identities=27%  Similarity=0.739  Sum_probs=40.5

Q ss_pred             CCCccceeeccccCccC--c--EEcCCCCcccHHhHHHHHhc-CCCCccccccccccCceee
Q 042225           68 VGEVRFTCGICLDTMKE--E--SSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~--p--~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~  124 (135)
                      .+++++ |++|++.+..  .  .-.+||-..|.-|+...... ...||.||.....+.++-+
T Consensus        11 edeed~-cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~   71 (480)
T COG5175          11 EDEEDY-CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV   71 (480)
T ss_pred             cccccc-CcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence            345555 9999997653  2  23478988899998776553 4689999998887776544

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

Probab=95.71  E-value=0.0033  Score=50.09  Aligned_cols=44  Identities=25%  Similarity=0.788  Sum_probs=34.9

Q ss_pred             cceeeccccCccC-c---EEcCCCCcccHHhHHHHHhcC--CCCcccccc
Q 042225           72 RFTCGICLDTMKE-E---SSTKCGHVFCKSCIVDAIRLQ--GRCPTCRTR  115 (135)
Q Consensus        72 ~~~C~IC~~~~~~-p---~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~  115 (135)
                      .+.|..|.+.+-. +   ..+||.|+||..|+.+++.+.  .+||.||+-
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crkl  414 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKL  414 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHH
Confidence            5679999986642 2   357999999999999998754  589999943

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

Probab=95.69  E-value=0.0082  Score=44.61  Aligned_cols=44  Identities=20%  Similarity=0.573  Sum_probs=35.8

Q ss_pred             ceeeccccCccC--cEEcCCCCcccHHhHHHHHhcC--------CCCccccccc
Q 042225           73 FTCGICLDTMKE--ESSTKCGHVFCKSCIVDAIRLQ--------GRCPTCRTRM  116 (135)
Q Consensus        73 ~~C~IC~~~~~~--p~~~~CgH~fc~~Ci~~~~~~~--------~~CP~Cr~~~  116 (135)
                      --|..|...+..  .+.+-|-|.|+++|+.+|..+-        ..||.|...+
T Consensus        51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei  104 (299)
T KOG3970|consen   51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI  104 (299)
T ss_pred             CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence            349999998874  5788999999999999998731        3699997765

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

Probab=95.68  E-value=0.012  Score=32.52  Aligned_cols=38  Identities=21%  Similarity=0.718  Sum_probs=23.9

Q ss_pred             eeccccCccCcEEcC---CCCcccHHhHHHHHhcCC--CCccc
Q 042225           75 CGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQG--RCPTC  112 (135)
Q Consensus        75 C~IC~~~~~~p~~~~---CgH~fc~~Ci~~~~~~~~--~CP~C  112 (135)
                      |.+|.++....+.-+   |+-.++..|+..++....  .||.|
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   999999999999998655  69987

; PDB: 3NW0_A 2CT0_A.

>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=95.52  E-value=0.0043  Score=40.25  Aligned_cols=33  Identities=30%  Similarity=0.561  Sum_probs=27.0

Q ss_pred             CCCccceeeccccCccCcE--EcCCCCcccHHhHH
Q 042225           68 VGEVRFTCGICLDTMKEES--STKCGHVFCKSCIV  100 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~--~~~CgH~fc~~Ci~  100 (135)
                      .+.+...|++|...+.+..  ..||||.||..|+.
T Consensus        74 ~i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   74 VITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             EECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            3556778999999998764  45999999999975

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 [].

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

Probab=95.34  E-value=0.0054  Score=47.31  Aligned_cols=48  Identities=27%  Similarity=0.681  Sum_probs=37.5

Q ss_pred             ccceeeccccCccCc---EEcCCCCcccHHhHHHHHh-----------------------cCCCCccccccccc
Q 042225           71 VRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIR-----------------------LQGRCPTCRTRMSV  118 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~-----------------------~~~~CP~Cr~~~~~  118 (135)
                      ....|.||+--|.+.   +.+.|-|-|+..|+.+++.                       ....||+||..+..
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~  187 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI  187 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence            456799999887753   5789999999999988765                       11249999998853

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

Probab=95.09  E-value=0.016  Score=45.00  Aligned_cols=47  Identities=26%  Similarity=0.726  Sum_probs=38.5

Q ss_pred             CCCccceeeccccCccCcE-EcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           68 VGEVRFTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ...+-+.||||.+.+..|+ +-.=||..|.+|-.+   ....||.||.++.
T Consensus        44 ~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~---~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   44 LDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTK---VSNKCPTCRLPIG   91 (299)
T ss_pred             cchhhccCchhhccCcccceecCCCcEehhhhhhh---hcccCCccccccc
Confidence            4556788999999999885 456699999999753   3678999999887

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

Probab=94.95  E-value=0.015  Score=50.40  Aligned_cols=42  Identities=24%  Similarity=0.640  Sum_probs=35.2

Q ss_pred             ccceeeccccCccCcE-EcCCCCcccHHhHHHHHhcCCCCcccccc
Q 042225           71 VRFTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGRCPTCRTR  115 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~  115 (135)
                      ....|..|...+.-|+ .-.|||.||.+|+.   .....||.|+..
T Consensus       839 q~skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e  881 (933)
T KOG2114|consen  839 QVSKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPE  881 (933)
T ss_pred             eeeeecccCCccccceeeeecccHHHHHhhc---cCcccCCccchh
Confidence            3468999999999884 57999999999998   456789999763

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

Probab=94.79  E-value=0.027  Score=51.81  Aligned_cols=50  Identities=20%  Similarity=0.557  Sum_probs=38.1

Q ss_pred             CCccceeeccccCcc---CcEEcCCCCcccHHhHHHHHhcC----------CCCccccccccc
Q 042225           69 GEVRFTCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQ----------GRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~----------~~CP~Cr~~~~~  118 (135)
                      ...+..|.||+..--   ..+++.|+|.|+..|....+.+.          ..||+|..++..
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            345778999997443   34789999999999998877643          269999877754

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=94.55  E-value=0.065  Score=37.75  Aligned_cols=49  Identities=20%  Similarity=0.452  Sum_probs=35.4

Q ss_pred             CCccceeeccccCccCcEEcCCCCc-----ccHHhHHHHHhcC--CCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHV-----FCKSCIVDAIRLQ--GRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~-----fc~~Ci~~~~~~~--~~CP~Cr~~~~~  118 (135)
                      ...+..|-||++.... ...||...     .|.+|+.+|+..+  ..|+.|+.....
T Consensus         5 s~~~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          5 SLMDKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            3456679999987542 33466543     3999999999854  579999887753

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

Probab=94.38  E-value=0.031  Score=40.20  Aligned_cols=49  Identities=29%  Similarity=0.738  Sum_probs=33.7

Q ss_pred             ccceeeccccCccCcE-------EcCCCCcccHHhHHHHHhc------C-----CCCcccccccccc
Q 042225           71 VRFTCGICLDTMKEES-------STKCGHVFCKSCIVDAIRL------Q-----GRCPTCRTRMSVR  119 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~-------~~~CgH~fc~~Ci~~~~~~------~-----~~CP~Cr~~~~~~  119 (135)
                      +..-|-||..+--+.+       ...||..|+.-|+..|++.      +     ..||.|..++..+
T Consensus       164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            3445666665433322       2369999999999999982      1     2599999888653

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

Probab=94.27  E-value=0.012  Score=44.12  Aligned_cols=61  Identities=18%  Similarity=0.453  Sum_probs=44.2

Q ss_pred             CccceeeccccC-ccCc-EEc----CCCCcccHHhHHHHHhcC-CCCc--cccccccccCceeecCCCCC
Q 042225           70 EVRFTCGICLDT-MKEE-SST----KCGHVFCKSCIVDAIRLQ-GRCP--TCRTRMSVRSIRRIFFPQLQ  130 (135)
Q Consensus        70 ~~~~~C~IC~~~-~~~p-~~~----~CgH~fc~~Ci~~~~~~~-~~CP--~Cr~~~~~~~~~~~~~~~~~  130 (135)
                      ..+.+||+|... +-+| +.+    .|-|..|.+|+.+.+... ..||  -|.+-+....++...|..++
T Consensus         8 ~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK~kf~~qtFeD~~   77 (314)
T COG5220           8 MEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRKIKFIKQTFEDIT   77 (314)
T ss_pred             hhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHHhcccccccchhh
Confidence            346689999973 3344 221    499999999999998854 6799  88887777776666665543

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

Probab=94.27  E-value=0.03  Score=43.61  Aligned_cols=57  Identities=23%  Similarity=0.421  Sum_probs=44.5

Q ss_pred             CccceeeccccCcc---CcEEcCCCCcccHHhHHHHHhcC---CCCccccccccccCceeecC
Q 042225           70 EVRFTCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        70 ~~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      ..-+.||+=.+...   .|+.+.|||+.-+.-+....++.   +.||.|-..-...++.++||
T Consensus       334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~~~~~~~rvrf  396 (396)
T COG5109         334 HSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMSKYENILRVRF  396 (396)
T ss_pred             cceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcchhhhhhhcccC
Confidence            45788998776544   37899999999999998877643   57999987777777777765

>PHA02862 5L protein; Provisional

Probab=94.26  E-value=0.08  Score=36.76  Aligned_cols=45  Identities=27%  Similarity=0.548  Sum_probs=33.6

Q ss_pred             ceeeccccCccCcEEcCCCCc-----ccHHhHHHHHhcC--CCCccccccccc
Q 042225           73 FTCGICLDTMKEESSTKCGHV-----FCKSCIVDAIRLQ--GRCPTCRTRMSV  118 (135)
Q Consensus        73 ~~C~IC~~~~~~p~~~~CgH~-----fc~~Ci~~~~~~~--~~CP~Cr~~~~~  118 (135)
                      ..|-||++.-.+. .-||...     .|.+|+.+|++..  ..|++|+....-
T Consensus         3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            3599999976544 3566542     4899999999854  579999988753

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

Probab=94.15  E-value=0.025  Score=43.87  Aligned_cols=44  Identities=27%  Similarity=0.588  Sum_probs=31.3

Q ss_pred             cceeeccccCccC-cEEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           72 RFTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        72 ~~~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      .-.|.-|-..+.. ...++|.|.||.+|..  ....+.||.|-..+.
T Consensus        90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr--~~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   90 VHFCDRCDFPIAIYGRMIPCKHVFCLECAR--SDSDKICPLCDDRVQ  134 (389)
T ss_pred             eEeecccCCcceeeecccccchhhhhhhhh--cCccccCcCcccHHH
Confidence            3456777665443 4578999999999974  344678999966553

>PHA03096 p28-like protein; Provisional

Probab=93.76  E-value=0.037  Score=42.63  Aligned_cols=42  Identities=29%  Similarity=0.454  Sum_probs=29.9

Q ss_pred             ceeeccccCccCc--------EEcCCCCcccHHhHHHHHhcC---CCCccccc
Q 042225           73 FTCGICLDTMKEE--------SSTKCGHVFCKSCIVDAIRLQ---GRCPTCRT  114 (135)
Q Consensus        73 ~~C~IC~~~~~~p--------~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~  114 (135)
                      ..|.||++.....        +...|.|.||..|+..|....   ..||.|+.
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            5699999955432        334799999999999998733   34555543

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

Probab=93.40  E-value=0.11  Score=45.29  Aligned_cols=49  Identities=31%  Similarity=0.688  Sum_probs=37.1

Q ss_pred             CCccceeeccccCccC--cE--EcCCCCcccHHhHHHHHhc-------CCCCcccccccc
Q 042225           69 GEVRFTCGICLDTMKE--ES--STKCGHVFCKSCIVDAIRL-------QGRCPTCRTRMS  117 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~--p~--~~~CgH~fc~~Ci~~~~~~-------~~~CP~Cr~~~~  117 (135)
                      ....+.|.||.+.+..  ++  -..|-|+|+..||..|-..       ...||.|.....
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~  247 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK  247 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence            4468999999998774  32  2369999999999999873       236999984443

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

Probab=92.88  E-value=0.025  Score=51.03  Aligned_cols=45  Identities=33%  Similarity=0.754  Sum_probs=39.7

Q ss_pred             CCccceeeccccCcc-CcEEcCCCCcccHHhHHHHHhcCCCCcccc
Q 042225           69 GEVRFTCGICLDTMK-EESSTKCGHVFCKSCIVDAIRLQGRCPTCR  113 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~-~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr  113 (135)
                      ......|.||.+.+. ......|||.+|..|...|+..+..||.|.
T Consensus      1150 ~~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~k 1195 (1394)
T KOG0298|consen 1150 LSGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICK 1195 (1394)
T ss_pred             hhcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchh
Confidence            335568999999999 557889999999999999999999999996

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

Probab=92.86  E-value=0.054  Score=41.60  Aligned_cols=49  Identities=24%  Similarity=0.746  Sum_probs=38.8

Q ss_pred             CccceeeccccCccCcEEcCC----CCcccHHhHHHHHhcCC-----------CCccccccccc
Q 042225           70 EVRFTCGICLDTMKEESSTKC----GHVFCKSCIVDAIRLQG-----------RCPTCRTRMSV  118 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~C----gH~fc~~Ci~~~~~~~~-----------~CP~Cr~~~~~  118 (135)
                      ...+.|.+|.+.+++.....|    .|.||..|-.+.++.+.           .||+-...+.+
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sgevYCPSGdkCPLvgS~vPW  329 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASGEVYCPSGDKCPLVGSNVPW  329 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCCceeCCCCCcCcccCCcccH
Confidence            356899999999999987777    78999999999998442           46766665554

