Psyllid ID: psy8828

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-
Protein Sequence
MLGGQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Secondary Structure (PSIPRED)
cccccccccccHHHHHHcccccccccccccccEEEccccccHHHHHHHHHHcccccccccccccccccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccHHccccccHHHHHHcccccEEEHHHcccccEcccccEccHHHHHHHHHHHccccccEEEEEccccccccccccEEEcc
Coil and Loop (DISEMBL)
mlggqlgvsptketllgvgcicpichdefktpvqltcchifcescvtkwfdreqtcplcratlvddpawrdgatsYFVQIF
Flexible Loop (DISEMBL)
mlggqlgvsptketLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRAtlvddpawrdGATSYFVQIF
Low Complexity Region (SEG)
MLGGQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Disordered region (IsUnstruct)
************ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI*
Disordered Region (DISOPRED)
******G****KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV******DGATSYFVQIF
Disordered Region (DISEMBL)
MLGGQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Disordered Region (DISPRO)
*****LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLGGQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	81	2.2.26 [Sep-21-2011]
Q5M7Z0	435	RING finger and transmemb	yes	N/A	0.925	0.172	0.513	4e-16
Q96EX2	444	RING finger and transmemb	no	N/A	0.925	0.168	0.486	5e-16
Q5RAG4	444	RING finger and transmemb	yes	N/A	0.925	0.168	0.473	5e-15
Q6NZ21	419	RING finger and transmemb	yes	N/A	0.925	0.178	0.460	6e-15
Q3UF64	445	RING finger and transmemb	yes	N/A	0.925	0.168	0.473	7e-15
Q28GL3	416	RING finger and transmemb	no	N/A	0.925	0.180	0.447	9e-15
Q9DCN7	395	RING finger and transmemb	no	N/A	0.925	0.189	0.486	2e-14
Q6NTV1	416	RING finger and transmemb	N/A	N/A	0.938	0.182	0.443	6e-14
Q9DBY1	612	E3 ubiquitin-protein liga	no	N/A	0.617	0.081	0.490	1e-07
Q803I8	625	E3 ubiquitin-protein liga	no	N/A	0.617	0.08	0.470	2e-07

>sp|Q5M7Z0|RNFT1_HUMAN RING finger and transmembrane domain-containing protein 1 OS=Homo sapiens GN=RNFT1 PE=2 SV=2

 Score = 83.2 bits (204), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 39/76 (51%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           GV+ +K     V  IC IC  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct: 360 GVAASKRQCSDVDDICSICQAEFQKPILLICQHIFCEECMTLWFNREKTCPLCRTVISDH 419

Query: 67  -PAWRDGATSYFVQIF 81
              W+DGATS  +QI+
Sbjct: 420 INKWKDGATSSHLQIY 435

Homo sapiens (taxid: 9606)

>sp|Q96EX2|RNFT2_HUMAN RING finger and transmembrane domain-containing protein 2 OS=Homo sapiens GN=RNFT2 PE=2 SV=2

 Score = 83.2 bits (204), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 37/76 (48%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           GV  T +     G IC IC  EF+ P+ L C H+FCE C+  W DRE+TCPLCR+  VD 
Sbjct: 369 GVRATGQQCTEAGDICAICQAEFREPLILLCQHVFCEECLCLWLDRERTCPLCRSVAVDT 428

Query: 67  -PAWRDGATSYFVQIF 81
              W+DGATS   Q++
Sbjct: 429 LRCWKDGATSAHFQVY 444

Homo sapiens (taxid: 9606)

>sp|Q5RAG4|RNFT2_PONAB RING finger and transmembrane domain-containing protein 2 OS=Pongo abelii GN=RNFT2 PE=2 SV=1

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 36/76 (47%), Positives = 46/76 (60%), Gaps = 1/76 (1%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           GV  T +     G IC IC  EF+ P+ L C H+FCE C+  W DRE+TCPL R+  VD 
Sbjct: 369 GVRATGQQCTEAGDICAICQAEFREPLILLCQHVFCEECLCLWLDRERTCPLSRSVAVDT 428

Query: 67  -PAWRDGATSYFVQIF 81
              W+DGATS   Q++
Sbjct: 429 LRCWKDGATSAHFQVY 444

Pongo abelii (taxid: 9601)

>sp|Q6NZ21|RNFT1_DANRE RING finger and transmembrane domain-containing protein 1 OS=Danio rerio GN=rnft1 PE=2 SV=2

 Score = 79.3 bits (194), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 35/76 (46%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           G   +   +   G ICPIC  +FK P  L C HIFCE C+ +W ++E+TCPLCR  + D 
Sbjct: 344 GAPASPAQIREAGDICPICQADFKQPRVLVCQHIFCEECIAQWLNQERTCPLCRTVITDK 403

Query: 67  -PAWRDGATSYFVQIF 81
              W+DGATS  +QI+
Sbjct: 404 VHKWKDGATSAHLQIY 419

Danio rerio (taxid: 7955)

>sp|Q3UF64|RNFT2_MOUSE RING finger and transmembrane domain-containing protein 2 OS=Mus musculus GN=Rnft2 PE=2 SV=2

