Citrus Sinensis ID: 033497

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------12
Protein Sequence
MASPYYLAINTNIVSGSPIIDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA
Secondary Structure (PSIPRED)
ccccEEEEEEcccccccccccccccHHHHHHHHHcccccccccccccccccccccHHHHHHcccEEcccccccccccccccccccEEccccccccHHHHHHHHccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEcccccccccccccccccHHHHHHHHHcccccccccccccccccccccHHHHHHccEEEEccccccccHHHccccHHHcccccccccccccEHHHHHHccccccEcccccc
Coil and Loop (DISEMBL)
maspyylaintnivsgspiidesfnLDEALTMItntsstppdqdqpkshdgqtnseltvsslptvaategrCTVCMENFlqafpgkqvpcghvfHATCISTWIslsnscpvcrsgvia
Flexible Loop (DISEMBL)
MASPYYLAIntnivsgspiIDESFNLDEALTMITNTsstppdqdqpkshDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWislsnscpvcrsgvia
Low Complexity Region (SEG)
MASPYYLAINTNIVSGSPIIDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA
Disordered region (IsUnstruct)
****YYLAINTNIVSGSPIIDESFNLDEALTM*******************************TVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS****
Disordered Region (DISOPRED)
**SPYYLAINTNIVSGSPIIDESFNLDEAL*********************************TVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA
Disordered Region (DISEMBL)
MASPYYLAINTNIVSGSPIIDESFNLDEALTMITNT******************SELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA
Disordered Region (DISPRO)
*ASPYYLAINTNIVSGSPIIDESFNLDEALTMITNTSSTPPD*D***SHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASPYYLAINTNIVSGSPIIDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA
Positional Conservation
no confident homologs detected

---

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	118	2.2.26 [Sep-21-2011]
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.601	0.216	0.384	2e-10
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.601	0.210	0.346	7e-10
Q9D0C1	305	E3 ubiquitin-protein liga	yes	no	0.644	0.249	0.315	4e-09
Q9Y4L5	304	E3 ubiquitin-protein liga	yes	no	0.644	0.25	0.315	5e-09
Q91YL2	313	RING finger protein 126 O	no	no	0.694	0.261	0.326	1e-08
Q9SPL2	334	E3 ubiquitin-protein liga	no	no	0.415	0.146	0.433	2e-08
Q20798	610	E3 ubiquitin-protein liga	yes	no	0.533	0.103	0.365	3e-08
Q6GPV5	156	E3 ubiquitin-protein liga	N/A	no	0.525	0.397	0.382	3e-08
Q9NVW2	624	E3 ubiquitin-protein liga	no	no	0.644	0.121	0.311	4e-08
Q9WTV7	600	E3 ubiquitin-protein liga	no	no	0.644	0.126	0.298	4e-08

>sp|Q8LPN7|RNG1L_ARATH E3 ubiquitin-protein ligase RING1-like OS=Arabidopsis thaliana GN=At3g19950 PE=2 SV=1

 Score = 64.7 bits (156), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 42/78 (53%), Gaps = 7/78 (8%)

Query: 43  QDQPKSHDGQTNSELTVSSLPTVAATE-------GRCTVCMENFLQAFPGKQVPCGHVFH 95
           ++ P  +     S+  + +LPTV  T+        +C VCM+ F      KQ+PC HVFH
Sbjct: 180 ENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAVCMDEFEDGSDVKQMPCKHVFH 239

Query: 96  ATCISTWISLSNSCPVCR 113
             C+  W+ L NSCPVCR
Sbjct: 240 QDCLLPWLELHNSCPVCR 257

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|P0CH30|RING1_GOSHI E3 ubiquitin-protein ligase RING1 OS=Gossypium hirsutum GN=RING1 PE=2 SV=1

 Score = 62.8 bits (151), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 7/78 (8%)

Query: 43  QDQPKSHDGQTNSELTVSSLPTVAATE-------GRCTVCMENFLQAFPGKQVPCGHVFH 95
           ++ P  +     S+  + +LP V  T+        +C VCM++F +    KQ+PC H++H
Sbjct: 188 ENDPNRYGTPPASKSAIEALPLVNITKSNLNSEFNQCAVCMDDFEEGTEAKQMPCKHLYH 247

Query: 96  ATCISTWISLSNSCPVCR 113
             C+  W+ L NSCPVCR
Sbjct: 248 KDCLLPWLELHNSCPVCR 265

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.

Gossypium hirsutum (taxid: 3635)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9D0C1|RN115_MOUSE E3 ubiquitin-protein ligase RNF115 OS=Mus musculus GN=Rnf115 PE=1 SV=1

 Score = 60.1 bits (144), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 49/95 (51%), Gaps = 19/95 (20%)

Query: 28  EALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGR------CTVCMENFLQ 81
           + L  + NT   P D+++             ++SLPTV  T+ +      C VC E++  
Sbjct: 192 QLLGQLENTGPPPADKEK-------------ITSLPTVTVTQEQVNTGLECPVCKEDYTV 238

Query: 82  AFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
               +Q+PC H FH++CI  W+ L ++CPVCR  +
Sbjct: 239 EEKVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSL 273

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9Y4L5|RN115_HUMAN E3 ubiquitin-protein ligase RNF115 OS=Homo sapiens GN=RNF115 PE=1 SV=2

 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 49/95 (51%), Gaps = 19/95 (20%)

Query: 28  EALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGR------CTVCMENFLQ 81
           + L  + NT   P D+++             ++SLPTV  T+ +      C VC E++  
Sbjct: 191 QLLGQLENTGPPPADKEK-------------ITSLPTVTVTQEQVDMGLECPVCKEDYTV 237

Query: 82  AFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
               +Q+PC H FH++CI  W+ L ++CPVCR  +
Sbjct: 238 EEEVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSL 272

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q91YL2|RN126_MOUSE RING finger protein 126 OS=Mus musculus GN=Rnf126 PE=1 SV=1

 Score = 58.9 bits (141), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 19/101 (18%)

Query: 26  LDEALTMITNT--SSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEG------RCTVCME 77
           LD  +T + N   ++ PP  D+ K           + +LPTV  TE        C VC E
Sbjct: 188 LDTIITQLLNQFENTGPPPADKEK-----------IQALPTVPVTEEHVGSGLECPVCKE 236

Query: 78  NFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA 118
           ++      +Q+PC H+FH +CI  W+   +SCPVCR  +  
Sbjct: 237 DYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTG 277

Mus musculus (taxid: 10090)

>sp|Q9SPL2|CIP8_ARATH E3 ubiquitin-protein ligase CIP8 OS=Arabidopsis thaliana GN=CIP8 PE=1 SV=1

 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 4/53 (7%)

Query: 65  VAATEGR----CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
           V+++EG     C VC +  +    GK++PCGH +H  CI  W+   NSCPVCR
Sbjct: 246 VSSSEGEMVMVCAVCKDGMVMGETGKKLPCGHCYHGDCIVPWLGTRNSCPVCR 298

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. Probably forms a minimal ubiquitin ligase complex in cooperation with the E2 enzyme UBC8. Its interaction with COP1 suggests that it may participate in proteasome-mediated degradation of HY5 in vivo.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q20798|HRD1_CAEEL E3 ubiquitin-protein ligase hrd-1 OS=Caenorhabditis elegans GN=sel-11 PE=3 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 34/63 (53%)

Query: 54  NSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
           NS+  V S   +AA +  C +C E        K++PC HVFHA C+ +W     +CP CR
Sbjct: 274 NSQFPVVSAEDLAAMDATCIICREEMTVDASPKRLPCSHVFHAHCLRSWFQRQQTCPTCR 333

Query: 114 SGV 116
           + +
Sbjct: 334 TDI 336

Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated ubc-7 E2 ligase and transfers it to substrates, promoting their degradation. Component of the endoplasmic reticulum quality control (ERQC) system, which is also called the ER-associated degradation (ERAD) system, involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. Also promotes the degradation of normal but naturally short-lived proteins. Protects cells from ER stress-induced apoptosis. Thought to play a role together with hsp-3 in developmental growth and function of intestinal cells and to play a role together with hsp-4 in gonad formation.

Caenorhabditis elegans (taxid: 6239)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6GPV5|RN181_XENLA E3 ubiquitin-protein ligase RNF181 OS=Xenopus laevis GN=rnf181 PE=2 SV=1

 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 6/68 (8%)

Query: 55  SELTVSSLPTVAATEG------RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS 108
           S+  V SLP V  T        +C VC+  F +    +Q+PC H+FH+ CI  W+  +NS
Sbjct: 56  SKKVVESLPKVTVTPEQADAALKCPVCLLEFEEGETVRQLPCEHLFHSACILPWLGKTNS 115

Query: 109 CPVCRSGV 116
           CP+CR  +
Sbjct: 116 CPLCRHEL 123

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9NVW2|RNF12_HUMAN E3 ubiquitin-protein ligase RLIM OS=Homo sapiens GN=RLIM PE=1 SV=3

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 42  DQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCIST 101
           D DQP+    +    L + S     A +  C+VC+  + +    +++PC H +H  CI  
Sbjct: 541 DDDQPRGLTKEQIDNLAMRSFGENDALKT-CSVCITEYTEGNKLRKLPCSHEYHVHCIDR 599

Query: 102 WISLSNSCPVCRSGVIA 118
           W+S +++CP+CR  V+A
Sbjct: 600 WLSENSTCPICRRAVLA 616

E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. Acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9WTV7|RNF12_MOUSE E3 ubiquitin-protein ligase RLIM OS=Mus musculus GN=Rlim PE=1 SV=2

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 42  DQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCIST 101
           D+DQP+    +    L + S     A +  C+VC+  + +    +++PC H +H  CI  
Sbjct: 517 DEDQPRGLTKEQIDNLAMRSFGENDALKT-CSVCITEYTEGNKLRKLPCSHEYHVHCIDR 575

Query: 102 WISLSNSCPVCRSGVIA 118
           W+S +++CP+CR  V++
Sbjct: 576 WLSENSTCPICRRAVLS 592

E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. Acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.

Mus musculus (taxid: 10090)

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	118
359484547	102	PREDICTED: E3 ubiquitin-protein ligase R	0.703	0.813	0.443	3e-14
297738762	168	unnamed protein product [Vitis vinifera]	0.703	0.494	0.443	4e-14
449488135	116	PREDICTED: E3 ubiquitin-protein ligase R	0.483	0.491	0.561	5e-14
255546337	109	hypothetical protein RCOM_1049910 [Ricin	0.745	0.807	0.436	3e-13
224114495	99	predicted protein [Populus trichocarpa]	0.754	0.898	0.415	2e-12
255546191	124	hypothetical protein RCOM_1048070 [Ricin	0.796	0.758	0.421	7e-11
242044428	254	hypothetical protein SORBIDRAFT_02g02252	0.762	0.354	0.373	5e-10
195645130	321	RHC1A [Zea mays]	0.474	0.174	0.491	1e-09
226499162	312	uncharacterized protein LOC100272564 [Ze	0.466	0.176	0.5	1e-09
308080430	310	RHC1A [Zea mays] gi|195612900|gb|ACG2828	0.474	0.180	0.491	1e-09

>gi|359484547|ref|XP_003633119.1| PREDICTED: E3 ubiquitin-protein ligase RNF115-like [Vitis vinifera]

 Score = 82.8 bits (203), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 57/97 (58%), Gaps = 14/97 (14%)

Query: 20  IDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENF 79
           ID  F+LD A+T + +TS               + S   VS++PTV A +  CTVC E F
Sbjct: 16  IDLCFDLDLAITAVDDTSEI-------------SKSTSMVSTMPTVTAVDA-CTVCREGF 61

Query: 80  LQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
                GKQ+PCGH +HA CI++W+SL NSCP+CR  V
Sbjct: 62  QSGEGGKQLPCGHFYHAGCIASWLSLRNSCPLCRCSV 98

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738762|emb|CBI28007.3| unnamed protein product [Vitis vinifera]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 57/97 (58%), Gaps = 14/97 (14%)

Query: 20  IDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENF 79
           ID  F+LD A+T + +TS               + S   VS++PTV A +  CTVC E F
Sbjct: 82  IDLCFDLDLAITAVDDTSEI-------------SKSTSMVSTMPTVTAVDA-CTVCREGF 127

Query: 80  LQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
                GKQ+PCGH +HA CI++W+SL NSCP+CR  V
Sbjct: 128 QSGEGGKQLPCGHFYHAGCIASWLSLRNSCPLCRCSV 164

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449488135|ref|XP_004157948.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus]

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 45/57 (78%)

Query: 57  LTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
           + V+ LPTVAA +  C VCME+FL    GKQ+PCGHV+H +C+S+W+S+ +SCP+CR
Sbjct: 43  VMVAELPTVAAADDVCAVCMEDFLPDEGGKQIPCGHVYHQSCLSSWLSIRDSCPLCR 99

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546337|ref|XP_002514228.1| hypothetical protein RCOM_1049910 [Ricinus communis] gi|223546684|gb|EEF48182.1| hypothetical protein RCOM_1049910 [Ricinus communis]

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 45/103 (43%), Positives = 62/103 (60%), Gaps = 15/103 (14%)

Query: 19  IIDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGR--CTVCM 76
           +ID SF++DEAL +       PP+     S      S+  V+ +PTV +T+    C++CM
Sbjct: 16  LIDVSFDMDEALAL-------PPNFGHQIS-----ESDSLVADMPTVTSTDDHDVCSICM 63

Query: 77  ENFLQ-AFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA 118
           E F      GKQVPCGHV+HA CIS+W+S  NSCP+CR  + A
Sbjct: 64  EGFQSPGVCGKQVPCGHVYHAPCISSWLSNCNSCPLCRFNISA 106

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114495|ref|XP_002332344.1| predicted protein [Populus trichocarpa] gi|222832065|gb|EEE70542.1| predicted protein [Populus trichocarpa]

 Score = 76.6 bits (187), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 42/101 (41%), Positives = 57/101 (56%), Gaps = 12/101 (11%)

Query: 17  SPIIDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAAT-EGRCTVC 75
           S +ID SF+LDEALT+       P +  Q  ++   T     V+ +PT   T +  C VC
Sbjct: 8   SCLIDTSFDLDEALTL-------PQNLSQQITYSNST----IVADMPTALTTGDAVCAVC 56

Query: 76  MENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
           ME F     GK+VPCGHV+H  CIS  +S  +SCP+CR  +
Sbjct: 57  MEGFQSGIGGKKVPCGHVYHEACISALLSHRHSCPLCRCDI 97

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546191|ref|XP_002514155.1| hypothetical protein RCOM_1048070 [Ricinus communis] gi|223546611|gb|EEF48109.1| hypothetical protein RCOM_1048070 [Ricinus communis]

 Score = 71.2 bits (173), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 48/114 (42%), Positives = 61/114 (53%), Gaps = 20/114 (17%)

Query: 23  SFNLDEALTMITNTSSTPPDQD-----QPKSHDGQT---NSELTV--------SSLPT-V 65
           SF+LDEAL +  N ++   D D     Q  SH   T   NS   V        + +PT +
Sbjct: 7   SFDLDEALCLTENAANLSFDLDVALTLQEISHHQTTPANNSPQVVVPADHRHHNHMPTTI 66

Query: 66  AATEGR--CTVCMENFLQA-FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
            ATE    C  CME F  +   GKQ PCGHV+HA CIS+W+S SN CP+CR  +
Sbjct: 67  PATEDDEVCIFCMEGFESSRIGGKQTPCGHVYHAACISSWLSYSNRCPLCRCHI 120

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242044428|ref|XP_002460085.1| hypothetical protein SORBIDRAFT_02g022520 [Sorghum bicolor] gi|241923462|gb|EER96606.1| hypothetical protein SORBIDRAFT_02g022520 [Sorghum bicolor]

 Score = 68.6 bits (166), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 37/99 (37%), Positives = 50/99 (50%), Gaps = 9/99 (9%)

Query: 19  IIDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSEL-TVSSLPTVAATEGRCTVCME 77
           + DE F   +A+  +      PPD  + +   G     L T S+ P     E  CTVC+E
Sbjct: 111 LTDEEFR--KAMDQLRKQEYRPPDPQKKQGDSGGGRGILRTRSAAPPATTEEKACTVCLE 168

Query: 78  NFLQAFPGKQV---PCGHVFHATCISTWISLSNSCPVCR 113
            FL   PG+QV   PC H+FH  CI+ W+    +CPVCR
Sbjct: 169 TFL---PGEQVAITPCNHMFHQGCIAPWVKGHGNCPVCR 204

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|195645130|gb|ACG42033.1| RHC1A [Zea mays]

 Score = 67.0 bits (162), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 38/57 (66%), Gaps = 1/57 (1%)

Query: 58  TVSSLPTVAATEG-RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
            V +LPTV   E   C+VC+++     P KQ+PCGH FH++CI  W+ L +SCPVCR
Sbjct: 182 AVEALPTVQIAEAVSCSVCLDDLELGSPAKQMPCGHRFHSSCILPWLELHSSCPVCR 238

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226499162|ref|NP_001140503.1| uncharacterized protein LOC100272564 [Zea mays] gi|194699744|gb|ACF83956.1| unknown [Zea mays] gi|413949698|gb|AFW82347.1| putative RING zinc finger domain superfamily protein isoform 1 [Zea mays] gi|413949699|gb|AFW82348.1| putative RING zinc finger domain superfamily protein isoform 2 [Zea mays]

 Score = 67.0 bits (162), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 59  VSSLPTVAATEG-RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
           V +LPTV   E   C+VC+++     P KQ+PCGH FH++CI  W+ L +SCPVCR
Sbjct: 181 VEALPTVQIAEAVSCSVCLDDLELGSPAKQMPCGHRFHSSCILPWLELHSSCPVCR 236

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|308080430|ref|NP_001182786.1| RHC1A [Zea mays] gi|195612900|gb|ACG28280.1| RHC1A [Zea mays]

 Score = 67.0 bits (162), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 38/57 (66%), Gaps = 1/57 (1%)

Query: 58  TVSSLPTVAATEG-RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
            V +LPTV   E   C+VC+++     P KQ+PCGH FH++CI  W+ L +SCPVCR
Sbjct: 179 AVEALPTVQIAEAVSCSVCLDDLELGSPAKQMPCGHRFHSSCILPWLELHSSCPVCR 235

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	118
MGI|MGI:1915095	305	Rnf115 "ring finger protein 11	0.491	0.190	0.390	9e-12
UNIPROTKB|E2QY59	319	RNF115 "Uncharacterized protei	0.491	0.181	0.390	1.1e-11
UNIPROTKB|Q9Y4L5	304	RNF115 "E3 ubiquitin-protein l	0.491	0.190	0.390	1.4e-11
TAIR|locus:2195573	327	AT1G60360 [Arabidopsis thalian	0.5	0.180	0.439	1.6e-11
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.601	0.216	0.384	3.5e-11
TAIR|locus:2131463	356	AT4G26400 [Arabidopsis thalian	0.601	0.199	0.383	1.6e-10
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.5	0.149	0.430	2e-10
ZFIN|ZDB-GENE-061215-82	310	rnf115 "ring finger protein 11	0.491	0.187	0.421	3e-10
TAIR|locus:2161058	396	ATCRT1 [Arabidopsis thaliana (	0.466	0.138	0.464	3.3e-10
TAIR|locus:2063912	401	RHC2A "RING-H2 finger C2A" [Ar	0.745	0.219	0.3	4.3e-10

MGI|MGI:1915095 Rnf115 "ring finger protein 115" [Mus musculus (taxid:10090)]

 Score = 143 (55.4 bits), Expect = 9.0e-12, Sum P(2) = 9.0e-12
 Identities = 25/64 (39%), Positives = 39/64 (60%)

Query:    59 VSSLPTVAATEGR------CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVC 112
             ++SLPTV  T+ +      C VC E++      +Q+PC H FH++CI  W+ L ++CPVC
Sbjct:   210 ITSLPTVTVTQEQVNTGLECPVCKEDYTVEEKVRQLPCNHFFHSSCIVPWLELHDTCPVC 269

Query:   113 RSGV 116
             R  +
Sbjct:   270 RKSL 273

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=ISO

UNIPROTKB|E2QY59 RNF115 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 143 (55.4 bits), Expect = 1.1e-11, Sum P(2) = 1.1e-11
 Identities = 25/64 (39%), Positives = 39/64 (60%)

Query:    59 VSSLPTVAATEGR------CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVC 112
             ++SLPTV  T+ +      C VC E++      +Q+PC H FH++CI  W+ L ++CPVC
Sbjct:   225 ITSLPTVTVTQEQVDMGLECPVCKEDYTVEEEVRQLPCNHFFHSSCIVPWLELHDTCPVC 284

Query:   113 RSGV 116
             R  +
Sbjct:   285 RKSL 288

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q9Y4L5 RNF115 "E3 ubiquitin-protein ligase RNF115" [Homo sapiens (taxid:9606)]

 Score = 143 (55.4 bits), Expect = 1.4e-11, Sum P(2) = 1.4e-11
 Identities = 25/64 (39%), Positives = 39/64 (60%)

Query:    59 VSSLPTVAATEGR------CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVC 112
             ++SLPTV  T+ +      C VC E++      +Q+PC H FH++CI  W+ L ++CPVC
Sbjct:   209 ITSLPTVTVTQEQVDMGLECPVCKEDYTVEEEVRQLPCNHFFHSSCIVPWLELHDTCPVC 268

Query:   113 RSGV 116
             R  +
Sbjct:   269 RKSL 272

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=ISS

GO:0051865 "protein autoubiquitination" evidence=IDA

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

TAIR|locus:2195573 AT1G60360 [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 1.6e-11, P = 1.6e-11
 Identities = 29/66 (43%), Positives = 41/66 (62%)

Query:    55 SELTVSSLPTVAATE-------GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN 107
             SE T++SLP+V  T         +CTVCME F+      ++PC H++H  CI  W+ L+N
Sbjct:   200 SEPTINSLPSVKITPQHLTNDMSQCTVCMEEFIVGGDATELPCKHIYHKDCIVPWLRLNN 259

Query:   108 SCPVCR 113
             SCP+CR
Sbjct:   260 SCPICR 265

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

TAIR|locus:2092231 AT3G19950 [Arabidopsis thaliana (taxid:3702)]

 Score = 159 (61.0 bits), Expect = 3.5e-11, P = 3.5e-11
 Identities = 30/78 (38%), Positives = 42/78 (53%)

Query:    43 QDQPKSHDGQTNSELTVSSLPTVAATE-------GRCTVCMENFLQAFPGKQVPCGHVFH 95
             ++ P  +     S+  + +LPTV  T+        +C VCM+ F      KQ+PC HVFH
Sbjct:   180 ENDPNRYGTPPASKSAIDALPTVKVTKDMLKSEMNQCAVCMDEFEDGSDVKQMPCKHVFH 239

Query:    96 ATCISTWISLSNSCPVCR 113
               C+  W+ L NSCPVCR
Sbjct:   240 QDCLLPWLELHNSCPVCR 257

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

GO:0010200 "response to chitin" evidence=RCA

TAIR|locus:2131463 AT4G26400 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 1.6e-10, P = 1.6e-10
 Identities = 28/73 (38%), Positives = 43/73 (58%)

Query:    42 DQDQPKSHDGQTNSELTVSSLPTVAATEG-RCTVCMENFLQAFPGKQVPCGHVFHATCIS 100
             D D  + H      +  V +LPTV  +E  +C++C+++F +    K++PC H FH  CI 
Sbjct:   211 DNDSIR-HGSLPARKEVVDNLPTVKISESLQCSICLDDFDKGSEAKEMPCKHKFHIRCIV 269

Query:   101 TWISLSNSCPVCR 113
              W+ L +SCPVCR
Sbjct:   270 PWLELHSSCPVCR 282

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

GO:0010200 "response to chitin" evidence=IEP

GO:0000303 "response to superoxide" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009733 "response to auxin stimulus" evidence=RCA

GO:0009737 "response to abscisic acid stimulus" evidence=RCA

GO:0009743 "response to carbohydrate stimulus" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

TAIR|locus:2075175 RDUF1 "RING and Domain of Unknown Function 1117 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 2.0e-10, P = 2.0e-10
 Identities = 28/65 (43%), Positives = 37/65 (56%)

Query:    55 SELTVSSLPTVAAT------EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS 108
             S+  + SLP V  +      E  C VC E F     G+++PC H+FH  CI  W+S+ NS
Sbjct:   192 SKSAIESLPRVEISDCHTKAEANCAVCTEVFEAGIEGREMPCKHIFHGDCIVPWLSIRNS 251

Query:   109 CPVCR 113
             CPVCR
Sbjct:   252 CPVCR 256

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

GO:0010200 "response to chitin" evidence=IEP;RCA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

GO:0002679 "respiratory burst involved in defense response" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

ZFIN|ZDB-GENE-061215-82 rnf115 "ring finger protein 115" [Danio rerio (taxid:7955)]

 Score = 150 (57.9 bits), Expect = 3.0e-10, P = 3.0e-10
 Identities = 27/64 (42%), Positives = 38/64 (59%)

Query:    59 VSSLPTVAATEGR------CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVC 112
             +SSLPTV  T+        C VC E++    P +Q+PC H FH+ CI  W+ L ++CPVC
Sbjct:   219 ISSLPTVIITQEHTDCNMECPVCKEDYTVGEPVRQLPCNHFFHSDCIVPWLELHDTCPVC 278

Query:   113 RSGV 116
             R  +
Sbjct:   279 RKSL 282

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

TAIR|locus:2161058 ATCRT1 [Arabidopsis thaliana (taxid:3702)]

 Score = 152 (58.6 bits), Expect = 3.3e-10, P = 3.3e-10
 Identities = 26/56 (46%), Positives = 37/56 (66%)

Query:    59 VSSLPTVAATEG-RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
             V +LPTV   E  +C+VC+++F +    K++PC H FH  CI  W+ L +SCPVCR
Sbjct:   245 VEALPTVKIMEPLQCSVCLDDFEKGTEAKEMPCKHKFHVRCIVPWLELHSSCPVCR 300

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

TAIR|locus:2063912 RHC2A "RING-H2 finger C2A" [Arabidopsis thaliana (taxid:3702)]

 Score = 151 (58.2 bits), Expect = 4.3e-10, P = 4.3e-10
 Identities = 27/90 (30%), Positives = 47/90 (52%)

Query:    26 LDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPT--VAATEGRCTVCMENFLQAF 83
             LD+   +  NT+      + P +      +   +   PT  ++ ++  C VC ENF+   
Sbjct:   153 LDQISQIELNTNRNLRSCEHPPASKSAIEALPLIEIDPTHLLSDSQSHCAVCKENFVLKS 212

Query:    84 PGKQVPCGHVFHATCISTWISLSNSCPVCR 113
               +++PC H++H  CI  W+++ NSCPVCR
Sbjct:   213 SAREMPCNHIYHPDCILPWLAIRNSCPVCR 242

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.02110006 hypothetical protein (99 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	118
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	4e-13
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	1e-10
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	1e-09
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-09
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	9e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-08
smart00184	40	smart00184, RING, Ring finger	9e-08
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	1e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	1e-05
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	2e-05
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	3e-05
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	2e-04
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	7e-04
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	0.003

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

 Score = 58.6 bits (142), Expect = 4e-13
 Identities = 18/43 (41%), Positives = 27/43 (62%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS 114
           C +C++ F        +PCGHVFH  C+  W+  SN+CP+CR+
Sbjct: 3   CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

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

 Score = 56.5 bits (136), Expect = 1e-10
 Identities = 28/99 (28%), Positives = 45/99 (45%), Gaps = 6/99 (6%)

Query: 21  DESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLP-TVAATEG-RCTVCMEN 78
              FN+   + +  +       +  P +    T   L   S+   V A +G  C +CM N
Sbjct: 276 GSRFNIILEIQINFDVGFYSSSEAIPTT---TTKGSLKPLSIERAVEADKGVECAICMSN 332

Query: 79  FLQAFPGKQVPCGHVFHATCISTWI-SLSNSCPVCRSGV 116
           F++    + +PC H FH  C+  W+   SN CPVCR+ +
Sbjct: 333 FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 49.4 bits (118), Expect = 1e-09
 Identities = 20/44 (45%), Positives = 29/44 (65%), Gaps = 3/44 (6%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWI-SLSNSCPVCRS 114
           C +C+E F +  P   +PCGHVF  +CI  W+ S  N+CP+CR+
Sbjct: 2   CPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43