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

Probab=92.76  E-value=0.03  Score=47.32  Aligned_cols=40  Identities=33%  Similarity=0.775  Sum_probs=31.0

Q ss_pred             CCccceeeccccCcc----CcEEcCCCCcccHHhHHHHHhcCCCCc
Q 042225           69 GEVRFTCGICLDTMK----EESSTKCGHVFCKSCIVDAIRLQGRCP  110 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~----~p~~~~CgH~fc~~Ci~~~~~~~~~CP  110 (135)
                      +.+.+.|.||...|.    .|+.+.|||+.|.+|+....+  .+||
T Consensus         8 w~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp   51 (861)
T KOG3161|consen    8 WVLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP   51 (861)
T ss_pred             hHHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC
Confidence            455678999987775    478889999999999986544  3466

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

Probab=92.68  E-value=0.062  Score=41.18  Aligned_cols=44  Identities=30%  Similarity=0.712  Sum_probs=36.3

Q ss_pred             ccceeeccccCcc----CcEEcCCCCcccHHhHHHHHhcCCCCccccc
Q 042225           71 VRFTCGICLDTMK----EESSTKCGHVFCKSCIVDAIRLQGRCPTCRT  114 (135)
Q Consensus        71 ~~~~C~IC~~~~~----~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~  114 (135)
                      ....||||.+.+.    .+..++|||..+..|..........||+|.+
T Consensus       157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             ccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            3444999998665    3567899999999999998887789999988

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

Probab=92.41  E-value=0.095  Score=41.65  Aligned_cols=33  Identities=24%  Similarity=0.722  Sum_probs=24.7

Q ss_pred             CCCcccHHhHHHHHh-------------cCCCCccccccccccCce
Q 042225           90 CGHVFCKSCIVDAIR-------------LQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        90 CgH~fc~~Ci~~~~~-------------~~~~CP~Cr~~~~~~~~~  122 (135)
                      |...-|.+|+.+|+.             .+..||.||+.+...|+-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilDV~  356 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILDVC  356 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeeeee
Confidence            344458899999986             223699999999877763

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

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.24  E-value=0.1  Score=39.39  Aligned_cols=37  Identities=19%  Similarity=0.239  Sum_probs=32.6

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHh
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR  104 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~  104 (135)
                      .+.+..-|.+|+..+.+|+.++=||.||..||.+++.
T Consensus        39 siK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~il   75 (303)
T KOG3039|consen   39 SIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYIL   75 (303)
T ss_pred             ccCCcceeeeecccccCCccCCCCeeeeHHHHHHHHH
Confidence            4555667899999999999999999999999998865

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

Probab=91.90  E-value=0.027  Score=47.90  Aligned_cols=51  Identities=33%  Similarity=0.742  Sum_probs=40.7

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHhc---CCCCccccccccccCc
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL---QGRCPTCRTRMSVRSI  121 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~~~~~  121 (135)
                      -...|+||...+.+|+.+.|.|.||..|+...+..   ...|++|+..+.....
T Consensus        20 k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~s~   73 (684)
T KOG4362|consen   20 KILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKRSL   73 (684)
T ss_pred             hhccCCceeEEeeccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhhhc
Confidence            35679999999999999999999999998665543   4579999877665544

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.80  E-value=0.12  Score=39.93  Aligned_cols=38  Identities=29%  Similarity=0.848  Sum_probs=29.1

Q ss_pred             CCCcccHHhHHHHHh-------------cCCCCccccccccccCceeecCC
Q 042225           90 CGHVFCKSCIVDAIR-------------LQGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        90 CgH~fc~~Ci~~~~~-------------~~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      |....|.+|+.+|+.             .+.+||.||+.+...|+.-+=++
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~~v~~~  375 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVHCVDFD  375 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeeeEEEee
Confidence            555668899998876             33479999999998888766444

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

Probab=91.76  E-value=0.078  Score=39.03  Aligned_cols=39  Identities=26%  Similarity=0.625  Sum_probs=31.6

Q ss_pred             eeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCcccccccc
Q 042225           75 CGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        75 C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      |-.|.+.-..-..+||.|. +|..|-..    ...||+|+....
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            9999998888778899996 89999754    456999986554

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

Probab=91.12  E-value=0.17  Score=28.34  Aligned_cols=38  Identities=32%  Similarity=0.714  Sum_probs=23.2

Q ss_pred             eeccccCccC--cEEcCCCC-----cccHHhHHHHHhc--CCCCccc
Q 042225           75 CGICLDTMKE--ESSTKCGH-----VFCKSCIVDAIRL--QGRCPTC  112 (135)
Q Consensus        75 C~IC~~~~~~--p~~~~CgH-----~fc~~Ci~~~~~~--~~~CP~C  112 (135)
                      |-||++...+  +...||+-     ..|..|+.+|+..  ...|++|
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            5678875543  46677654     3589999999984  3568876

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.99  E-value=0.37  Score=36.54  Aligned_cols=55  Identities=18%  Similarity=0.393  Sum_probs=43.2

Q ss_pred             CCCccceeeccccCccCc----EEcCCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           68 VGEVRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      .....+.|+|-.-.+...    ..-.|||+|-..-+.+.-  ...|++|.+.+...+++.+
T Consensus       107 ~~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKeik--as~C~~C~a~y~~~dvIvl  165 (293)
T KOG3113|consen  107 TQRARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEIK--ASVCHVCGAAYQEDDVIVL  165 (293)
T ss_pred             cccceeecccccceecceEEEEEEeccceeccHHHHHHhh--hccccccCCcccccCeEee
Confidence            345678899988777764    344899999998877652  5679999999999998765

>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=90.97  E-value=0.14  Score=35.15  Aligned_cols=36  Identities=25%  Similarity=0.559  Sum_probs=26.8

Q ss_pred             cceeeccccCccC--c-EEcCCC------CcccHHhHHHHHhcCC
Q 042225           72 RFTCGICLDTMKE--E-SSTKCG------HVFCKSCIVDAIRLQG  107 (135)
Q Consensus        72 ~~~C~IC~~~~~~--p-~~~~Cg------H~fc~~Ci~~~~~~~~  107 (135)
                      ...|.||++.+.+  . +.++||      |.||..|+.+|.+..+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~   70 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERN   70 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhcc
Confidence            6779999998876  3 344555      5689999999955433

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.

>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=90.82  E-value=0.091  Score=29.54  Aligned_cols=32  Identities=28%  Similarity=0.791  Sum_probs=22.3

Q ss_pred             EcCCC-CcccHHhHHHHHhcCCCCccccccccc
Q 042225           87 STKCG-HVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        87 ~~~Cg-H~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      .+.|. |-.|..|+...+.....||+|.+++..
T Consensus        15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             EEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             eeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            45564 557999999999999999999998864

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.

>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=90.77  E-value=0.18  Score=28.65  Aligned_cols=43  Identities=16%  Similarity=0.522  Sum_probs=21.2

Q ss_pred             cceeeccccCccCcEEc-CCCCcccHHhHHHHHh-----cCCCCcccccc
Q 042225           72 RFTCGICLDTMKEESST-KCGHVFCKSCIVDAIR-----LQGRCPTCRTR  115 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~  115 (135)
                      .+.|++....+..|+.. .|.|..|.+- ..|+.     ....||+|.++
T Consensus         2 sL~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    2 SLRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             ESB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred             eeeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence            36799999999999764 7999876542 22333     23479999763

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.

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

Probab=86.84  E-value=1  Score=39.41  Aligned_cols=48  Identities=10%  Similarity=0.135  Sum_probs=33.4

Q ss_pred             CCccceeeccccCccCcE----Ec---CCCCcccHHhHHHHHhc------CCCCccccccc
Q 042225           69 GEVRFTCGICLDTMKEES----ST---KCGHVFCKSCIVDAIRL------QGRCPTCRTRM  116 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~----~~---~CgH~fc~~Ci~~~~~~------~~~CP~Cr~~~  116 (135)
                      ..+...|.+|...+.+++    ..   .|+|.||..||..|...      ...|++|..-|
T Consensus        93 ~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci  153 (1134)
T KOG0825|consen   93 TAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV  153 (1134)
T ss_pred             cccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence            345566777777777632    23   49999999999999872      23577776555

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

Probab=86.62  E-value=0.42  Score=38.99  Aligned_cols=58  Identities=22%  Similarity=0.647  Sum_probs=41.3

Q ss_pred             CccceeeccccCccC-cEEcCCCCcccHHhHHHHHhcC--------CCCc--cccccccccCceeecCC
Q 042225           70 EVRFTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQ--------GRCP--TCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~~~--------~~CP--~Cr~~~~~~~~~~~~~~  127 (135)
                      .....|-||.+.+.. .+.+.|||.||..|+..++..+        -+||  -|++.+....+..+.-+
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            445789999998885 6677999999999999988732        2354  56666665555444433

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

Probab=86.39  E-value=0.34  Score=38.92  Aligned_cols=35  Identities=43%  Similarity=0.915  Sum_probs=26.5

Q ss_pred             ccceeeccccCccCc----EEcCCCCcccHHhHHHHHhc
Q 042225           71 VRFTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRL  105 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~  105 (135)
                      ....|.||.......    ....|+|.||..|+.+++..
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEV  183 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhh
Confidence            467899999433322    25689999999999998873

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=85.34  E-value=1.2  Score=25.76  Aligned_cols=41  Identities=24%  Similarity=0.706  Sum_probs=28.7

Q ss_pred             cceeeccccCcc--CcEEc--CCCCcccHHhHHHHHhcCCCCcc--ccccc
Q 042225           72 RFTCGICLDTMK--EESST--KCGHVFCKSCIVDAIRLQGRCPT--CRTRM  116 (135)
Q Consensus        72 ~~~C~IC~~~~~--~p~~~--~CgH~fc~~Ci~~~~~~~~~CP~--Cr~~~  116 (135)
                      ...|++|.+.|.  +.++.  .||-.|+..|+..    ...|-.  |...+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~~~c~~~~   51 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCINYSCGTGF   51 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEeccCCCCc
Confidence            456999999994  44443  7999999999764    445554  55444

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

Probab=85.13  E-value=1  Score=39.56  Aligned_cols=53  Identities=17%  Similarity=0.483  Sum_probs=39.3

Q ss_pred             CCccceeeccccCc--cCcEEcCCCCc-----ccHHhHHHHHhcC--CCCccccccccccCc
Q 042225           69 GEVRFTCGICLDTM--KEESSTKCGHV-----FCKSCIVDAIRLQ--GRCPTCRTRMSVRSI  121 (135)
Q Consensus        69 ~~~~~~C~IC~~~~--~~p~~~~CgH~-----fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~~  121 (135)
                      .+++..|.||...-  .+|..-||..+     .|.+|+.+|+...  +.|-.|..++..+++
T Consensus         9 N~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~I   70 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDI   70 (1175)
T ss_pred             CccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeee
Confidence            44567899998643  35666676553     4899999999854  579999998886665

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

Probab=84.68  E-value=1  Score=26.15  Aligned_cols=28  Identities=29%  Similarity=0.778  Sum_probs=21.7

Q ss_pred             CcccHHhHHHHHhcCCCCccccccccccCc
Q 042225           92 HVFCKSCIVDAIRLQGRCPTCRTRMSVRSI  121 (135)
Q Consensus        92 H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~  121 (135)
                      .+||..|....+  ...||.|...+..+.+
T Consensus        29 CTFC~~C~e~~l--~~~CPNCgGelv~RP~   56 (57)
T PF06906_consen   29 CTFCADCAETML--NGVCPNCGGELVRRPR   56 (57)
T ss_pred             CcccHHHHHHHh--cCcCcCCCCccccCCC
Confidence            369999998876  4579999988865543

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

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

Probab=84.17  E-value=0.54  Score=41.28  Aligned_cols=36  Identities=22%  Similarity=0.503  Sum_probs=28.2

Q ss_pred             CCccceeeccccCccC-c-EEcCCCCcccHHhHHHHHh
Q 042225           69 GEVRFTCGICLDTMKE-E-SSTKCGHVFCKSCIVDAIR  104 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~-p-~~~~CgH~fc~~Ci~~~~~  104 (135)
                      .+....|.+|...+.. | +.-+|||.|++.|+.+...
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            4456789999996653 4 5569999999999987654

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

Probab=83.74  E-value=0.53  Score=37.85  Aligned_cols=41  Identities=29%  Similarity=0.623  Sum_probs=30.4

Q ss_pred             cceeeccccCccC-----cEEcCCCCcccHHhHHHHHhcCCCCccc
Q 042225           72 RFTCGICLDTMKE-----ESSTKCGHVFCKSCIVDAIRLQGRCPTC  112 (135)
Q Consensus        72 ~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~~~~CP~C  112 (135)
                      -..|+.|...+..     -++-.|||-||+.|...|......|..|
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence            4569999886653     3555699999999999998876656433

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

Probab=81.89  E-value=1.9  Score=35.19  Aligned_cols=60  Identities=27%  Similarity=0.403  Sum_probs=52.8

Q ss_pred             ceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCccccccccccCceeecCCCCCCC
Q 042225           73 FTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQPP  132 (135)
Q Consensus        73 ~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~~  132 (135)
                      +.|+|-.++.++|+.- .-||.|=+.-|++++.....+|+-..++..+++.++--+.+.-|
T Consensus         1 m~CaISgEvP~~PVvS~~Sg~vfEkrLIEqyI~e~G~DPIt~~pLs~eelV~Ik~~~~v~p   61 (506)
T KOG0289|consen    1 MVCAISGEVPEEPVVSPVSGHVFEKRLIEQYIAETGKDPITNEPLSIEELVEIKVPAQVRP   61 (506)
T ss_pred             CeecccCCCCCCccccccccchHHHHHHHHHHHHcCCCCCCCCcCCHHHeeeccccccccC
Confidence            3599999999999876 58999999999999999999999999999999999977766544

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

Probab=80.41  E-value=1.3  Score=38.65  Aligned_cols=39  Identities=33%  Similarity=0.749  Sum_probs=29.8

Q ss_pred             cceeeccccCccCc--EEcCCCCcccHHhHHHHHhcCCCCc
Q 042225           72 RFTCGICLDTMKEE--SSTKCGHVFCKSCIVDAIRLQGRCP  110 (135)
Q Consensus        72 ~~~C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~~~~~~CP  110 (135)
                      .+.|.+|.-.....  +...|||..+.+|..+|+...-.||
T Consensus      1028 ~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cp 1068 (1081)
T KOG0309|consen 1028 TFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCP 1068 (1081)
T ss_pred             eeeeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCC
Confidence            45577776555432  3457999999999999999888887

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	135
4ap4_A	133	Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex Le		2e-06
1jm7_A	112	Solution Structure Of The Brca1/bard1 Ring-domain H		3e-06
2ckl_B	165	Ring1b-Bmi1 E3 Catalytic Domain Structure Length =		9e-06
2eci_A	86	Solution Structure Of The Ring Domain Of The Human		1e-05
3hct_A	118	Crystal Structure Of Traf6 In Complex With Ubc13 In		1e-05
3rpg_C	121	Bmi1RING1B-Ubch5c Complex Structure Length = 121		1e-05
3hcs_A	170	Crystal Structure Of The N-Terminal Domain Of Traf6		1e-05
2h0d_B	100	Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquiti		2e-05
3ng2_A	71	Crystal Structure Of The Rnf4 Ring Domain Dimer Len		2e-05
2xeu_A	64	Ring Domain Length = 64		2e-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		9e-05
2ecw_A	85	Solution Structure Of The Zinc Finger, C3hc4 Type (		5e-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 = 28/93 (30%), Positives = 45/93 (48%), Gaps = 9/93 (9%)
Query: 43  IEDVPKVSNDKEKCR--VCESRNGMVVVGEVRFTCGICLDTMKEES-------STKCGHV 93
           + D  K +N    CR  +   R   + +G    +C IC+D   E         ST+CGHV
Sbjct: 41  LRDSLKNANTCPTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHV 100
Query: 94  FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF 126
           FC  C+ D+++    CPTCR +++ +    I+ 
Sbjct: 101 FCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 133

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 4/75 (5%)
Query: 52  DKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ---GR 108
           D    RV E +N +  + ++   C ICL+ +KE  STKC H+FCK C++  +  +    +
Sbjct: 2   DLSALRVEEVQNVINAMQKI-LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQ 60
Query: 109 CPTCRTRMSVRSIRR 123
           CP C+  ++ RS++ 
Sbjct: 61  CPLCKNDITKRSLQE 75

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 73  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGR-CPTCRTRM-SVRSIR 122
             C ICLD +K   +TK C H FC  CI+ A+R   + CPTCR ++ S RS+R
Sbjct: 55  LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 107

>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 = 20/43 (46%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPT 111
           E ++ C ICL  ++E   T CGH FCK+CI+ +IR  G +CP 
Sbjct: 23  ESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 65

>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 = 20/43 (46%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPT 111
           E ++ C ICL  ++E   T CGH FCK+CI+ +IR  G +CP 
Sbjct: 16  ESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 58

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 73  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGR-CPTCRTRM-SVRSIR 122
             C ICLD +K   +TK C H FC  CI+ A+R   + CPTCR ++ S RS+R
Sbjct: 54  LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 106

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPT 111
           E ++ C ICL  ++E   T CGH FCK+CI+ +IR  G +CP 
Sbjct: 16  ESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 58

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 73  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGR-CPTCRTRM-SVRSIR 122
             C ICLD +K   +TK C H FC  CI+ A+R   + CPTCR ++ S RS+R
Sbjct: 35  LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 87

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 74  TCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF 126
           +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 = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 74  TCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF 126
           +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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 72  RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPT 111
           ++ C ICL  ++E   T CGH FCK+CI+ +IR  G +CP 
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 = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 7/51 (13%)
Query: 74  TCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGRCPTCRTRMS 117
           +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 = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRL------QGRCPTCRTRMSVRSIR 122
           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	135
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-16
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	5e-16
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	5e-14
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-14
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-12
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	4e-12
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	4e-12
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-11
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-11
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	3e-11
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	4e-11
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	8e-11
1z6u_A	150	NP95-like ring finger protein isoform B; structura	9e-11
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	1e-10
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-10
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-10
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	4e-10
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	4e-10
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	9e-10
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	1e-09
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	1e-09
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	2e-09
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	3e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-09
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-08
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	4e-09
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	1e-08
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-08
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	2e-08
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	2e-08
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	4e-08
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	5e-08
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	9e-08
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	1e-07
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	1e-07
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-07
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	2e-07
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	2e-06
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	2e-06
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	9e-06
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-05
2ect_A	78	Ring finger protein 126; metal binding protein, st	3e-05
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	5e-05
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	6e-05
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	8e-05
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	2e-04
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	2e-04
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	4e-04
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	4e-04

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

 Score = 67.1 bits (164), Expect = 3e-16
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 7/61 (11%)

Query: 72  RFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI 124
             +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +    I
Sbjct: 3   MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 62

Query: 125 F 125
           +
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 = 66.8 bits (163), Expect = 5e-16
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 7/60 (11%)

Query: 73  FTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF 125
            +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 = 61.8 bits (150), Expect = 5e-14
 Identities = 17/45 (37%), Positives = 22/45 (48%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRT 114
           E+ F C IC    +    TKC H FC+SC ++  R   RC  C  
Sbjct: 13  EIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQ 57

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

 Score = 61.4 bits (149), Expect = 6e-14
 Identities = 18/50 (36%), Positives = 21/50 (42%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIR 122
             C ICL T     S  C HVFC  C+  A  L  RC  CR  +    + 
Sbjct: 16  PECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLD 65

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

 Score = 57.6 bits (139), Expect = 2e-12
 Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 7/54 (12%)

Query: 73  FTCGICLDTMKEES-------STKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR 119
            +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +
Sbjct: 16  VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 69

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

 Score = 57.5 bits (139), Expect = 4e-12
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 73  FTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRR 123
             CGIC +         +C H +C  CI   +  + +CPTC   ++   ++ 
Sbjct: 23  LRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKN 74

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

 Score = 58.5 bits (141), Expect = 4e-12
 Identities = 20/73 (27%), Positives = 33/73 (45%)

Query: 48  KVSNDKEKCRVCESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG 107
           K   +K + +  E  + M  V E    C IC +   E  +  C H FC  CI + ++ + 
Sbjct: 40  KEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKI 99

Query: 108 RCPTCRTRMSVRS 120
            CP CR  +  ++
Sbjct: 100 ECPICRKDIKSKT 112

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

 Score = 55.5 bits (134), Expect = 1e-11
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 73  FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGRCPTCRT 114
             C IC   + + ++ T+C H FCKSCIV       RCP C  
Sbjct: 16  ILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNI 58

>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 = 59.8 bits (144), Expect = 1e-11
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 60  ESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMS 117
           E       +G     C IC +  K+     CGH+ C SC+      +G+ CP CR  + 
Sbjct: 320 EQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK 378

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

 Score = 54.4 bits (131), Expect = 3e-11
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 60  ESRNGMVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSV 118
              +G V   E ++ C  C   +     T+CGH FC+SC+   +     +C  C+  +  
Sbjct: 3   SGSSGFVKTVEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVK 62

Query: 119 RSI 121
             +
Sbjct: 63  DKV 65

>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 = 55.1 bits (133), Expect = 4e-11
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG---RCPTCRTRMSVRSIRR 123
             C ICL+ +KE  STKC H+FCK C++  +  +    +CP C+  ++ RS++ 
Sbjct: 22  LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE 75

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

 Score = 54.1 bits (130), Expect = 8e-11
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 73  FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSVRSIRRIFF 126
           F C IC++ +++      C  + C SCI   +  Q  +CP CR  + +R +    +
Sbjct: 23  FRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRW 78

>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 = 55.0 bits (132), Expect = 9e-11
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVR 119
           F C  C + + +  +T+C H  CK C+  + + Q   CP CR  +   
Sbjct: 79  FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 126

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

 Score = 52.8 bits (127), Expect = 1e-10
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG---RCPTCRTRMSVRSIR 122
             C ICLD +++  +  CGH FC  CI           +CP C+T +   +IR
Sbjct: 21  VICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAIR 73

>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 = 54.2 bits (130), Expect = 1e-10
 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSVR 119
           F C  C + +    +T C H  CK C+  + R Q   CP CR  +   
Sbjct: 53  FQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRS 100

>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 = 53.3 bits (128), Expect = 2e-10
 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 73  FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGRCPTCRT 114
             C +C     + ++  +C H FCK+CIV  +     CP C  
Sbjct: 16  LMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDV 58

>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 = 52.6 bits (126), Expect = 4e-10
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 73  FTCGICLDTMKE-ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRR 123
             C  C + ++E      C H+FC +C+ D I     CP C T   ++ ++ 
Sbjct: 23  LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPAWIQDLKI 72

>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 = 53.4 bits (128), Expect = 4e-10
 Identities = 25/53 (47%), Positives = 33/53 (62%), Gaps = 3/53 (5%)

Query: 73  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGR-CPTCRTR-MSVRSIR 122
             C ICLD +K   +TK C H FC  CI+ A+R   + CPTCR + +S RS+R
Sbjct: 55  LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLR 107

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

 Score = 50.5 bits (121), Expect = 9e-10
 Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 74  TCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF 125
            C ICL+     S +  C H FC  CI   IR    CP C+    V S+    
Sbjct: 7   RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKV--PVESVVHTI 57

>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 = 50.7 bits (122), Expect = 1e-09
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 7/58 (12%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCI-------VDAIRLQGRCPTCRTRMSVRSIRR 123
            TC ICL+ + E  S  CGH  C++CI       V ++  +  CP C    S   ++ 
Sbjct: 13  VTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQA 70

>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 = 51.5 bits (123), Expect = 1e-09
 Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIRR 123
             CGIC++ + E  +  C H  CK C    +      CP CR R+S  +   
Sbjct: 16  CQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYH 67

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

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 6/57 (10%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG------RCPTCRTRMSVRSIRR 123
            TC ICL+ +KE  S  C H FC++CI               CP CR      +++ 
Sbjct: 20  VTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKP 76

>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 = 50.6 bits (121), Expect = 3e-09
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 72  RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSVRSIRR 123
           ++ C ICL  ++E   T CGH FCK+CI+ +IR  G +CP     +    +  
Sbjct: 18  KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP 70

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

 Score = 50.6 bits (120), Expect = 3e-09
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 7/63 (11%)

Query: 73  FTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF 125
            +C IC+D   E         ST+CGHVFC  C+ D+++    CPTCR +++ +    I+
Sbjct: 8   VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY 67

Query: 126 FPQ 128
              
Sbjct: 68  IGS 70

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

 Score = 49.0 bits (116), Expect = 2e-08
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 54  EKCRVCESRNGMVVVGEVRFTCGICLDTMKEESS-------TKCGHVFCKSCIVDAIRLQ 106
            + ++   R   + +G    +C IC+D   E          T+CGHVFC  C+ D+++  
Sbjct: 54  CRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA 113

Query: 107 GRCPTCRTRMSVRSIRRIF 125
             CPTCR +++ +    I+
Sbjct: 114 NTCPTCRKKINHKRYHPIY 132

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

 Score = 49.2 bits (118), Expect = 4e-09
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVD------AIRLQGRCPTCRTRMSVRSIRR 123
            TC ICL+ + +  S  CGH FC++C+          + +  CP CR      +IR 
Sbjct: 20  VTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRP 76

>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 = 48.8 bits (116), Expect = 1e-08
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIRR 123
            +C IC   + +   T C H+FC+ CI+  +++ G  CP+CR       +  
Sbjct: 24  ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES 75

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

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 7/58 (12%)

Query: 72  RFTCGICLDTMKEESST----KCGHVFCKSCIVDAIRLQG---RCPTCRTRMSVRSIR 122
              C IC+++  EE        CGH  C+ C+   +       RCP C     + S+ 
Sbjct: 15  VLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLT 72

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 1/65 (1%)

Query: 70  EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIRRIFFPQ 128
           E ++ C  C + ++     +CGH +C  C+   +    + C  C           I    
Sbjct: 29  EAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEEGISILESS 88

Query: 129 LQPPA 133
              P 
Sbjct: 89  SAFPD 93

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

 Score = 46.6 bits (111), Expect = 2e-08
 Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 3/43 (6%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG---RCPTC 112
             C ICLD +++  +  CGH FC  CI           +CP C
Sbjct: 21  VICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

>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 = 46.3 bits (110), Expect = 4e-08
 Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 73  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGR--CPTCRTRMSVR 119
             C IC D M +      CG+ +C  CI  A+       CPTC       
Sbjct: 16  LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSP 65

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

 Score = 45.8 bits (109), Expect = 5e-08
 Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS 117
            C IC+D  + +    C H FC+ CI         CP CR +M+
Sbjct: 17  ECCICMD-GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMT 59

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

 Score = 45.0 bits (107), Expect = 9e-08
 Identities = 10/45 (22%), Positives = 14/45 (31%), Gaps = 3/45 (6%)

Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV 118
            C  C    K      C H  C  C+        +CP C+    +
Sbjct: 8   RCQQCQAEAKCPKLLPCLHTLCSGCLE---ASGMQCPICQAPWPL 49