Length = 45

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

 Score = 49.0 bits (117), Expect = 2e-09
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 68  TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS 114
            E  C +C++      P    PCGHVF   CI  ++   + CP+CR+
Sbjct: 1   EELECPICLDLLRD--PVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 51.5 bits (123), Expect = 9e-09
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 10/76 (13%)

Query: 52  QTNSELTVSSLPTVAATEGRCTVCMENFLQA----------FPGKQVPCGHVFHATCIST 101
             N+    ++   +  ++  CT+CM+                  K++PCGH+ H  C+  
Sbjct: 270 DLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKN 329

Query: 102 WISLSNSCPVCRSGVI 117
           W+    +CP+CR  VI
Sbjct: 330 WLERQQTCPICRRPVI 345

Length = 491

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

 Score = 48.2 bits (115), Expect = 1e-08
 Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 10/55 (18%)

Query: 69  EGRCTVCMENFLQA-----FPGKQVP-----CGHVFHATCISTWISLSNSCPVCR 113
           +  C +C  +F         PG   P     CGH FH  CIS W+   N+CP+CR
Sbjct: 19  DDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 44.8 bits (106), Expect = 9e-08
 Identities = 17/42 (40%), Positives = 27/42 (64%), Gaps = 3/42 (7%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWI-SLSNSCPVC 112
           C +C+E +L+      +PCGH F  +CI  W+ S +N+CP+C
Sbjct: 1   CPICLEEYLKDP--VILPCGHTFCRSCIRKWLESGNNTCPIC 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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 5/47 (10%)

Query: 72  CTVCME-----NFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
           C +CME          + G    C HVF   CI  W    N+CPVCR
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 6/49 (12%)

Query: 72   CTVC---MENFLQAFPGKQVP-CGHVFHATCISTWISLSNS--CPVCRS 114
            C +C   ++   ++ P K+   C + FH  C+  W + S    CP+CRS
Sbjct: 1472 CAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRS 1520

Length = 1525

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

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 14/56 (25%)

Query: 66  AATEGRCTVCMENFLQAFPGKQVP-----CGHVFHATCISTWISLSNS---CPVCR 113
            + +G C  C       FPG   P     C H FH  CI  W++   S   CP+CR
Sbjct: 29  VSFDGTCPQC------KFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCR 78

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

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

 Score = 38.6 bits (90), Expect = 2e-05
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 3/42 (7%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN-SCPVC 112
           C +C+E      P   +PCGH+F + CI +W+   N +CP+C
Sbjct: 1   CPICLEEPKD--PVTILPCGHLFCSKCILSWLESGNVTCPLC 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|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 39.4 bits (92), Expect = 3e-05
 Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 5/44 (11%)

Query: 75  CMENFLQAFPGKQVP-----CGHVFHATCISTWISLSNSCPVCR 113
           C E      PG + P     C H FH  CI  W+     CP+ R
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 5/67 (7%)

Query: 49  HDGQTNSELTVSSLPTVAA--TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS 106
            D    S+   + +P++    +  RC +C           +  CGH F + CI   +   
Sbjct: 3   LDATDPSDWNQTKIPSLKGLDSMLRCRICDCRISIPC---ETTCGHTFCSLCIRRHLGTQ 59

Query: 107 NSCPVCR 113
             CPVCR
Sbjct: 60  PFCPVCR 66

Length = 391

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

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 5/67 (7%)

Query: 50  DGQTNSELTVSSLPTVAATEG--RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN 107
           D   +S+   + +P++   +   RC +C + F          C H F + CI   +S   
Sbjct: 5   DITDSSDWLTTPIPSLYPLDTSLRCHICKDFFDVPV---LTSCSHTFCSLCIRRCLSNQP 61

Query: 108 SCPVCRS 114
            CP+CR+
Sbjct: 62  KCPLCRA 68

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|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger)

 Score = 33.1 bits (76), Expect = 0.003
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 5/49 (10%)

Query: 69  EGRCTVCMENFLQAFPGKQVPCGH-VFHATCISTWISLSNSCPVCRSGV 116
           +  C +C+E          +PCGH      C     S    CP+CR  +
Sbjct: 2   DDLCVICLERPRNVV---FLPCGHLCLCEECAKRLRS-KKKCPICRQPI 46

Length = 49

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	118
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.68
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.54
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.51
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.48
PHA02929	238	N1R/p28-like protein; Provisional	99.47
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.45
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.41
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.4
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.37
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.36
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.32
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.31
PF14634	44	zf-RING_5: zinc-RING finger domain	99.29
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.28
PHA02926	242	zinc finger-like protein; Provisional	99.25
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.25
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.25
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.2
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.18
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.15
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.13
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.12
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	99.11
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.01
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.99
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.99
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.97
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.86
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.83
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.81
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.76
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.73
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.71
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.71
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	98.71
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.67
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.65
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.61
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.61
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.59
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.58
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.52
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.5
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.49
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.47
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.43
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.37
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.35
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	98.17
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.1
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.98
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.92
KOG2660	331	consensus Locus-specific chromosome binding protei	97.85
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.84
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.8
COG5152	259	Uncharacterized conserved protein, contains RING a	97.72
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.71
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.71
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.68
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	97.66
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.63
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.61
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	97.43
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.35
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.34
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.25
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.23
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.17
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.11
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	97.08
PHA02862	156	5L protein; Provisional	97.08
COG5222	427	Uncharacterized conserved protein, contains RING Z	97.07
PHA03096	284	p28-like protein; Provisional	97.04
KOG4739	233	consensus Uncharacterized protein involved in syna	97.01
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.0
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.8
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	96.77
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.77
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.75
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.73
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.63
KOG1940	276	consensus Zn-finger protein [General function pred	96.56
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.38
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.38
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.29
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.22
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	96.07
PF04641	260	Rtf2: Rtf2 RING-finger	95.95
KOG4367	699	consensus Predicted Zn-finger protein [Function un	95.93
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.92
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.89
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.62
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	95.56
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.47
KOG3002	299	consensus Zn finger protein [General function pred	95.3
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	95.03
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	94.97
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	94.91
KOG3053	293	consensus Uncharacterized conserved protein [Funct	94.87
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	94.8
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	94.52
KOG1609	323	consensus Protein involved in mRNA turnover and st	94.47
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	94.46
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	94.43
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	94.41
KOG3899	381	consensus Uncharacterized conserved protein [Funct	94.12
KOG0298	1394	consensus DEAD box-containing helicase-like transc	94.09
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	93.62
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	92.91
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	91.91
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	91.38
KOG0269	839	consensus WD40 repeat-containing protein [Function	90.95
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	90.21
COG5109	396	Uncharacterized conserved protein, contains RING Z	87.4
KOG2068	327	consensus MOT2 transcription factor [Transcription	87.21
KOG1829	580	consensus Uncharacterized conserved protein, conta	87.01
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	86.98
KOG0825	1134	consensus PHD Zn-finger protein [General function	86.73
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	85.9
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	85.62
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	85.58
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	85.41
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	84.8
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	84.78
KOG3039	303	consensus Uncharacterized conserved protein [Funct	84.25
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	84.04
KOG2807	378	consensus RNA polymerase II transcription initiati	83.02
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	82.46
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	80.62

>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=99.68  E-value=8.6e-18  Score=86.91  Aligned_cols=44  Identities=48%  Similarity=1.198  Sum_probs=39.7

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccC
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR  113 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr  113 (118)
                      ++|+||++.+..++.++.++|+|.||.+||.+|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            36999999998888889999999999999999999999999997

...

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

Probab=99.54  E-value=2.4e-15  Score=106.76  Aligned_cols=48  Identities=31%  Similarity=0.996  Sum_probs=44.1

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCc-ccccCcccC
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS-CPVCRSGVI  117 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~-CP~Cr~~~~  117 (118)
                      ..|.||+|.|..++..++|||+|.||..||++|+...++ ||+|++.+.
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~  278 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIR  278 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence            489999999999999999999999999999999987765 999998764

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

Probab=99.51  E-value=1.9e-14  Score=99.09  Aligned_cols=57  Identities=33%  Similarity=0.832  Sum_probs=49.4

Q ss_pred             cccCCCCccCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           58 TVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        58 ~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .....+........|.+|++....   +..+||||+||+.||..|...+..||+||..+.
T Consensus       228 ~s~~~~~i~~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~  284 (293)
T KOG0317|consen  228 DSNSLSSIPEATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKAECPLCREKFQ  284 (293)
T ss_pred             hccCCccCCCCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccccCCCcccccCC
Confidence            334455566777999999999877   999999999999999999999999999998765

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

Probab=99.48  E-value=3.1e-14  Score=81.06  Aligned_cols=48  Identities=38%  Similarity=0.924  Sum_probs=37.1

Q ss_pred             cCccccccccccccccC---------CC-ceeeCCCChhhHHHHHHHhhCCCcccccC
Q 033497           66 AATEGRCTVCMENFLQA---------FP-GKQVPCGHVFHATCISTWISLSNSCPVCR  113 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~---------~~-~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr  113 (118)
                      ...+..|+||++.+...         .. +...+|||.||..||.+|++.+.+||+||
T Consensus        16 ~~~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   16 DIADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             SSCCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCcCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            33455699999999431         12 34457999999999999999999999998

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.47  E-value=3.3e-14  Score=96.96  Aligned_cols=51  Identities=37%  Similarity=0.867  Sum_probs=41.9

Q ss_pred             CccccccccccccccCCC-----ceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFP-----GKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~-----~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+.+|+||++.+..+..     +++.+|+|.||..||.+|++.+.+||+||..+.
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            345789999999765321     245579999999999999999999999999875

>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=99.45  E-value=5.5e-14  Score=74.46  Aligned_cols=46  Identities=30%  Similarity=0.839  Sum_probs=40.5

Q ss_pred             cccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      +..|.||++....   +..+||||. ||..|+.+|++....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            5679999999777   899999999 999999999999999999999874

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.41  E-value=3.3e-13  Score=88.91  Aligned_cols=47  Identities=32%  Similarity=0.814  Sum_probs=40.0

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----------------CCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----------------SNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----------------~~~CP~Cr~~~~  117 (118)
                      ++..|+||++.+..   +++++|||.||+.||.+|+..                ...||.||..+.
T Consensus        17 ~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is   79 (193)
T PLN03208         17 GDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS   79 (193)
T ss_pred             CccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence            46889999999877   888999999999999999742                236999998764

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

Probab=99.40  E-value=1.4e-13  Score=97.75  Aligned_cols=52  Identities=35%  Similarity=1.079  Sum_probs=44.7

Q ss_pred             cCcccccccccccccc-C---------CCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQ-A---------FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~-~---------~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ...+..|.||+|++.. +         ..+..+||||.+|..|++.|++++.+||+||.++.
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            5677899999999543 2         34688999999999999999999999999999864

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

Probab=99.37  E-value=3.6e-13  Score=68.67  Aligned_cols=38  Identities=34%  Similarity=0.945  Sum_probs=30.4

Q ss_pred             ccccccccccCCCceeeCCCChhhHHHHHHHhhCC----Cccccc
Q 033497           72 CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS----NSCPVC  112 (118)
Q Consensus        72 C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~----~~CP~C  112 (118)
                      |+||++.|.+   ++.++|||.||..||.+|++..    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999999   9999999999999999999643    359987

>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=99.36  E-value=3.7e-13  Score=67.67  Aligned_cols=38  Identities=34%  Similarity=1.045  Sum_probs=33.0

Q ss_pred             ccccccccccCCCc-eeeCCCChhhHHHHHHHhhCCCccccc
Q 033497           72 CTVCMENFLQAFPG-KQVPCGHVFHATCISTWISLSNSCPVC  112 (118)
Q Consensus        72 C~IC~~~~~~~~~~-~~~~C~H~f~~~Ci~~~~~~~~~CP~C  112 (118)
                      |+||++.+.+   + +.++|||.||..|+.+|++.+..||+|
T Consensus         1 C~iC~~~~~~---~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD---PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS---EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC---cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999887   6 678899999999999999988899987

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

Probab=99.32  E-value=2.7e-12  Score=83.01  Aligned_cols=49  Identities=29%  Similarity=0.768  Sum_probs=41.4

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      +..+.|+|||+.+.+. .++...|||.||..||+..++....||+|++.+
T Consensus       129 ~~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkI  177 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKI  177 (187)
T ss_pred             ccccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCccccc
Confidence            4448999999998762 235577999999999999999999999999765

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

Probab=99.31  E-value=1e-12  Score=91.27  Aligned_cols=51  Identities=37%  Similarity=0.970  Sum_probs=45.4

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccCC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVIA  118 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~~  118 (118)
                      ...+|.||++.|...++.+.+||.|.||..|+.+|+. -+..||.||.++++
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            3478999999999888899999999999999999997 55579999999874

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.29  E-value=3.4e-12  Score=65.76  Aligned_cols=44  Identities=30%  Similarity=0.873  Sum_probs=38.1

Q ss_pred             cccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCc
Q 033497           71 RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS  114 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~  114 (118)
                      .|+||++.+.....+.+++|||+||..|+..+......||+||+
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            48999999965666888999999999999999866678999985

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

Probab=99.28  E-value=2.2e-12  Score=86.59  Aligned_cols=49  Identities=29%  Similarity=0.722  Sum_probs=41.6

Q ss_pred             ccCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC---CCcccccCccc
Q 033497           65 VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL---SNSCPVCRSGV  116 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~---~~~CP~Cr~~~  116 (118)
                      .+...+.|-||++.-.+   +++..|||.||+-||-+|+..   .+.||+|+..+
T Consensus        43 ~~~~~FdCNICLd~akd---PVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~V   94 (230)
T KOG0823|consen   43 RDGGFFDCNICLDLAKD---PVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEV   94 (230)
T ss_pred             CCCCceeeeeeccccCC---CEEeecccceehHHHHHHHhhcCCCeeCCcccccc
Confidence            35567899999999777   999999999999999999963   34599999865

>PHA02926 zinc finger-like protein; Provisional

Probab=99.25  E-value=5.2e-12  Score=84.50  Aligned_cols=51  Identities=31%  Similarity=0.786  Sum_probs=38.5

Q ss_pred             cCccccccccccccccC-----C-CceeeCCCChhhHHHHHHHhhCC------CcccccCccc
Q 033497           66 AATEGRCTVCMENFLQA-----F-PGKQVPCGHVFHATCISTWISLS------NSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~-----~-~~~~~~C~H~f~~~Ci~~~~~~~------~~CP~Cr~~~  116 (118)
                      ...+.+|+||+|.....     . ..++.+|+|.||..||..|...+      ++||+||..+
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f  229 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRF  229 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCccee
Confidence            34568899999987442     1 13445699999999999998643      3599999865

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

Probab=99.25  E-value=8.4e-12  Score=72.04  Aligned_cols=49  Identities=31%  Similarity=0.681  Sum_probs=38.1

Q ss_pred             cccccccccccccc---------CCCceee-CCCChhhHHHHHHHhhC---CCcccccCccc
Q 033497           68 TEGRCTVCMENFLQ---------AFPGKQV-PCGHVFHATCISTWISL---SNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~---------~~~~~~~-~C~H~f~~~Ci~~~~~~---~~~CP~Cr~~~  116 (118)
                      +++.|+||...|..         ++.+..+ .|+|.||..||.+|+..   +..||+||++.
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w   81 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW   81 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence            47789999998863         2334333 59999999999999974   45799999875

>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=99.25  E-value=7.6e-12  Score=64.04  Aligned_cols=44  Identities=43%  Similarity=1.222  Sum_probs=35.6

Q ss_pred             cccccccccccCCCceeeCCCChhhHHHHHHHhhC-CCcccccCccc
Q 033497           71 RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGV  116 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~  116 (118)
                      .|+||++.+..  .....+|+|.||..|+..|+.. +..||.||..+
T Consensus         1 ~C~iC~~~~~~--~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhC--ceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            49999999843  2344459999999999999986 67799999764

>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=99.20  E-value=8.8e-12  Score=63.19  Aligned_cols=38  Identities=39%  Similarity=1.130  Sum_probs=33.5

Q ss_pred             ccccccccccCCCce-eeCCCChhhHHHHHHHhh--CCCccccc
Q 033497           72 CTVCMENFLQAFPGK-QVPCGHVFHATCISTWIS--LSNSCPVC  112 (118)
Q Consensus        72 C~IC~~~~~~~~~~~-~~~C~H~f~~~Ci~~~~~--~~~~CP~C  112 (118)
                      |+||++.+..   +. .++|||.||..|+.+|++  ....||.|
T Consensus         1 C~iC~~~~~~---~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED---PVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS---EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC---CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999999887   66 888999999999999998  55579987

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 ....

>smart00504 Ubox Modified RING finger domain

Probab=99.18  E-value=2.3e-11  Score=67.09  Aligned_cols=44  Identities=18%  Similarity=0.416  Sum_probs=40.5

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ..|+||.+.+.+   ++.++|||.|+..||.+|++.+..||.|+..+
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~   45 (63)
T smart00504        2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPL   45 (63)
T ss_pred             cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCC
Confidence            569999999988   88899999999999999998888999999876

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

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

Probab=99.15  E-value=1.5e-11  Score=93.19  Aligned_cols=51  Identities=33%  Similarity=1.015  Sum_probs=44.3

Q ss_pred             cCccccccccccccccCCC--ceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFP--GKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~--~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ...+..|.||+|.+.....  +..++|+|+||..|+..|+++..+||+||..+
T Consensus       288 ~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  288 ALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             hhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence            3456889999999987544  78899999999999999999999999999843

>smart00184 RING Ring finger

Probab=99.13  E-value=7.7e-11  Score=58.30  Aligned_cols=38  Identities=39%  Similarity=1.205  Sum_probs=32.9

Q ss_pred             ccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCccccc
Q 033497           72 CTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVC  112 (118)
Q Consensus        72 C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~C  112 (118)
                      |+||++....   +..++|+|.||..|+..|+. .+..||.|
T Consensus         1 C~iC~~~~~~---~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKD---PVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCC---cEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899988544   88899999999999999998 66679987

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.12  E-value=4.6e-11  Score=86.90  Aligned_cols=48  Identities=31%  Similarity=0.666  Sum_probs=42.6

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ......|+||++.|..   +++++|||.||..||..|+.....||.||..+
T Consensus        23 Le~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~   70 (397)
T TIGR00599        23 LDTSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAED   70 (397)
T ss_pred             cccccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCCCCCCCCcc
Confidence            3456899999999987   78899999999999999998888899999865

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

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

Probab=99.11  E-value=5.1e-11  Score=81.44  Aligned_cols=57  Identities=30%  Similarity=0.775  Sum_probs=47.3

Q ss_pred             cccCCCCccCccccccccccccccCCCceeeCCCChhhHHHHHH-HhhCCCc-ccccCcccC
Q 033497           58 TVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCIST-WISLSNS-CPVCRSGVI  117 (118)
Q Consensus        58 ~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~-~~~~~~~-CP~Cr~~~~  117 (118)
                      ....++-....++.|.||++....   +..++|||+||+.||.. |-..+.. ||+||+...
T Consensus       204 ~kn~~pfip~~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~  262 (271)
T COG5574         204 KKNGLPFIPLADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY  262 (271)
T ss_pred             ccccCCcccccccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence            444555566788999999999877   99999999999999999 8766666 999998753

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

Probab=99.01  E-value=2.9e-10  Score=64.27  Aligned_cols=47  Identities=26%  Similarity=0.639  Sum_probs=36.7

Q ss_pred             cccccccccccc------------CCCceeeC-CCChhhHHHHHHHhhCCCcccccCccc
Q 033497           70 GRCTVCMENFLQ------------AFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~------------~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      +.|.||...+..            ++.++... |.|.||..||.+|+..+..||++|++.
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w   80 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTW   80 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCcee
Confidence            567777766542            23344444 999999999999999999999999875

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

Probab=98.99  E-value=1.9e-10  Score=84.81  Aligned_cols=45  Identities=33%  Similarity=0.857  Sum_probs=38.5

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhC-----CCcccccCccc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-----SNSCPVCRSGV  116 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-----~~~CP~Cr~~~  116 (118)
                      +..||||++....   +..+.|||+||..||.++|..     ...||+||..+
T Consensus       186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I  235 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTI  235 (513)
T ss_pred             CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhc
Confidence            7899999999776   788889999999999999853     34699999765

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

Probab=98.99  E-value=2.1e-10  Score=81.00  Aligned_cols=46  Identities=35%  Similarity=0.775  Sum_probs=42.5

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      -++|.||.+.|..   +.+.||+|.||.-||+.++..+..||.|+.++.
T Consensus        23 lLRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~   68 (442)
T KOG0287|consen   23 LLRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVT   68 (442)
T ss_pred             HHHHhHHHHHhcC---ceeccccchHHHHHHHHHhccCCCCCceecccc
Confidence            3889999999998   999999999999999999999999999988653

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

Probab=98.97  E-value=3.7e-10  Score=57.62  Aligned_cols=38  Identities=39%  Similarity=0.911  Sum_probs=22.9

Q ss_pred             cccccccccc-CCCceeeCCCChhhHHHHHHHhhCC----Cccc
Q 033497           72 CTVCMENFLQ-AFPGKQVPCGHVFHATCISTWISLS----NSCP  110 (118)
Q Consensus        72 C~IC~~~~~~-~~~~~~~~C~H~f~~~Ci~~~~~~~----~~CP  110 (118)
                      |+||.+ +.. .+.++.|+|||.||.+|+.++.+..    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 644 5667889999999999999998743    3476

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

Probab=98.86  E-value=5.8e-10  Score=62.55  Aligned_cols=49  Identities=31%  Similarity=0.678  Sum_probs=38.0

Q ss_pred             cccccccccccccc---------CCCceeeC-CCChhhHHHHHHHhhCC---CcccccCccc
Q 033497           68 TEGRCTVCMENFLQ---------AFPGKQVP-CGHVFHATCISTWISLS---NSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~---------~~~~~~~~-C~H~f~~~Ci~~~~~~~---~~CP~Cr~~~  116 (118)
                      .+..|.||.-.|..         ++.+.++. |.|.||..||.+|+...   ..||+||+..
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~   80 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTW   80 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhee
Confidence            44589999888753         45566555 99999999999999643   3599999865

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

Probab=98.83  E-value=3.2e-09  Score=73.80  Aligned_cols=45  Identities=31%  Similarity=0.685  Sum_probs=41.6

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      -++|.||-+.+..   +...+|||.||.-||+..+..+..||+||.+.
T Consensus        25 ~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~   69 (391)
T COG5432          25 MLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQPFCPVCREDP   69 (391)
T ss_pred             HHHhhhhhheeec---ceecccccchhHHHHHHHhcCCCCCccccccH
Confidence            3789999999988   88999999999999999999999999999864

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

Probab=98.81  E-value=4.3e-09  Score=59.83  Aligned_cols=47  Identities=21%  Similarity=0.432  Sum_probs=38.5

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      +.+.|+|+.+.|.+   ++++++||.|...+|.+|+.. ...||+++.++.
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~   50 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLS   50 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-S
T ss_pred             cccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCC
Confidence            56889999999999   999999999999999999988 788999988764

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

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

Probab=98.76  E-value=7.7e-09  Score=61.29  Aligned_cols=54  Identities=26%  Similarity=0.578  Sum_probs=39.9

Q ss_pred             CCCccCcccccccccccccc-------------CCCceeeC-CCChhhHHHHHHHhhCCCcccccCcc
Q 033497           62 LPTVAATEGRCTVCMENFLQ-------------AFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSG  115 (118)
Q Consensus        62 ~~~~~~~~~~C~IC~~~~~~-------------~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~  115 (118)
                      +-.-+...+.|.||...+.+             ++..+... |.|.||..||.+|++.+..||+|.+.
T Consensus        39 lWaWDi~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   39 LWAWDIVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             eeeeeeeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence            33345666889999766532             12233333 99999999999999999999999764

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

Probab=98.73  E-value=4.5e-09  Score=72.29  Aligned_cols=56  Identities=32%  Similarity=0.775  Sum_probs=42.9

Q ss_pred             CCCCccCccccccccccccccCC-------CceeeCCCChhhHHHHHHHh--hCCCcccccCccc
Q 033497           61 SLPTVAATEGRCTVCMENFLQAF-------PGKQVPCGHVFHATCISTWI--SLSNSCPVCRSGV  116 (118)
Q Consensus        61 ~~~~~~~~~~~C~IC~~~~~~~~-------~~~~~~C~H~f~~~Ci~~~~--~~~~~CP~Cr~~~  116 (118)
                      .+|....++..|.||-..+....       ....+.|+|.||+.||+.|-  ..+.+||.|+..+
T Consensus       216 glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV  280 (328)
T KOG1734|consen  216 GLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV  280 (328)
T ss_pred             CCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence            34444556778999988876543       45678999999999999996  4666899998754

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

Probab=98.71  E-value=6.1e-09  Score=72.62  Aligned_cols=45  Identities=38%  Similarity=0.828  Sum_probs=40.1

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR  113 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr  113 (118)
                      ..+...|+||++.|..   +.+++|+|.||..|+..++.....||.||
T Consensus        10 ~~~~~~C~iC~~~~~~---p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   10 LQEELTCPICLEYFRE---PVLLPCGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             ccccccChhhHHHhhc---CccccccchHhHHHHHHhcCCCcCCcccC
Confidence            4567889999999998   68899999999999999988556799998

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

Probab=98.71  E-value=4.6e-09  Score=55.27  Aligned_cols=46  Identities=28%  Similarity=0.704  Sum_probs=38.2

Q ss_pred             ccccccccccccccCCCceeeCCCCh-hhHHHHHHHhh-CCCcccccCccc
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWIS-LSNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~-~~~~CP~Cr~~~  116 (118)
                      .+.+|.||+|...+   .++..|||. +|..|..+.++ .+..||+||+++
T Consensus         6 ~~dECTICye~pvd---sVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi   53 (62)
T KOG4172|consen    6 WSDECTICYEHPVD---SVLYTCGHMCMCYACGLRLKKALHGCCPICRAPI   53 (62)
T ss_pred             cccceeeeccCcch---HHHHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence            34789999998766   677789998 89999888776 666899999876

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

Probab=98.71  E-value=1.6e-09  Score=78.13  Aligned_cols=47  Identities=34%  Similarity=0.870  Sum_probs=39.1

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhh--CCCcccccCccc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS--LSNSCPVCRSGV  116 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~--~~~~CP~Cr~~~  116 (118)
                      ..-..|.||-|.-.+   +.+-||||..|..|+..|-.  ...+||+||..+
T Consensus       367 sTFeLCKICaendKd---vkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI  415 (563)
T KOG1785|consen  367 STFELCKICAENDKD---VKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI  415 (563)
T ss_pred             chHHHHHHhhccCCC---cccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence            344789999988555   88999999999999999973  356899999865

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.67  E-value=1.9e-08  Score=70.94  Aligned_cols=49  Identities=22%  Similarity=0.514  Sum_probs=34.8

Q ss_pred             cccccccccccc--ccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCccc
Q 033497           68 TEGRCTVCMENF--LQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~--~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~  116 (118)
                      ++..||+|...-  .......+-+|||.||.+|+...+. ....||.|+..+
T Consensus         2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~l   53 (309)
T TIGR00570         2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPL   53 (309)
T ss_pred             CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCcc
Confidence            346799999853  2222122226999999999999764 455799998765

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).

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

Probab=98.65  E-value=3.3e-08  Score=51.87  Aligned_cols=42  Identities=24%  Similarity=0.721  Sum_probs=31.9

Q ss_pred             cccccccccccCCCceeeCCC-----ChhhHHHHHHHhhC--CCcccccC
Q 033497           71 RCTVCMENFLQAFPGKQVPCG-----HVFHATCISTWISL--SNSCPVCR  113 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~C~-----H~f~~~Ci~~~~~~--~~~CP~Cr  113 (118)
                      .|.||++ ...+..+.+.||.     |.+|.+|+.+|+..  +.+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            3899998 3334446677874     88999999999954  44799995

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

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

Probab=98.61  E-value=2.6e-08  Score=73.60  Aligned_cols=53  Identities=28%  Similarity=0.716  Sum_probs=40.4

Q ss_pred             cCccccccccccccccCC--------------CceeeCCCChhhHHHHHHHhhCCC-cccccCcccCC
Q 033497           66 AATEGRCTVCMENFLQAF--------------PGKQVPCGHVFHATCISTWISLSN-SCPVCRSGVIA  118 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~--------------~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~~~  118 (118)
                      ......|.||+..+..-.              .-...||.|+||..|+..|....+ .||.||.++++
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            345577999998875310              012458999999999999998555 89999999874

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

Probab=98.61  E-value=2.7e-08  Score=70.82  Aligned_cols=48  Identities=23%  Similarity=0.690  Sum_probs=41.9

Q ss_pred             CccccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ....+|-||+....+   ..+|||.|. .|..|.+...-.++.||+||+++.
T Consensus       288 ~~gkeCVIClse~rd---t~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            335789999999777   999999999 999999988777889999999874

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

Probab=98.59  E-value=2.4e-08  Score=72.86  Aligned_cols=50  Identities=34%  Similarity=0.806  Sum_probs=39.2

Q ss_pred             ccCccccccccccccccCCCc-eeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           65 VAATEGRCTVCMENFLQAFPG-KQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~-~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ...+-.+|++|+|.+..+... +...|.|.||..|+.+|..  .+||+||...
T Consensus       171 ~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~--~scpvcR~~q  221 (493)
T KOG0804|consen  171 GLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD--SSCPVCRYCQ  221 (493)
T ss_pred             CcccCCCcchhHhhcCccccceeeeecccccchHHHhhccc--CcChhhhhhc
Confidence            345567899999999875433 3445999999999999954  7899999743

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

Probab=98.58  E-value=5.6e-09  Score=58.86  Aligned_cols=49  Identities=33%  Similarity=0.718  Sum_probs=22.1

Q ss_pred             cccccccccccc-cCCCce-ee---CCCChhhHHHHHHHhhC---CC--------cccccCcccC
Q 033497           69 EGRCTVCMENFL-QAFPGK-QV---PCGHVFHATCISTWISL---SN--------SCPVCRSGVI  117 (118)
Q Consensus        69 ~~~C~IC~~~~~-~~~~~~-~~---~C~H~f~~~Ci~~~~~~---~~--------~CP~Cr~~~~  117 (118)
                      +..|.||+..+. .+..+. ..   .|+..||..||.+|+..   .+        .||.|+.+|.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            457999999876 322222 22   49999999999999851   11        4999998763

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

Probab=98.52  E-value=3.4e-08  Score=75.99  Aligned_cols=46  Identities=28%  Similarity=0.676  Sum_probs=40.6

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccC
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVI  117 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~  117 (118)
                      -..|+.|-+.+.+   .++..|+|.||..|+...+. +++.||.|...|-
T Consensus       643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg  689 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG  689 (698)
T ss_pred             ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence            3789999988888   88889999999999999886 6678999998875

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

Probab=98.50  E-value=1.6e-08  Score=55.25  Aligned_cols=44  Identities=30%  Similarity=0.757  Sum_probs=23.6

Q ss_pred             ccccccccccccccCCCcee-eCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           68 TEGRCTVCMENFLQAFPGKQ-VPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~-~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      +-..|++|.+.+.+   ++. ..|.|.||..||..-+.  ..||+|+.+.
T Consensus         6 ~lLrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Pa   50 (65)
T PF14835_consen    6 ELLRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPA   50 (65)
T ss_dssp             HTTS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-
T ss_pred             HhcCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC--CCCCCcCChH
Confidence            34689999999988   765 45999999999987544  4599998764

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

Probab=98.49  E-value=6.7e-08  Score=69.57  Aligned_cols=45  Identities=29%  Similarity=0.961  Sum_probs=34.6

Q ss_pred             ccccccccccccCCCceeeC-CCChhhHHHHHHHhh---CCCcccccCc
Q 033497           70 GRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWIS---LSNSCPVCRS  114 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~---~~~~CP~Cr~  114 (118)
                      ..|.||.+-+.......... |||+||..|+.+|+.   .++.||+|+-
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~i   53 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQI   53 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceee
Confidence            46999966665544444444 999999999999996   3467999983

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

Probab=98.47  E-value=2e-08  Score=71.37  Aligned_cols=50  Identities=24%  Similarity=0.560  Sum_probs=40.3

Q ss_pred             cCccccccccccccccCCCceeeC-CCChhhHHHHHHHhh-CCCcccccCcccCC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWIS-LSNSCPVCRSGVIA  118 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~~  118 (118)
                      ...+..|+||++.+..   ....+ |.|.||.+||..-++ .++.||.||+.+.+
T Consensus        40 ~~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   40 FDIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            4456889999999876   44444 999999999988775 66689999997653

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

Probab=98.43  E-value=1.1e-07  Score=68.28  Aligned_cols=50  Identities=36%  Similarity=0.780  Sum_probs=37.9

Q ss_pred             CccccccccccccccCC-----CceeeCCCChhhHHHHHHHhh--C-----CCcccccCccc
Q 033497           67 ATEGRCTVCMENFLQAF-----PGKQVPCGHVFHATCISTWIS--L-----SNSCPVCRSGV  116 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~-----~~~~~~C~H~f~~~Ci~~~~~--~-----~~~CP~Cr~~~  116 (118)
                      ..+..|.||++......     -.++.+|.|.||..||..|-.  +     .+.||.||...
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            55788999999987633     122345999999999999983  3     45799999753

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

Probab=98.37  E-value=1.8e-07  Score=65.36  Aligned_cols=47  Identities=23%  Similarity=0.440  Sum_probs=39.1

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccCC
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVIA  118 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~~  118 (118)
                      +..|.||+.....   ++.++|+|.||.-||+-... .+++|++||.++.+
T Consensus         7 ~~eC~IC~nt~n~---Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids   54 (324)
T KOG0824|consen    7 KKECLICYNTGNC---PVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDS   54 (324)
T ss_pred             CCcceeeeccCCc---CccccccchhhhhhhcchhhcCCCCCceecCCCCc
Confidence            4569999887655   89999999999999998765 55569999998753

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

Probab=98.35  E-value=1.6e-07  Score=74.14  Aligned_cols=51  Identities=25%  Similarity=0.774  Sum_probs=37.5

Q ss_pred             Ccccccccccccccc-CC--C-ceeeCCCChhhHHHHHHHhh--CCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQ-AF--P-GKQVPCGHVFHATCISTWIS--LSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~-~~--~-~~~~~C~H~f~~~Ci~~~~~--~~~~CP~Cr~~~~  117 (118)
                      ++..+|+||+..+.- +.  . .+.-.|.|.||..|+-+|++  .+.+||+||..+.
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            445889999987762 11  1 12234999999999999997  4557999998764

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

Probab=98.17  E-value=9.8e-07  Score=64.63  Aligned_cols=52  Identities=29%  Similarity=0.749  Sum_probs=44.8

Q ss_pred             CCccCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           63 PTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        63 ~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      +.....++.|.||+..+..   ++.+||||.||..||.+.+.....||.||..+.
T Consensus        78 ~~~~~sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~  129 (398)
T KOG4159|consen   78 PEEIRSEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELV  129 (398)
T ss_pred             CccccchhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCcccccccc
Confidence            3344677999999999888   888899999999999998887778999998765

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

Probab=98.10  E-value=1.5e-06  Score=63.10  Aligned_cols=46  Identities=26%  Similarity=0.897  Sum_probs=36.1

Q ss_pred             ccccccccccccc--CCCceeeCCCChhhHHHHHHHhh--CCCcccccCc
Q 033497           69 EGRCTVCMENFLQ--AFPGKQVPCGHVFHATCISTWIS--LSNSCPVCRS  114 (118)
Q Consensus        69 ~~~C~IC~~~~~~--~~~~~~~~C~H~f~~~Ci~~~~~--~~~~CP~Cr~  114 (118)
                      ...|+||++.+..  +.+.+.+.|||.|..+||.+|+.  ....||.|..
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~   53 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSG   53 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCC
Confidence            4679999999865  34456778999999999999994  2225999965

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

Probab=97.98  E-value=1.4e-06  Score=67.78  Aligned_cols=48  Identities=23%  Similarity=0.643  Sum_probs=39.6

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ...|++|+-.+..+......+|+|.||..||..|-+...+||+||..|
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF  170 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEF  170 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhh
Confidence            366888887776655555667999999999999999999999999755

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

Probab=97.92  E-value=6.3e-06  Score=61.90  Aligned_cols=91  Identities=20%  Similarity=0.421  Sum_probs=64.1

Q ss_pred             ccccCcccccCCCChHHHHhhhhcCCCCCCCCCCCCCCCCCCCccccccCCCCccCccccccccccccccCCCceeeCCC
Q 033497           12 NIVSGSPIIDESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCG   91 (118)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~   91 (118)
                      .++..|.+.+...+...++...++...+|.-....           ....++....++..|.+|.+.-.+   .+...|.
T Consensus       490 tyieeGvvlNNYAnIF~LitRmRQ~aDHP~LVl~S-----------~~~n~~~enk~~~~C~lc~d~aed---~i~s~Ch  555 (791)
T KOG1002|consen  490 TYIEEGVVLNNYANIFTLITRMRQAADHPDLVLYS-----------ANANLPDENKGEVECGLCHDPAED---YIESSCH  555 (791)
T ss_pred             hHHhhhhhhhhHHHHHHHHHHHHHhccCcceeeeh-----------hhcCCCccccCceeecccCChhhh---hHhhhhh
Confidence            34555667777777777777777777666443221           223344445566789999988666   7888899


Q ss_pred             ChhhHHHHHHHhh-----CCCcccccCccc
Q 033497           92 HVFHATCISTWIS-----LSNSCPVCRSGV  116 (118)
Q Consensus        92 H~f~~~Ci~~~~~-----~~~~CP~Cr~~~  116 (118)
                      |.||.-|+..+..     .+.+||.|-..+
T Consensus       556 H~FCrlCi~eyv~~f~~~~nvtCP~C~i~L  585 (791)
T KOG1002|consen  556 HKFCRLCIKEYVESFMENNNVTCPVCHIGL  585 (791)
T ss_pred             HHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence            9999999999874     345799997654

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

Probab=97.85  E-value=4.2e-06  Score=59.29  Aligned_cols=46  Identities=24%  Similarity=0.670  Sum_probs=39.4

Q ss_pred             ccccccccccccccCCCceeeC-CCChhhHHHHHHHhhCCCcccccCccc
Q 033497           68 TEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ....|.+|-..|.+   +..+. |-|.||.+||.+.+...+.||.|...+
T Consensus        14 ~~itC~LC~GYliD---ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~i   60 (331)
T KOG2660|consen   14 PHITCRLCGGYLID---ATTITECLHTFCKSCIVKYLEESKYCPTCDIVI   60 (331)
T ss_pred             cceehhhccceeec---chhHHHHHHHHHHHHHHHHHHHhccCCccceec
Confidence            34679999999988   66555 999999999999999999999997644

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

Probab=97.84  E-value=9.2e-06  Score=59.75  Aligned_cols=48  Identities=33%  Similarity=0.707  Sum_probs=41.7

Q ss_pred             cCccccccccccccccCCCcee-eCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQ-VPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~-~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ..++..|+||...+.+   +.. ..|||.||..|+..|+..+..||.|+..+
T Consensus        18 ~~~~l~C~~C~~vl~~---p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~   66 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRD---PVQTTTCGHRFCAGCLLESLSNHQKCPVCRQEL   66 (391)
T ss_pred             CcccccCccccccccC---CCCCCCCCCcccccccchhhccCcCCccccccc
Confidence            4567889999999887   666 58999999999999999888999998754

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

Probab=97.80  E-value=1.5e-05  Score=57.31  Aligned_cols=49  Identities=22%  Similarity=0.580  Sum_probs=43.7

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      +.++..|+||+.....   .+..||+|.-|..||.+-+...+.|=+|+..++
T Consensus       419 ~sEd~lCpICyA~pi~---Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  419 DSEDNLCPICYAGPIN---AVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             CcccccCcceecccch---hhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence            4678899999988766   889999999999999999999999999988764

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

Probab=97.72  E-value=1.5e-05  Score=52.98  Aligned_cols=43  Identities=23%  Similarity=0.583  Sum_probs=38.6

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSG  115 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~  115 (118)
                      +.|.||-..|..   ++...|||.||..|...-++....|-+|-+.
T Consensus       197 F~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~  239 (259)
T COG5152         197 FLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKA  239 (259)
T ss_pred             eeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchh
Confidence            589999999998   8999999999999999888888889999654

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

Probab=97.71  E-value=1.2e-05  Score=56.57  Aligned_cols=34  Identities=24%  Similarity=0.750  Sum_probs=31.2

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHh
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWI  103 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~  103 (118)
                      -.|.||+.-|..+...+.++|-|.||..|+.+++
T Consensus       116 gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl  149 (368)
T KOG4445|consen  116 GQCVICLYGFASSPAFTVTACDHYMHFACLARYL  149 (368)
T ss_pred             CceEEEEEeecCCCceeeehhHHHHHHHHHHHHH
Confidence            6799999999988878889999999999999987

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

Probab=97.71  E-value=1.2e-05  Score=58.37  Aligned_cols=48  Identities=33%  Similarity=0.716  Sum_probs=37.7

Q ss_pred             CccccccccccccccC-CCceeeCCCChhhHHHHHHHhhC--CCcccccCc
Q 033497           67 ATEGRCTVCMENFLQA-FPGKQVPCGHVFHATCISTWISL--SNSCPVCRS  114 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~-~~~~~~~C~H~f~~~Ci~~~~~~--~~~CP~Cr~  114 (118)
                      +-+..|..|-+.+-.. +....+||.|+||.+|+..++..  .++||.||+
T Consensus       363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            3457899999887653 33567899999999999999854  447999984

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

Probab=97.68  E-value=4.8e-05  Score=52.85  Aligned_cols=49  Identities=31%  Similarity=0.591  Sum_probs=37.9

Q ss_pred             cCccccccccccccccCCCce-eeCCCChhhHHHHHHHhh--CCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGK-QVPCGHVFHATCISTWIS--LSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~-~~~C~H~f~~~Ci~~~~~--~~~~CP~Cr~~~~  117 (118)
                      ...+.+|++|-+....   |. ..+|+|+||..||..-..  ...+||.|.....
T Consensus       236 ~t~~~~C~~Cg~~Pti---P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  236 GTSDTECPVCGEPPTI---PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccCCceeeccCCCCCC---CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            4566789999988666   54 456999999999998764  3468999987654

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

Probab=97.66  E-value=5.1e-06  Score=58.10  Aligned_cols=41  Identities=29%  Similarity=0.740  Sum_probs=35.1

Q ss_pred             cccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCccc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      +..|.||++...+   -+.|+|||. -|.+|.+.+    ..||+||+.+
T Consensus       300 ~~LC~ICmDaP~D---CvfLeCGHmVtCt~CGkrm----~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLECGHMVTCTKCGKRM----NECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcCCcc---eEEeecCcEEeehhhcccc----ccCchHHHHH
Confidence            5789999999877   899999998 789998765    4899999865

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

Probab=97.63  E-value=6.7e-05  Score=38.89  Aligned_cols=45  Identities=22%  Similarity=0.490  Sum_probs=22.7

Q ss_pred             ccccccccccCCC-ceeeCCCChhhHHHHHHHhh-CCCcccccCccc
Q 033497           72 CTVCMENFLQAFP-GKQVPCGHVFHATCISTWIS-LSNSCPVCRSGV  116 (118)
Q Consensus        72 C~IC~~~~~~~~~-~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~  116 (118)
                      |++|.+.+...+. ..--+|++.+|..|+...+. ....||-||.+.
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            7899999854332 22335899999999999886 567899999863

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

Probab=97.61  E-value=3.6e-05  Score=41.53  Aligned_cols=41  Identities=29%  Similarity=0.668  Sum_probs=27.5

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHHHHhhC--CCcccc
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISL--SNSCPV  111 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~--~~~CP~  111 (118)
                      -...|+|-+..|.+   ++.- .|+|.|-.+.|.+|++.  ...||.
T Consensus        10 ~~~~CPiT~~~~~~---PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED---PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS---EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhC---CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            34789999999887   6654 69999999999999943  335998

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

Probab=97.43  E-value=4.2e-05  Score=53.64  Aligned_cols=44  Identities=25%  Similarity=0.577  Sum_probs=39.4

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      +.|-||...|..   ++...|+|.||..|...-++....|.+|.+.+
T Consensus       242 f~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  242 FKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             cccccccccccc---chhhcCCceeehhhhccccccCCcceeccccc
Confidence            569999999998   99999999999999988888888899997654

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

Probab=97.35  E-value=0.0001  Score=38.18  Aligned_cols=40  Identities=28%  Similarity=0.785  Sum_probs=26.4

Q ss_pred             ccccccccccCCCceeeCC--CC---hhhHHHHHHHhh--CCCccccc
Q 033497           72 CTVCMENFLQAFPGKQVPC--GH---VFHATCISTWIS--LSNSCPVC  112 (118)
Q Consensus        72 C~IC~~~~~~~~~~~~~~C--~H---~f~~~Ci~~~~~--~~~~CP~C  112 (118)
                      |.||++.-..+. +.+.||  .-   ..|.+|+.+|+.  .+..|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            789998866544 556675  33   689999999996  45569887

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

Probab=97.34  E-value=0.00017  Score=60.17  Aligned_cols=51  Identities=29%  Similarity=0.776  Sum_probs=39.2

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC----------cccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN----------SCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~----------~CP~Cr~~~  116 (118)
                      ...++.|-||+.+-...-..+.+.|+|+||..|.++.++++-          +||+|+.++
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence            345678999988755545567889999999999988775322          599998875

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

Probab=97.33  E-value=0.00017  Score=52.76  Aligned_cols=35  Identities=29%  Similarity=0.723  Sum_probs=31.9

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhh
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS  104 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~  104 (118)
                      ..|.||++...-.+..+.+||+|.||.+|+..++.
T Consensus       185 f~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFT  219 (445)
T ss_pred             ccceeeehhhcCcceeeecccchHHHHHHHHHHHH
Confidence            88999999987667889999999999999999984

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

Probab=97.25  E-value=0.00068  Score=48.89  Aligned_cols=48  Identities=23%  Similarity=0.690  Sum_probs=39.2

Q ss_pred             ccCccccccccccccccCCCceeeCCCChhhHHHHHHH--hhCCCcccccCcc
Q 033497           65 VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTW--ISLSNSCPVCRSG  115 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~--~~~~~~CP~Cr~~  115 (118)
                      .+++...|-||.+.+.-   ..++||+|..|.-|..+.  +..++.||+||..
T Consensus        57 tDEen~~C~ICA~~~TY---s~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE  106 (493)
T COG5236          57 TDEENMNCQICAGSTTY---SARYPCGHQICHACAVRLRALYMQKGCPLCRTE  106 (493)
T ss_pred             cccccceeEEecCCceE---EEeccCCchHHHHHHHHHHHHHhccCCCccccc
Confidence            34556889999988765   788999999999998765  4578899999863

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

Probab=97.23  E-value=0.00032  Score=47.65  Aligned_cols=48  Identities=21%  Similarity=0.614  Sum_probs=37.2

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhC--------CCcccccCcccC
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL--------SNSCPVCRSGVI  117 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~--------~~~CP~Cr~~~~  117 (118)
                      ...|..|-..+..++. +.+-|-|.||++|+.+|-..        ...||.|...+.
T Consensus        50 ~pNC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF  105 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF  105 (299)
T ss_pred             CCCCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence            3569999998887664 45569999999999999742        235999987653

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

Probab=97.17  E-value=0.00034  Score=43.91  Aligned_cols=36  Identities=22%  Similarity=0.452  Sum_probs=29.3

Q ss_pred             cccccccccccccCCCceeeCCC------ChhhHHHHHHHhh
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCG------HVFHATCISTWIS  104 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~------H~f~~~Ci~~~~~  104 (118)
                      ..+|.||++.+.....++.++|+      |.||.+|+.+|-+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            57899999999874556666775      8899999999954

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.

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.11  E-value=0.00079  Score=43.39  Aligned_cols=47  Identities=21%  Similarity=0.681  Sum_probs=33.1

Q ss_pred             cCccccccccccccccCCCceeeC--CCC---hhhHHHHHHHhhC--CCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP--CGH---VFHATCISTWISL--SNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~--C~H---~f~~~Ci~~~~~~--~~~CP~Cr~~~  116 (118)
                      ...+..|-||.+.-..    ..-|  |..   ..|.+|+.+|+..  ...|++|+...
T Consensus         5 s~~~~~CRIC~~~~~~----~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y   58 (162)
T PHA02825          5 SLMDKCCWICKDEYDV----VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY   58 (162)
T ss_pred             CCCCCeeEecCCCCCC----ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence            3456789999988432    2235  444   5699999999964  44699998764

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

Probab=97.08  E-value=0.00043  Score=49.06  Aligned_cols=46  Identities=28%  Similarity=0.733  Sum_probs=37.4

Q ss_pred             ccccccccccccC---CCceeeCCCChhhHHHHHHHhhCCC-cccccCcc
Q 033497           70 GRCTVCMENFLQA---FPGKQVPCGHVFHATCISTWISLSN-SCPVCRSG  115 (118)
Q Consensus        70 ~~C~IC~~~~~~~---~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~  115 (118)
                      ..|-||-++|...   ..++.+.|||.+|..|+.+.+.... .||+||.+
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~   53 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRET   53 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCc
Confidence            4699999999764   4477888999999999988775433 59999986

>PHA02862 5L protein; Provisional

Probab=97.08  E-value=0.00073  Score=42.86  Aligned_cols=43  Identities=23%  Similarity=0.647  Sum_probs=31.4

Q ss_pred             ccccccccccccCCCceeeC--C---CChhhHHHHHHHhh--CCCcccccCccc
Q 033497           70 GRCTVCMENFLQAFPGKQVP--C---GHVFHATCISTWIS--LSNSCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~--C---~H~f~~~Ci~~~~~--~~~~CP~Cr~~~  116 (118)
                      ..|-||++.-.++    .-|  |   -...|.+|+.+|+.  ++..|++|+.+.
T Consensus         3 diCWIC~~~~~e~----~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY   52 (156)
T PHA02862          3 DICWICNDVCDER----NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKY   52 (156)
T ss_pred             CEEEEecCcCCCC----cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeE
Confidence            4699999884332    244  4   25689999999996  445699998764

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

Probab=97.07  E-value=0.00042  Score=49.00  Aligned_cols=42  Identities=31%  Similarity=0.741  Sum_probs=34.4

Q ss_pred             ccccccccccccCCCceeeC-CCChhhHHHHHHHh-hCCCcccccCc
Q 033497           70 GRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWI-SLSNSCPVCRS  114 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~-~~~~~CP~Cr~  114 (118)
                      +.|+.|...+..   +...+ |+|.||..||...+ ..-..||.|..
T Consensus       275 LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhC---cccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            789999988877   66665 89999999998765 46668999943

>PHA03096 p28-like protein; Provisional

Probab=97.04  E-value=0.00046  Score=48.78  Aligned_cols=44  Identities=25%  Similarity=0.489  Sum_probs=30.7

Q ss_pred             ccccccccccccC----CCceeeC-CCChhhHHHHHHHhhC---CCcccccC
Q 033497           70 GRCTVCMENFLQA----FPGKQVP-CGHVFHATCISTWISL---SNSCPVCR  113 (118)
Q Consensus        70 ~~C~IC~~~~~~~----~~~~~~~-C~H~f~~~Ci~~~~~~---~~~CP~Cr  113 (118)
                      ..|.||++.....    ..-..++ |.|.||..|+..|...   +..||.||
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~  230 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENR  230 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCcccc
Confidence            5799999987652    1223454 9999999999999742   23455554

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

Probab=97.01  E-value=0.00026  Score=48.41  Aligned_cols=42  Identities=26%  Similarity=0.665  Sum_probs=30.6

Q ss_pred             ccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           72 CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        72 C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      |--|..--. ++.-.++.|+|+||..|...-.  ...||+|++++
T Consensus         6 Cn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~i   47 (233)
T KOG4739|consen    6 CNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSI   47 (233)
T ss_pred             eccccccCC-CCceeeeechhhhhhhhcccCC--cccccccccee
Confidence            666665544 5556677899999999986642  23899999875

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

Probab=97.00  E-value=0.00039  Score=50.07  Aligned_cols=46  Identities=33%  Similarity=0.694  Sum_probs=33.7

Q ss_pred             ccCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           65 VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      .......|.||++...+   ...+||||.-|  |..-. +....||+||..+
T Consensus       301 ~~~~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI  346 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCS-KHLPQCPVCRQRI  346 (355)
T ss_pred             ccCCCCceEEecCCccc---eeeecCCcEEE--chHHH-hhCCCCchhHHHH
Confidence            34455789999999887   99999999966  54433 2334599999754

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.80  E-value=0.00044  Score=36.72  Aligned_cols=42  Identities=29%  Similarity=0.677  Sum_probs=29.8

Q ss_pred             cccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           71 RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .|-.|...   +....+++|||..|..|..-+  +-+.||+|-.++.
T Consensus         9 ~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~   50 (55)
T PF14447_consen    9 PCVFCGFV---GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFE   50 (55)
T ss_pred             eEEEcccc---ccccccccccceeeccccChh--hccCCCCCCCccc
Confidence            35555433   334778899999999997654  4567999987763

>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=96.77  E-value=0.00057  Score=35.09  Aligned_cols=43  Identities=26%  Similarity=0.733  Sum_probs=25.9

Q ss_pred             cccccccccccCCCceeeCC-CChhhHHHHHHHhhCCCcccccCcccCC
Q 033497           71 RCTVCMENFLQAFPGKQVPC-GHVFHATCISTWISLSNSCPVCRSGVIA  118 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~C-~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~  118 (118)
                      .|.-|+  |..   ..++.| .|-.|..|+..++.....||+|..+++.
T Consensus         4 nCKsCW--f~~---k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen    4 NCKSCW--FAN---KGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             ---SS---S-----SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             cChhhh--hcC---CCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            466665  223   445667 4889999999999999999999998863

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.

>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=96.77  E-value=0.0015  Score=42.13  Aligned_cols=34  Identities=21%  Similarity=0.561  Sum_probs=24.2

Q ss_pred             ccccccccccccccCCCceeeC------------CCCh-hhHHHHHHHhh
Q 033497           68 TEGRCTVCMENFLQAFPGKQVP------------CGHV-FHATCISTWIS  104 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~------------C~H~-f~~~Ci~~~~~  104 (118)
                      ++.+|+||||...+   .++|-            |+.. -|..|++++.+
T Consensus         1 ed~~CpICme~PHN---AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPHN---AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCCc---eEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            46789999999777   66653            3322 47889998863

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.

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

Probab=96.75  E-value=0.0013  Score=43.27  Aligned_cols=47  Identities=28%  Similarity=0.845  Sum_probs=30.7

Q ss_pred             ccccccccccccCCCc----eeeCCCChhhHHHHHHHhhC----CC-------cccccCccc
Q 033497           70 GRCTVCMENFLQAFPG----KQVPCGHVFHATCISTWISL----SN-------SCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~----~~~~C~H~f~~~Ci~~~~~~----~~-------~CP~Cr~~~  116 (118)
                      -.|.||+..-..+..+    --..||..||.-|+..|++.    +.       .||.|..++
T Consensus       166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pi  227 (234)
T KOG3268|consen  166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPI  227 (234)
T ss_pred             hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcc
Confidence            4466665543332222    22459999999999999962    11       499998875

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

Probab=96.73  E-value=0.00055  Score=54.15  Aligned_cols=48  Identities=35%  Similarity=0.798  Sum_probs=34.4

Q ss_pred             CccccccccccccccCCCce-eeCCCChhhHHHHHHHhhCCC-------cccccCc
Q 033497           67 ATEGRCTVCMENFLQAFPGK-QVPCGHVFHATCISTWISLSN-------SCPVCRS  114 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~-~~~C~H~f~~~Ci~~~~~~~~-------~CP~Cr~  114 (118)
                      ...++|.||++.+.....+- --.|=|+||..||.+|-+...       .||.|..
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            34589999999987633222 223779999999999975311       4999974

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

Probab=96.63  E-value=0.00054  Score=41.20  Aligned_cols=35  Identities=34%  Similarity=0.677  Sum_probs=27.5

Q ss_pred             ccCccccccccccccccCCCceeeCCCChhhHHHHH
Q 033497           65 VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCIS  100 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~  100 (118)
                      ...++..|++|...+.. ......||||.||..|+.
T Consensus        74 ~i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   74 VITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             EECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            34556789999999876 335677999999999975

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 [].