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

 Score = 44.6 bits (106), Expect = 1e-07
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 3/43 (6%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIV---DAIRLQGRCPTC 112
            +C +CL+ +KE    +CGH FCK+CI    + +     CP C
Sbjct: 16  ASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58

>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 = 47.6 bits (112), Expect = 1e-07
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 5/63 (7%)

Query: 65  MVVVGEVRFTCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQG--RCPT--CRTRMSVR 119
            +  G++  TC I     +    S KC HVF +  I + ++      CP   C   +S+R
Sbjct: 174 QIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMR 233

Query: 120 SIR 122
              
Sbjct: 234 DFV 236

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

 Score = 45.1 bits (107), Expect = 2e-07
 Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 3/46 (6%)

Query: 73  FTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGR--CPTCRTR 115
             C IC D M +      CG+ +C  CI  A+       CPTC   
Sbjct: 14  LLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN 59

>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 = 46.6 bits (110), Expect = 2e-07
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 72  RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSVRSIRRIFF 126
           ++ C ICL  ++E   T CGH FCK+CI+ +IR  G +CP     +    +    F
Sbjct: 18  KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNF 73

>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 = 2e-06
 Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 1/53 (1%)

Query: 73  FTCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI 124
             C I     +    S K   +F KS +   ++  G  P     +S+  I  I
Sbjct: 4   MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEI 56

>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 = 41.1 bits (97), Expect = 2e-06
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 4/43 (9%)

Query: 75  CGICLDTMKEESST----KCGHVFCKSCIVDAIRLQGRCPTCR 113
           C ICL+ +           CGH+  ++C  + ++   RCP C 
Sbjct: 8   CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

>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 = 42.6 bits (100), Expect = 9e-06
 Identities = 9/51 (17%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRC-PTCRTRMSVRSIR 122
               I  + M+E   T  G  + +  I + ++  G   P  R+ ++   + 
Sbjct: 209 LCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLI 259

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

 Score = 40.4 bits (95), Expect = 1e-05
 Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 3/45 (6%)

Query: 75  CGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQGRCPTCRTRM 116
           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 = 38.9 bits (91), Expect = 3e-05
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 74  TCGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQGRCPTCRTRMSVRS 120
            C +C +      S +   C H+F  SCIV  +     CP CR  ++ ++
Sbjct: 17  ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQN 66

>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 = 38.7 bits (90), Expect = 5e-05
 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 3/37 (8%)

Query: 73  FTCGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQ 106
             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 = 38.3 bits (89), Expect = 6e-05
 Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 4/44 (9%)

Query: 74  TCGICLDTMKEESST----KCGHVFCKSCIVDAIRLQGRCPTCR 113
            C  C    K+E       +C H F   C+   ++   RCP C+
Sbjct: 28  ACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 37.4 bits (87), Expect = 8e-05
 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 74  TCGICLDTMKEESSTK---CGHVFCKSCIVDAIRLQGRCPTCRTRM 116
            C +CL+  K         C H F + C++  + ++  CP C   +
Sbjct: 17  LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>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 Length = 79

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 74  TCGICLDTMKEESSTKCGHVF-CKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQP 131
            C +C +     +   CGH   C+SC   A +LQ  CP CR+R  V  ++ ++ P    
Sbjct: 20  LCMVCCEEEINSTFCPCGHTVCCESC---AAQLQ-SCPVCRSR--VEHVQHVYLPTHTS 72

>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 Length = 64

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 5/56 (8%)

Query: 75  CGICLDTMKEES--STKCGHVF-CKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP 127
           C IC    K       K GH+  C +C     +    CP CR    ++ I   +FP
Sbjct: 11  CVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQP--IQMIVLTYFP 64

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

 Score = 35.7 bits (82), Expect = 4e-04
 Identities = 11/44 (25%), Positives = 15/44 (34%), Gaps = 3/44 (6%)

Query: 74  TCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQG--RCPTCRT 114
            C IC   + +  S   CG      C+    +     RCP C  
Sbjct: 17  ICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCND 60

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

 Score = 36.7 bits (84), Expect = 4e-04
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 23/64 (35%)

Query: 74  TCGICLDTMKEESS------------------TKCGHVFCKSCIVDAIRLQG-----RCP 110
            C IC++ +   S                   TKC H F   C++            +CP
Sbjct: 27  DCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCP 86

Query: 111 TCRT 114
           +C+T
Sbjct: 87  SCKT 90

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	135
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.66
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.64
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.62
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.62
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.62
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.58
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.58
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.58
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.57
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.57
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.57
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.57
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.56
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.56
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.56
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.56
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.55
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.54
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.54
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.53
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.52
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.52
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.5
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.5
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.49
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.49
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.49
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.49
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.48
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.46
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.46
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.46
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.45
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.45
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.44
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.44
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.44
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.43
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.42
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.42
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.42
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.41
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.4
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.38
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.38
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.38
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.37
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.37
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.37
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.35
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.35
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.34
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.31
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.3
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.3
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.27
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.25
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.24
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.21
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.19
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.17
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.15
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.12
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.04
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.93
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.92
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	98.86
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.83
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.36
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.28
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.19
3nw0_A	238	Non-structural maintenance of chromosomes element	97.52
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	97.0
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.82
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	94.92
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	94.89
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	89.78
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	89.13
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	86.5
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	84.32
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	84.21

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

Probab=99.66  E-value=3.9e-17  Score=99.11  Aligned_cols=58  Identities=36%  Similarity=0.889  Sum_probs=53.4

Q ss_pred             CCccceeeccccCccCc-------EEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           69 GEVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      ..+...|+||++.+.++       +.++|||.||..|+.+|++....||+||..+..++++++|+
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~l   71 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI   71 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCCCCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhheeeccC
Confidence            34577899999999887       88999999999999999999899999999999999999986

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

Probab=99.64  E-value=8.8e-17  Score=95.49  Aligned_cols=56  Identities=38%  Similarity=0.940  Sum_probs=51.9

Q ss_pred             ccceeeccccCccCc-------EEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           71 VRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      +.+.|+||++.+.++       +.++|||.||..|+.+|++....||+||..+..++++++|+
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            356799999999887       78999999999999999999899999999999999999986

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

Probab=99.62  E-value=5.2e-16  Score=94.68  Aligned_cols=57  Identities=28%  Similarity=0.575  Sum_probs=51.1

Q ss_pred             CCCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           68 VGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      ...+.+.|+||++.+.+|+.+ +|||.||..||..|++....||+||+.+...++...
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   68 (72)
T 2djb_A           11 ELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSG   68 (72)
T ss_dssp             CCCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCC
T ss_pred             hcCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccccc
Confidence            456788999999999999987 999999999999999988999999999988776544

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

Probab=99.62  E-value=4.1e-16  Score=96.39  Aligned_cols=58  Identities=19%  Similarity=0.346  Sum_probs=51.8

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc-CCCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|+||++.+.+|+.++|||+||..||.+|+.. ...||+||..+...++.+++
T Consensus         4 ~~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n~   62 (78)
T 1t1h_A            4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNY   62 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECT
T ss_pred             CCcccCCCCCccccccCCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccCH
Confidence            35678899999999999999999999999999999986 67899999999887777654

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

Probab=99.62  E-value=4.7e-16  Score=93.29  Aligned_cols=55  Identities=24%  Similarity=0.652  Sum_probs=48.9

Q ss_pred             CCCCccceeeccccCccCcEEcCCCCcccHHhHHHHHh-cCCCCccccccccccCc
Q 042225           67 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGRCPTCRTRMSVRSI  121 (135)
Q Consensus        67 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~  121 (135)
                      ....+.+.|+||++.+.+|+.++|||.||..|+..|+. ....||+||+.+..+++
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A           10 KTVEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV   65 (66)
T ss_dssp             CSCCCCEECTTTCCEESSCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTC
T ss_pred             hcCCcCCCCCCCChHhcCeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhc
Confidence            34567899999999999999999999999999999995 55789999999987765

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

Probab=99.58  E-value=2.5e-15  Score=93.69  Aligned_cols=59  Identities=32%  Similarity=0.770  Sum_probs=52.4

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc------CCCCccccccccccCceeecC
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL------QGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~------~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      ...+.+.|+||++.+.+|+.++|||.||..|+..|+..      ...||.||..+...++.+++.
T Consensus        15 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~   79 (85)
T 2ecw_A           15 MIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNLH   79 (85)
T ss_dssp             CCCTTTSCTTTCSCCSSCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEECSC
T ss_pred             hCccCCCCcCCChhhCcceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCcCHH
Confidence            35567889999999999999999999999999999987      568999999999888887743

>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=99.58  E-value=8.4e-16  Score=99.59  Aligned_cols=57  Identities=26%  Similarity=0.653  Sum_probs=51.8

Q ss_pred             CCccceeeccccCccCcEE-cCCCCcccHHhHHHHHhcC-CCCccccccccccCceeec
Q 042225           69 GEVRFTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~  125 (135)
                      +.+.+.|+||++.+.+|+. ++|||.||..||..|+... ..||+||..+...++..++
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            4567889999999999999 9999999999999999987 6999999999988887764

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

Probab=99.58  E-value=1.9e-15  Score=92.08  Aligned_cols=54  Identities=31%  Similarity=0.693  Sum_probs=47.9

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHh---cCCCCccccccccccCc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR---LQGRCPTCRTRMSVRSI  121 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~---~~~~CP~Cr~~~~~~~~  121 (135)
                      ...+.+.|+||++.+.+|+.++|||.||..|+..|++   ....||+||..+..+++
T Consensus        16 ~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~   72 (73)
T 2ysl_A           16 KLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI   72 (73)
T ss_dssp             CCCCCCBCTTTCSBCSSEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCCC
T ss_pred             hCccCCEeccCCcccCCeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcccC
Confidence            4567889999999999999999999999999999997   34689999999987665

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

Probab=99.57  E-value=2e-15  Score=92.63  Aligned_cols=51  Identities=29%  Similarity=0.633  Sum_probs=45.5

Q ss_pred             CCCccceeeccccCccCcEEcC-CCCcccHHhHHHHHhcC--CCCccccccccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQ--GRCPTCRTRMSV  118 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~  118 (135)
                      ...+.+.|+||++.+.+|+.++ |||.||..||..|+...  ..||+||+.+..
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           11 PIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CSCGGGSCSSSCCCCTTCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             cCCCCCCCcCCChHHhCCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            4567889999999999999999 99999999999999865  689999997643

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

Probab=99.57  E-value=2.6e-15  Score=94.71  Aligned_cols=58  Identities=14%  Similarity=0.090  Sum_probs=53.0

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|+||++++.+|++++|||+||..||..|+....+||+|+..+...+++++.
T Consensus        10 ~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn~   67 (85)
T 2kr4_A           10 DAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPVP   67 (85)
T ss_dssp             TCCTTTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEECH
T ss_pred             cCchheECcccCchhcCCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchHH
Confidence            4567899999999999999999999999999999999888999999999988887763

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

Probab=99.57  E-value=5.8e-16  Score=95.71  Aligned_cols=58  Identities=29%  Similarity=0.665  Sum_probs=51.3

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc-------CCCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-------QGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-------~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|+||++.+.+|+.++|||.||..|+..|+..       ...||+||..+...++.+++
T Consensus         8 ~~~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~   72 (79)
T 2egp_A            8 NVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQANQ   72 (79)
T ss_dssp             CCCCCCEETTTTEECSSCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGTCS
T ss_pred             hcccCCCCcCCCcccCCeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCcCH
Confidence            45678899999999999999999999999999999986       56899999999887776654

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

Probab=99.57  E-value=9.6e-16  Score=93.24  Aligned_cols=54  Identities=33%  Similarity=0.639  Sum_probs=48.7

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCce
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~  122 (135)
                      ..+.+.|+||++.+.+++.++|||.||..|+..|+.....||+||..+...++.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   65 (71)
T 2d8t_A           12 SLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDFLD   65 (71)
T ss_dssp             SSSCCBCSSSSSBCSSEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHHHS
T ss_pred             CCCCCCCccCCcccCCCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhhcc
Confidence            456788999999999999999999999999999999889999999999876553

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

Probab=99.56  E-value=2.3e-15  Score=89.95  Aligned_cols=57  Identities=26%  Similarity=0.605  Sum_probs=50.0

Q ss_pred             ccceeecccc-CccCc----EEcCCCCcccHHhHHHHHhc-CCCCccccccccccCceeecCC
Q 042225           71 VRFTCGICLD-TMKEE----SSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        71 ~~~~C~IC~~-~~~~p----~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      +++.|+||++ .+.++    +.++|||.||..|+.+|+.. ...||+||+.+..+++.+++|.
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            3577999999 88888    57899999999999999764 4679999999999999998875

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

Probab=99.56  E-value=4.9e-15  Score=94.22  Aligned_cols=57  Identities=28%  Similarity=0.568  Sum_probs=48.2

Q ss_pred             CCCccceeeccccCccCcEEcC-CCCcccHHhHHHHHhcC--CCCccccccc-cccCceee
Q 042225           68 VGEVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQ--GRCPTCRTRM-SVRSIRRI  124 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~-~~~~~~~~  124 (135)
                      ...+.+.|+||++.+.+|++++ |||+||..||..|+...  ..||+||..+ ...++.+.
T Consensus         9 ~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~~~~n   69 (92)
T 3ztg_A            9 PIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIAN   69 (92)
T ss_dssp             CCCTTTEETTTTEECSSCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCTTSCEEC
T ss_pred             cCCcCCCCCCCChhhcCceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCccccCcC
Confidence            4567899999999999999999 99999999999999743  5899999997 44455443