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

Probab=96.56  E-value=0.0017  Score=45.69  Aligned_cols=47  Identities=30%  Similarity=0.812  Sum_probs=38.5

Q ss_pred             ccccccccccccccCC-CceeeCCCChhhHHHHHHHhhCCCcccccCc
Q 033497           68 TEGRCTVCMENFLQAF-PGKQVPCGHVFHATCISTWISLSNSCPVCRS  114 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~-~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~  114 (118)
                      ....|+||.+.+.... .+..++|||..|..|+........+||+|.+
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            3355999999877643 3567889999999999999877789999976

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

Probab=96.38  E-value=0.0022  Score=50.90  Aligned_cols=41  Identities=27%  Similarity=0.779  Sum_probs=32.6

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS  114 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~  114 (118)
                      ...|.+|-..+..  +.+...|||.||..|+.   .....||.|+.
T Consensus       840 ~skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~  880 (933)
T KOG2114|consen  840 VSKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLP  880 (933)
T ss_pred             eeeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccch
Confidence            3679999877765  35667799999999997   45567999975

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

Probab=96.38  E-value=0.0017  Score=32.98  Aligned_cols=41  Identities=24%  Similarity=0.630  Sum_probs=21.3

Q ss_pred             ccccccccccCCCceeeCCCChhhHHHHHHHhhCCC--ccccc
Q 033497           72 CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN--SCPVC  112 (118)
Q Consensus        72 C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~--~CP~C  112 (118)
                      |.+|-+....+..=....|+-.+|..|+..+++.+.  .||.|
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            566766655521111123888899999999997666  69987

; PDB: 3NW0_A 2CT0_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.29  E-value=0.0042  Score=44.78  Aligned_cols=48  Identities=27%  Similarity=0.602  Sum_probs=35.3

Q ss_pred             ccccccccccccccCCCc-eeeCCCChhhHHHHHHHhh-CCCcccccCcc
Q 033497           68 TEGRCTVCMENFLQAFPG-KQVPCGHVFHATCISTWIS-LSNSCPVCRSG  115 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~-~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~  115 (118)
                      +++-|+.|+|++...+.- .-.+||-..|.-|+....+ -+..||.||+.
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~   62 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRK   62 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhh
Confidence            444599999999875433 4467999988888776643 34579999874

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

Probab=96.22  E-value=0.0023  Score=50.26  Aligned_cols=43  Identities=30%  Similarity=0.715  Sum_probs=34.7

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC--cccccCccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN--SCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~--~CP~Cr~~~  116 (118)
                      ..|.||++ ...   ....+|+|.||..|+...+....  .||.||..+
T Consensus       455 ~~c~ic~~-~~~---~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l  499 (674)
T KOG1001|consen  455 HWCHICCD-LDS---FFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL  499 (674)
T ss_pred             cccccccc-ccc---ceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence            78999999 333   78889999999999999875333  599998754

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

Probab=96.07  E-value=0.0058  Score=44.72  Aligned_cols=47  Identities=23%  Similarity=0.428  Sum_probs=39.8

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC---cccccCc
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN---SCPVCRS  114 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~---~CP~Cr~  114 (118)
                      ..+.|||=-+.-.+++.|..+.|||+.+.+-+.+..+...   .||.|-.
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            3478999888888888999999999999999999986444   6999953

>PF04641 Rtf2: Rtf2 RING-finger

Probab=95.95  E-value=0.0065  Score=42.51  Aligned_cols=51  Identities=25%  Similarity=0.423  Sum_probs=38.7

Q ss_pred             cCccccccccccccccCCCce-eeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGK-QVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~-~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ....+.|||....|......+ +.+|||.|...+|.... ....||+|-.++.
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~  161 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFT  161 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccc
Confidence            345589999999986544343 45799999999999973 3457999987753

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

Probab=95.93  E-value=0.0052  Score=45.76  Aligned_cols=34  Identities=24%  Similarity=0.580  Sum_probs=30.3

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHh
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWI  103 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~  103 (118)
                      +++..|+||..-|.+   +++++|+|..|..|....+
T Consensus         2 eeelkc~vc~~f~~e---piil~c~h~lc~~ca~~~~   35 (699)
T KOG4367|consen    2 EEELKCPVCGSFYRE---PIILPCSHNLCQACARNIL   35 (699)
T ss_pred             cccccCceehhhccC---ceEeecccHHHHHHHHhhc
Confidence            467889999999888   9999999999999988665

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

Probab=95.92  E-value=0.0058  Score=43.76  Aligned_cols=47  Identities=23%  Similarity=0.486  Sum_probs=37.2

Q ss_pred             cCccccccccccccccCCCceeeC-CCChhhHHHHHHHhhCCCcccccCcc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSG  115 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~  115 (118)
                      ......|++|+-.-.+   +..+. -|-.||..|+..++...+.||+=..+
T Consensus       297 ~~~~~~CpvClk~r~N---ptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p  344 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQN---PTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYP  344 (357)
T ss_pred             CCccccChhHHhccCC---CceEEecceEEeHHHHHHHHHhcCCCCccCCc
Confidence            3345679999988766   55555 69999999999999999999975444

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.89  E-value=0.0076  Score=41.64  Aligned_cols=49  Identities=22%  Similarity=0.376  Sum_probs=40.2

Q ss_pred             ccccccccccccccCCCcee-eCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           68 TEGRCTVCMENFLQAFPGKQ-VPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~-~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ..+.|++|.+.+.+...-.. -+|||.|+..|..++++.-..||+|-.++
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~pl  269 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPL  269 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcC
Confidence            34889999999987554444 46999999999999988888899997664

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.62  E-value=0.013  Score=31.11  Aligned_cols=34  Identities=26%  Similarity=0.606  Sum_probs=27.4

Q ss_pred             ccccccccccccccCCCceeeC-CCChhhHHHHHH
Q 033497           68 TEGRCTVCMENFLQAFPGKQVP-CGHVFHATCIST  101 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~  101 (118)
                      ....|.+|-+.|..++.+++-+ |+-.+|+.|..+
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            3467999999998666677766 999999999654

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

Probab=95.56  E-value=0.0041  Score=42.12  Aligned_cols=38  Identities=32%  Similarity=0.709  Sum_probs=30.3

Q ss_pred             ccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCccc
Q 033497           72 CTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        72 C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      |..|.+.-..   +.++||.|. +|..|-..    ...||+|+...
T Consensus       161 Cr~C~~~~~~---VlllPCrHl~lC~~C~~~----~~~CPiC~~~~  199 (207)
T KOG1100|consen  161 CRKCGEREAT---VLLLPCRHLCLCGICDES----LRICPICRSPK  199 (207)
T ss_pred             ceecCcCCce---EEeecccceEeccccccc----CccCCCCcChh
Confidence            9999888555   889999988 88888643    35699998754

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

Probab=95.47  E-value=0.01  Score=43.26  Aligned_cols=27  Identities=26%  Similarity=0.950  Sum_probs=21.2

Q ss_pred             CCChhhHHHHHHHhhCCC-------------cccccCccc
Q 033497           90 CGHVFHATCISTWISLSN-------------SCPVCRSGV  116 (118)
Q Consensus        90 C~H~f~~~Ci~~~~~~~~-------------~CP~Cr~~~  116 (118)
                      |...-|.+|+.+|+..+.             .||.||+++
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F  350 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF  350 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence            667779999999994222             499999975

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

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

Probab=95.30  E-value=0.013  Score=41.82  Aligned_cols=45  Identities=27%  Similarity=0.558  Sum_probs=33.4

Q ss_pred             cCccccccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ..+-++||||.+.+..   ++.. .=||..|.+|-.+   ....||.||.++
T Consensus        45 ~~~lleCPvC~~~l~~---Pi~QC~nGHlaCssC~~~---~~~~CP~Cr~~~   90 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSP---PIFQCDNGHLACSSCRTK---VSNKCPTCRLPI   90 (299)
T ss_pred             chhhccCchhhccCcc---cceecCCCcEehhhhhhh---hcccCCcccccc
Confidence            3445889999999876   3332 3489999999753   556799999876

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

Probab=95.03  E-value=0.01  Score=42.27  Aligned_cols=43  Identities=33%  Similarity=0.760  Sum_probs=29.2

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      -.|.-|--.+  ....+.++|.|.||.+|.+.  ..-+.||.|-..+
T Consensus        91 HfCd~Cd~PI--~IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPI--AIYGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCcc--eeeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            4466664332  23457789999999999754  3456799996554

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

Probab=94.97  E-value=0.028  Score=35.32  Aligned_cols=46  Identities=24%  Similarity=0.661  Sum_probs=35.6

Q ss_pred             ccccccccccccccCCCceee-C---CCChhhHHHHHHHhhC---CCcccccCccc
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-P---CGHVFHATCISTWISL---SNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~---C~H~f~~~Ci~~~~~~---~~~CP~Cr~~~  116 (118)
                      .-.+|-||.|...+   .+.+ |   ||-..|..|....|+.   ...||.|+..+
T Consensus        79 ~lYeCnIC~etS~e---e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSF  131 (140)
T PF05290_consen   79 KLYECNICKETSAE---ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSF  131 (140)
T ss_pred             CceeccCcccccch---hhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccc
Confidence            45789999998766   4433 2   9999999999888864   44699998765

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

Probab=94.91  E-value=0.0011  Score=48.28  Aligned_cols=48  Identities=27%  Similarity=0.675  Sum_probs=38.8

Q ss_pred             cccccccccccccC-CCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           69 EGRCTVCMENFLQA-FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        69 ~~~C~IC~~~~~~~-~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ...|.||.+.+... .....+-|||.+|..||.+|+.....||.||..+
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel  244 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRREL  244 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhh
Confidence            36799999887652 2244567999999999999998888899998765

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.87  E-value=0.017  Score=40.13  Aligned_cols=50  Identities=28%  Similarity=0.613  Sum_probs=33.5

Q ss_pred             cCccccccccccccccCCCc-eeeCC-----CChhhHHHHHHHhhCC--------CcccccCcc
Q 033497           66 AATEGRCTVCMENFLQAFPG-KQVPC-----GHVFHATCISTWISLS--------NSCPVCRSG  115 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~-~~~~C-----~H~f~~~Ci~~~~~~~--------~~CP~Cr~~  115 (118)
                      .+.+..|-||+..-.+.... -+-||     .|..|.+|+..|+..+        .+||.|+..
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE   80 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE   80 (293)
T ss_pred             cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence            45677899999874332211 12344     3889999999998422        259999764

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

Probab=94.80  E-value=0.0085  Score=46.86  Aligned_cols=45  Identities=22%  Similarity=0.690  Sum_probs=37.6

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC---cccccCcc
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN---SCPVCRSG  115 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~---~CP~Cr~~  115 (118)
                      ...+|+||...+..   +..+.|.|.|+..|+..-+...+   .||+|+..
T Consensus        20 k~lEc~ic~~~~~~---p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~   67 (684)
T KOG4362|consen   20 KILECPICLEHVKE---PSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSD   67 (684)
T ss_pred             hhccCCceeEEeec---cchhhhhHHHHhhhhhceeeccCccccchhhhhh
Confidence            45789999999988   78889999999999998876444   59999854

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

Probab=94.52  E-value=0.023  Score=45.04  Aligned_cols=41  Identities=27%  Similarity=0.670  Sum_probs=29.1

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPV  111 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~  111 (118)
                      ..|.||--.+. +...+...|+|..|.+|...|++....||.
T Consensus      1029 ~~C~~C~l~V~-gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAVR-GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeeEeeEee-ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            44666643322 222345569999999999999999999874

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

Probab=94.47  E-value=0.059  Score=38.29  Aligned_cols=50  Identities=24%  Similarity=0.571  Sum_probs=35.0

Q ss_pred             CccccccccccccccCCC-ceeeCCC-----ChhhHHHHHHHhh--CCCcccccCccc
Q 033497           67 ATEGRCTVCMENFLQAFP-GKQVPCG-----HVFHATCISTWIS--LSNSCPVCRSGV  116 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~-~~~~~C~-----H~f~~~Ci~~~~~--~~~~CP~Cr~~~  116 (118)
                      ..+..|.||.+....... ....||.     ...|..|+..|+.  .+..|.+|....
T Consensus        76 ~~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~  133 (323)
T KOG1609|consen   76 SSGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF  133 (323)
T ss_pred             CCCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence            335789999997654221 3455652     5579999999997  555699997643

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

Probab=94.46  E-value=0.047  Score=38.59  Aligned_cols=46  Identities=24%  Similarity=0.548  Sum_probs=31.3

Q ss_pred             ccccccccccc--CCCceeeCCCChhhHHHHHHHhhC-CCcccccCccc
Q 033497           71 RCTVCMENFLQ--AFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGV  116 (118)
Q Consensus        71 ~C~IC~~~~~~--~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~  116 (118)
                      .|++|-.....  +....+-+|+|..|.+|....+.. ...||-|...+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            48888655332  222223369999999999999864 44699997643

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

Probab=94.43  E-value=0.0078  Score=39.03  Aligned_cols=27  Identities=26%  Similarity=0.770  Sum_probs=24.6

Q ss_pred             ccccccccccccCCCceeeCCCChhhH
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHA   96 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~   96 (118)
                      -+|.||+|++..++.+..|||--+||.
T Consensus       178 GECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  178 GECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             CcEEEEhhhccCCCceeccceEEEeec
Confidence            689999999999999999999888885

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

Probab=94.41  E-value=0.025  Score=45.33  Aligned_cols=42  Identities=29%  Similarity=0.611  Sum_probs=31.4

Q ss_pred             CCCCccCccccccccccccccCCCceeeCCCChhhHHHHHHHh
Q 033497           61 SLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWI  103 (118)
Q Consensus        61 ~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~  103 (118)
                      ..-.+...+..|.+|...+... .-.+.+|||.||++||.+-.
T Consensus       809 ~ry~v~ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  809 QRYRVLEPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             cceEEecCccchHHhcchhhcC-cceeeeccchHHHHHHHHHH
Confidence            3334556678899998887652 24566899999999998875

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.12  E-value=0.034  Score=39.46  Aligned_cols=27  Identities=26%  Similarity=0.751  Sum_probs=21.7

Q ss_pred             CCChhhHHHHHHHhhC-------------CCcccccCccc
Q 033497           90 CGHVFHATCISTWISL-------------SNSCPVCRSGV  116 (118)
Q Consensus        90 C~H~f~~~Ci~~~~~~-------------~~~CP~Cr~~~  116 (118)
                      |....|.+|+.+|+..             +-.||+||+.+
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~f  364 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNF  364 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhce
Confidence            6788999999999843             22599999875

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

Probab=94.09  E-value=0.018  Score=47.88  Aligned_cols=43  Identities=30%  Similarity=0.801  Sum_probs=36.8

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS  114 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~  114 (118)
                      ..|.||++.+..  ...+..|||-+|..|...|+..+..||.|+.
T Consensus      1154 ~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1154 FVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             cchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence            589999999874  1455569999999999999999999999964

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

Probab=93.62  E-value=0.026  Score=41.75  Aligned_cols=38  Identities=24%  Similarity=0.540  Sum_probs=27.5

Q ss_pred             ccccccccc-cccccCCCceeeCCCChhhHHHHHHHhhC
Q 033497           68 TEGRCTVCM-ENFLQAFPGKQVPCGHVFHATCISTWISL  105 (118)
Q Consensus        68 ~~~~C~IC~-~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~  105 (118)
                      ....|.||+ +............|+|.||..|+++.+..
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            356899999 44333233345679999999999999863

>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=92.91  E-value=0.11  Score=27.13  Aligned_cols=43  Identities=19%  Similarity=0.524  Sum_probs=18.2

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHh---hCCC--cccccCcc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWI---SLSN--SCPVCRSG  115 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~---~~~~--~CP~Cr~~  115 (118)
                      +.|+|-...+..  .++...|.|.-|.+- ..|+   ..+.  .||+|.++
T Consensus         3 L~CPls~~~i~~--P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI--PVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS--EEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe--CccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence            468888887766  234445999854322 2233   2222  59999764

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

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

Probab=91.91  E-value=0.13  Score=35.71  Aligned_cols=46  Identities=26%  Similarity=0.555  Sum_probs=31.8

Q ss_pred             cccccccccccccc-CCCc-eeeC-CCChhhHHHHHHHhhCC-Cccc--ccC
Q 033497           68 TEGRCTVCMENFLQ-AFPG-KQVP-CGHVFHATCISTWISLS-NSCP--VCR  113 (118)
Q Consensus        68 ~~~~C~IC~~~~~~-~~~~-~~~~-C~H~f~~~Ci~~~~~~~-~~CP--~Cr  113 (118)
                      .+..||||..+-.. .+.. .+-| |-|.+|.+|..+.+... ..||  -|.
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~   60 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCG   60 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHH
Confidence            45689999866432 2222 2335 99999999999998644 4698  563

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

Probab=91.38  E-value=0.17  Score=38.14  Aligned_cols=37  Identities=22%  Similarity=0.614  Sum_probs=30.5

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhh
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS  104 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~  104 (118)
                      ......|.||.+.+..  ....+.|+|.||..|+..++.
T Consensus        67 ~~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~  103 (444)
T KOG1815|consen   67 KKGDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLG  103 (444)
T ss_pred             CCccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhh
Confidence            4556789999998764  367778999999999999874

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

Probab=90.95  E-value=0.21  Score=39.76  Aligned_cols=39  Identities=26%  Similarity=0.530  Sum_probs=29.0

Q ss_pred             ccccccccccccCCCceee--CCCChhhHHHHHHHhhCCCcccc
Q 033497           70 GRCTVCMENFLQAFPGKQV--PCGHVFHATCISTWISLSNSCPV  111 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~--~C~H~f~~~Ci~~~~~~~~~CP~  111 (118)
                      ..|.+|-..+..   +...  -|+|..|.+|+.+|+.....||.
T Consensus       780 ~~CtVC~~vi~G---~~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRG---VDVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceeee---eEeecccccccccHHHHHHHHhcCCCCcc
Confidence            467788655443   3332  39999999999999988887766

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

Probab=90.21  E-value=0.39  Score=38.80  Aligned_cols=49  Identities=18%  Similarity=0.592  Sum_probs=34.4

Q ss_pred             CccccccccccccccCCCceeeCC--C---ChhhHHHHHHHhh--CCCcccccCccc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPC--G---HVFHATCISTWIS--LSNSCPVCRSGV  116 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C--~---H~f~~~Ci~~~~~--~~~~CP~Cr~~~  116 (118)
                      .++..|.||..+=..++ +..-||  .   .-.|.+|+.+|+.  ....|-+|..++
T Consensus        10 ~d~~~CRICr~e~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~   65 (1175)
T COG5183          10 EDKRSCRICRTEDIRDD-PLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY   65 (1175)
T ss_pred             ccchhceeecCCCCCCC-cCcccccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence            45578999998855544 444444  3   3389999999996  344699998754

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

Probab=87.40  E-value=0.54  Score=33.94  Aligned_cols=46  Identities=26%  Similarity=0.422  Sum_probs=36.3

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCC---CcccccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS---NSCPVCR  113 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~---~~CP~Cr  113 (118)
                      .-..||+=-+.-.+.+.+..+.|||+.-..-+....+..   ..||.|-
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP  383 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP  383 (396)
T ss_pred             ceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence            337899877776777789999999999999998876533   2599994

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=87.21  E-value=0.56  Score=33.91  Aligned_cols=47  Identities=26%  Similarity=0.494  Sum_probs=36.1

Q ss_pred             ccccccccccccCC-CceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           70 GRCTVCMENFLQAF-PGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~-~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ..|+||.+.....+ ...-.+|++..|.-|+........+||.||++.
T Consensus       250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~  297 (327)
T KOG2068|consen  250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPY  297 (327)
T ss_pred             CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcc
Confidence            67999999874322 233446898889989888888888999999764

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

Probab=87.01  E-value=0.27  Score=38.21  Aligned_cols=23  Identities=39%  Similarity=0.882  Sum_probs=17.5

Q ss_pred             eeCCCChhhHHHHHHHhhCCCccccc
Q 033497           87 QVPCGHVFHATCISTWISLSNSCPVC  112 (118)
Q Consensus        87 ~~~C~H~f~~~Ci~~~~~~~~~CP~C  112 (118)
                      ...|++.||..|+..   ....||.|
T Consensus       534 C~~C~avfH~~C~~r---~s~~CPrC  556 (580)
T KOG1829|consen  534 CSTCLAVFHKKCLRR---KSPCCPRC  556 (580)
T ss_pred             HHHHHHHHHHHHHhc---cCCCCCch
Confidence            345999999999755   33449999

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

Probab=86.98  E-value=0.26  Score=25.85  Aligned_cols=42  Identities=21%  Similarity=0.468  Sum_probs=20.2

Q ss_pred             ccccccccccCC------Cceee-CCCChhhHHHHHHHhhCCCcccccC
Q 033497           72 CTVCMENFLQAF------PGKQV-PCGHVFHATCISTWISLSNSCPVCR  113 (118)
Q Consensus        72 C~IC~~~~~~~~------~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr  113 (118)
                      |.-|+..|....      ....- .|++.||.+|=.-.=+.-..||.|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            555666665521      11223 3999999999644334555799883

It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.

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

Probab=86.73  E-value=1  Score=36.41  Aligned_cols=49  Identities=12%  Similarity=0.220  Sum_probs=33.3

Q ss_pred             ccccccccccccccCC-CceeeC---CCChhhHHHHHHHhhC------CCcccccCccc
Q 033497           68 TEGRCTVCMENFLQAF-PGKQVP---CGHVFHATCISTWISL------SNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~-~~~~~~---C~H~f~~~Ci~~~~~~------~~~CP~Cr~~~  116 (118)
                      ....|.+|...+..+. ..-.++   |+|.||..||..|..+      +-.|++|..-|
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci  153 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECV  153 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHh
Confidence            3477888887776622 122333   9999999999999842      22478886544

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

Probab=85.90  E-value=0.42  Score=37.62  Aligned_cols=39  Identities=26%  Similarity=0.726  Sum_probs=30.3

Q ss_pred             cccccccccccc-CCCceeeCCCChhhHHHHHHHhhCCCccc
Q 033497           70 GRCTVCMENFLQ-AFPGKQVPCGHVFHATCISTWISLSNSCP  110 (118)
Q Consensus        70 ~~C~IC~~~~~~-~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP  110 (118)
                      ..|+||+..|.. ...++.+-|||..|..|+....+  .+||
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp   51 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP   51 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC
Confidence            679999777654 34477788999999999988644  5677

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

Probab=85.62  E-value=0.5  Score=32.13  Aligned_cols=42  Identities=26%  Similarity=0.672  Sum_probs=33.5

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccC
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR  113 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr  113 (118)
                      ..|-+|......+  .+.-.|+-.+|..|+..++++...||.|.
T Consensus       182 k~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc~  223 (235)
T KOG4718|consen  182 KNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHCG  223 (235)
T ss_pred             HHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCchh
Confidence            6799998876551  33445888899999999999988899993

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

Probab=85.58  E-value=0.33  Score=38.89  Aligned_cols=44  Identities=27%  Similarity=0.569  Sum_probs=31.1

Q ss_pred             ccccccccccccccC----CCceeeCCCChhhHHHHHHHhhCCCccccc
Q 033497           68 TEGRCTVCMENFLQA----FPGKQVPCGHVFHATCISTWISLSNSCPVC  112 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~----~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~C  112 (118)
                      .+.+|..|++.....    ...+.+.|+|.||..|+.....++. |..|
T Consensus       783 ~e~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~~~~~-~~~~  830 (846)
T KOG2066|consen  783 VEERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMESLRNA-CNIE  830 (846)
T ss_pred             ehhhhhhhcccccccCcccceeeEEEccchhhhcccccHHHhcc-cChh
Confidence            345899999886532    2356778999999999977654443 5444

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

Probab=85.41  E-value=0.76  Score=32.71  Aligned_cols=38  Identities=26%  Similarity=0.471  Sum_probs=29.2

Q ss_pred             CccccccccccccccCCCceeeCC----CChhhHHHHHHHhhCCC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPC----GHVFHATCISTWISLSN  107 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C----~H~f~~~Ci~~~~~~~~  107 (118)
                      ..-+.|-+|.|.+.+   ...+.|    .|.||.-|-++.++.+.
T Consensus       266 ~apLcCTLC~ERLED---THFVQCPSVp~HKFCFPCSResIK~Qg  307 (352)
T KOG3579|consen  266 SAPLCCTLCHERLED---THFVQCPSVPSHKFCFPCSRESIKQQG  307 (352)
T ss_pred             CCceeehhhhhhhcc---CceeecCCCcccceecccCHHHHHhhc
Confidence            344899999999887   444444    69999999999886543

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

Probab=84.80  E-value=0.62  Score=25.69  Aligned_cols=12  Identities=33%  Similarity=0.894  Sum_probs=8.6

Q ss_pred             hhhHHHHHHHhh
Q 033497           93 VFHATCISTWIS  104 (118)
Q Consensus        93 ~f~~~Ci~~~~~  104 (118)
                      .||+.|+.+|..
T Consensus        11 gFCRNCLskWy~   22 (68)
T PF06844_consen   11 GFCRNCLSKWYR   22 (68)
T ss_dssp             S--HHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            399999999984

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

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

Probab=84.78  E-value=0.53  Score=34.91  Aligned_cols=43  Identities=23%  Similarity=0.545  Sum_probs=29.6

Q ss_pred             cccccccccccc--CCCceeeCCCChhhHHHHHHHhhCCCccccc
Q 033497           70 GRCTVCMENFLQ--AFPGKQVPCGHVFHATCISTWISLSNSCPVC  112 (118)
Q Consensus        70 ~~C~IC~~~~~~--~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~C  112 (118)
                      ..|++|.-.+..  +-......|||.||..|...|...+..|..|
T Consensus       307 r~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  307 RQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             CcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence            568888665432  2122334599999999999998877766443

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.25  E-value=0.5  Score=32.95  Aligned_cols=34  Identities=18%  Similarity=0.298  Sum_probs=30.0

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhh
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS  104 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~  104 (118)
                      .-..|+.|+.++..   +++.+=||+|+..||.+++.
T Consensus        42 ~FdcCsLtLqPc~d---Pvit~~GylfdrEaILe~il   75 (303)
T KOG3039|consen   42 PFDCCSLTLQPCRD---PVITPDGYLFDREAILEYIL   75 (303)
T ss_pred             CcceeeeecccccC---CccCCCCeeeeHHHHHHHHH
Confidence            34679999999988   99999999999999999874

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=84.04  E-value=0.67  Score=31.28  Aligned_cols=40  Identities=30%  Similarity=0.708  Sum_probs=25.3

Q ss_pred             cccccccccc-----cccCCCceeeCCCChhhHHHHHHHhhCCCcccccC
Q 033497           69 EGRCTVCMEN-----FLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR  113 (118)
Q Consensus        69 ~~~C~IC~~~-----~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr  113 (118)
                      +..|-+|-..     |..+...+-..|+..||..|..     +..||.|.
T Consensus       152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-----~~~CpkC~  196 (202)
T PF13901_consen  152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-----KKSCPKCA  196 (202)
T ss_pred             CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-----CCCCCCcH
Confidence            3667777643     1221222333499999999975     26799993

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

Probab=83.02  E-value=0.71  Score=33.46  Aligned_cols=45  Identities=22%  Similarity=0.426  Sum_probs=32.4

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS  114 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~  114 (118)
                      ..|-.|.+........+.-.|.+.||.+|=.-.-..-..||.|..
T Consensus       331 ~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh  375 (378)
T KOG2807|consen  331 RFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH  375 (378)
T ss_pred             cceeeeccccCCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence            558888777665444455569999999997655455567999964