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

Probab=99.56  E-value=2.8e-15  Score=93.52  Aligned_cols=58  Identities=31%  Similarity=0.718  Sum_probs=51.6

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc------CCCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL------QGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~------~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|+||++.+.+|+.++|||.||..|+..|+..      ...||.||..+...++.+++
T Consensus        15 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~   78 (85)
T 2ecv_A           15 NVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNR   78 (85)
T ss_dssp             CCCCCCCCTTTCSCCSSCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCSC
T ss_pred             HccCCCCCCCCCcccCCceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCccH
Confidence            45567889999999999999999999999999999986      67899999999988777664

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

Probab=99.56  E-value=5.5e-15  Score=91.97  Aligned_cols=50  Identities=34%  Similarity=0.769  Sum_probs=46.1

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      .....+.|+||++.+.+|+.++|||.||..|+..|+.....||+||..+.
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           11 EEEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCCSBCSSSCSBCCSEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             cCCCCCCCcCCCchhcCeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34567889999999999999999999999999999998889999999986

>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=99.55  E-value=4.5e-15  Score=96.00  Aligned_cols=58  Identities=16%  Similarity=0.047  Sum_probs=52.9

Q ss_pred             CCCccceeeccccCccCcEEcCCC-CcccHHhHHHHHhcCCCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCG-HVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~Cg-H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|+||+++|.+|++++|| |+||..||..|+.....||+|+..+...++++++
T Consensus        18 ~~p~~~~CpI~~~~m~dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn~   76 (98)
T 1wgm_A           18 DACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNT   76 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECH
T ss_pred             cCcHhcCCcCccccccCCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEcH
Confidence            356789999999999999999999 9999999999999888999999999988887763

>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=99.54  E-value=6.3e-15  Score=95.64  Aligned_cols=58  Identities=12%  Similarity=0.096  Sum_probs=53.0

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|+||++++.+|++++|||+||..||..|+....+||+|+..+...++++++
T Consensus        25 ~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn~   82 (100)
T 2kre_A           25 DAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVP   82 (100)
T ss_dssp             SCSTTTBCTTTCSBCSSEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEECH
T ss_pred             cCcHhhCCcCccCcccCCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceECH
Confidence            4567899999999999999999999999999999999888999999999988887763

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

Probab=99.54  E-value=6e-15  Score=92.77  Aligned_cols=54  Identities=26%  Similarity=0.707  Sum_probs=47.8

Q ss_pred             CCCccceeeccccCccC----cEEcCCCCcccHHhHHHHHhcC---CCCccccccccccCc
Q 042225           68 VGEVRFTCGICLDTMKE----ESSTKCGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVRSI  121 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~  121 (135)
                      ...+.+.|+||++.+.+    ++.++|||.||..|+..|++..   ..||+||..+...++
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~i   71 (88)
T 2ct2_A           11 ALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSL   71 (88)
T ss_dssp             CCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSST
T ss_pred             hccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchhH
Confidence            45667889999999998    9999999999999999999875   789999999876544

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

Probab=99.53  E-value=5.1e-15  Score=89.00  Aligned_cols=51  Identities=39%  Similarity=0.922  Sum_probs=45.6

Q ss_pred             CCCccceeeccccCccCc-------EEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           68 VGEVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      ...+...|+||++.+.++       +.++|||.||..|+..|++....||+||..+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           11 RPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            345678899999999887       889999999999999999998999999998864

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

Probab=99.52  E-value=6.7e-15  Score=94.88  Aligned_cols=56  Identities=23%  Similarity=0.653  Sum_probs=50.1

Q ss_pred             CCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           69 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      ..+.+.|+||++.+.+|+.+ +|||.||..|+..|+.....||+||..+...++.++
T Consensus        19 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~n   75 (99)
T 2y43_A           19 IDDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNN   75 (99)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             CCCCCCcccCChhhCCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCCcC
Confidence            34578899999999999988 899999999999999988899999999987777654

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

Probab=99.52  E-value=4.5e-15  Score=101.27  Aligned_cols=50  Identities=30%  Similarity=0.756  Sum_probs=45.7

Q ss_pred             CccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCcccccccccc
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR  119 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  119 (135)
                      .+++.|+||++.+.+|+.++|||.||..||..|+.....||+||+.+...
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            35678999999999999999999999999999999999999999998643

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

Probab=99.50  E-value=1.4e-14  Score=89.39  Aligned_cols=56  Identities=23%  Similarity=0.568  Sum_probs=47.8

Q ss_pred             CCCccceeeccccCccCc---EEcCCCCcccHHhHHHHHhcCCCCccccccccccCcee
Q 042225           68 VGEVRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRR  123 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~  123 (135)
                      .......|+||++.+.++   +.++|||.||..||.+|++....||+||+.+...++..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   69 (78)
T 2ect_A           11 HVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTAT   69 (78)
T ss_dssp             TSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCC
T ss_pred             cCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCC
Confidence            345677899999999865   56799999999999999998899999999998776654

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

Probab=99.50  E-value=9.9e-15  Score=97.73  Aligned_cols=50  Identities=32%  Similarity=0.664  Sum_probs=45.1

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC-CCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~  118 (135)
                      ..+.+.|+||++.+.+|+.++|||+||..||..|+... ..||.||..+..
T Consensus        49 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           49 VEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CccCCCCCcCChHHcCcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            34678899999999999999999999999999999854 489999999976

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

Probab=99.49  E-value=3.1e-14  Score=84.42  Aligned_cols=45  Identities=33%  Similarity=0.757  Sum_probs=40.5

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHh---cCCCCccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR---LQGRCPTC  112 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~---~~~~CP~C  112 (135)
                      ...+.+.|+||++.+.+|+.++|||.||..||.+|++   ....||+|
T Consensus        16 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           16 KLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCBCTTTCSBCSSCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             hCccCCCCCcCCchhCCeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            4567889999999999999999999999999999998   34589988

>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=99.49  E-value=2e-14  Score=95.53  Aligned_cols=60  Identities=33%  Similarity=0.695  Sum_probs=52.1

Q ss_pred             CcCCCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCC-CCccccccccccCceee
Q 042225           65 MVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        65 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~~~~  124 (135)
                      ......+.+.|+||++.+.+|+.++|||+||..||..|+.... .||+||..+...++++.
T Consensus        11 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~   71 (118)
T 3hct_A           11 FDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD   71 (118)
T ss_dssp             BSSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEEC
T ss_pred             hccCCCCCCCCCcCChhhcCeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhcccC
Confidence            3345778899999999999999999999999999999998664 89999999988766543

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

Probab=99.49  E-value=9.9e-15  Score=88.29  Aligned_cols=55  Identities=27%  Similarity=0.553  Sum_probs=47.9

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccccCcee
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRR  123 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~  123 (135)
                      ...+...|+||++.+.+ +.++|||.||..|+..|+.....||+||..+...+...
T Consensus        11 ~~~~~~~C~IC~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   65 (70)
T 2ecn_A           11 QLTDEEECCICMDGRAD-LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESS   65 (70)
T ss_dssp             CCCCCCCCSSSCCSCCS-EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCCC
T ss_pred             cCCCCCCCeeCCcCccC-cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCccc
Confidence            34567889999999999 99999999999999999998899999999998655433

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

Probab=99.49  E-value=1.5e-14  Score=96.99  Aligned_cols=59  Identities=36%  Similarity=0.875  Sum_probs=54.3

Q ss_pred             CccceeeccccCccCc-------EEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeecCCC
Q 042225           70 EVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQ  128 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~  128 (135)
                      .+.+.|+||++.+.++       +.++|||.||..||.+|++....||+||+.+..+++.++|+..
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            4567899999999988       8999999999999999999999999999999999999988764

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

Probab=99.48  E-value=2.3e-14  Score=93.79  Aligned_cols=51  Identities=25%  Similarity=0.656  Sum_probs=46.9

Q ss_pred             CCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCcccccccccc
Q 042225           69 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR  119 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  119 (135)
                      ..+.+.|+||++.+.+|+.+ +|||+||..||..|+.....||.||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HGGGTBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCcCCCccCChHHhCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            45688899999999999997 9999999999999999889999999998764

>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=99.46  E-value=6.8e-14  Score=84.33  Aligned_cols=50  Identities=24%  Similarity=0.670  Sum_probs=43.3

Q ss_pred             CCccceeeccccCcc---CcEEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           69 GEVRFTCGICLDTMK---EESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      ......|+||++.+.   .++.++|||.||..|+..|++....||+||..+..
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   63 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEA   63 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCS
T ss_pred             CCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccC
Confidence            455678999999885   35778999999999999999988899999998864

>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=99.46  E-value=2.7e-14  Score=93.65  Aligned_cols=56  Identities=36%  Similarity=0.879  Sum_probs=49.0

Q ss_pred             CccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC---CCCccccccccccCceeec
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~~~~  125 (135)
                      .+.+.|+||++.+.+|+.++|||.||..|+..|+...   ..||+||..+...++..++
T Consensus        19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~~~   77 (112)
T 1jm7_A           19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQEST   77 (112)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCC
T ss_pred             cCCCCCcccChhhcCeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCccH
Confidence            3467899999999999999999999999999999865   3899999999987776653

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

Probab=99.46  E-value=2.2e-14  Score=96.23  Aligned_cols=58  Identities=38%  Similarity=0.935  Sum_probs=53.4

Q ss_pred             CCccceeeccccCccCc-------EEcCCCCcccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           69 GEVRFTCGICLDTMKEE-------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      ..+...|+||++.+.++       +.++|||.||..|+.+|++..++||+||..+..++++++|+
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  133 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI  133 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGEEEECC
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcceeeeC
Confidence            34677899999999876       88999999999999999999999999999999999999986

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

Probab=99.45  E-value=1.4e-13  Score=87.58  Aligned_cols=50  Identities=26%  Similarity=0.613  Sum_probs=44.4

Q ss_pred             CCccceeeccccCccC---cEEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      ..+...|+||++.+.+   .+.++|||.||..||..|++....||+||+.+..
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            4567889999998887   6788999999999999999988999999998763

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

Probab=99.45  E-value=9.8e-14  Score=83.33  Aligned_cols=47  Identities=34%  Similarity=0.735  Sum_probs=42.9

Q ss_pred             ccceeeccccCccCc-EEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           71 VRFTCGICLDTMKEE-SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ....|+||++.+.++ +.++|||.||..|+..|++....||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            456799999999986 78899999999999999998899999999886

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

Probab=99.44  E-value=5.6e-14  Score=81.03  Aligned_cols=48  Identities=25%  Similarity=0.670  Sum_probs=42.3

Q ss_pred             CccceeeccccCccC---cEEcC-CCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           70 EVRFTCGICLDTMKE---ESSTK-CGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~---p~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ++...|+||++.+.+   ++.++ |||.||..|+.+|++....||+||+.+.
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            456779999999987   67776 9999999999999999899999998764

>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=99.44  E-value=6.4e-14  Score=80.69  Aligned_cols=47  Identities=28%  Similarity=0.685  Sum_probs=41.9

Q ss_pred             ccceeeccccCccC----cEEcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           71 VRFTCGICLDTMKE----ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        71 ~~~~C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ....|+||++.+.+    ++.++|||.||..|+.+|++....||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            45679999999865    678899999999999999998899999998775

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

Probab=99.44  E-value=5e-14  Score=97.55  Aligned_cols=51  Identities=29%  Similarity=0.688  Sum_probs=46.2

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCC-CCcccccccccc
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMSVR  119 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~  119 (135)
                      ..+.+.|+||++.+.+|+.++|||+||..||..|+.... .||+||..+...
T Consensus        75 l~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           75 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CccCCEeecCChhhcCCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            346789999999999999999999999999999998654 899999999866

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

Probab=99.43  E-value=9.1e-14  Score=80.83  Aligned_cols=45  Identities=38%  Similarity=0.847  Sum_probs=39.6

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHh---cCCCCccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR---LQGRCPTC  112 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~---~~~~CP~C  112 (135)
                      ...+.+.|+||++.+.+|+.++|||.||..||..|+.   ....||+|
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           11 NLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CSCCCCBCSSSCCBCSSCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccccCCCCccCCcccCccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4556788999999999999999999999999999955   45689987

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

Probab=99.42  E-value=7.7e-14  Score=85.51  Aligned_cols=50  Identities=20%  Similarity=0.561  Sum_probs=44.2

Q ss_pred             CCccceeeccccCccCc---EEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      ..+...|+||++.+.++   +.++|||.||..|+..|++....||+||+.+..
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            34567899999999876   678999999999999999988999999998864

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

Probab=99.42  E-value=7.2e-14  Score=92.42  Aligned_cols=55  Identities=25%  Similarity=0.695  Sum_probs=48.8

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc-CCCCccccccccccCcee
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRR  123 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~  123 (135)
                      ..+.+.|+||++.+.+|+.++|||.||..||..|+.. ...||+||..+...++..
T Consensus        20 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (116)
T 1rmd_A           20 FVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (116)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             ccCCCCCCCCCcHhcCcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhccc
Confidence            3457889999999999999999999999999999986 678999999998776643

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

Probab=99.42  E-value=9.8e-14  Score=84.72  Aligned_cols=51  Identities=22%  Similarity=0.628  Sum_probs=43.7

Q ss_pred             CCCccceeeccccCccCc---EEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           68 VGEVRFTCGICLDTMKEE---SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      .......|+||++.+.++   +.++|||.||..||.+|++....||+||+.+..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2ep4_A           11 ELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQ   64 (74)
T ss_dssp             CCCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSS
T ss_pred             cCCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccc
Confidence            345677899999999865   345999999999999999988899999998864

>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=99.41  E-value=3.1e-14  Score=94.08  Aligned_cols=51  Identities=31%  Similarity=0.772  Sum_probs=45.7

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc-CCCCccccccccc
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSV  118 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~  118 (135)
                      ...+++.|+||++.+.+|+.++|||+||..|+..|+.. ...||.||..+..
T Consensus        11 ~~~~~~~C~iC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           11 PSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CCHHHHBCTTTCSBCSSCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCCCccCCcccCceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            45568999999999999999999999999999999976 5689999998863

>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=99.40  E-value=1.5e-13  Score=88.05  Aligned_cols=56  Identities=30%  Similarity=0.628  Sum_probs=48.1

Q ss_pred             CCccceeeccccCccCcEEcC-CCCcccHHhHHHHHhcC------CCCcc--cccc-ccccCceee
Q 042225           69 GEVRFTCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQ------GRCPT--CRTR-MSVRSIRRI  124 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~------~~CP~--Cr~~-~~~~~~~~~  124 (135)
                      ..+.+.|+||+++|.+|++++ |||+||..||..|+...      ..||+  |+.. +...+|+++
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            346788999999999999996 99999999999999853      48999  8877 777777765

>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=99.38  E-value=2.5e-13  Score=101.24  Aligned_cols=57  Identities=14%  Similarity=0.121  Sum_probs=51.0

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC-CCCccccccccccCceee
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~  124 (135)
                      ...+.+.|+||++.+.+|++++|||+||..||..|+... ..||+|+.++...+++++
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            456789999999999999999999999999999999864 459999999998888765

>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=99.38  E-value=2e-13  Score=95.52  Aligned_cols=50  Identities=40%  Similarity=0.922  Sum_probs=45.1

Q ss_pred             CCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhc-CCCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRL-QGRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~  118 (135)
                      ..+.+.|+||++.+.+|+.+ +|||.||..||..|+.. ...||+||..+..
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            45678999999999999987 99999999999999997 6789999999854

>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=99.38  E-value=3.2e-13  Score=80.63  Aligned_cols=57  Identities=28%  Similarity=0.563  Sum_probs=49.8

Q ss_pred             CCccceeeccccCccCcEEc--CCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecCC
Q 042225           69 GEVRFTCGICLDTMKEESST--KCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~--~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      ..++..|+||++...+++.+  +|||. ||..|+..|.+....||+||..+.  .++++|++
T Consensus         5 ~~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~--~~i~i~~~   64 (64)
T 2vje_A            5 LNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ--MIVLTYFP   64 (64)
T ss_dssp             CGGGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC--EEEEEECC
T ss_pred             CCCcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh--ceEeeecC
Confidence            34566799999999999877  99999 899999999998889999999986  48888864

>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=99.37  E-value=2.9e-13  Score=95.02  Aligned_cols=59  Identities=32%  Similarity=0.683  Sum_probs=51.7

Q ss_pred             CcCCCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC-CCCccccccccccCcee
Q 042225           65 MVVVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSVRSIRR  123 (135)
Q Consensus        65 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~  123 (135)
                      +...+.+.+.|+||++.+.+|++++|||+||..|+..|+... ..||.||..+...++++
T Consensus        11 ~~~~~~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   70 (170)
T 3hcs_A           11 FDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFP   70 (170)
T ss_dssp             ESSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEE
T ss_pred             hccCCCCCCCCCCCChhhcCcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhh
Confidence            344677899999999999999999999999999999999864 48999999998876654

>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=99.37  E-value=1.6e-13  Score=94.14  Aligned_cols=51  Identities=20%  Similarity=0.632  Sum_probs=45.7

Q ss_pred             CCCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCC-CCcccccccc
Q 042225           67 VVGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG-RCPTCRTRMS  117 (135)
Q Consensus        67 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~  117 (135)
                      ....+.+.|+||++.+.+|++++|||+||..||..|+.... .||+||..+.
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            35678899999999999999999999999999999998664 8999999764

>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=99.37  E-value=5.9e-14  Score=93.13  Aligned_cols=53  Identities=28%  Similarity=0.748  Sum_probs=46.7

Q ss_pred             CccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           70 EVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      .+.+.|+||++.+.+|+.+ +|||+||..||..|+.  ..||+||..+...++.++
T Consensus        20 ~~~~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~n   73 (117)
T 1jm7_B           20 EKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKIN   73 (117)
T ss_dssp             HHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCC
T ss_pred             hhCCCCCCCChHhhCccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcccccccc
Confidence            4578899999999999999 9999999999999987  789999999976666543

>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=99.35  E-value=6.3e-13  Score=87.48  Aligned_cols=48  Identities=29%  Similarity=0.604  Sum_probs=40.5

Q ss_pred             ccceeeccccCccCcE------------------EcCCCCcccHHhHHHHHh-----cCCCCccccccccc
Q 042225           71 VRFTCGICLDTMKEES------------------STKCGHVFCKSCIVDAIR-----LQGRCPTCRTRMSV  118 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~------------------~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~  118 (135)
                      .+..|+||++.|.++.                  .++|||.||..||..|+.     ....||+||..+..
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCC
Confidence            3468999999987653                  789999999999999994     45689999998864

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

Probab=99.35  E-value=4.1e-13  Score=83.68  Aligned_cols=50  Identities=26%  Similarity=0.568  Sum_probs=41.6

Q ss_pred             ccceeeccccCccC--------------cEEc-CCCCcccHHhHHHHHhcCCCCccccccccccC
Q 042225           71 VRFTCGICLDTMKE--------------ESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRS  120 (135)
Q Consensus        71 ~~~~C~IC~~~~~~--------------p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  120 (135)
                      ++..|+||++.+.+              .+.+ +|||.||..||.+|++...+||+||+.+...+
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~   78 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQR   78 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchhh
Confidence            45569999998865              3444 59999999999999999999999999987554

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=99.34  E-value=7.9e-13  Score=93.87  Aligned_cols=58  Identities=14%  Similarity=0.124  Sum_probs=52.1

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC-CCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|+||++++.+|++++|||+||..||..|+... .+||+|+.++...++++++
T Consensus       102 ~ip~~f~CPI~~elm~DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN~  160 (179)
T 2f42_A          102 EIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNL  160 (179)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECH
T ss_pred             CCcHhhcccCccccCCCCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcchH
Confidence            456899999999999999999999999999999999864 4699999999988888763

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

Probab=99.31  E-value=5.5e-13  Score=81.76  Aligned_cols=51  Identities=29%  Similarity=0.718  Sum_probs=44.5

Q ss_pred             CccceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      .+...|+||++.+.+++.++|||. ||..|+..|    ..||+||+.+..  ...+|+
T Consensus        22 ~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~--~~~i~~   73 (74)
T 4ic3_A           22 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF--KQKILM   73 (74)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE--EEECBC
T ss_pred             ccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC--cEEEee
Confidence            356789999999999999999999 999999887    789999998875  566665

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

Probab=99.30  E-value=3.5e-13  Score=78.32  Aligned_cols=46  Identities=22%  Similarity=0.552  Sum_probs=40.7

Q ss_pred             CccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      .+.+.|+||++.+.+|+.++|||+||..|+..|   ...||+||+.+..
T Consensus         4 ~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSC
T ss_pred             ccCCCceEeCCccCCeEEcCCCCcccHHHHccC---CCCCCcCCcEeec
Confidence            457789999999999999999999999999773   5689999998864

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

Probab=99.30  E-value=2.5e-12  Score=79.75  Aligned_cols=54  Identities=22%  Similarity=0.559  Sum_probs=43.6

Q ss_pred             CCccceeeccccCcc--CcEEcC--CCCcccHHhHHHHHhc-CCCCccccccccccCce
Q 042225           69 GEVRFTCGICLDTMK--EESSTK--CGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~--~p~~~~--CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~  122 (135)
                      ..+++.|+||++.+.  ++..++  |||.||..|+..++.. ...||.||+.+....+.
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             cccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            456788999999884  345554  9999999999998753 46899999999877664

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

Probab=99.27  E-value=2.3e-12  Score=76.63  Aligned_cols=55  Identities=18%  Similarity=0.596  Sum_probs=47.5

Q ss_pred             CccceeeccccCccCcEEc--CCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           70 EVRFTCGICLDTMKEESST--KCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~--~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      .....|.||++...+++.+  +|||. ||..|+..|.+....||+||+.+.  +++++|+
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~--~~i~i~~   62 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ--LVIKVFI   62 (63)
T ss_dssp             GGGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC--EEEEEEE
T ss_pred             CcCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh--ceEEEec
Confidence            3456799999999999877  99998 999999999988889999999985  4777764

>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=99.25  E-value=3e-12  Score=75.80  Aligned_cols=56  Identities=20%  Similarity=0.284  Sum_probs=51.4

Q ss_pred             cceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCccccccccccCceeecCC
Q 042225           72 RFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      .+.|+|+++.+.+|+.+ ++||+|++.||.+|++...+||+.+.++..++++++...
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            46799999999999999 999999999999999977789999999999999998754

>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=99.24  E-value=5e-12  Score=82.72  Aligned_cols=48  Identities=23%  Similarity=0.476  Sum_probs=41.2

Q ss_pred             ccceeeccccCccCc------------------EEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           71 VRFTCGICLDTMKEE------------------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p------------------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      ++..|+||++.+.++                  +.++|||.||..||..|+....+||+||+.+..
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            345699999988854                  457999999999999999999999999998753

>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=99.21  E-value=5.7e-12  Score=98.76  Aligned_cols=51  Identities=27%  Similarity=0.617  Sum_probs=45.7

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHh-cCCCCccccccccccCc
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIR-LQGRCPTCRTRMSVRSI  121 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~  121 (135)
                      ....|+||++.+.+++.++|||.||..|+..|+. ....||+||..+....+
T Consensus       331 ~~~~C~ICle~~~~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~  382 (389)
T 2y1n_A          331 TFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP  382 (389)
T ss_dssp             SSSBCTTTSSSBCCEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEE
T ss_pred             CCCCCCccCcCCCCeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCcee
Confidence            3468999999999999999999999999999998 67899999999986544

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

Probab=99.19  E-value=4.5e-12  Score=77.74  Aligned_cols=51  Identities=31%  Similarity=0.740  Sum_probs=42.7

Q ss_pred             CccceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      .+...|+||++.+.+++.++|||. ||..|+..    ...||+||..+..  .+.+|+
T Consensus        23 ~~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~--~~~i~~   74 (75)
T 2ecg_A           23 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITF--KQKIFM   74 (75)
T ss_dssp             HHHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCC--CCBCCC
T ss_pred             CCCCCCCcCCCCCCCEEEecCCCHHHHHHHhhC----CCCCccCCceecC--cEEEec
Confidence            346679999999999999999999 99999964    4789999998865  455554

>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=99.17  E-value=1.2e-11  Score=92.18  Aligned_cols=57  Identities=28%  Similarity=0.532  Sum_probs=50.2

Q ss_pred             CCCccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcC--CCCcc--ccccccccCceee
Q 042225           68 VGEVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQ--GRCPT--CRTRMSVRSIRRI  124 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~--~~CP~--Cr~~~~~~~~~~~  124 (135)
                      .....+.||||+++|.+||+. .|||+||+.||..|+...  ..||+  |++.+...++.+.
T Consensus       177 ~~~~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN  238 (267)
T 3htk_C          177 GGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRD  238 (267)
T ss_dssp             SSBCCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEEC
T ss_pred             CCceeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcC
Confidence            456789999999999999985 999999999999999854  47999  9999998888765

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

Probab=99.15  E-value=4.5e-11  Score=72.10  Aligned_cols=53  Identities=23%  Similarity=0.478  Sum_probs=44.8

Q ss_pred             CCccceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecCC
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      ..+...|.||++...+++.++|||. ||..|+..    ...||+||..+..  ++.+|.+
T Consensus        12 ~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~--~~~i~~~   65 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE--SFALSGP   65 (68)
T ss_dssp             CCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC--EECCCSS
T ss_pred             CCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhc----CCCCCCCCcchhc--eEEeecC
Confidence            4457789999999999999999999 99999984    5789999998875  6666654

>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=99.12  E-value=1.3e-11  Score=76.62  Aligned_cols=52  Identities=27%  Similarity=0.820  Sum_probs=45.3

Q ss_pred             ccceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecCCC
Q 042225           71 VRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQ  128 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~  128 (135)
                      +...|+||++.+.+++.++|||. ||..|+..|    ..||+||..+..  .+.+|++.
T Consensus        17 ~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~--~~~i~~p~   69 (79)
T 2yho_A           17 EAMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEH--VQHVYLPT   69 (79)
T ss_dssp             HHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE--EEECBCTT
T ss_pred             CCCEeEEeCcccCcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhC--eEEEEeCc
Confidence            45679999999999999999999 999999865    489999999876  67788765

>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=99.04  E-value=2.6e-11  Score=80.55  Aligned_cols=47  Identities=21%  Similarity=0.463  Sum_probs=0.4

Q ss_pred             cceeeccccCccCc------------------EEcCCCCcccHHhHHHHHhcCCCCccccccccc
Q 042225           72 RFTCGICLDTMKEE------------------SSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV  118 (135)
Q Consensus        72 ~~~C~IC~~~~~~p------------------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  118 (135)
                      +..|+||++.+.++                  +.++|+|.||..||.+|++....||+||+.+..
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             C----------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            45799999998763                  125899999999999999999999999998754

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

Probab=98.93  E-value=5.9e-10  Score=69.26  Aligned_cols=49  Identities=20%  Similarity=0.438  Sum_probs=40.8