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

Probab=82.46  E-value=1  Score=34.89  Aligned_cols=43  Identities=26%  Similarity=0.939  Sum_probs=34.6

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      .....|.||+... .   .+..+|.   |..|+.+|...+..||.|+..+
T Consensus       477 ~~~~~~~~~~~~~-~---~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~  519 (543)
T KOG0802|consen  477 EPNDVCAICYQEM-S---ARITPCS---HALCLRKWLYVQEVCPLCHTYM  519 (543)
T ss_pred             cccCcchHHHHHH-H---hcccccc---chhHHHhhhhhccccCCCchhh
Confidence            3447799999887 3   6666777   7899999999999999997654

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

Probab=80.62  E-value=0.44  Score=26.20  Aligned_cols=37  Identities=24%  Similarity=0.544  Sum_probs=18.7

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHh
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWI  103 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~  103 (118)
                      .+...|.+|...|..-.....- .||+.||..|.....
T Consensus         7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~   44 (69)
T PF01363_consen    7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI   44 (69)
T ss_dssp             GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred             CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence            3457799999999663333333 399999999986544

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	118
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		2e-08
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		1e-07
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		1e-07
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-07
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		6e-07
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		3e-06
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		3e-06
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		6e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-04

>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HETERODIMER Length = 149

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/108 (26%), Positives = 46/108 (42%), Gaps = 10/108 (9%)
Query: 16  GSPIIDESFNLDEALTM-------ITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAAT 68
           GSP   E + L E L         I    +   +Q + +    Q   E  +S +  V   
Sbjct: 4   GSPGFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLEN 63
Query: 69  EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
           E +C +C E F++A     + C H F + CI+ W+     CP+CR  +
Sbjct: 64  ELQCIICSEYFIEAVT---LNCAHSFCSYCINEWMKRKIECPICRKDI 108

>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure Length = 138

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 3/84 (3%)
Query: 33  ITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGH 92
           I    +   +Q + +    Q   E  +S +  V   E +C +C E F++A     + C H
Sbjct: 17  IIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVT---LNCAH 73
Query: 93  VFHATCISTWISLSNSCPVCRSGV 116
            F + CI+ W+     CP+CR  +
Sbjct: 74  SFCSYCINEWMKRKIECPICRKDI 97

>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure Length = 138

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 3/84 (3%)
Query: 33  ITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGH 92
           I    +   +Q + +    Q   E  +S +  V   E +C +C E F++A     + C H
Sbjct: 17  IIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVT---LNCAH 73
Query: 93  VFHATCISTWISLSNSCPVCRSGV 116
            F + CI+ W+     CP+CR  +
Sbjct: 74  SFCSYCINEWMKRKIECPICRKDI 97

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

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 27/43 (62%)
Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
            C VC E++      +Q+PC H+FH +CI  W+   +SCPVCR
Sbjct: 17  ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 59

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 8/67 (11%)
Query: 55  SELTVSSLPTVAATEGR--------CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS 106
           S+ ++ +LP +  TE          C +C   +++     ++PC H FH  C+S W+  S
Sbjct: 18  SKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS 77
Query: 107 NSCPVCR 113
            +CPVCR
Sbjct: 78  GTCPVCR 84

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 28/48 (58%)
Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA 118
           +CT+C+    +    +++PC H+FH  C+  W+  +  CP+CR  + A
Sbjct: 16  KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEA 63

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS 114
           C VCM +F      + +PC H FHA C+  W+  + +CP+CR+
Sbjct: 26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRA 68

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 72  CTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGVI 117
           C VC+         + +P CGH FHA C+  W+   ++CP+CR  V+
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI 117
           C VC+E+F         PC H FH  C+  W+ +   CP+C   V+
Sbjct: 18  CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	118
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	5e-17
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-14
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	8e-14
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-13
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	4e-13
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	6e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	6e-13
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	1e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	1e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-12
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	5e-12
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-10
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-10
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-10
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	5e-10
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	8e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-09
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	6e-09
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	8e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	6e-06
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	6e-08
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-07
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	1e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	1e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-06
3nw0_A	238	Non-structural maintenance of chromosomes element	3e-06
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	1e-05
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	1e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	4e-05
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	6e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	6e-05
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	7e-05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	7e-05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	1e-04
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	2e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	5e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	7e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	9e-04

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

 Score = 69.3 bits (170), Expect = 5e-17
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 8/67 (11%)

Query: 55  SELTVSSLPTVAATEGR--------CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS 106
           S+ ++ +LP +  TE          C +C   +++     ++PC H FH  C+S W+  S
Sbjct: 18  SKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKS 77

Query: 107 NSCPVCR 113
            +CPVCR
Sbjct: 78  GTCPVCR 84

>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 = 62.4 bits (152), Expect = 2e-14
 Identities = 19/48 (39%), Positives = 28/48 (58%)

Query: 66  AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
             +   C VC E++      +Q+PC H+FH +CI  W+   +SCPVCR
Sbjct: 12  VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 59

>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 = 60.7 bits (148), Expect = 5e-14
 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 7/52 (13%)

Query: 66  AATEGRCTVCMENFLQAFPGKQV----PCGHVFHATCISTWISLSNSCPVCR 113
           ++    C +C+E+       + V    PCGH+ H TC    +     CP+C 
Sbjct: 2   SSGSSGCPICLEDI---HTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 60.5 bits (147), Expect = 8e-14
 Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 65  VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
           +A    RC +C+E+         +PC H F   CI+ WI  + +CP+C+  V
Sbjct: 1   MATVAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

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

 Score = 59.3 bits (144), Expect = 3e-13
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 7/66 (10%)

Query: 58  TVSSLPTVAATEGR-------CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCP 110
           +   LP+              C VCM +F      + +PC H FHA C+  W+  + +CP
Sbjct: 5   SSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCP 64

Query: 111 VCRSGV 116
           +CR+  
Sbjct: 65  ICRADS 70

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69

 Score = 58.5 bits (142), Expect = 4e-13
 Identities = 17/51 (33%), Positives = 30/51 (58%)

Query: 68  TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA 118
           TE +CT+C+    +    +++PC H+FH  C+  W+  +  CP+CR  + A
Sbjct: 13  TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEA 63

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

 Score = 58.2 bits (141), Expect = 6e-13
 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 4/48 (8%)

Query: 69  EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
           E  C +CM+          +PC H F   CI  W     +CP+CR  +
Sbjct: 15  EEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQM 58

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

 Score = 57.9 bits (140), Expect = 6e-13
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 72  CTVCMENFLQAFPGKQV----PCGHVFHATCISTWISLSNSCPVCRSGV 116
           C +CM+ + +     ++     CGHVF + C+   +  +N+CP CR  +
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

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

 Score = 57.5 bits (139), Expect = 1e-12
 Identities = 16/47 (34%), Positives = 23/47 (48%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI 117
            C VC+E+F         PC H FH  C+  W+ +   CP+C   V+
Sbjct: 17  LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL 63

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

 Score = 57.2 bits (138), Expect = 1e-12
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 72  CTVCMENFLQAFPGKQV----PCGHVFHATCISTWISLSNSCPVCRSGV 116
           C +CM+ + +     ++     CGHVF + C+   +  +N+CP CR  +
Sbjct: 18  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

>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 = 56.8 bits (137), Expect = 2e-12
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 72  CTVCMENFLQAFPGKQV----PCGHVFHATCISTWISLSNSCPVCRSGV 116
           C +CM+ + +     ++     CGHVF + C+   +  +N+CP CR  +
Sbjct: 13  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

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

 Score = 55.3 bits (134), Expect = 5e-12
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 72  CTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGVI 117
           C VC+         + +P CGH FHA C+  W+   ++CP+CR  V+
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>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 = 55.9 bits (134), Expect = 1e-10
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 4/51 (7%)

Query: 67  ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWI-SLSNSCPVCRSGV 116
           +T   C +C EN       K  PCGH+   +C+++W  S    CP CR  +
Sbjct: 330 STFQLCKICAENDKDV---KIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 52.7 bits (126), Expect = 5e-10
 Identities = 29/106 (27%), Positives = 45/106 (42%), Gaps = 10/106 (9%)

Query: 15  SGSPIIDESFNLDEAL-------TMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAA 67
            GSP   E + L E L         I    +   +Q + +    Q   E  +S +  V  
Sbjct: 3   LGSPGFQEHWALMEELNRSKKDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLE 62

Query: 68  TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
            E +C +C E F++A     + C H F + CI+ W+     CP+CR
Sbjct: 63  NELQCIICSEYFIEAV---TLNCAHSFCSYCINEWMKRKIECPICR 105

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

 Score = 51.1 bits (122), Expect = 5e-10
 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 69  EGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCR 113
              C  C     Q         C H FH  C+S W+  +N CP+C+
Sbjct: 26  MDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 50.5 bits (121), Expect = 5e-10
 Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 2/46 (4%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
            C++C    + A       C H F  +CI      SN CP C   V
Sbjct: 17  LCSICKGYLIDAT--TITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

>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 = 51.4 bits (123), Expect = 8e-10
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 2/43 (4%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
            C +C   F+       + C H F  TCI  ++  S  CP+C 
Sbjct: 17  MCVLCGGYFID--ATTIIECLHSFCKTCIVRYLETSKYCPICD 57

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

 Score = 49.5 bits (118), Expect = 3e-09
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 48  SHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN 107
            H    +S +   S+ ++A    RC +CME            C  +   +CI  W++   
Sbjct: 2   GHHHHHHSHMDEQSVESIAE-VFRCFICMEKLRD--ARLCPHCSKLCCFSCIRRWLTEQR 58

Query: 108 -SCPVCRSGV 116
             CP CR+ +
Sbjct: 59  AQCPHCRAPL 68

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

 Score = 48.3 bits (115), Expect = 6e-09
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 3/46 (6%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
           RC +C + F          C H F  +C       +  C +C    
Sbjct: 17  RCFICRQAFQNPV---VTKCRHYFCESCALEHFRATPRCYICDQPT 59

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

 Score = 47.9 bits (114), Expect = 8e-09
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 3/48 (6%)

Query: 66  AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
           + T   C +C++  +       +PC HVF   C+     L   C +CR
Sbjct: 12  SLTVPECAICLQTCVHPV---SLPCKHVFCYLCVKGASWLGKRCALCR 56

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

 Score = 47.9 bits (113), Expect = 2e-08
 Identities = 19/93 (20%), Positives = 26/93 (27%), Gaps = 21/93 (22%)

Query: 42  DQDQPKSHDGQTNSE-LTVSSLPTVA-----ATEGRCTVCMENFLQAFPGKQVP------ 89
           D D P   +     +   V     VA          C +C  + +      Q        
Sbjct: 4   DVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATS 63

Query: 90  ---------CGHVFHATCISTWISLSNSCPVCR 113
                    C H FH  CIS W+     CP+  
Sbjct: 64  EECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

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

 Score = 48.2 bits (114), Expect = 2e-08
 Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 72  CTVCMENFLQAFPGKQVP----CGHVFHATCISTWISLSNSCPVCR 113
           C +CM+ + +     ++     CGHVF + C+   +  +N+CP CR
Sbjct: 10  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 55

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

 Score = 41.7 bits (97), Expect = 6e-06
 Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 72  CTVCMENFLQAFPGKQV----PCGHVFHATCISTWISLSNSCPVCR 113
           C +CM+ + +     ++     CGHVF + C+   +  +N+CP CR
Sbjct: 75  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 120

>4a0k_B E3 ubiquitin-protein ligase RBX1; ligase-DNA-binding protein-DNA complex, DNA-binding protein- complex; HET: DNA 3DR; 5.93A {Mus musculus} Length = 117

 Score = 46.4 bits (109), Expect = 6e-08
 Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 15/57 (26%)

Query: 72  CTVCMENFLQAFPGKQVP---------------CGHVFHATCISTWISLSNSCPVCR 113
           C +C  + +      Q                 C H FH  CIS W+     CP+  
Sbjct: 51  CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

>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 = 45.6 bits (107), Expect = 1e-07
 Identities = 15/66 (22%), Positives = 20/66 (30%), Gaps = 20/66 (30%)

Query: 69  EGRCTVCMENFL---------------QAFPGKQVPCGHVFHATCISTWISLSN-----S 108
           E  C +CME                      G+   C H FH  C+       N      
Sbjct: 25  EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQ 84

Query: 109 CPVCRS 114
           CP C++
Sbjct: 85  CPSCKT 90

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

 Score = 44.8 bits (106), Expect = 2e-07
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 4/45 (8%)

Query: 71  RCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRS 114
           RC +C E F  A     +P C H + + CI  ++S    CP C  
Sbjct: 24  RCGICFEYFNIAM---IIPQCSHNYCSLCIRKFLSYKTQCPTCCV 65

>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 = 42.2 bits (99), Expect = 1e-06
 Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 4/45 (8%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS--CPVCRS 114
           C +C    +Q        CG   H  C++ +   +    CP C  
Sbjct: 18  CNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCND 60

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

 Score = 44.5 bits (104), Expect = 1e-06
 Identities = 19/110 (17%), Positives = 30/110 (27%), Gaps = 28/110 (25%)

Query: 21  DESFNLDEALTMITNTSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFL 80
           D   N+ + L  + +    P           + ++E            E RC +C    L
Sbjct: 272 DSEMNIHKNLLRMFDLCYFPMPDWSDGPKLDEEDNE------------ELRCNICFAYRL 319

Query: 81  QAFPGKQV-----PCGHVFHATCISTWI-----------SLSNSCPVCRS 114
                  V      C    HA C+  W                 CP C++
Sbjct: 320 DGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKA 369

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

 Score = 41.7 bits (98), Expect = 1e-06
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN-SCPVCRSGV 116
           C  C           Q  CGH F  +C++  +S S+  C  C+  +
Sbjct: 18  CEKCHLVLCSPK---QTECGHRFCESCMAALLSSSSPKCTACQESI 60

>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 = 42.6 bits (100), Expect = 2e-06
 Identities = 17/95 (17%), Positives = 30/95 (31%), Gaps = 6/95 (6%)

Query: 22  ESFNL-DEALTMITN-TSSTPPDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENF 79
           E ++L  +  ++I    S+     +   S   +  S        +      +C  C E  
Sbjct: 3   EPYSLTAQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEETFQCICCQELV 62

Query: 80  LQAFPGKQVPCGHVFHATCISTWI-SLSNSCPVCR 113
            +        C H     C+     +   SCP CR
Sbjct: 63  FRP---ITTVCQHNVCKDCLDRSFRAQVFSCPACR 94

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

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 9/49 (18%), Positives = 15/49 (30%), Gaps = 3/49 (6%)

Query: 69  EGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNS--CPVCRS 114
                +C         G+    CG   H  C++ +   +    CP C  
Sbjct: 177 PDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

>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 = 40.7 bits (95), Expect = 1e-05
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 4/44 (9%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS 114
           RC+ C     +  P     C H+F + C+S  I     CPVC +
Sbjct: 24  RCSRCTNILRE--PVCLGGCEHIFCSNCVSDCI--GTGCPVCYT 63

>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 = 40.2 bits (94), Expect = 1e-05
 Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 4/44 (9%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS-CPVCRS 114
           C +C+    +A    Q PCGH F   CI   I  +   CPV   
Sbjct: 21  CPICLMALREAV---QTPCGHRFCKACIIKSIRDAGHKCPVDNE 61

>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 = 39.1 bits (91), Expect = 4e-05
 Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 4/46 (8%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCI-STWISLSNSCPVCRSGV 116
           C +CME  ++      +PC H     C  ST    S  CP CR  V
Sbjct: 18  CGICMEILVEP---VTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV 60

>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 = 39.9 bits (92), Expect = 6e-05
 Identities = 14/77 (18%), Positives = 23/77 (29%), Gaps = 10/77 (12%)

Query: 41  PDQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCIS 100
           P    P   +     +L +         E  C +  + +    P     C HVF    I 
Sbjct: 157 PTCVIPDLQNPADEDDLQIEGGKI----ELTCPITCKPYEA--PLISRKCNHVFDRDGIQ 210

Query: 101 TWISLSNS--CPV--CR 113
            ++    +  CP   C 
Sbjct: 211 NYLQGYTTRDCPQAACS 227

>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 = 38.8 bits (90), Expect = 6e-05
 Identities = 15/73 (20%), Positives = 19/73 (26%), Gaps = 4/73 (5%)

Query: 42  DQDQPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCIST 101
           D    K  D   +  +   +          C  C E   Q        C H     C+  
Sbjct: 51  DCQNQKLWDEVLSHLVEGPNFLKKLEQSFMCVCCQELVYQP---VTTECFHNVCKDCLQR 107

Query: 102 WISLSN-SCPVCR 113
                  SCP CR
Sbjct: 108 SFKAQVFSCPACR 120

>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 = 39.3 bits (91), Expect = 7e-05
 Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 4/44 (9%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS-CPVCRS 114
           C +C+    +A    Q PCGH F   CI   I  +   CPV   
Sbjct: 21  CPICLMALREAV---QTPCGHRFCKACIIKSIRDAGHKCPVDNE 61

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

 Score = 37.0 bits (86), Expect = 7e-05
 Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 6/46 (13%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
           RC  C          K +PC H   + C+    +    CP+C++  
Sbjct: 8   RCQQCQAEAKCP---KLLPCLHTLCSGCLE---ASGMQCPICQAPW 47

>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 = 38.2 bits (88), Expect = 1e-04
 Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 4/44 (9%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS-CPVCR 113
            C+ C     + F   Q  CGH + + C+++ +S     C  C 
Sbjct: 33  LCSACRNVLRRPF---QAQCGHRYCSFCLASILSSGPQNCAACV 73

>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 = 37.2 bits (86), Expect = 2e-04
 Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 4/44 (9%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNS-CPVCR 113
            C +C           +  C H+F   CI   + +  S CP CR
Sbjct: 25  SCQICEHILADPV---ETSCKHLFCRICILRCLKVMGSYCPSCR 65

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

 Score = 36.6 bits (84), Expect = 2e-04
 Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 2/58 (3%)

Query: 59  VSSLPTVAATEGRCTVCMENF-LQAFPGKQVPCGHVFHATCISTWISLSN-SCPVCRS 114
           +S  P        C +CME   +         CG+     C     +  N  CP CR 
Sbjct: 1   MSRSPDAKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 58

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

 Score = 35.5 bits (82), Expect = 5e-04
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 6/47 (12%)

Query: 71  RCTVCMENFLQAFPGKQVP-CGHVFHATCISTWI--SLSNSCPVCRS 114
            C +C +    A     +P CG+ +   CI T +  S  ++CP C  
Sbjct: 15  LCLICKDIMTDAV---VIPCCGNSYCDECIRTALLESDEHTCPTCHQ 58

>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 = 36.1 bits (83), Expect = 7e-04
 Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 45  QPKSHDGQTNSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS 104
           Q    +  T+    V S  ++ + E  C +C++            C H F A CI T + 
Sbjct: 31  QRTPQEAITDGLEIVVSPRSLHS-ELMCPICLDMLKNTM--TTKECLHRFCADCIITALR 87

Query: 105 LSN-SCPVCR 113
             N  CP CR
Sbjct: 88  SGNKECPTCR 97

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

 Score = 34.7 bits (80), Expect = 9e-04
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 72  CTVCMENF-LQAFPGKQVPCGHVFHATCISTWISLSN---SCPVCR 113
           C +CME+F  +    K + CGH     C+   ++ S     CP C 
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	118
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.7
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.68
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.68
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.67
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.67
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.65
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.63
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.61
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.61
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.61
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.61
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.6
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.59
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.58
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.57
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.57
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.57
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.56
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.56
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.55
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.55
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.55
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.54
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.54
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.54
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.54
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.53
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.52
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.51
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.5
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.5
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.5
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.49
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.47
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.47
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.46
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.45
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.45
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.45
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.43
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.43
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.43
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.43
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.42
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.42
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.41
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.41
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.41
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.4
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.37
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.36
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.34
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.32
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.32
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.32
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.3
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.29
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.23
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.2
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.2
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.2
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.15
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.14
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.12
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.01
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.0
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.96
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.95
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.95
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.86
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.65
3nw0_A	238	Non-structural maintenance of chromosomes element	98.12
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.48
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.82
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	95.22
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	95.17
1we9_A	64	PHD finger family protein; structural genomics, PH	93.95
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	93.12
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	92.67
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	92.21
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	90.81
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	90.22
1weu_A	91	Inhibitor of growth family, member 4; structural g	90.01
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	89.49
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	89.45
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	88.63
1z60_A	59	TFIIH basal transcription factor complex P44 subun	88.03
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	87.93
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	87.79
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	87.29
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	86.61
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	85.82
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	85.79
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	85.73
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	85.66
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	85.31
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	84.51
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	84.05
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	83.96
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	83.55
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	83.55
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	83.49
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	83.32
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	83.23
1wew_A	78	DNA-binding family protein; structural genomics, P	83.19
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	83.04
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	82.96
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	82.54
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	81.66
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	81.11
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	80.97
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	80.92
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	80.69
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	80.61
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	80.6
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	80.4
1wem_A	76	Death associated transcription factor 1; structura	80.39
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	80.08

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

Probab=99.70  E-value=1.6e-17  Score=97.62  Aligned_cols=51  Identities=33%  Similarity=0.882  Sum_probs=46.2

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+..|+||++.+..+..++.++|+|.||..||..|++.+.+||+||..+.
T Consensus        38 ~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~   88 (91)
T 2l0b_A           38 GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFP   88 (91)
T ss_dssp             SSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSS
T ss_pred             CCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCC
Confidence            455789999999988777888999999999999999999999999999875

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

Probab=99.68  E-value=1.4e-17  Score=89.04  Aligned_cols=51  Identities=33%  Similarity=0.924  Sum_probs=45.7

Q ss_pred             CccccccccccccccCCCceeeC-CCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..++.+..++ |+|.||..||.+|++.+.+||+||+.+.
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            35678999999998877788887 9999999999999999999999999874

>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=99.68  E-value=4.4e-17  Score=90.96  Aligned_cols=51  Identities=31%  Similarity=0.920  Sum_probs=45.3

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+..|+||++.+..+..++.++|+|.||..||.+|+..+.+||+||..+.
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   62 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIE   62 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCcccc
Confidence            455789999999987667888999999999999999998899999999874

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

Probab=99.67  E-value=2.7e-17  Score=93.31  Aligned_cols=52  Identities=33%  Similarity=0.856  Sum_probs=46.2

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..+..++.++|+|.||..||.+|++.+.+||+||+.+.
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~   71 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSG   71 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCC
Confidence            3456789999999988666788999999999999999998999999999875

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

Probab=99.67  E-value=5.3e-17  Score=91.79  Aligned_cols=51  Identities=31%  Similarity=0.828  Sum_probs=45.2

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+..|+||++.+........++|+|.||..||.+|++.+.+||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~   63 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVL   63 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCS
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccc
Confidence            345789999999988777778899999999999999998889999999875

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

Probab=99.65  E-value=7.1e-17  Score=92.15  Aligned_cols=51  Identities=37%  Similarity=0.964  Sum_probs=45.1

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+..|+||++.|........++|+|.||..||.+|++.+.+||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   63 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLT   63 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCC
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccC
Confidence            456789999999987666778899999999999999998899999999874

>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=99.63  E-value=1.3e-16  Score=85.15  Aligned_cols=52  Identities=25%  Similarity=0.738  Sum_probs=44.1

Q ss_pred             CccccccccccccccC-CCceeeCCCChhhHHHHHHHhhCCCcccccCcccCC
Q 033497           67 ATEGRCTVCMENFLQA-FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVIA  118 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~-~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~  118 (118)
                      ..+..|+||++.+..+ ..++.++|+|.||..||.+|++.+.+||+||+.+.+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~g   55 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSSG   55 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSCC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            3457899999998653 346778899999999999999988999999998864

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

Probab=99.61  E-value=6.6e-16  Score=88.89  Aligned_cols=52  Identities=25%  Similarity=0.673  Sum_probs=41.5

Q ss_pred             cCcccccccccccccc-----------CCCceeeC-CCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQ-----------AFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~-----------~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.|..           ++.++.++ |+|.||..||.+|++.+.+||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   75 (81)
T 2ecl_A           12 DVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWV   75 (81)
T ss_dssp             SCCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCC
T ss_pred             cCCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcc
Confidence            3456778888888854           33355554 9999999999999999999999999864

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

Probab=99.61  E-value=2.8e-16  Score=87.46  Aligned_cols=52  Identities=27%  Similarity=0.694  Sum_probs=43.8

Q ss_pred             cCccccccccccccccC----CCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQA----FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~----~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+...    ..++.++|||.||..||.+|+..+..||+||..+.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   67 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN   67 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccC
Confidence            34567899999998762    22378899999999999999998899999999874

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

Probab=99.61  E-value=2.8e-16  Score=87.97  Aligned_cols=52  Identities=27%  Similarity=0.694  Sum_probs=44.0

Q ss_pred             cCccccccccccccccC----CCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQA----FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~----~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+...    ..++.++|||.||..||.+|++.+.+||+||..+.
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   62 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN   62 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccC
Confidence            34567899999998762    33478899999999999999998899999999764

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

Probab=99.61  E-value=2.9e-16  Score=98.78  Aligned_cols=47  Identities=32%  Similarity=0.911  Sum_probs=43.1

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ++..|+||++.+..   ++.++|||.||..||..|+..+.+||+||.++.
T Consensus        52 ~~~~C~iC~~~~~~---~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   98 (138)
T 4ayc_A           52 NELQCIICSEYFIE---AVTLNCAHSFCSYCINEWMKRKIECPICRKDIK   98 (138)
T ss_dssp             HHSBCTTTCSBCSS---EEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCC
T ss_pred             ccCCCcccCcccCC---ceECCCCCCccHHHHHHHHHcCCcCCCCCCcCC
Confidence            45789999999987   899999999999999999999999999999874

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

Probab=99.60  E-value=3.6e-16  Score=87.77  Aligned_cols=49  Identities=27%  Similarity=0.688  Sum_probs=43.6

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++|||.||..||..|+..+..||+||..+.
T Consensus        12 ~~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (71)
T 2d8t_A           12 SLTVPECAICLQTCVH---PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIP   60 (71)
T ss_dssp             SSSCCBCSSSSSBCSS---EEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCC
T ss_pred             CCCCCCCccCCcccCC---CEEccCCCHHHHHHHHHHHHCCCcCcCcCchhC
Confidence            3456789999999887   888999999999999999998899999999763

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

Probab=99.59  E-value=1.6e-15  Score=85.33  Aligned_cols=49  Identities=27%  Similarity=0.623  Sum_probs=42.4

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhh---CCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS---LSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~---~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++|||.||..||..|+.   ....||+||..+.
T Consensus        17 ~~~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~   68 (73)
T 2ysl_A           17 LQEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVR   68 (73)
T ss_dssp             CCCCCBCTTTCSBCSS---EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCC
T ss_pred             CccCCEeccCCcccCC---eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCC
Confidence            4456889999999987   88889999999999999996   4557999999864

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

Probab=99.58  E-value=1.3e-15  Score=85.73  Aligned_cols=48  Identities=27%  Similarity=0.610  Sum_probs=42.5

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.+ +|||.||..||..|++.+..||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   61 (72)
T 2djb_A           13 TPYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVH   61 (72)
T ss_dssp             CGGGSCTTTSSCCSS---CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCC
T ss_pred             CCCCCCCCCChHHHC---cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccC
Confidence            456889999999987   7766 89999999999999998889999998764

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

Probab=99.57  E-value=1.7e-15  Score=86.98  Aligned_cols=48  Identities=21%  Similarity=0.486  Sum_probs=42.9

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .....|+||++.+..   ++.++|||.||..||..|+.....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            345789999999987   888999999999999999998889999998763

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

Probab=99.57  E-value=8.2e-16  Score=84.31  Aligned_cols=50  Identities=28%  Similarity=0.711  Sum_probs=42.6

Q ss_pred             ccccccccccccccC----CCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQA----FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~----~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ++..|+||++.+...    ..++.++|||.||..|+.+|+..+.+||+||..+.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   55 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN   55 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCC
Confidence            456899999998762    33478899999999999999998899999999864

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

Probab=99.57  E-value=2.3e-15  Score=83.28  Aligned_cols=49  Identities=27%  Similarity=0.677  Sum_probs=42.1

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++|||.||..||.+|+. .+..||+||..+.
T Consensus        12 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCS---PKQTECGHRFCESCMAALLSSSSPKCTACQESIV   61 (66)
T ss_dssp             CCCCEECTTTCCEESS---CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCC
T ss_pred             CCcCCCCCCCChHhcC---eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCC
Confidence            3456889999999987   77789999999999999994 5668999999864

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

Probab=99.56  E-value=1.8e-15  Score=85.57  Aligned_cols=49  Identities=27%  Similarity=0.678  Sum_probs=42.5

Q ss_pred             cCccccccccccccccCCCceeeC-CCChhhHHHHHHHhhCC--CcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLS--NSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~--~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++ |||.||..||..|+..+  ..||+||+.+.
T Consensus        12 ~~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   63 (74)
T 2yur_A           12 IPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   63 (74)
T ss_dssp             SCGGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSC
T ss_pred             CCCCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCC
Confidence            3456889999999987   88899 99999999999999755  68999999754

>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=99.56  E-value=2e-15  Score=91.89  Aligned_cols=50  Identities=32%  Similarity=0.666  Sum_probs=39.6

Q ss_pred             ccccccccccccccCC---------------CceeeCCCChhhHHHHHHHh-----hCCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAF---------------PGKQVPCGHVFHATCISTWI-----SLSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~---------------~~~~~~C~H~f~~~Ci~~~~-----~~~~~CP~Cr~~~~  117 (118)
                      .+..|+||++.|....               ....++|+|.||..||..|+     ..+.+||+||..+.
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~   93 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYG   93 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccC
Confidence            3468999999986532               22367899999999999999     45668999998763

>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=99.55  E-value=3.7e-15  Score=89.77  Aligned_cols=51  Identities=24%  Similarity=0.598  Sum_probs=42.6

Q ss_pred             cCccccccccccccccC---------------CCceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQA---------------FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~---------------~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      ..++..|+||++.|...               ..++.++|+|.||..||.+|+..+.+||+||+.+
T Consensus        34 d~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~   99 (106)
T 3dpl_R           34 DIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREW   99 (106)
T ss_dssp             SSCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBC
T ss_pred             CCCCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcc
Confidence            34678899999998753               1245678999999999999999999999999875

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

Probab=99.55  E-value=8.2e-15  Score=80.26  Aligned_cols=44  Identities=27%  Similarity=0.651  Sum_probs=38.7

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhh---CCCccccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS---LSNSCPVC  112 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~---~~~~CP~C  112 (118)
                      ..++..|+||++.+..   ++.++|||.||..||.+|++   .+..||+|
T Consensus        17 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSS---CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCC---eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            4566889999999987   88889999999999999997   45589998

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

Probab=99.55  E-value=1.7e-15  Score=84.19  Aligned_cols=49  Identities=33%  Similarity=0.842  Sum_probs=42.0

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+..|+||++.+..  .++.++|||.||..|+.+|+..+.+||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~   51 (68)
T 1chc_A            3 TVAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhH
Confidence            345689999999865  2477899999999999999998899999998764

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

Probab=99.54  E-value=7.4e-15  Score=84.63  Aligned_cols=49  Identities=29%  Similarity=0.628  Sum_probs=42.5

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC------CCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL------SNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~------~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++|||.||..||..|+..      ...||.||..+.
T Consensus        16 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~   70 (85)
T 2ecw_A           16 IKEEVTCPICLELLKE---PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYP   70 (85)
T ss_dssp             CCTTTSCTTTCSCCSS---CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCC
T ss_pred             CccCCCCcCCChhhCc---ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCC
Confidence            3456789999999987   788999999999999999976      667999998764

>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=5e-15  Score=86.04  Aligned_cols=51  Identities=27%  Similarity=0.623  Sum_probs=43.2

Q ss_pred             cCccccccccccccccCCC-ceeeCCCChhhHHHHHHHhhCC---CcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFP-GKQVPCGHVFHATCISTWISLS---NSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~-~~~~~C~H~f~~~Ci~~~~~~~---~~CP~Cr~~~  116 (118)
                      ..+...|+||++.+..... ++.++|||.||..||..|+..+   ..||+||..+
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   66 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKIT   66 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCB
T ss_pred             ccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcc
Confidence            3456789999999987554 7788999999999999999865   6899999875

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

Probab=99.54  E-value=4.2e-15  Score=84.71  Aligned_cols=49  Identities=18%  Similarity=0.485  Sum_probs=43.4

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.|.+   ++.++|||.||..||.+|+.. +.+||+||..+.
T Consensus         5 ~~~~~~C~IC~~~~~~---Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~   54 (78)
T 1t1h_A            5 FPEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLL   54 (78)
T ss_dssp             CSSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCS
T ss_pred             CcccCCCCCccccccC---CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCC
Confidence            3467889999999988   889999999999999999986 778999998763

>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=99.54  E-value=1.9e-15  Score=90.19  Aligned_cols=48  Identities=29%  Similarity=0.742  Sum_probs=42.5

Q ss_pred             CccccccccccccccCCCcee-eCCCChhhHHHHHHHhhCC-CcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQ-VPCGHVFHATCISTWISLS-NSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~-~~C~H~f~~~Ci~~~~~~~-~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++. ++|||.||..||..|+... ..||.||..+.
T Consensus        20 ~~~~~C~IC~~~~~~---p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   69 (100)
T 3lrq_A           20 AEVFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQ   69 (100)
T ss_dssp             HHHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccccC---ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCC
Confidence            456889999999987   887 8999999999999999877 68999998763

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

Probab=99.53  E-value=2.1e-15  Score=84.25  Aligned_cols=47  Identities=32%  Similarity=0.889  Sum_probs=41.5

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..    +.++|+|.||..||.+|+..+..||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   59 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMT   59 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCSSCHHHHHCTT
T ss_pred             CCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcCcCCCcCCccc
Confidence            456789999999765    78899999999999999998899999998764

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

Probab=99.52  E-value=8.6e-15  Score=84.36  Aligned_cols=49  Identities=33%  Similarity=0.719  Sum_probs=42.5

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC------CCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL------SNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~------~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++|||.||..|+..|+..      ...||.||..+.
T Consensus        16 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~   70 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQ   70 (85)
T ss_dssp             CCCCCCCTTTCSCCSS---CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSC
T ss_pred             ccCCCCCCCCCcccCC---ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccC
Confidence            3456789999999987   788899999999999999976      678999998764

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

Probab=99.51  E-value=3e-15  Score=85.38  Aligned_cols=49  Identities=29%  Similarity=0.636  Sum_probs=42.3

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-------CCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-------SNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-------~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++|||.||..||..|+..       ...||+||..+.
T Consensus         9 ~~~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~   64 (79)
T 2egp_A            9 VQEEVTCPICLELLTE---PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYS   64 (79)
T ss_dssp             CCCCCEETTTTEECSS---CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCC
T ss_pred             cccCCCCcCCCcccCC---eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCC
Confidence            3456889999999987   778899999999999999976       567999998764

>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=8.6e-15  Score=90.37  Aligned_cols=48  Identities=23%  Similarity=0.493  Sum_probs=42.2

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC-cccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN-SCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.++|||.||..||..|+..+. .||+||..+.
T Consensus        50 ~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   98 (124)
T 3fl2_A           50 EETFQCICCQELVFR---PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLG   98 (124)
T ss_dssp             HHHTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             ccCCCCCcCChHHcC---cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCC
Confidence            456889999999987   88899999999999999997544 8999999874

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

Probab=99.50  E-value=8.2e-15  Score=87.11  Aligned_cols=48  Identities=29%  Similarity=0.704  Sum_probs=42.5

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.+ +|||.||..||..|+..+..||.||..+.
T Consensus        20 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   68 (99)
T 2y43_A           20 DDLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVT   68 (99)
T ss_dssp             HHHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             CCCCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCC
Confidence            356889999999987   7777 89999999999999998889999998764

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

Probab=99.50  E-value=1.5e-14  Score=84.83  Aligned_cols=48  Identities=27%  Similarity=0.671  Sum_probs=41.9

Q ss_pred             cCccccccccccccccCCCceeeC-CCChhhHHHHHHHhhCC--CcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLS--NSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~--~~CP~Cr~~~  116 (118)
                      ..++..|+||++.|..   ++.++ |||.||..||..|+...  ..||+||..+
T Consensus        10 ~~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           10 IPDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             CCTTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             CCcCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            3466889999999987   89999 99999999999999643  5899999986

>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=99.49  E-value=1.6e-14  Score=87.12  Aligned_cols=48  Identities=29%  Similarity=0.700  Sum_probs=43.1

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.+ +|||.||..||..|+.....||.||..+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   61 (108)
T 2ckl_A           13 NPHLMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVH   61 (108)
T ss_dssp             GGGTBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSC
T ss_pred             CCcCCCccCChHHhC---cCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccc
Confidence            456889999999987   7877 99999999999999998899999998764

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

Probab=99.47  E-value=3.3e-14  Score=76.42  Aligned_cols=44  Identities=36%  Similarity=0.918  Sum_probs=37.5

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhh---CCCccccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS---LSNSCPVC  112 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~---~~~~CP~C  112 (118)
                      ..++..|+||++.+..   ++.++|||.||..||.+|+.   .+..||+|
T Consensus        12 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLKE---PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCSS---CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccCc---cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            3456789999999987   78889999999999999954   55679998

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

Probab=99.47  E-value=2.1e-14  Score=89.03  Aligned_cols=51  Identities=27%  Similarity=0.705  Sum_probs=43.7

Q ss_pred             CccccccccccccccC----CCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQA----FPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~----~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+...    ..++.++|||.||..||.+|++.+.+||+||+.+.
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   59 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN   59 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCT
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCc
Confidence            4567899999999762    23388999999999999999999999999999764

>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=99.46  E-value=2.8e-15  Score=91.60  Aligned_cols=52  Identities=23%  Similarity=0.550  Sum_probs=2.7

Q ss_pred             ccCccccccccccccccC--------------C-CceeeCCCChhhHHHHHHHhhCCCcccccCccc
Q 033497           65 VAATEGRCTVCMENFLQA--------------F-PGKQVPCGHVFHATCISTWISLSNSCPVCRSGV  116 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~--------------~-~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~  116 (118)
                      .+..+..|+||++.|...              + .+..++|+|.||..||.+|++.+.+||+||+.+
T Consensus        44 wd~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~  110 (117)
T 4a0k_B           44 WDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREW  110 (117)
T ss_dssp             ECCCC--------------------------------------------------------------
T ss_pred             ecCCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCee
Confidence            345668899999998641              1 123457999999999999999999999999874

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

Probab=99.45  E-value=2.8e-14  Score=81.78  Aligned_cols=52  Identities=27%  Similarity=0.701  Sum_probs=42.0

Q ss_pred             ccCccccccccccccccCCCceeeCCC-----ChhhHHHHHHHhhCC--CcccccCcccC
Q 033497           65 VAATEGRCTVCMENFLQAFPGKQVPCG-----HVFHATCISTWISLS--NSCPVCRSGVI  117 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~~~~~C~-----H~f~~~Ci~~~~~~~--~~CP~Cr~~~~  117 (118)
                      ...++..|.||++.+..++. .++||+     |.||..||.+|+..+  .+||+||..+.
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~-l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~   69 (80)
T 2d8s_A           11 TPSSQDICRICHCEGDDESP-LITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFI   69 (80)
T ss_dssp             CCTTSCCCSSSCCCCCSSSC-EECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCC
T ss_pred             CCCCCCCCeEcCccccCCCe-eEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeee
Confidence            34556789999999876554 568896     999999999999754  48999998764

>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=99.45  E-value=1e-13  Score=82.35  Aligned_cols=49  Identities=14%  Similarity=0.093  Sum_probs=44.7

Q ss_pred             cCccccccccccccccCCCceeeCCC-ChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCG-HVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~-H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+++.|+||++.|.+   ++.++|| |.||..||.+|+..+.+||+||.++.
T Consensus        19 ~p~~~~CpI~~~~m~d---PV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~   68 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLT   68 (98)
T ss_dssp             CCTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCC
T ss_pred             CcHhcCCcCccccccC---CeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCC
Confidence            3567899999999999   9999999 99999999999988889999998764

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

Probab=99.45  E-value=4.2e-14  Score=77.86  Aligned_cols=50  Identities=18%  Similarity=0.524  Sum_probs=39.4

Q ss_pred             cccccccccc-ccccCCCc-eeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           68 TEGRCTVCME-NFLQAFPG-KQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~-~~~~~~~~-~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      ++..|+||++ .+...... +.++|||.||..||.+|+.. ...||+||..+.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   54 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR   54 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCS
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccc
Confidence            4578999999 77663322 46789999999999999754 457999998764

>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=99.43  E-value=1.4e-14  Score=88.23  Aligned_cols=48  Identities=31%  Similarity=0.787  Sum_probs=42.2

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-CCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~  116 (118)
                      ..++..|+||++.+..   ++.++|||.||..||..|+.. ...||+||..+
T Consensus        12 ~~~~~~C~iC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   60 (115)
T 3l11_A           12 SLSECQCGICMEILVE---PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV   60 (115)
T ss_dssp             CHHHHBCTTTCSBCSS---CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBC
T ss_pred             CCCCCCCccCCcccCc---eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCccc
Confidence            3456889999999987   888999999999999999975 66899999876

>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=99.43  E-value=8.7e-14  Score=89.70  Aligned_cols=48  Identities=29%  Similarity=0.686  Sum_probs=41.9

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.+ +|||.||..||..|+.. ...||+||..+.
T Consensus        52 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~  101 (165)
T 2ckl_B           52 HSELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLV  101 (165)
T ss_dssp             HHHHBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             CCCCCCcccChHhhC---cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCC
Confidence            456789999999987   7776 89999999999999986 678999998763

>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=99.43  E-value=5.8e-14  Score=89.39  Aligned_cols=47  Identities=26%  Similarity=0.477  Sum_probs=41.8

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC-cccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN-SCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~~  117 (118)
                      +...|+||++.+..   ++.++|||.||..||..|+.... .||+||..+.
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~  124 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG  124 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             cCCEeecCChhhcC---CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCC
Confidence            45789999999988   88899999999999999998654 8999999764

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

Probab=99.43  E-value=1.2e-13  Score=80.02  Aligned_cols=49  Identities=20%  Similarity=0.169  Sum_probs=44.5

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+++.|+||++.|.+   ++.++|||.|+..||.+|+..+.+||+||.++.
T Consensus        11 ~p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~   59 (85)
T 2kr4_A           11 APDEFRDPLMDTLMTD---PVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLT   59 (85)
T ss_dssp             CCTTTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CchheECcccCchhcC---CeECCCCCEECHHHHHHHHhcCCCCCCCcCCCC
Confidence            3467899999999999   999999999999999999998889999998764

>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=99.42  E-value=7.3e-14  Score=85.52  Aligned_cols=50  Identities=28%  Similarity=0.622  Sum_probs=43.3

Q ss_pred             ccCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC-cccccCcccC
Q 033497           65 VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN-SCPVCRSGVI  117 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~~  117 (118)
                      ...++..|+||++.+..   ++.++|||.||..||..|+.... .||+||..+.
T Consensus        14 ~~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   64 (118)
T 3hct_A           14 PLESKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL   64 (118)
T ss_dssp             CCCGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CCCCCCCCCcCChhhcC---eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcC
Confidence            34567899999999987   88899999999999999997655 8999998764

>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=99.42  E-value=5.5e-14  Score=85.06  Aligned_cols=47  Identities=21%  Similarity=0.687  Sum_probs=40.8

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC---cccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN---SCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~---~CP~Cr~~~~  117 (118)
                      +...|+||++.+..   ++.++|||.||..||..|+..+.   .||+||..+.
T Consensus        20 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~   69 (112)
T 1jm7_A           20 KILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT   69 (112)
T ss_dssp             HHTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCC
T ss_pred             CCCCCcccChhhcC---eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCC
Confidence            45789999999877   77889999999999999997654   7999998764

>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=99.41  E-value=2.9e-13  Score=80.65  Aligned_cols=49  Identities=18%  Similarity=0.183  Sum_probs=44.8

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+++.|+||++.|.+   ++.++|||.||..||.+|+..+.+||+||.++.
T Consensus        26 ~p~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~   74 (100)
T 2kre_A           26 APDEFRDPLMDTLMTD---PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLT   74 (100)
T ss_dssp             CSTTTBCTTTCSBCSS---EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCC
T ss_pred             CcHhhCCcCccCcccC---CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCC
Confidence            3567899999999999   999999999999999999998889999998764

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

Probab=99.41  E-value=5.4e-14  Score=85.80  Aligned_cols=49  Identities=22%  Similarity=0.588  Sum_probs=42.9

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+..   ++.++|||.||..||..|+.. ...||+||..+.
T Consensus        20 ~~~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   69 (116)
T 1rmd_A           20 FVKSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF   69 (116)
T ss_dssp             HHHHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             ccCCCCCCCCCcHhcC---cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCC
Confidence            3456889999999987   888999999999999999986 678999998764

>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=99.41  E-value=6.3e-14  Score=88.39  Aligned_cols=49  Identities=20%  Similarity=0.501  Sum_probs=42.7

Q ss_pred             ccCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC-cccccCccc
Q 033497           65 VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN-SCPVCRSGV  116 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~-~CP~Cr~~~  116 (118)
                      ...++..|+||++.+..   ++.++|||.||..||.+|+.... .||.||.++
T Consensus        27 ~l~~~~~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~   76 (141)
T 3knv_A           27 KLEAKYLCSACRNVLRR---PFQAQCGHRYCSFCLASILSSGPQNCAACVHEG   76 (141)
T ss_dssp             GCCGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTT
T ss_pred             cCCcCcCCCCCChhhcC---cEECCCCCccCHHHHHHHHhcCCCCCCCCCCcc
Confidence            34577899999999988   88899999999999999997554 899999864

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

Probab=99.40  E-value=2.6e-13  Score=77.41  Aligned_cols=51  Identities=22%  Similarity=0.387  Sum_probs=39.6

Q ss_pred             cCccccccccccccccCCCceee--CCCChhhHHHHHHHhh-CCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQV--PCGHVFHATCISTWIS-LSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~--~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~  117 (118)
                      ..++..|+||++.+...+ +..+  +|||.||..|+..++. ....||.||+.+.
T Consensus         8 ~~~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~   61 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP   61 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCS
T ss_pred             cccCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccC
Confidence            456788999999886432 3344  4999999999999984 4567999999763

>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=99.37  E-value=1.8e-13  Score=75.23  Aligned_cols=47  Identities=28%  Similarity=0.550  Sum_probs=41.2

Q ss_pred             ccccccccccccccCCCceee--CCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQV--PCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~--~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ++..|.||++...+   ++.+  ||||. ||..|+..|+..+..||+||+++.
T Consensus         7 ~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKN---GCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSC---EEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCC---EEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            45679999999877   7766  99999 899999999988889999999764

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

Probab=99.36  E-value=2.3e-13  Score=84.31  Aligned_cols=52  Identities=27%  Similarity=0.703  Sum_probs=43.9

Q ss_pred             cCcccccccccccccc----CCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQ----AFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~----~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+...|+||++.+..    ...++.++|||.||..||.+|++.+++||+||..+.
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~  124 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN  124 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCC
Confidence            4566889999999876    122378899999999999999999999999999764

>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=99.34  E-value=4e-13  Score=73.64  Aligned_cols=48  Identities=21%  Similarity=0.524  Sum_probs=41.2

Q ss_pred             CccccccccccccccCCCceee--CCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV--PCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~--~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+..|.||++...+   +..+  ||||. ||..|+..|.+....||+||+++.
T Consensus         5 ~~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRD---GNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSC---EEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CcCCCCcccCCcCCC---eEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            345679999998766   6666  99998 999999999988889999999864

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

Probab=99.32  E-value=1.9e-13  Score=73.25  Aligned_cols=45  Identities=24%  Similarity=0.540  Sum_probs=38.8

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.++|||.||..|+..   ....||+||+.+.
T Consensus         4 ~~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~---~~~~CP~Cr~~~~   48 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEA---SGMQCPICQAPWP   48 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSS---SSSSCSSCCSSSS
T ss_pred             ccCCCceEeCCccCC---eEEcCCCCcccHHHHcc---CCCCCCcCCcEee
Confidence            456789999999987   88999999999999977   3568999998764

>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=99.32  E-value=7.6e-13  Score=95.10  Aligned_cols=46  Identities=33%  Similarity=0.842  Sum_probs=41.6

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccC
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVI  117 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~  117 (118)
                      ...|+||++.+..   ++.++|||.||..|+..|+. ....||+||..+.
T Consensus       332 ~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~  378 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK  378 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccC
Confidence            3689999999877   89999999999999999998 7789999999764

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

Probab=99.32  E-value=3.3e-13  Score=76.19  Aligned_cols=44  Identities=30%  Similarity=0.754  Sum_probs=39.2

Q ss_pred             CccccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+.+   ++.++|||. ||..|+..|    ..||+||..+.
T Consensus        22 ~~~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~   66 (74)
T 4ic3_A           22 QEEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV----DKCPMCYTVIT   66 (74)
T ss_dssp             HHHTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC----SBCTTTCCBCS
T ss_pred             ccCCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC----ccCCCcCcCcc
Confidence            345789999999887   899999999 999999998    88999999764

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

Probab=99.30  E-value=2.5e-13  Score=83.04  Aligned_cols=46  Identities=28%  Similarity=0.668  Sum_probs=40.8

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.+ +|||.||..||..|+.  ..||+||..+.
T Consensus        20 ~~~~~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           20 EKLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             HHTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hhCCCCCCCChHhhC---ccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            456889999999987   8888 8999999999999987  78999998763

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

Probab=99.29  E-value=2.2e-12  Score=72.65  Aligned_cols=49  Identities=20%  Similarity=0.532  Sum_probs=39.4

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCC--CcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS--NSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~--~~CP~Cr~~~~  117 (118)
                      .....|.||.+.+..+.  ....|+|.||..||.+|++.+  .+||+||..+.
T Consensus        13 ~~i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~   63 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP   63 (74)
T ss_dssp             SSSCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCC
T ss_pred             CCCCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCC
Confidence            34577999999997632  223799999999999999877  78999998753

>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=99.23  E-value=4.1e-12  Score=82.17  Aligned_cols=49  Identities=29%  Similarity=0.652  Sum_probs=42.8

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCC-CcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS-NSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~-~~CP~Cr~~~~  117 (118)
                      ..+++.|+||++.+..   ++.++|||.||..||.+|+... ..||.||..+.
T Consensus        15 ~~~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   64 (170)
T 3hcs_A           15 LESKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL   64 (170)
T ss_dssp             CCGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCC
T ss_pred             CCCCCCCCCCChhhcC---cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcc
Confidence            4567899999999988   8889999999999999999754 48999998764

>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=99.20  E-value=6.5e-12  Score=86.45  Aligned_cols=49  Identities=16%  Similarity=0.142  Sum_probs=42.9

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      ......|+||++.|.+   |++++|||.||..||..|+.. ..+||+||.++.
T Consensus       205 ~~~~~~c~i~~~~~~d---Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~  254 (281)
T 2c2l_A          205 IPDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLT  254 (281)
T ss_dssp             CCSTTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCC
T ss_pred             CCcccCCcCcCCHhcC---CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCc
Confidence            3467899999999998   999999999999999999975 445999998764

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

Probab=99.20  E-value=1.6e-12  Score=73.55  Aligned_cols=44  Identities=30%  Similarity=0.754  Sum_probs=37.5

Q ss_pred             CccccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.++|||. ||..|+..+    ..||+||.++.
T Consensus        23 ~~~~~C~IC~~~~~~---~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~   67 (75)
T 2ecg_A           23 QEEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV----DKCPMCYTVIT   67 (75)
T ss_dssp             HHHHSCSSSCSSCCC---BCCSSSCCCCBCHHHHHHC----SBCTTTCCBCC
T ss_pred             CCCCCCCcCCCCCCC---EEEecCCCHHHHHHHhhCC----CCCccCCceec
Confidence            345789999999877   888999999 999999643    78999998764

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

Probab=99.20  E-value=6.1e-12  Score=74.07  Aligned_cols=46  Identities=22%  Similarity=0.503  Sum_probs=39.9

Q ss_pred             CccccccccccccccCCCceeeC-CCChhhHHHHHHHhhCC------Ccccc--cCcc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLS------NSCPV--CRSG  115 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~------~~CP~--Cr~~  115 (118)
                      ..++.|+||++.|.+   ++.++ |||.||..||.+|+..+      .+||+  |+..
T Consensus         5 ~~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            456889999999998   99996 99999999999999753      47999  9754

>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=1.9e-11  Score=67.82  Aligned_cols=45  Identities=27%  Similarity=0.656  Sum_probs=38.3

Q ss_pred             cCccccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..++..|.||++....   ++.+||||. ||..|+..    ...||+||..+.
T Consensus        12 ~~~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~   57 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQ   57 (68)
T ss_dssp             CCCSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH----CSSCTTTCCCCC
T ss_pred             CCCCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc----CCCCCCCCcchh
Confidence            3456789999999877   999999999 99999984    478999999874

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

Probab=99.14  E-value=2.6e-11  Score=78.99  Aligned_cols=49  Identities=16%  Similarity=0.123  Sum_probs=43.1

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCC-CcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS-NSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~-~~CP~Cr~~~~  117 (118)
                      ....+.|+||++.|.+   |++++|||.|+..||..|+... .+||+||.++.
T Consensus       103 ip~~f~CPI~~elm~D---PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~  152 (179)
T 2f42_A          103 IPDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLT  152 (179)
T ss_dssp             CCGGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CcHhhcccCccccCCC---CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCC
Confidence            3567899999999998   9999999999999999999753 47999998764

>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=8.4e-12  Score=71.26  Aligned_cols=43  Identities=40%  Similarity=0.828  Sum_probs=37.7

Q ss_pred             ccccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ++..|.||++.+..   ++.+||||. ||..|+..|    ..||+||..+.
T Consensus        17 ~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~   60 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCPCGHTVCCESCAAQL----QSCPVCRSRVE   60 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEETTCBCCBCHHHHTTC----SBCTTTCCBCC
T ss_pred             CCCEeEEeCcccCc---EEEECCCCHHHHHHHHHhc----CcCCCCCchhh
Confidence            45689999999887   899999999 999999877    49999999764

>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=99.01  E-value=7.1e-10  Score=75.81  Aligned_cols=48  Identities=23%  Similarity=0.477  Sum_probs=40.9

Q ss_pred             cCccccccccccccccCCCceee-CCCChhhHHHHHHHhhCC--Ccccc--cCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLS--NSCPV--CRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~--~~CP~--Cr~~~  116 (118)
                      ...+..|+||++.|..   ++.. .|||.||..||..|+..+  ..||.  ||+.+
T Consensus       178 ~~~el~CPIcl~~f~D---PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l  230 (267)
T 3htk_C          178 GKIELTCPITCKPYEA---PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVV  230 (267)
T ss_dssp             SBCCSBCTTTSSBCSS---EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEE
T ss_pred             CceeeECcCccCcccC---CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcC
Confidence            3566899999999988   8875 899999999999999754  46999  99865

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

Probab=99.00  E-value=1.1e-10  Score=68.46  Aligned_cols=48  Identities=21%  Similarity=0.619  Sum_probs=36.7

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhC--------CCcccc--cCcc
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL--------SNSCPV--CRSG  115 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~--------~~~CP~--Cr~~  115 (118)
                      +...|+||++.+.......+.+|||.||..||..++..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            45789999999876332233479999999999999852        236999  9887

>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=98.96  E-value=7.7e-11  Score=83.89  Aligned_cols=44  Identities=32%  Similarity=0.830  Sum_probs=39.3