Q ss_pred             CccceeeccccCcc--CcEEcCCC-----CcccHHhHHHHHhcC--CCCccccccccc
Q 042225           70 EVRFTCGICLDTMK--EESSTKCG-----HVFCKSCIVDAIRLQ--GRCPTCRTRMSV  118 (135)
Q Consensus        70 ~~~~~C~IC~~~~~--~p~~~~Cg-----H~fc~~Ci~~~~~~~--~~CP~Cr~~~~~  118 (135)
                      .+...|.||++.+.  ++..++|+     |.||..||.+|+...  ..||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~   70 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIM   70 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCC
T ss_pred             CCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeec
Confidence            34567999998774  56788996     999999999999865  589999998864

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.92  E-value=2.2e-10  Score=88.82  Aligned_cols=50  Identities=30%  Similarity=0.734  Sum_probs=43.2

Q ss_pred             ccceeeccccCccCcEEcCCCCc-ccHHhHHHHHhcCCCCccccccccccCceeecC
Q 042225           71 VRFTCGICLDTMKEESSTKCGHV-FCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFF  126 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~  126 (135)
                      +...|+||++.+.+++.++|||. ||..|+..|    ..||+||..+..  ...+|+
T Consensus       294 ~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~--~~~i~~  344 (345)
T 3t6p_A          294 EERTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKG--TVRTFL  344 (345)
T ss_dssp             TTCBCTTTSSSBCCEEEETTCCEEECTTTGGGC----SBCTTTCCBCCE--EEECC-
T ss_pred             CCCCCCccCCcCCceEEcCCCChhHhHHHHhcC----CcCCCCCCCccC--eEEeec
Confidence            46789999999999999999999 999999877    689999999874  556654

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

Probab=98.86  E-value=4.7e-09  Score=64.20  Aligned_cols=48  Identities=23%  Similarity=0.578  Sum_probs=40.3

Q ss_pred             CccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcC--CCCcccccccc
Q 042225           70 EVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQ--GRCPTCRTRMS  117 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~  117 (135)
                      +....|+||.+.+.....- .|+|.|+..||.+|++..  ..||+|+..+.
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             CCCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            3456799999998865443 899999999999999977  78999998775

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

Probab=98.83  E-value=4.5e-10  Score=71.46  Aligned_cols=52  Identities=27%  Similarity=0.673  Sum_probs=41.1

Q ss_pred             ccceeeccccCccCcEEc---CCCCcccHHhHHHHHhc--------CCCCcc--cccc--ccccCce
Q 042225           71 VRFTCGICLDTMKEESST---KCGHVFCKSCIVDAIRL--------QGRCPT--CRTR--MSVRSIR  122 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~~--------~~~CP~--Cr~~--~~~~~~~  122 (135)
                      +.+.|+||++.+..+..+   +|||.||..|+..++..        ...||.  |+..  +....+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~~i~   70 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIE   70 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHH
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHHHHH
Confidence            467799999999877443   79999999999999873        136999  9998  6655444

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

Probab=98.36  E-value=3.4e-07  Score=53.57  Aligned_cols=49  Identities=22%  Similarity=0.493  Sum_probs=39.1

Q ss_pred             CccceeeccccCccCcEEcCCC--C---cccHHhHHHHHhc--CCCCccccccccc
Q 042225           70 EVRFTCGICLDTMKEESSTKCG--H---VFCKSCIVDAIRL--QGRCPTCRTRMSV  118 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~Cg--H---~fc~~Ci~~~~~~--~~~CP~Cr~~~~~  118 (135)
                      ++...|.||++...++..+||.  +   .||..|+.+|+..  ...||+|+..+..
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            4556799999877667677865  4   7999999999984  5689999988753

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

Probab=98.28  E-value=1.3e-07  Score=72.96  Aligned_cols=49  Identities=22%  Similarity=0.615  Sum_probs=38.8

Q ss_pred             CccceeeccccCccC----cE----EcCCCCcccHHhHHHHHhcC-----------CCCccccccccc
Q 042225           70 EVRFTCGICLDTMKE----ES----STKCGHVFCKSCIVDAIRLQ-----------GRCPTCRTRMSV  118 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~----p~----~~~CgH~fc~~Ci~~~~~~~-----------~~CP~Cr~~~~~  118 (135)
                      +....|+||+..+.+    |.    ...|||.||..|+.+|++..           ..||+||+++..
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            456779999998876    21    23799999999999999732           369999998863

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.19  E-value=1.2e-06  Score=56.07  Aligned_cols=45  Identities=27%  Similarity=0.580  Sum_probs=37.4

Q ss_pred             eeeccccCccC-cEEcCCCCcccHHhHHHHHh-cCCCCccccccccc
Q 042225           74 TCGICLDTMKE-ESSTKCGHVFCKSCIVDAIR-LQGRCPTCRTRMSV  118 (135)
Q Consensus        74 ~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~  118 (135)
                      .|++|.-.+.. ...+||.|.||.+|+..|.+ ..+.||.|+..+..
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            48888887775 45779999999999999986 45889999998864

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

Probab=97.52  E-value=7.2e-05  Score=55.04  Aligned_cols=47  Identities=23%  Similarity=0.571  Sum_probs=39.1

Q ss_pred             cceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCC--CCccccccccc
Q 042225           72 RFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQG--RCPTCRTRMSV  118 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~--~CP~Cr~~~~~  118 (135)
                      ...|.+|.+.......- .|+|.||..|+..|++...  .||.|+.....
T Consensus       180 i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             CCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            56799999988876655 4999999999999998654  89999887654

>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=97.00  E-value=0.00067  Score=58.46  Aligned_cols=58  Identities=12%  Similarity=0.019  Sum_probs=52.7

Q ss_pred             CCCccceeeccccCccCcEEcCCC-CcccHHhHHHHHhcCCCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCG-HVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~Cg-H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      ...+.+.|||-.+.+.+||.++.| ++|=...|.+|+....+||.-|.++...++++++
T Consensus       887 ~iP~~F~cPIs~~lM~DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN~  945 (968)
T 3m62_A          887 DVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNE  945 (968)
T ss_dssp             CSCGGGBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECH
T ss_pred             CCcHHhCCcchhhHHhCCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcccccccH
Confidence            456799999999999999999998 5899999999999888999999999988888763

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.82  E-value=0.0005  Score=43.49  Aligned_cols=32  Identities=16%  Similarity=0.626  Sum_probs=27.0

Q ss_pred             ccceeeccccC-ccCcEE--cCCCCcccHHhHHHH
Q 042225           71 VRFTCGICLDT-MKEESS--TKCGHVFCKSCIVDA  102 (135)
Q Consensus        71 ~~~~C~IC~~~-~~~p~~--~~CgH~fc~~Ci~~~  102 (135)
                      +++.|.||.+. +.+++.  +.|+|.||..|+..+
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            35779999975 677777  899999999999983

>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=94.89  E-value=0.04  Score=33.64  Aligned_cols=36  Identities=25%  Similarity=0.736  Sum_probs=29.7

Q ss_pred             CCccceeeccccCccCcEEcCC----CCcccHHhHHHHHh
Q 042225           69 GEVRFTCGICLDTMKEESSTKC----GHVFCKSCIVDAIR  104 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~C----gH~fc~~Ci~~~~~  104 (135)
                      ....+.|.+|.+.+++.....|    +|.||..|-...++
T Consensus        12 ~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk   51 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   51 (93)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             CCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHH
Confidence            3456789999999999855544    88999999999888

>3i2d_A E3 SUMO-protein ligase SIZ1; signal transduction, replication, ring E3, PIAS, ubiquitin, UBC9, metal-binding, nucleus; 2.60A {Saccharomyces cerevisiae}

Probab=89.78  E-value=0.35  Score=37.56  Aligned_cols=53  Identities=21%  Similarity=0.514  Sum_probs=38.9

Q ss_pred             CccceeeccccCccCcEE-cCCCCcccHHh--HHHHHh--cCCCCccccccccccCce
Q 042225           70 EVRFTCGICLDTMKEESS-TKCGHVFCKSC--IVDAIR--LQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~-~~CgH~fc~~C--i~~~~~--~~~~CP~Cr~~~~~~~~~  122 (135)
                      .-.+.||+-...+..|+. ..|.|..|.+-  +..+..  ....||+|.+.+...+|+
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            357889999999999976 57999966543  333332  345799999999877664

>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=89.13  E-value=0.43  Score=36.91  Aligned_cols=53  Identities=17%  Similarity=0.369  Sum_probs=38.7

Q ss_pred             CccceeeccccCccCcEE-cCCCCcccHH--hHHHHHh--cCCCCccccccccccCce
Q 042225           70 EVRFTCGICLDTMKEESS-TKCGHVFCKS--CIVDAIR--LQGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~-~~CgH~fc~~--Ci~~~~~--~~~~CP~Cr~~~~~~~~~  122 (135)
                      .-.+.||+-...+..|+. ..|.|.-|.+  -+..+..  ....||+|.+.+..++|+
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            347789999999999976 5899995543  3333333  345799999999877764

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=86.50  E-value=1.8  Score=26.48  Aligned_cols=34  Identities=24%  Similarity=0.336  Sum_probs=24.7

Q ss_pred             CCCccceeeccccCccCcEEc---CCCCcccHHhHHHH
Q 042225           68 VGEVRFTCGICLDTMKEESST---KCGHVFCKSCIVDA  102 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~  102 (135)
                      .+..+..|.||...-.+ ...   -|+-.||..|+.+.
T Consensus        11 ~~~~D~~C~VC~~~t~~-~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           11 PVVNDEMCDVCEVWTAE-SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTTCCCCSS-CCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCCcccCcccccccc-ceeccccccccccHhhcccc
Confidence            45567889999854333 233   48899999999986

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=84.32  E-value=0.88  Score=26.41  Aligned_cols=44  Identities=25%  Similarity=0.488  Sum_probs=30.3

Q ss_pred             ccceeeccccCccCcEEc--CCCCcccHHhHHHHHhc----CCCCccccccc
Q 042225           71 VRFTCGICLDTMKEESST--KCGHVFCKSCIVDAIRL----QGRCPTCRTRM  116 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~~----~~~CP~Cr~~~  116 (135)
                      ....|.||.+.-.  +.+  .|...||..|+...+..    ...|+.|....
T Consensus        11 ~~~~C~vC~~~~~--ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDGTD--VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCCTT--CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCCCe--EEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            3456999986422  222  69999999999766653    24799997543

>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=84.21  E-value=0.55  Score=30.23  Aligned_cols=51  Identities=18%  Similarity=0.300  Sum_probs=39.1

Q ss_pred             ccceeeccccCccC---cEEcCCCCcccHHhHHHHHhcCCCCccccccccccCc
Q 042225           71 VRFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSI  121 (135)
Q Consensus        71 ~~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~  121 (135)
                      +-+.|..|...+.+   .....=|..||..|..+.+.....|-.|.+.+....+
T Consensus        31 ~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~   84 (122)
T 1m3v_A           31 RCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDV   84 (122)
T ss_dssp             HHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEES
T ss_pred             hCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchhe
Confidence            35789999998863   3455678889999998877665589999998876544

---

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	135
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-11
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	7e-10
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	7e-09
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-08
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-08
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-07
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	3e-05
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	4e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	8e-05
d2c2la2	80	g.44.1.2 (A:225-304) STIP1 homology and U box-cont	2e-04
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-04
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	0.002
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	0.002

>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 = 54.9 bits (132), Expect = 1e-11
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIR 122
            +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 = 50.5 bits (120), Expect = 7e-10
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQG---RCPTCRTRMSVRSIRR 123
             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 = 47.2 bits (112), Expect = 7e-09
 Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 75  CGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGRCPTCRTRMS 117
           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 = 46.0 bits (109), Expect = 1e-08
 Identities = 10/46 (21%), Positives = 14/46 (30%), Gaps = 3/46 (6%)

Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR 119
            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 = 46.9 bits (111), Expect = 1e-08
 Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 3/56 (5%)

Query: 74  TCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIRRIFFPQ 128
            C IC +  K+     CGH+ C SC+      +G+ CP CR    ++    I    
Sbjct: 25  LCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRC--EIKGTEPIVVDP 78

>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 = 42.5 bits (100), Expect = 2e-07
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 74  TCGICLDTMKEESS----TKCGHVFCKSCIVDAIRLQGRCPTCRTRMSV 118
            C +CL  +++        +CGH F   C+   +     CP CR  + V
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 1e-05
 Identities = 17/60 (28%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 74  TCGICLDTMKEESS-----TKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRRIFFP 127
            C  C  T     S       CGH  C+SC+        G CP C T +   + R   F 
Sbjct: 5   GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE 64

>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 = 38.2 bits (88), Expect = 3e-05
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 73  FTCGICLDTMKEESS-TKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRR 123
             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 = 37.4 bits (86), Expect = 4e-05
 Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGR-CPTCRTRMSVRSIR 122
           F C I L+ MK+      G  + +S I   +    + CP  +  +    + 
Sbjct: 9   FRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLT 59

>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 = 36.3 bits (83), Expect = 8e-05
 Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 1/52 (1%)

Query: 74  TCGICLDTMKEESSTK-CGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI 124
            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 = 35.6 bits (81), Expect = 2e-04
 Identities = 9/58 (15%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 73  FTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIFFPQLQ 130
               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 = 35.1 bits (80), Expect = 3e-04
 Identities = 10/59 (16%), Positives = 16/59 (27%), Gaps = 18/59 (30%)

Query: 74  TCGICLDTMKEES------------------STKCGHVFCKSCIVDAIRLQGRCPTCRT 114
            C IC + + +                       C H F   CI   ++ +  CP    
Sbjct: 23  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 32.9 bits (74), Expect = 0.002
 Identities = 10/53 (18%), Positives = 17/53 (32%), Gaps = 7/53 (13%)