Q ss_pred             CccccccccccccccCCCceeeCCCCh-hhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHV-FHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~-f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++..|+||++.+..   ++.+||||. ||..|+..|    ..||+||.++.
T Consensus       293 ~~~~~C~IC~~~~~~---~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~  337 (345)
T 3t6p_A          293 QEERTCKVCMDKEVS---VVFIPCGHLVVCQECAPSL----RKCPICRGIIK  337 (345)
T ss_dssp             HTTCBCTTTSSSBCC---EEEETTCCEEECTTTGGGC----SBCTTTCCBCC
T ss_pred             cCCCCCCccCCcCCc---eEEcCCCChhHhHHHHhcC----CcCCCCCCCcc
Confidence            356889999999988   999999999 999999988    78999999864

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

Probab=98.95  E-value=9.1e-11  Score=82.86  Aligned_cols=51  Identities=25%  Similarity=0.627  Sum_probs=38.6

Q ss_pred             Ccccccccccccccc-CCCce----eeCCCChhhHHHHHHHhhCC-----------CcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQ-AFPGK----QVPCGHVFHATCISTWISLS-----------NSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~-~~~~~----~~~C~H~f~~~Ci~~~~~~~-----------~~CP~Cr~~~~  117 (118)
                      .....|+||++.+.. +..+.    ...|+|.||..||.+|++..           .+||.||+++.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs  372 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLS  372 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEE
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCC
Confidence            345679999999876 32222    23699999999999999632           35999999874

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

Probab=98.95  E-value=5.3e-10  Score=60.43  Aligned_cols=48  Identities=23%  Similarity=0.581  Sum_probs=37.1

Q ss_pred             CccccccccccccccCCCceeeCC--CC---hhhHHHHHHHhh--CCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPC--GH---VFHATCISTWIS--LSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C--~H---~f~~~Ci~~~~~--~~~~CP~Cr~~~~  117 (118)
                      .++..|.||++....   ..++||  .+   .||..||.+|+.  .+.+||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~---~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGN---ERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSC---CCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCCC---ceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            456789999987433   446785  45   899999999996  4678999998764

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.86  E-value=7.8e-10  Score=59.99  Aligned_cols=45  Identities=7%  Similarity=0.135  Sum_probs=40.8

Q ss_pred             ccccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           70 GRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      +.|+|+++.+.+   ++.. ++||.|.+.||.+|++.+.+||+.+.++.
T Consensus         4 ~~CpIs~~~m~d---PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~   49 (61)
T 2bay_A            4 MLCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLS   49 (61)
T ss_dssp             CCCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCC
T ss_pred             EEecCCCCCCCC---CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCC
Confidence            579999999998   8888 89999999999999988788999998763

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

Probab=98.65  E-value=1.5e-08  Score=59.40  Aligned_cols=45  Identities=29%  Similarity=0.554  Sum_probs=36.3

Q ss_pred             cccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccC
Q 033497           71 RCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVI  117 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~  117 (118)
                      -|++|--++..  ..+.+||+|.||.+|+..|.+ ..+.||.|+.++.
T Consensus         3 fC~~C~~Pi~i--ygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCSE--EEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeEE--EeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            37788666544  567899999999999999975 5678999998874

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

Probab=98.12  E-value=1.9e-06  Score=58.47  Aligned_cols=45  Identities=24%  Similarity=0.704  Sum_probs=36.7

Q ss_pred             cccccccccccccCCCceeeC-CCChhhHHHHHHHhhCCC--cccccCccc
Q 033497           69 EGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSN--SCPVCRSGV  116 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~--~CP~Cr~~~  116 (118)
                      ...|.||.+....   ....+ |+|.||..|+.+|++.+.  .||.|+...
T Consensus       180 i~~C~iC~~iv~~---g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W  227 (238)
T 3nw0_A          180 VKICNICHSLLIQ---GQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYW  227 (238)
T ss_dssp             CCBCTTTCSBCSS---CEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBC
T ss_pred             CCcCcchhhHHhC---CcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCC
Confidence            4779999999876   34443 999999999999997654  799998764

>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=0.00052  Score=40.08  Aligned_cols=32  Identities=16%  Similarity=0.433  Sum_probs=25.2

Q ss_pred             cccccccccccc-ccCCCcee--eCCCChhhHHHHHHH
Q 033497           68 TEGRCTVCMENF-LQAFPGKQ--VPCGHVFHATCISTW  102 (118)
Q Consensus        68 ~~~~C~IC~~~~-~~~~~~~~--~~C~H~f~~~Ci~~~  102 (118)
                      ++..|+||.+.+ ..   ++.  +.|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~---av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQD---AVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCB---CCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCC---ceEECCcCChHHhHHHCHHH
Confidence            457899999763 33   444  889999999999983

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

Probab=95.22  E-value=0.012  Score=31.81  Aligned_cols=46  Identities=24%  Similarity=0.431  Sum_probs=30.7

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC----cccccCcc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN----SCPVCRSG  115 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~----~CP~Cr~~  115 (118)
                      ..+..|.||.+.   ++.+.--.|...||..|+...+....    .||.|+..
T Consensus        10 ~~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           10 APGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             CTTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            345679999753   22222234999999999987764322    59999753

>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=95.17  E-value=0.028  Score=31.76  Aligned_cols=33  Identities=27%  Similarity=0.702  Sum_probs=23.4

Q ss_pred             cCccccccccccccccCCCceeeC---CCChhhHHHHHHH
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP---CGHVFHATCISTW  102 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~---C~H~f~~~Ci~~~  102 (118)
                      ...+..|.||- .+..   -.++|   |+..||..|+.+.
T Consensus        12 ~~~D~~C~VC~-~~t~---~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           12 VVNDEMCDVCE-VWTA---ESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTTC-CCCS---SCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCcccCccc-cccc---cceeccccccccccHhhcccc
Confidence            34678899994 2222   23333   8899999999997

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=93.95  E-value=0.0059  Score=32.66  Aligned_cols=48  Identities=23%  Similarity=0.520  Sum_probs=32.1

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhh-----CCCcccccCc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWIS-----LSNSCPVCRS  114 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~-----~~~~CP~Cr~  114 (118)
                      .++..|+||...+..+...+.- .|...||..|+.--..     ....||.|+.
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            4567799998877543333333 4899999999864322     2345999964

>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=93.12  E-value=0.087  Score=42.12  Aligned_cols=49  Identities=10%  Similarity=0.034  Sum_probs=43.0

Q ss_pred             cCccccccccccccccCCCceeeCCC-ChhhHHHHHHHhhCCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCG-HVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~-H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..++..|||=++.+.+   |++++-| +.|-+..|.+|+..+.+||+=|.++.
T Consensus       888 iP~~F~cPIs~~lM~D---PVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~  937 (968)
T 3m62_A          888 VPDEFLDPLMYTIMKD---PVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLK  937 (968)
T ss_dssp             SCGGGBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             CcHHhCCcchhhHHhC---CeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCC
Confidence            4567899999999999   9999987 68999999999998889999877653

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.67  E-value=0.044  Score=27.73  Aligned_cols=45  Identities=24%  Similarity=0.496  Sum_probs=27.3

Q ss_pred             cccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCcc
Q 033497           71 RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRSG  115 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~~  115 (118)
                      .|.||...-..+..+.--.|...||..|+..=+..    .-.||.|+..
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~~   50 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQPA   50 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSCC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCcccc
Confidence            48888765322222222348999999999753322    1249999653

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=92.21  E-value=0.018  Score=31.70  Aligned_cols=48  Identities=19%  Similarity=0.337  Sum_probs=31.0

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhhC----CCcccccCcc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISL----SNSCPVCRSG  115 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~----~~~CP~Cr~~  115 (118)
                      .+...|.||..... +...+.. .|...||..|+..-...    .-.||.|+..
T Consensus        16 ~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~   68 (75)
T 2k16_A           16 NQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANK   68 (75)
T ss_dssp             CEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHH
T ss_pred             CCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCc
Confidence            34567999987643 2223332 48999999999764432    2359999654

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=90.81  E-value=0.072  Score=28.12  Aligned_cols=45  Identities=22%  Similarity=0.505  Sum_probs=29.1

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRS  114 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~  114 (118)
                      ..+..|.+|...   ++.+.--.|...||..|+..-+..    .-.||.|+.
T Consensus         9 ~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            445779999863   211222248899999999874321    224999965

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=90.22  E-value=0.062  Score=34.84  Aligned_cols=46  Identities=20%  Similarity=0.372  Sum_probs=32.1

Q ss_pred             ccccccccccccCCC---ceee-CCCChhhHHHHHHHh------h-----CCCcccccCcc
Q 033497           70 GRCTVCMENFLQAFP---GKQV-PCGHVFHATCISTWI------S-----LSNSCPVCRSG  115 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~---~~~~-~C~H~f~~~Ci~~~~------~-----~~~~CP~Cr~~  115 (118)
                      ..|+||...+..++.   .+.. .|...||..|..---      .     ....||.|+..
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~   63 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTER   63 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCC
Confidence            469999988877542   3333 499999999984321      1     14679999865

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=90.01  E-value=0.41  Score=27.41  Aligned_cols=47  Identities=19%  Similarity=0.332  Sum_probs=27.4

Q ss_pred             CccccccccccccccCCCceeeC--CC-ChhhHHHHHHHhh--CCCcccccCcc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVP--CG-HVFHATCISTWIS--LSNSCPVCRSG  115 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~--C~-H~f~~~Ci~~~~~--~~~~CP~Cr~~  115 (118)
                      .+...| ||..... +..+.--.  |. ..||..|+.--..  .+-.||.|+..
T Consensus        34 ~e~~yC-iC~~~~~-g~MI~CD~~dC~~~WfH~~CVgl~~~p~g~W~Cp~C~~~   85 (91)
T 1weu_A           34 NEPTYC-LCHQVSY-GEMIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQE   85 (91)
T ss_dssp             CCCBCS-TTCCBCC-SCCCCCSCSSCSCCCCCSTTTTCSSCCCSSCCCTTTCCC
T ss_pred             CCCcEE-ECCCCCC-CCEeEecCCCCCCCCEecccCCcCcCCCCCEECcCccCc
Confidence            344667 9987643 32222233  55 6899999972111  22359999754

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=89.49  E-value=0.2  Score=27.73  Aligned_cols=47  Identities=19%  Similarity=0.412  Sum_probs=29.7

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHHHHhh-----CCCcccccCcc
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWIS-----LSNSCPVCRSG  115 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~-----~~~~CP~Cr~~  115 (118)
                      +...| ||......+..++.. .|...||..|+.--..     ....||.|+..
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~   63 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccc
Confidence            34556 898776433334433 4999999999853221     34469999754

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=89.45  E-value=0.047  Score=28.85  Aligned_cols=48  Identities=19%  Similarity=0.371  Sum_probs=30.8

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCccc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRSGV  116 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~~~  116 (118)
                      ...+..|.+|.+.   ++.+.--.|...||..|+..-+..    .-.||.|+...
T Consensus         6 d~~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             cCCCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            3456779999753   222333358899999999754322    22499997653

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=88.63  E-value=0.061  Score=34.64  Aligned_cols=45  Identities=27%  Similarity=0.477  Sum_probs=29.7

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCcc
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRSG  115 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~~  115 (118)
                      ++..|.+|...   ++....-.|...||..|+.+-+..    .-.||.|+..
T Consensus         3 ~~~~C~~C~~~---g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~   51 (184)
T 3o36_A            3 NEDWCAVCQNG---GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDL   51 (184)
T ss_dssp             SCSSCTTTCCC---SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCccccCCCC---CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCc
Confidence            45679999754   332222348999999998765432    2259999764

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=88.03  E-value=0.13  Score=27.11  Aligned_cols=43  Identities=23%  Similarity=0.383  Sum_probs=28.7

Q ss_pred             ccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCccccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVC  112 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~C  112 (118)
                      ..|-.|+..+.......-..|++.||.+|=.-.-..-..||.|
T Consensus        16 ~~C~~C~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCCccEECCccCcCcccchhHHHHhhccCCcCC
Confidence            3599999888541111123499999999965433455579988

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=87.93  E-value=0.087  Score=30.56  Aligned_cols=45  Identities=18%  Similarity=0.301  Sum_probs=27.3

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhh---CCCcccccCc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS---LSNSCPVCRS  114 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~---~~~~CP~Cr~  114 (118)
                      ...| ||......+..+.--.|...||..|+..-..   ....||.|+.
T Consensus        28 ~vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CEEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            3567 8866544322122224999999999865322   1235999974

>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=87.79  E-value=0.39  Score=26.83  Aligned_cols=37  Identities=27%  Similarity=0.392  Sum_probs=27.2

Q ss_pred             CccccccccccccccCCCceeeC--CCChhhHHHHHHHhh
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVP--CGHVFHATCISTWIS  104 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~--C~H~f~~~Ci~~~~~  104 (118)
                      .....|.+|.+.+.... -+..|  =.|.||.-|-+..++
T Consensus        13 ~a~l~CtlC~erLEdtH-FVQCPsv~~HkFCFpCsr~sIk   51 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTH-FVQCPSVPSHKFCFPCSRESIK   51 (93)
T ss_dssp             CCSCCCSSSCSCCSSTT-SEECSSCSSCEECHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCc-eeeCCCccCCeeeccccHHHHH
Confidence            34577999999987633 23333  369999999999885

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=87.29  E-value=0.04  Score=33.31  Aligned_cols=46  Identities=24%  Similarity=0.471  Sum_probs=28.2

Q ss_pred             CccccccccccccccCCCcee-eCCCChhhHHHHHHHhhCCCccccc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQ-VPCGHVFHATCISTWISLSNSCPVC  112 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~-~~C~H~f~~~Ci~~~~~~~~~CP~C  112 (118)
                      .....|..|...|..-.+... -.||.+||..|........+.|-.|
T Consensus        17 ~~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C   63 (120)
T 1y02_A           17 GLEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLC   63 (120)
T ss_dssp             ---CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHH
T ss_pred             cccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHH
Confidence            344679999999876322333 3599999999976655555566666

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=86.61  E-value=0.44  Score=25.43  Aligned_cols=35  Identities=17%  Similarity=0.399  Sum_probs=24.2

Q ss_pred             CccccccccccccccCCCceee--CCCChhhHHHHHH
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV--PCGHVFHATCIST  101 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~--~C~H~f~~~Ci~~  101 (118)
                      .....|++|...+..+...+..  .|...||..|+.-
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvgl   42 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGM   42 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTC
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccCC
Confidence            3456799999987665444443  5999999999743

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=85.82  E-value=0.14  Score=30.20  Aligned_cols=39  Identities=18%  Similarity=0.364  Sum_probs=25.6

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhh
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS  104 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~  104 (118)
                      ..++..|.||.+.=...+.+.-..|+..||..|+.....
T Consensus         4 ~~~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~   42 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVT   42 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCC
T ss_pred             CCCCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccc
Confidence            346778999976632211122335999999999987654

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=85.79  E-value=0.24  Score=26.97  Aligned_cols=50  Identities=16%  Similarity=0.308  Sum_probs=30.7

Q ss_pred             ccCccccccccccccc-cCCCceee-CCCChhhHHHHHHHhhCC--CcccccCc
Q 033497           65 VAATEGRCTVCMENFL-QAFPGKQV-PCGHVFHATCISTWISLS--NSCPVCRS  114 (118)
Q Consensus        65 ~~~~~~~C~IC~~~~~-~~~~~~~~-~C~H~f~~~Ci~~~~~~~--~~CP~Cr~  114 (118)
                      ...++..|.||...-. .++..+.- .|.-.||..|+..-....  -.||.|+.
T Consensus        12 ~~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           12 LIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CCCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            3456778999986631 12223332 489999999997533222  24888854

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=85.73  E-value=0.13  Score=26.13  Aligned_cols=43  Identities=19%  Similarity=0.345  Sum_probs=27.1

Q ss_pred             cccccccccccCCCceee--CCCChhhHHHHHHHh----hCCCcccccC
Q 033497           71 RCTVCMENFLQAFPGKQV--PCGHVFHATCISTWI----SLSNSCPVCR  113 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~--~C~H~f~~~Ci~~~~----~~~~~CP~Cr  113 (118)
                      .|.+|...+..+...+.-  .|...||..|+.--.    .....||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            477887776544334433  488899999975322    2455688885

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=85.66  E-value=0.76  Score=25.67  Aligned_cols=37  Identities=19%  Similarity=0.384  Sum_probs=26.7

Q ss_pred             cCccccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           66 AATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      +.+...|.+|...|..-.+...- .||.+||..|....
T Consensus        18 d~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   55 (84)
T 1z2q_A           18 DEDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHR   55 (84)
T ss_dssp             TTTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCE
T ss_pred             CCCCCCCcCcCCccccchhcccccCCCcEEChHHhCCe
Confidence            34456799999999764333333 49999999997654

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=85.31  E-value=0.11  Score=34.19  Aligned_cols=45  Identities=29%  Similarity=0.500  Sum_probs=29.5

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHhhC----CCcccccCcc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISL----SNSCPVCRSG  115 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~----~~~CP~Cr~~  115 (118)
                      ..+..|.+|...   ++ .... .|...||..|+.+-+..    .-.||.|+..
T Consensus         5 ~~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~   54 (207)
T 3u5n_A            5 PNEDWCAVCQNG---GD-LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDI   54 (207)
T ss_dssp             SSCSSBTTTCCC---EE-EEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCS
T ss_pred             CCCCCCCCCCCC---Cc-eEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCc
Confidence            355679999754   21 2222 48999999999765432    2259999763

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=84.51  E-value=0.46  Score=28.71  Aligned_cols=35  Identities=23%  Similarity=0.566  Sum_probs=25.7

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      +...|.+|...|......... .||++||..|....
T Consensus        68 ~~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           68 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CCCCCcCcCCccccccccccCCCCCeEEChHHhCCc
Confidence            346799999998764333344 49999999997654

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=84.05  E-value=0.14  Score=32.46  Aligned_cols=47  Identities=21%  Similarity=0.411  Sum_probs=29.5

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHHh-----hCCCcccccCc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWI-----SLSNSCPVCRS  114 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~-----~~~~~CP~Cr~  114 (118)
                      .+...| +|......+...+.. .|..+||..|+.--.     ...-.||.|+.
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~   58 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQS   58 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcc
Confidence            455678 998775433323333 489999999985321     12346999964

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=83.96  E-value=0.081  Score=30.37  Aligned_cols=49  Identities=18%  Similarity=0.233  Sum_probs=28.9

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRS  114 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~  114 (118)
                      ..++..|.||...-..+..+.--.|...||..|+.+-+..    .-.||.|+.
T Consensus        13 ~~~~~~C~vC~~~~~~~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~   65 (92)
T 2e6r_A           13 FIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCIL   65 (92)
T ss_dssp             CCCCCCCSSSCCSGGGGGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHH
T ss_pred             ccCCCCCccCCCcCCCCCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcC
Confidence            3455679999876432111222248889999998743321    114888854

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=83.55  E-value=0.23  Score=29.35  Aligned_cols=44  Identities=23%  Similarity=0.463  Sum_probs=26.7

Q ss_pred             cccccccccccCCCceee-CCCChhhHHHHHHHhhC----CCcccccCc
Q 033497           71 RCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISL----SNSCPVCRS  114 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~----~~~CP~Cr~  114 (118)
                      .|.||...-..+.....- .|...||..|+.+-+..    .-.||.|+.
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            577887542222223322 49999999999754432    125999975

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=83.55  E-value=0.56  Score=25.48  Aligned_cols=32  Identities=25%  Similarity=0.521  Sum_probs=23.6

Q ss_pred             ccccccccccccCCCceee-CCCChhhHHHHHH
Q 033497           70 GRCTVCMENFLQAFPGKQV-PCGHVFHATCIST  101 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~  101 (118)
                      ..|.+|...|..-.....- .||.+||..|...
T Consensus        12 ~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~   44 (73)
T 1vfy_A           12 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   44 (73)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             CcccCCCCccCCccccccCCCCCEEEcccccCC
Confidence            4799999998763333333 4999999999754

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=83.49  E-value=0.047  Score=28.28  Aligned_cols=46  Identities=24%  Similarity=0.550  Sum_probs=28.8

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRS  114 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~  114 (118)
                      ...+..|.+|...   +..+.--.|...||..|+.+-+..    .-.||.|+.
T Consensus         6 ~~~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            3456779999864   222223358999999999754322    114888853

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=83.32  E-value=0.58  Score=26.55  Aligned_cols=35  Identities=23%  Similarity=0.507  Sum_probs=25.5

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      +...|.+|...|..-...... .||++||..|...+
T Consensus        19 ~~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~   54 (90)
T 3t7l_A           19 EAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRK   54 (90)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             cCCcCcCCCCcccchhhCccccCCCCEECCcccCCe
Confidence            346799999998764333333 49999999997654

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=83.23  E-value=0.24  Score=28.23  Aligned_cols=46  Identities=22%  Similarity=0.397  Sum_probs=30.2

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCC----CcccccCc
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS----NSCPVCRS  114 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~----~~CP~Cr~  114 (118)
                      ...+..|.+|...   ++...--.|...||..|+.+=+...    -.||.|+.
T Consensus        22 d~n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~   71 (88)
T 1fp0_A           22 DDSATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHV   71 (88)
T ss_dssp             SSSSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCC
T ss_pred             CCCCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccC
Confidence            4566789999864   2212223488999999997654321    14999964

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=83.19  E-value=0.21  Score=27.58  Aligned_cols=46  Identities=24%  Similarity=0.331  Sum_probs=28.2

Q ss_pred             ccccccccccccccCCCceee--CCCChhhHHHHHHHhh---------CCCcccccCc
Q 033497           68 TEGRCTVCMENFLQAFPGKQV--PCGHVFHATCISTWIS---------LSNSCPVCRS  114 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~--~C~H~f~~~Ci~~~~~---------~~~~CP~Cr~  114 (118)
                      +...| ||......+..+.--  .|...||..|+.--..         .+..||.|+.
T Consensus        15 ~~~~C-iC~~~~~~g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~   71 (78)
T 1wew_A           15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRL   71 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHH
T ss_pred             CCEEe-ECCCcCCCCCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCc
Confidence            44667 888763333222223  5889999999854322         2346999964

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=83.04  E-value=0.54  Score=26.16  Aligned_cols=36  Identities=28%  Similarity=0.589  Sum_probs=25.7

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      .+...|.+|...|........- .||.+||..|....
T Consensus        17 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~   53 (82)
T 2yw8_A           17 DEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNE   53 (82)
T ss_dssp             CCCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCEE
T ss_pred             ccCCcccCcCCcccCccccccCCCCCCEEChHHhCCe
Confidence            3446799999999763333333 49999999997643

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=82.96  E-value=0.65  Score=26.26  Aligned_cols=35  Identities=29%  Similarity=0.525  Sum_probs=24.5

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHH
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCIST  101 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~  101 (118)
                      .+...|.+|...|..-...... .||.+||..|...
T Consensus         7 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   42 (88)
T 1wfk_A            7 GMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSF   42 (88)
T ss_dssp             CCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCE
T ss_pred             CcCCCCcCcCCcccCccccccCCCCCCEEChhHcCC
Confidence            3445799999998763333333 4999999999754

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=82.54  E-value=0.26  Score=27.96  Aligned_cols=49  Identities=18%  Similarity=0.316  Sum_probs=29.6

Q ss_pred             cCcccccccccccccc-CCCceee-CCCChhhHHHHHHHhhC--CCcccccCc
Q 033497           66 AATEGRCTVCMENFLQ-AFPGKQV-PCGHVFHATCISTWISL--SNSCPVCRS  114 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~-~~~~~~~-~C~H~f~~~Ci~~~~~~--~~~CP~Cr~  114 (118)
                      ..++..|.||...-.. .+..+.. .|.-.||..|+..-...  .-.||.|..
T Consensus        22 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~   74 (88)
T 2l43_A           22 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   74 (88)
T ss_dssp             CCCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccC
Confidence            3456789999865311 1112222 48889999999753322  224888854

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.66  E-value=0.63  Score=25.98  Aligned_cols=35  Identities=29%  Similarity=0.563  Sum_probs=25.0

Q ss_pred             CccccccccccccccCCCceee-CCCChhhHHHHHH
Q 033497           67 ATEGRCTVCMENFLQAFPGKQV-PCGHVFHATCIST  101 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~  101 (118)
                      .+...|.+|...|..-.+...- .||.+||..|...
T Consensus        12 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           12 NNFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CCCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCE
T ss_pred             CCCCcCcCcCCccccchhhhhhcCCCcEEChhhcCC
Confidence            3446799999998764333333 4999999999754

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=81.11  E-value=0.13  Score=26.93  Aligned_cols=45  Identities=24%  Similarity=0.544  Sum_probs=28.3

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRS  114 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~  114 (118)
                      ..+..|.+|...   +..+.--.|...||..|+.+-+..    .-.||.|+.
T Consensus         3 ~~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~   51 (60)
T 2puy_A            3 IHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   51 (60)
T ss_dssp             CCCSSCTTTCCC---SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHH
T ss_pred             CCCCCCcCCCCC---CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccC
Confidence            456779999764   222223348899999998753321    124888854

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=80.97  E-value=0.5  Score=27.65  Aligned_cols=45  Identities=20%  Similarity=0.393  Sum_probs=30.5

Q ss_pred             ccccccccccccCCCceee--CCCChhhHHHHHHHhh----------CCCcccccCc
Q 033497           70 GRCTVCMENFLQAFPGKQV--PCGHVFHATCISTWIS----------LSNSCPVCRS  114 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~--~C~H~f~~~Ci~~~~~----------~~~~CP~Cr~  114 (118)
                      ..|.||...+..+...+..  .|...||..|+.--..          ....||.|+.
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~   60 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLK   60 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHH
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccC
Confidence            5699999887654444444  5899999999853210          2335999964

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=80.92  E-value=3.5  Score=23.43  Aligned_cols=49  Identities=16%  Similarity=0.304  Sum_probs=33.1

Q ss_pred             ccccccccccccccC---CCcee-eCCCChhhHHHHHHHh-hCCCcccccCccc
Q 033497           68 TEGRCTVCMENFLQA---FPGKQ-VPCGHVFHATCISTWI-SLSNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~---~~~~~-~~C~H~f~~~Ci~~~~-~~~~~CP~Cr~~~  116 (118)
                      ....|.||-+.+-..   +.-+. --|+--.|..|+.--. ..+..||.|+...
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrY   68 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRY   68 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcc
Confidence            446799999886432   21122 2388889999987654 4667899997654

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

Probab=80.69  E-value=1.4  Score=31.59  Aligned_cols=45  Identities=24%  Similarity=0.522  Sum_probs=29.6

Q ss_pred             ccccccccccccCCCceeeCCCCh--hhHHHHHHHhhCC--CcccccCccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHV--FHATCISTWISLS--NSCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~--f~~~Ci~~~~~~~--~~CP~Cr~~~  116 (118)
                      +.|+|=...+..  .++...|.|.  |-..-+..+....  -.||+|.+.+
T Consensus       250 L~CPlS~~ri~~--PvRg~~C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~  298 (371)
T 3i2d_A          250 LQCPISYTRMKY--PSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDI  298 (371)
T ss_dssp             SBCTTTSSBCSS--EEEETTCCSSCCEEHHHHHHHHHHSCCCBCTTTCCBC
T ss_pred             ecCCCccccccc--cCcCCcCCCcceECHHHHHHHhhcCCceeCCCCCccc
Confidence            779988777765  2345569998  5554454444333  3599998765

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=80.61  E-value=0.6  Score=25.34  Aligned_cols=46  Identities=20%  Similarity=0.366  Sum_probs=26.3

Q ss_pred             CccccccccccccccCCCcee-eC--CC-ChhhHHHHHHHhh--CCCcccccCcc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQ-VP--CG-HVFHATCISTWIS--LSNSCPVCRSG  115 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~-~~--C~-H~f~~~Ci~~~~~--~~~~CP~Cr~~  115 (118)
                      .+...| ||..... +. ++. -.  |. ..||..|+.--..  .+-.||.|+..
T Consensus        14 ~~~~~C-~C~~~~~-g~-MI~CD~~~C~~~wfH~~Cvgl~~~p~g~w~Cp~C~~~   65 (71)
T 1wen_A           14 NEPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQE   65 (71)
T ss_dssp             TSCCCS-TTCCCSC-SS-EECCSCSSCSCCCEETTTTTCSSCCSSCCCCTTTSSC
T ss_pred             CCCCEE-ECCCCCC-CC-EeEeeCCCCCCccEecccCCcCcCCCCCEECCCCCcc
Confidence            344567 8977532 22 222 23  55 6899999972111  22259999754

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=80.60  E-value=0.13  Score=27.58  Aligned_cols=45  Identities=24%  Similarity=0.484  Sum_probs=28.6

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRS  114 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~  114 (118)
                      .++..|.||.+.   ++.+.--.|...||..|+.+-+..    .-.||.|..
T Consensus         6 ~~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~   54 (66)
T 1xwh_A            6 KNEDECAVCRDG---GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQ   54 (66)
T ss_dssp             SCCCSBSSSSCC---SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCccCCCC---CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccC
Confidence            456789999864   222222348899999999753321    124888854

>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=80.40  E-value=1.5  Score=31.36  Aligned_cols=45  Identities=24%  Similarity=0.456  Sum_probs=30.2

Q ss_pred             ccccccccccccCCCceeeCCCCh--hhHHHHHHHhhCCC--cccccCccc
Q 033497           70 GRCTVCMENFLQAFPGKQVPCGHV--FHATCISTWISLSN--SCPVCRSGV  116 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~~C~H~--f~~~Ci~~~~~~~~--~CP~Cr~~~  116 (118)
                      +.|+|=...+..  ..+...|.|.  |-..-+..+.....  .||+|.+.+
T Consensus       216 L~CPlS~~ri~~--P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~  264 (360)
T 4fo9_A          216 LMCPLGKMRLTI--PCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKA  264 (360)
T ss_dssp             SBCTTTCSBCSS--EEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBC
T ss_pred             eeCCCccceecc--CCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCccc
Confidence            679988777765  2344569999  66555555544333  599998865

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=80.39  E-value=1.3  Score=24.15  Aligned_cols=45  Identities=20%  Similarity=0.391  Sum_probs=28.5

Q ss_pred             ccccccccccccccCCCcee-eCCCChhhHHHHHHHh---------hCCCcccccCc
Q 033497           68 TEGRCTVCMENFLQAFPGKQ-VPCGHVFHATCISTWI---------SLSNSCPVCRS  114 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~-~~C~H~f~~~Ci~~~~---------~~~~~CP~Cr~  114 (118)
                      +...| ||......+ .++. -.|...||..|+.--.         .....||.|+.
T Consensus        15 ~~~~C-~C~~~~~~~-~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~   69 (76)
T 1wem_A           15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             CCCEE-ECCCccCCC-CEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcC
Confidence            34567 898775432 2333 3499999999985321         24557999964

>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix, transferase; HET: CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2 g.50.1.1

Probab=80.08  E-value=0.6  Score=30.80  Aligned_cols=34  Identities=24%  Similarity=0.511  Sum_probs=25.5

Q ss_pred             cccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           69 EGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      +..|.+|...|..-.+.... .||++||..|....
T Consensus       161 ~~~C~~C~~~F~~~~rrhhCr~CG~v~C~~Cs~~~  195 (220)
T 1dvp_A          161 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ  195 (220)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCccCCCCCccCCcccccccCCcCCEEChHHhCCe
Confidence            46899999998764444444 49999999997653

---

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	118
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-12
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-12
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	3e-09
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	9e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	2e-06
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-06
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	6e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	3e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	5e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	0.004

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 55.3 bits (133), Expect = 2e-12
 Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 72  CTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGVI 117
           C VC+         + +P CGH FHA C+  W+   ++CP+CR  V+
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 55.3 bits (133), Expect = 3e-12
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 65  VAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCR 113
           +A    RC +C+E+         +PC H F   CI+ WI  + +CP+C+
Sbjct: 1   MATVAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCK 47

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 1e-09
 Identities = 13/58 (22%), Positives = 18/58 (31%), Gaps = 15/58 (25%)

Query: 72  CTVCMENFLQAFPGKQV---------------PCGHVFHATCISTWISLSNSCPVCRS 114
           C +C  + +      Q                 C H FH  CIS W+     CP+   
Sbjct: 24  CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

>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 = 48.1 bits (114), Expect = 3e-09
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 4/46 (8%)

Query: 72  CTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGV 116
           C +C EN       K  PCGH+   +C+++W       CP CR  +
Sbjct: 26  CKICAENDKDV---KIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>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 = 45.6 bits (108), Expect = 1e-08
 Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 6/46 (13%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGV 116
           RC  C          K +PC H   + C+         CP+C++  
Sbjct: 8   RCQQCQAEAKCP---KLLPCLHTLCSGCLEAS---GMQCPICQAPW 47

>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 = 42.5 bits (99), Expect = 2e-07
 Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 3/49 (6%)

Query: 69  EGRCTVCMENFLQAFPGKQV--PCGHVFHATCISTWISL-SNSCPVCRS 114
           +  C  C     +    K +   CGH    +C+       + +CP C +
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGT 51

>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 = 42.0 bits (98), Expect = 9e-07
 Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 6/47 (12%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN---SCPVCRS 114
            C +C+E   +        C H+F   C+   ++       CP+C++
Sbjct: 23  ECPICLELIKEP---VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKN 66

>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 = 40.7 bits (95), Expect = 2e-06
 Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 4/61 (6%)

Query: 54  NSELTVSSLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWI-SLSNSCPVC 112
           +++L     P        C +C           +  C H+F   CI   +  + + CP C
Sbjct: 8   STKLLAVDFPAHFVKSISCQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSC 64

Query: 113 R 113
           R
Sbjct: 65  R 65

>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 = 38.5 bits (89), Expect = 6e-06
 Identities = 12/45 (26%), Positives = 15/45 (33%), Gaps = 2/45 (4%)

Query: 72  CTVCMENFLQAFPG-KQVPCGHVFHATCISTWISLSN-SCPVCRS 114
           C +CME             CG+     C     +  N  CP CR 
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 47

>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 = 38.7 bits (89), Expect = 6e-06
 Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 72  CTVCMENF--LQAFPGKQVPCGHVFHATCISTWISLS--NSCPVCRS 114
           C +C E     +             H +C+STW+++S   +C +C  
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGV 55

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.1 bits (87), Expect = 3e-05
 Identities = 16/69 (23%), Positives = 21/69 (30%), Gaps = 20/69 (28%)

Query: 66  AATEGRCTVCMENFLQAFPGKQV---------------PCGHVFHATCISTWISLSN--- 107
            A E  C +CME    A     +                C H FH  C+       N   
Sbjct: 22  VAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDG 81

Query: 108 --SCPVCRS 114
              CP C++
Sbjct: 82  SLQCPSCKT 90

>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 = 37.1 bits (85), Expect = 5e-05
 Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 4/44 (9%)

Query: 71  RCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRS 114
           RC+ C        P     C H+F + C+S    +   CPVC +
Sbjct: 24  RCSRCTNIL--REPVCLGGCEHIFCSNCVSDC--IGTGCPVCYT 63

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.0 bits (72), Expect = 0.004
 Identities = 9/56 (16%), Positives = 18/56 (32%), Gaps = 8/56 (14%)

Query: 66  AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN--------SCPVCR 113
           ++    C +C+  +          C  +F   C+  ++ L          SCP   
Sbjct: 2   SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	118
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.78
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.65
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.6
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.6
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.6
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.59
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.54
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.52
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.51
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.5
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.43
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.41
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.35
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.34
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.26
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.88
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.75
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.49
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	93.39
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	91.1
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	90.97
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.62
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	90.16
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	89.43
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	88.88
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	88.58
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	87.54
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	84.85
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	83.97
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	83.23
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	83.1
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	82.79
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	82.36

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.78  E-value=4.6e-20  Score=97.60  Aligned_cols=51  Identities=33%  Similarity=0.924  Sum_probs=45.3

Q ss_pred             CccccccccccccccCCCceeeC-CCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .++.+|+||++.|..++.++.++ |+|.||..||.+|++.+.+||+||++++
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            35567999999999887787765 9999999999999999999999999875

>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=99.65  E-value=1.7e-17  Score=91.30  Aligned_cols=47  Identities=34%  Similarity=0.873  Sum_probs=40.8

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ...|+||++.+.+  .++.++|||.||..||.+|++.+.+||+||+++.
T Consensus         5 ~d~C~IC~~~~~~--~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCccC--CcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            4569999999865  3566899999999999999999999999999763

>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=99.64  E-value=3.5e-17  Score=92.46  Aligned_cols=47  Identities=34%  Similarity=0.842  Sum_probs=40.9

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~  117 (118)
                      ....|+||++.+..   +++++|||.||..||..|+. +.+.||+||..+.
T Consensus        22 ~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~   69 (79)
T d1fbva4          22 TFQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIK   69 (79)
T ss_dssp             CTTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCC
T ss_pred             CCCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCcc
Confidence            34569999999887   89999999999999999997 4567999999874

>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=99.60  E-value=1.2e-16  Score=91.28  Aligned_cols=54  Identities=22%  Similarity=0.594  Sum_probs=44.5

Q ss_pred             CCCCccCccccccccccccccCCCceeeCCCChhhHHHHHHHhh-CCCcccccCcccC
Q 033497           61 SLPTVAATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWIS-LSNSCPVCRSGVI  117 (118)
Q Consensus        61 ~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~-~~~~CP~Cr~~~~  117 (118)
                      .++....++..|+||++.+..   ++.++|||.||..||.+|++ .+..||.||.++.
T Consensus        15 d~~~d~~~~l~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~   69 (86)
T d1rmda2          15 DFPAHFVKSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF   69 (86)
T ss_dssp             CCCHHHHHHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             cchhhhccCcCCccCCcchhc---ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCC
Confidence            334334456889999999988   99999999999999999996 4567999998764

>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=99.60  E-value=1.5e-16  Score=82.93  Aligned_cols=48  Identities=23%  Similarity=0.373  Sum_probs=39.5

Q ss_pred             ccccccccccccCCC-ceeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           70 GRCTVCMENFLQAFP-GKQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~-~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      .+|+||++.|..++. +..++|||.||..|+.+|++. +.+||+||+++.
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~   50 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP   50 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCS
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCC
Confidence            369999999976543 455689999999999999975 447999999875

>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=99.60  E-value=3e-16  Score=85.42  Aligned_cols=50  Identities=18%  Similarity=0.503  Sum_probs=39.4

Q ss_pred             ccccccccccccccC--CCceeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQA--FPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~--~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      ++..|+||++.+..+  ....+++|||.||..||.+|+.. +..||+||+++.
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~   54 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLR   54 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCS
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcc
Confidence            567899999986432  23355689999999999999954 557999999763

>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=99.59  E-value=4.9e-16  Score=89.35  Aligned_cols=51  Identities=24%  Similarity=0.582  Sum_probs=41.6

Q ss_pred             CccccccccccccccCC---------------CceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAF---------------PGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~---------------~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      ..+..|+||++.+....               .+..++|+|.||..||.+|++.+.+||+||+.+.
T Consensus        19 ~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          19 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            35567999998875421               2456789999999999999999999999999763

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.54  E-value=1.5e-15  Score=91.12  Aligned_cols=49  Identities=33%  Similarity=0.736  Sum_probs=38.0

Q ss_pred             ccccccccccccccC---------------CCceeeCCCChhhHHHHHHHhhC-----CCcccccCccc
Q 033497           68 TEGRCTVCMENFLQA---------------FPGKQVPCGHVFHATCISTWISL-----SNSCPVCRSGV  116 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~---------------~~~~~~~C~H~f~~~Ci~~~~~~-----~~~CP~Cr~~~  116 (118)
                      .+..|+||++.+...               ....+++|+|.||..||..|++.     +.+||+||+.+
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~   92 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIY   92 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchh
Confidence            356799999998531               22356789999999999999964     34799999865

>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=99.52  E-value=1.4e-15  Score=80.41  Aligned_cols=44  Identities=9%  Similarity=0.227  Sum_probs=40.2

Q ss_pred             cccccccccccCCCceeeC-CCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           71 RCTVCMENFLQAFPGKQVP-CGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .|+||++.+.+   ++.++ |||.||.+||.+|++.+.+||+||.++.
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~   46 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLS   46 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCC
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCC
Confidence            59999999988   88875 9999999999999999999999999764

>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=99.51  E-value=3.2e-15  Score=88.24  Aligned_cols=47  Identities=21%  Similarity=0.687  Sum_probs=40.8

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC---cccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN---SCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~---~CP~Cr~~~~  117 (118)
                      +...|+||++.|..   ++.++|||.||..||..|+..++   .||.||..+.
T Consensus        20 ~~l~CpIC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~   69 (103)
T d1jm7a_          20 KILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT   69 (103)
T ss_dssp             HHTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCC
T ss_pred             cCcCCCccCchhCC---eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCC
Confidence            44789999999987   88899999999999999996543   6999998764

>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=99.50  E-value=7.7e-16  Score=81.23  Aligned_cols=44  Identities=25%  Similarity=0.560  Sum_probs=38.2

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      +...|+||++.+.+   +++++|||.||..||.+|   +.+||+||..+.
T Consensus         5 ~~l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~   48 (56)
T d1bora_           5 QFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWP   48 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSS
T ss_pred             CCCCCcccCcccCC---CEEecCCCHHhHHHHHcC---CCcCcCCCCccc
Confidence            44689999999987   889999999999999765   567999999875

>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=99.43  E-value=3.5e-14  Score=80.03  Aligned_cols=49  Identities=16%  Similarity=0.142  Sum_probs=43.0

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-CCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-SNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-~~~CP~Cr~~~~  117 (118)
                      ..+++.|+||++.|.+   ++.++|||.||..||.+|+.. +..||.||.++.
T Consensus         4 iP~~l~CpIc~~l~~d---Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~   53 (80)
T d2c2la2           4 IPDYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLT   53 (80)
T ss_dssp             CCSTTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCC
T ss_pred             CCccccCcCcCchhhh---hcccCCcCeecHHHHHHHHhcCCccCCCcccccc
Confidence            3477899999999998   999999999999999999964 557999998763

>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=99.41  E-value=8.4e-14  Score=78.08  Aligned_cols=49  Identities=18%  Similarity=0.489  Sum_probs=43.1

Q ss_pred             cCccccccccccccccCCCceeeCCCChhhHHHHHHHhhCC-CcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLS-NSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~-~~CP~Cr~~~~  117 (118)
                      ..+++.|+||++.|.+   ++.++|||.||..||.+|++.+ ..||.|+.++.
T Consensus         5 iP~~l~CpIc~~~m~d---PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~   54 (78)
T d1t1ha_           5 FPEYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLL   54 (78)
T ss_dssp             CSSSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCS
T ss_pred             CCccCCCcCcCchhhC---ceEccCCCcchHHHHHHHHHHCCCCCCcccccCC
Confidence            4477899999999998   8999999999999999999754 56999998764

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=99.35  E-value=2.4e-13  Score=72.54  Aligned_cols=49  Identities=20%  Similarity=0.459  Sum_probs=37.7

Q ss_pred             cCccccccccccccccCCCceeeC-----CCChhhHHHHHHHhh--CCCcccccCcccC
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP-----CGHVFHATCISTWIS--LSNSCPVCRSGVI  117 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~-----C~H~f~~~Ci~~~~~--~~~~CP~Cr~~~~  117 (118)
                      ..+...|.||++.+..   ....+     |+|.||..||.+|+.  .+.+||+||+++.
T Consensus         3 ded~~~C~IC~~~~~~---~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           3 DEDVPVCWICNEELGN---ERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             TCSCCEETTTTEECSC---CCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCCccCCccCCC---ceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            3456789999998765   33333     469999999999984  5568999999864

>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=99.34  E-value=5.4e-14  Score=81.98  Aligned_cols=45  Identities=29%  Similarity=0.683  Sum_probs=37.9

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccCcccC
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      +...|+||++.|..   ++.+ +|||.||..||.+|+.  ..||.||.++.
T Consensus        21 ~~l~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (97)
T d1jm7b_          21 KLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (97)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hcCCCccCCchhhc---CceeCCCCCchhHHHHHHHHh--ccccccCCcCc
Confidence            45789999999987   6654 7999999999999974  46999998653

>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=99.26  E-value=3.3e-12  Score=74.33  Aligned_cols=48  Identities=13%  Similarity=0.078  Sum_probs=43.0

Q ss_pred             CccccccccccccccCCCceeeCCC-ChhhHHHHHHHhhCCCcccccCcccC
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCG-HVFHATCISTWISLSNSCPVCRSGVI  117 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~-H~f~~~Ci~~~~~~~~~CP~Cr~~~~  117 (118)
                      .+++.|+||.+.|.+   +++++|+ |.|++.||.+|+..+..||+||.++.
T Consensus        20 P~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~   68 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLT   68 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCC
T ss_pred             cHHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCccccccccc
Confidence            457999999999999   9999866 58999999999999999999998764

>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=98.88  E-value=2.6e-10  Score=65.48  Aligned_cols=47  Identities=19%  Similarity=0.541  Sum_probs=36.1

Q ss_pred             ccccccccccccccCCCceeeCCCChhhHHHHHHHhhC-----C---CcccccCc
Q 033497           68 TEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL-----S---NSCPVCRS  114 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~-----~---~~CP~Cr~  114 (118)
                      ....|+||++.+...+.+..++|+|.||..||..|+..     .   -.||.|+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            45679999999876555566689999999999999842     1   15998653

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.75  E-value=0.0015  Score=32.13  Aligned_cols=43  Identities=26%  Similarity=0.574  Sum_probs=28.3

Q ss_pred             cccccccccccCCCceee-CCCChhhHHHHHHHhhCCC----cccccCc
Q 033497           71 RCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSN----SCPVCRS  114 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~----~CP~Cr~  114 (118)
                      +|.||...-..+. .+.- .|...||..|+..-+....    .||.||.
T Consensus         2 ~C~vC~~~~~~~~-~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDK-LILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSC-CEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCC-EEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            5888976533322 3332 4999999999987653222    4999975

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.49  E-value=0.0056  Score=33.07  Aligned_cols=33  Identities=30%  Similarity=0.759  Sum_probs=25.2

Q ss_pred             cCccccccccccccccCCCceeeC---CCChhhHHHHHHH
Q 033497           66 AATEGRCTVCMENFLQAFPGKQVP---CGHVFHATCISTW  102 (118)
Q Consensus        66 ~~~~~~C~IC~~~~~~~~~~~~~~---C~H~f~~~Ci~~~  102 (118)
                      ...+..|.|| +.+..   -.++|   |+..||..|+.+.
T Consensus        12 v~~D~mC~vC-~v~t~---~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          12 VVNDEMCDVC-EVWTA---ESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCS---SCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCcCcccccc-Ccccc---cceecceeecchhhHHHHHHh
Confidence            5577889999 66554   33334   7899999999998

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.39  E-value=0.01  Score=30.00  Aligned_cols=44  Identities=25%  Similarity=0.401  Sum_probs=29.9

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhCCCccccc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSNSCPVC  112 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~C  112 (118)
                      ...|.-|+..+.......-..|++.||.+|=.-.-+.-.+||.|
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            46699999887652222233499999999964433455579988

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=91.10  E-value=0.027  Score=28.66  Aligned_cols=48  Identities=23%  Similarity=0.509  Sum_probs=32.0

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHHHHhh-----CCCcccccCcc
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTWIS-----LSNSCPVCRSG  115 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~-----~~~~CP~Cr~~  115 (118)
                      ....|.+|......+...+.- .|+..||..|+..-..     ....||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            345799998876655444433 4999999999853211     23359999653

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.97  E-value=0.012  Score=29.85  Aligned_cols=47  Identities=19%  Similarity=0.381  Sum_probs=30.2

Q ss_pred             CccccccccccccccCCCceeeCCCChhhHHHHHHHhhC----CCcccccCccc
Q 033497           67 ATEGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISL----SNSCPVCRSGV  116 (118)
Q Consensus        67 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~----~~~CP~Cr~~~  116 (118)
                      ..+..|.+|.+.   ++.+.--.|...||..|+...+..    .-.||.|+...
T Consensus         7 ~~~~~C~~C~~~---g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            344569999753   222333359999999998755432    22599997653

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.62  E-value=0.2  Score=25.96  Aligned_cols=36  Identities=28%  Similarity=0.393  Sum_probs=26.5

Q ss_pred             ccccccccccccccCCCceeeC--CCChhhHHHHHHHhh
Q 033497           68 TEGRCTVCMENFLQAFPGKQVP--CGHVFHATCISTWIS  104 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~~--C~H~f~~~Ci~~~~~  104 (118)
                      ....|.+|.+.+.+.. -+..|  =+|.||.-|-+..++
T Consensus         7 ~~l~CtlC~erLEdtH-FVQCPsv~~HkFCFpCsr~sik   44 (80)
T d2cs3a1           7 GPLCCTICHERLEDTH-FVQCPSVPSHKFCFPCSRESIK   44 (80)
T ss_dssp             CSCCCSSSCSCCSSTT-SEECSSCSSCEECHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCc-eEeCCCCcCCceeccccHHHHH
Confidence            3467999999987633 23333  379999999999885

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.16  E-value=0.0078  Score=29.64  Aligned_cols=43  Identities=23%  Similarity=0.492  Sum_probs=27.5

Q ss_pred             cccccccccccCCCceee-CCCChhhHHHHHHHhhCCCcccccC
Q 033497           71 RCTVCMENFLQAFPGKQV-PCGHVFHATCISTWISLSNSCPVCR  113 (118)
Q Consensus        71 ~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~~~~~~~CP~Cr  113 (118)
                      .|.+|...|........- .||..||..|........+.|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            588888888753323333 4999999999766555556677774

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.43  E-value=0.13  Score=26.73  Aligned_cols=45  Identities=20%  Similarity=0.409  Sum_probs=27.0

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHH----HH-----hhCCCcccccCc
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCIS----TW-----ISLSNSCPVCRS  114 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~----~~-----~~~~~~CP~Cr~  114 (118)
                      +...| ||......+ ..+.- .|.-.||..|+.    ..     ......||.|+.
T Consensus        15 ~~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~   69 (76)
T d1wema_          15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             CcCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcC
Confidence            34557 887654332 23332 489999999983    11     123457999954

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=88.88  E-value=0.14  Score=26.92  Aligned_cols=45  Identities=27%  Similarity=0.414  Sum_probs=28.2

Q ss_pred             ccccccccccccccCCCceee---CCCChhhHHHHHHHh----h-----CCCcccccCc
Q 033497           68 TEGRCTVCMENFLQAFPGKQV---PCGHVFHATCISTWI----S-----LSNSCPVCRS  114 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~---~C~H~f~~~Ci~~~~----~-----~~~~CP~Cr~  114 (118)
                      +...| ||......+ ..+..   .|...||..|+.---    .     ....||.|+.
T Consensus        15 ~~~~C-~C~~~~~~~-~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~   71 (78)
T d1wewa_          15 IKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRL   71 (78)
T ss_dssp             CCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHH
T ss_pred             CccEe-ECCCccCCC-cEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcC
Confidence            34568 898775432 24444   399999999984210    1     1246999954

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.58  E-value=0.33  Score=25.48  Aligned_cols=44  Identities=18%  Similarity=0.378  Sum_probs=28.4

Q ss_pred             ccccccccccCCCceee-CCCChhhHHHHHHH--h-h--CCCcccccCcc
Q 033497           72 CTVCMENFLQAFPGKQV-PCGHVFHATCISTW--I-S--LSNSCPVCRSG  115 (118)
Q Consensus        72 C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~--~-~--~~~~CP~Cr~~  115 (118)
                      +-||......+...+.- .|.-.||..|+.--  . .  .+..||.|+..
T Consensus        14 ~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~   63 (79)
T d1wepa_          14 YCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             CSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             EeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCC
Confidence            44998766544334433 49999999998522  1 1  23569999764

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.54  E-value=0.043  Score=28.46  Aligned_cols=43  Identities=23%  Similarity=0.438  Sum_probs=27.3

Q ss_pred             cccccccccccccCCCceeeCCCChhhHHHHHHHhhCCC----cccccCc
Q 033497           69 EGRCTVCMENFLQAFPGKQVPCGHVFHATCISTWISLSN----SCPVCRS  114 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~----~CP~Cr~  114 (118)
                      ...|.+|.+.   ++.+.--.|...||..|+...+....    .||.|+.
T Consensus         7 c~~C~~C~~~---~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~   53 (70)
T d1fp0a1           7 ATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHV   53 (70)
T ss_dssp             SSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCC
T ss_pred             CCCCCCCCCc---CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcC
Confidence            3457777543   22222234999999999987653222    4999965

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.85  E-value=0.072  Score=28.72  Aligned_cols=46  Identities=17%  Similarity=0.391  Sum_probs=28.2

Q ss_pred             cccccccccccccCC-Cceee-CCCChhhHHHHHHHh-----hC---CCcccccCc
Q 033497           69 EGRCTVCMENFLQAF-PGKQV-PCGHVFHATCISTWI-----SL---SNSCPVCRS  114 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~-~~~~~-~C~H~f~~~Ci~~~~-----~~---~~~CP~Cr~  114 (118)
                      ...|.||......+. .++.- .|...||..|+...+     ..   .-.||.|..
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~   71 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTR   71 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCc
Confidence            356999986544322 22322 489999999976322     11   235999853

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.97  E-value=0.26  Score=24.86  Aligned_cols=35  Identities=23%  Similarity=0.566  Sum_probs=25.3

Q ss_pred             ccccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           68 TEGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        68 ~~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      +...|.+|...|..-.....- .||++||..|....
T Consensus         7 ~~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~~   42 (64)
T d1joca1           7 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN   42 (64)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             cCCcCcCcCCcccCCccccchhhhCCeecccccCCc
Confidence            345799999998764333333 49999999997654

>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=83.23  E-value=0.21  Score=25.95  Aligned_cols=34  Identities=24%  Similarity=0.511  Sum_probs=24.7

Q ss_pred             cccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           69 EGRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        69 ~~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      +..|.+|...|..-.....- .||+.||..|....
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~~   47 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ   47 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhCCc
Confidence            35699999998764434443 49999999997543

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.10  E-value=0.29  Score=24.95  Aligned_cols=33  Identities=24%  Similarity=0.472  Sum_probs=23.9

Q ss_pred             ccccccccccccCCCceee-CCCChhhHHHHHHH
Q 033497           70 GRCTVCMENFLQAFPGKQV-PCGHVFHATCISTW  102 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~-~C~H~f~~~Ci~~~  102 (118)
                      ..|.+|...|..-.....- .||..||..|....
T Consensus         6 ~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           6 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             cccccCCCcccCcccccccccCCCEecccccCCc
Confidence            4699999988763333333 49999999997544

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=82.79  E-value=0.22  Score=26.18  Aligned_cols=12  Identities=33%  Similarity=0.905  Sum_probs=10.5

Q ss_pred             hhhHHHHHHHhh
Q 033497           93 VFHATCISTWIS  104 (118)
Q Consensus        93 ~f~~~Ci~~~~~  104 (118)
                      .||+.|+.+|+.
T Consensus        39 GFCRNCLskWy~   50 (79)
T d2o35a1          39 GFCRNCLSNWYR   50 (79)
T ss_dssp             SCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            399999999984

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.36  E-value=0.2  Score=25.99  Aligned_cols=42  Identities=26%  Similarity=0.501  Sum_probs=24.1

Q ss_pred             ccccccccccccCCCceee---CC-CChhhHHHHHHHhh---CCCcccccCcc
Q 033497           70 GRCTVCMENFLQAFPGKQV---PC-GHVFHATCISTWIS---LSNSCPVCRSG  115 (118)
Q Consensus        70 ~~C~IC~~~~~~~~~~~~~---~C-~H~f~~~Ci~~~~~---~~~~CP~Cr~~  115 (118)
                      .-| ||......  ..+..   .| ...||..|+. +..   ..-.||.|+..
T Consensus        17 ~~C-iC~~~~~~--~~i~c~~~~C~~~wfH~~Cvg-l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          17 TYC-LCNQVSYG--EMIGCDNEQCPIEWFHFSCVS-LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCS-TTCCCCCS--SEECCSCTTCSCCCEETTTTT-CSSCCSSCCCCTTTSSC
T ss_pred             CEE-EeCCCCCC--CEEEEECCCCCCcCccCccCC-CCcCCCCcEECcCCccc
Confidence            445 99876432  13333   24 4579999984 221   12249999753