Query: 74  TCGICLDTMKEE-----SSTKCGHVFCKSCIVDAIRLQG--RCPTCRTRMSVR 119
            C IC + +  E       T       +SC+   + +     C  C    + R
Sbjct: 8   VCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNTR 60

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.4 bits (73), Expect = 0.002
 Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 5/48 (10%)

Query: 75  CGICLDTMKEESS----TKCGHVFCKSCIVDAIRLQG-RCPTCRTRMS 117
           C +C++ ++ +        CG+  C+ C       +   CP CR    
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 50

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	135
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.61
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.58
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.57
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.57
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.57
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.52
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.47
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.43
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.41
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.41
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.4
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.35
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.23
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.21
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.99
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.42
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	95.14
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	90.46
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	83.59
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	80.28

>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=99.61  E-value=9.8e-17  Score=92.35  Aligned_cols=53  Identities=21%  Similarity=0.317  Sum_probs=49.0

Q ss_pred             ceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCccccccccccCceeec
Q 042225           73 FTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        73 ~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~  125 (135)
                      +.|+||++.+.+|+.+ .|||+||+.||.+|++....||+||.++..++++++.
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            3599999999999987 5999999999999999989999999999999998864

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=3.5e-16  Score=97.38  Aligned_cols=52  Identities=27%  Similarity=0.782  Sum_probs=46.6

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHhc-CCCCccccccccccCce
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIR  122 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~  122 (135)
                      +.+.|+||++.+.+|+.++|||+||+.||.+|++. ...||.||.++...++.
T Consensus        22 ~~l~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          22 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             cCcCCccCCcchhcceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            56789999999999999999999999999999974 46899999999877664

>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=99.57  E-value=1.2e-15  Score=93.26  Aligned_cols=58  Identities=19%  Similarity=0.333  Sum_probs=51.9

Q ss_pred             CCCccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC-CCCccccccccccCceeec
Q 042225           68 VGEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~  125 (135)
                      .+.+++.|+||+++|.+|++++|||+||+.||..|+... ..||.|+..+...++++++
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            356789999999999999999999999999999999854 5799999999988888764

>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=99.57  E-value=8.8e-16  Score=94.29  Aligned_cols=56  Identities=14%  Similarity=0.143  Sum_probs=50.3

Q ss_pred             CCccceeeccccCccCcEEcCCCCcccHHhHHHHHhc-CCCCccccccccccCceee
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~  124 (135)
                      +.+++.|+||+++|.+|++++|||+||..||.+|+.. ...||.|+..+...++.++
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 4579999999988888765

>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=99.57  E-value=5.1e-16  Score=99.64  Aligned_cols=56  Identities=36%  Similarity=0.879  Sum_probs=48.7

Q ss_pred             CccceeeccccCccCcEEcCCCCcccHHhHHHHHhcC---CCCccccccccccCceeec
Q 042225           70 EVRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQ---GRCPTCRTRMSVRSIRRIF  125 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~~~~  125 (135)
                      .+.+.|+||++.+.+|++++|||+||..||..|++..   ..||.||..+..+++.+.+
T Consensus        19 ~~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~   77 (103)
T d1jm7a_          19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQEST   77 (103)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCC
T ss_pred             ccCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcCH
Confidence            4567899999999999999999999999999999754   4799999999887776553

>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=99.54  E-value=2.3e-15  Score=92.30  Aligned_cols=49  Identities=29%  Similarity=0.664  Sum_probs=43.5

Q ss_pred             cceeeccccCccCcEEcCCCCcccHHhHHHHHhc-CCCCccccccccccC
Q 042225           72 RFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRS  120 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~  120 (135)
                      ...|+||++.+.+++.++|||.||..|+..|+.. ...||+||..+...+
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            3469999999999999999999999999999974 568999999997544

>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=99.52  E-value=3.5e-15  Score=88.19  Aligned_cols=57  Identities=28%  Similarity=0.568  Sum_probs=46.4

Q ss_pred             ccceeeccccCccC-----cEEcCCCCcccHHhHHHHHhc-CCCCccccccccccCceeecCC
Q 042225           71 VRFTCGICLDTMKE-----ESSTKCGHVFCKSCIVDAIRL-QGRCPTCRTRMSVRSIRRIFFP  127 (135)
Q Consensus        71 ~~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~~~  127 (135)
                      ++..|+||++.+..     .+.++|||.||..||.+|+.. ...||+||+.+..+++....|.
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            45789999986532     256799999999999999964 4679999999998888777664

>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=99.47  E-value=7.2e-15  Score=87.50  Aligned_cols=45  Identities=36%  Similarity=0.773  Sum_probs=40.4

Q ss_pred             ceeeccccCccCcE-EcCCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           73 FTCGICLDTMKEES-STKCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        73 ~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      ..|+||++.+.+++ .++|||.||..|+.+|++.+.+||+||..+.
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            45999999998764 5799999999999999999999999999875

>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=99.43  E-value=2.2e-14  Score=81.97  Aligned_cols=48  Identities=25%  Similarity=0.687  Sum_probs=40.5

Q ss_pred             CccceeeccccCccCc---EEc-CCCCcccHHhHHHHHhcCCCCcccccccc
Q 042225           70 EVRFTCGICLDTMKEE---SST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMS  117 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p---~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  117 (135)
                      +++..|+||++.+.+.   +.+ .|||.||..|+.+|++.+.+||+||+.+.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            4556799999999753   444 69999999999999999999999998763

>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=99.41  E-value=1.1e-14  Score=92.38  Aligned_cols=53  Identities=28%  Similarity=0.748  Sum_probs=44.9

Q ss_pred             CccceeeccccCccCcEEc-CCCCcccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           70 EVRFTCGICLDTMKEESST-KCGHVFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        70 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      .+.+.|+||++.|.+|+++ +|||+||..||.+|+.  ..||.||..+...++.+.
T Consensus        20 ~~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~n   73 (97)
T d1jm7b_          20 EKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKIN   73 (97)
T ss_dssp             HHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCC
T ss_pred             hhcCCCccCCchhhcCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhCccc
Confidence            3567899999999999875 8999999999999985  359999999887776543

>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=99.41  E-value=1.5e-13  Score=87.31  Aligned_cols=56  Identities=16%  Similarity=0.094  Sum_probs=50.7

Q ss_pred             CCccceeeccccCccCcEEcCCCC-cccHHhHHHHHhcCCCCccccccccccCceee
Q 042225           69 GEVRFTCGICLDTMKEESSTKCGH-VFCKSCIVDAIRLQGRCPTCRTRMSVRSIRRI  124 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~CgH-~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~  124 (135)
                      ..+++.||||.++|.+||+++||| +||+.||.+|++....||+|+.++...+|+++
T Consensus        19 ~P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN   75 (98)
T d1wgma_          19 ACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPN   75 (98)
T ss_dssp             CCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEEC
T ss_pred             CcHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhcch
Confidence            446899999999999999998775 79999999999988899999999998888765

>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=99.40  E-value=1.3e-14  Score=83.27  Aligned_cols=46  Identities=22%  Similarity=0.573  Sum_probs=40.6

Q ss_pred             ccceeeccccCccCcEEcCCCCcccHHhHHHHHhcCCCCcccccccccc
Q 042225           71 VRFTCGICLDTMKEESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR  119 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  119 (135)
                      +.+.|+||++.+.+|+.++|||.||..|+.+|   ...||+||..+...
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCCcccCcccCCCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            45689999999999999999999999999765   66899999998754

>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=99.35  E-value=1.8e-13  Score=77.23  Aligned_cols=46  Identities=24%  Similarity=0.705  Sum_probs=38.2

Q ss_pred             ceeeccccCccCc----EEcCCCCcccHHhHHHHHhcC-CCCccccccccc
Q 042225           73 FTCGICLDTMKEE----SSTKCGHVFCKSCIVDAIRLQ-GRCPTCRTRMSV  118 (135)
Q Consensus        73 ~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~  118 (135)
                      +.|+||++.+...    ..++|||.||..|+.+|++.. ..||+||+++..
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            4699999988642    345899999999999999864 579999998864

>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=99.23  E-value=3e-12  Score=79.54  Aligned_cols=46  Identities=22%  Similarity=0.537  Sum_probs=38.3

Q ss_pred             eeeccccCccC------------------cEEcCCCCcccHHhHHHHHhcCCCCcccccccccc
Q 042225           74 TCGICLDTMKE------------------ESSTKCGHVFCKSCIVDAIRLQGRCPTCRTRMSVR  119 (135)
Q Consensus        74 ~C~IC~~~~~~------------------p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  119 (135)
                      .|+||++.+.+                  .+.++|||.||..||.+|++...+||+||..+..+
T Consensus        23 ~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   86 (88)
T d3dplr1          23 NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQ   86 (88)
T ss_dssp             CCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCCEE
T ss_pred             cCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccccc
Confidence            48888776643                  24578999999999999999999999999988653

>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=99.21  E-value=5.4e-12  Score=81.64  Aligned_cols=49  Identities=27%  Similarity=0.595  Sum_probs=38.9

Q ss_pred             ccceeeccccCccCc------------------EEcCCCCcccHHhHHHHHhcC-----CCCcccccccccc
Q 042225           71 VRFTCGICLDTMKEE------------------SSTKCGHVFCKSCIVDAIRLQ-----GRCPTCRTRMSVR  119 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p------------------~~~~CgH~fc~~Ci~~~~~~~-----~~CP~Cr~~~~~~  119 (135)
                      .+..|+||++.+.++                  ..++|||.||..||..|++..     .+||+||..+..+
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            345799999977532                  457899999999999999853     3799999877543

>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=98.99  E-value=1.5e-10  Score=66.65  Aligned_cols=50  Identities=20%  Similarity=0.389  Sum_probs=40.3

Q ss_pred             CCccceeeccccCccCcEEcCC-----CCcccHHhHHHHHh--cCCCCccccccccc
Q 042225           69 GEVRFTCGICLDTMKEESSTKC-----GHVFCKSCIVDAIR--LQGRCPTCRTRMSV  118 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p~~~~C-----gH~fc~~Ci~~~~~--~~~~CP~Cr~~~~~  118 (135)
                      .++...|.||++.+.++...+|     +|.||..||..|+.  ...+||+||+.+..
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            3456779999998887766654     59999999999996  34589999998764

>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=98.42  E-value=4.8e-08  Score=60.41  Aligned_cols=43  Identities=23%  Similarity=0.647  Sum_probs=32.7

Q ss_pred             cceeeccccCccC---cEEcCCCCcccHHhHHHHHhcC--------CCCccccc
Q 042225           72 RFTCGICLDTMKE---ESSTKCGHVFCKSCIVDAIRLQ--------GRCPTCRT  114 (135)
Q Consensus        72 ~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~--------~~CP~Cr~  114 (135)
                      ...|+||++.+..   +..++|||.||..|+..|++.+        -.||.|+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            4569999998753   3456899999999999998721        25998643

>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=95.14  E-value=0.0092  Score=34.08  Aligned_cols=34  Identities=26%  Similarity=0.773  Sum_probs=28.5

Q ss_pred             ccceeeccccCccCcEEcCC----CCcccHHhHHHHHh
Q 042225           71 VRFTCGICLDTMKEESSTKC----GHVFCKSCIVDAIR  104 (135)
Q Consensus        71 ~~~~C~IC~~~~~~p~~~~C----gH~fc~~Ci~~~~~  104 (135)
                      ..+.|.+|.+.+++.....|    +|.||..|-..+++
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik   44 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   44 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHH
Confidence            35779999999999855544    89999999999888

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.46  E-value=0.13  Score=30.04  Aligned_cols=35  Identities=23%  Similarity=0.408  Sum_probs=26.7

Q ss_pred             CCCccceeeccccCccCcEEcC---CCCcccHHhHHHHH
Q 042225           68 VGEVRFTCGICLDTMKEESSTK---CGHVFCKSCIVDAI  103 (135)
Q Consensus        68 ~~~~~~~C~IC~~~~~~p~~~~---CgH~fc~~Ci~~~~  103 (135)
                      .+..+..|.|| +.+.....++   |+..||..|+.+.-
T Consensus        11 ~v~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~g   48 (89)
T d1wila_          11 PVVNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRMG   48 (89)
T ss_dssp             CCCCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHHT
T ss_pred             CCCcCcccccc-CcccccceecceeecchhhHHHHHHhc
Confidence            45678889999 6666554555   78899999999873

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=83.59  E-value=0.21  Score=28.19  Aligned_cols=32  Identities=25%  Similarity=0.546  Sum_probs=23.0

Q ss_pred             CCccceeeccccCccCc----EEcCCCCcccHHhHH
Q 042225           69 GEVRFTCGICLDTMKEE----SSTKCGHVFCKSCIV  100 (135)
Q Consensus        69 ~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~  100 (135)
                      +.++..|.+|...|.--    .--.||++||..|..
T Consensus        10 W~~~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~   45 (72)
T d1dvpa2          10 WADGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTA   45 (72)
T ss_dssp             CCCCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSC
T ss_pred             CCcCCccccCCCcccCccccccccccCCeeChhhhC
Confidence            44556799999877532    224799999999964

>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=80.28  E-value=0.72  Score=24.92  Aligned_cols=41  Identities=29%  Similarity=0.604  Sum_probs=28.4

Q ss_pred             cceeeccccCccCcEEc---CCCCcccHHhHHHHHhcCCCCccc
Q 042225           72 RFTCGICLDTMKEESST---KCGHVFCKSCIVDAIRLQGRCPTC  112 (135)
Q Consensus        72 ~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~~~~~CP~C  112 (135)
                      ...|.-|...+.+....   .|++.||.+|-.=....-..||-|
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            35688888888766433   689999999964322233568877