 Score = 79.3 bits (194), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 48/76 (63%), Gaps = 1/76 (1%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           GV  T +     G +C IC  EF+ P+ L C H+FCE C+  W DRE+TCPLCR+  VD 
Sbjct: 370 GVRATGQQCTEAGAVCAICQAEFRDPMILLCQHVFCEECLCLWLDRERTCPLCRSVAVDT 429

Query: 67  PA-WRDGATSYFVQIF 81
              W+DGATS  +Q++
Sbjct: 430 LRCWKDGATSAHLQVY 445

Mus musculus (taxid: 10090)

>sp|Q28GL3|RNFT1_XENTR RING finger and transmembrane domain-containing protein 1 OS=Xenopus tropicalis GN=rnft1 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 34/76 (44%), Positives = 48/76 (63%), Gaps = 1/76 (1%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           G + TK     V  +C IC  EF  P+ L C H+FCE C++ WF++E+TCPLCR  + + 
Sbjct: 341 GAAATKSQCSEVDGMCAICQAEFIKPIVLVCQHVFCEECISLWFNKEKTCPLCRTVISNQ 400

Query: 67  P-AWRDGATSYFVQIF 81
              W+DGATS  ++IF
Sbjct: 401 SHKWKDGATSLQLRIF 416

Xenopus tropicalis (taxid: 8364)

>sp|Q9DCN7|RNFT1_MOUSE RING finger and transmembrane domain-containing protein 1 OS=Mus musculus GN=Rnft1 PE=2 SV=1

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/76 (48%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD- 65
           GV  +K     +  IC IC  EF+ PV L C HIFCE C+T WF+RE+TCPLCR  + + 
Sbjct: 320 GVPASKRQCSDMDGICTICQAEFQKPVLLFCQHIFCEECITLWFNREKTCPLCRTVISEC 379

Query: 66  DPAWRDGATSYFVQIF 81
              W+DGATS  +Q++
Sbjct: 380 INKWKDGATSSHLQMY 395

Mus musculus (taxid: 10090)

>sp|Q6NTV1|RNFT1_XENLA RING finger and transmembrane domain-containing protein 1 OS=Xenopus laevis GN=rnft1 PE=2 SV=2

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 50/79 (63%), Gaps = 3/79 (3%)

Query: 5   QLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 64
             G + TK        +C IC  EF  P+ L C H+FCE C++ WF++E+TCPLCR TL+
Sbjct: 339 NYGTTATKRQCSEADGMCAICQAEFTKPIALICQHVFCEECISSWFNKEKTCPLCR-TLI 397

Query: 65  DDPA--WRDGATSYFVQIF 81
            + +  W+DGATS  ++IF
Sbjct: 398 SNHSHKWKDGATSLQLRIF 416

Xenopus laevis (taxid: 8355)

>sp|Q9DBY1|SYVN1_MOUSE E3 ubiquitin-protein ligase synoviolin OS=Mus musculus GN=Syvn1 PE=1 SV=3

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 25/51 (49%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 11  TKETLLGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCR 60
           T E L  V  +C IC +E  T  + L C HIF  SC+  WF R+QTCP CR
Sbjct: 280 TPEELQAVDNVCIICREEMVTGAKRLPCNHIFHTSCLRSWFQRQQTCPTCR 330

Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation. Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis. Required for embryogenesis.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q803I8|SYVN1_DANRE E3 ubiquitin-protein ligase synoviolin OS=Danio rerio GN=syvn1 PE=2 SV=2

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/51 (47%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 11  TKETLLGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCR 60
           T E L     +C IC +E  T  + L C HIF  SC+  WF R+QTCP CR
Sbjct: 280 TPEDLQATDNVCIICREEMVTGAKKLPCNHIFHSSCLRSWFQRQQTCPTCR 330

Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation. Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) 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. Sequesters p53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis.

Danio rerio (taxid: 7955)

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	81
328711386	484	PREDICTED: RING finger and transmembrane	0.938	0.157	0.710	2e-29
91079492	412	PREDICTED: similar to CG13605 CG13605-PA	0.938	0.184	0.657	1e-28
242009781	492	conserved hypothetical protein [Pediculu	0.938	0.154	0.657	2e-27
328704294	474	PREDICTED: RING finger and transmembrane	0.938	0.160	0.657	3e-27
157124022	692	hypothetical protein AaeL_AAEL009719 [Ae	0.925	0.108	0.64	2e-26
307183322	459	Ring finger and transmembrane domain-con	0.938	0.165	0.605	8e-26
347972340	684	AGAP004640-PA [Anopheles gambiae str. PE	0.925	0.109	0.64	1e-25
322790174	462	hypothetical protein SINV_00016 [Solenop	0.938	0.164	0.605	2e-25
198452503	674	GA12398 [Drosophila pseudoobscura pseudo	0.888	0.106	0.611	2e-25
195144928	667	GL24146 [Drosophila persimilis] gi|19410	0.888	0.107	0.611	2e-25

>gi|328711386|ref|XP_001945914.2| PREDICTED: RING finger and transmembrane domain-containing protein 2-like [Acyrthosiphon pisum]

 Score =  132 bits (332), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/76 (71%), Positives = 62/76 (81%)

Query: 6   LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD 65
           LG +P+KE L   G  CPICHDE+ TPV L C HIFCE+CV KWFDREQTCPLCRA LVD
Sbjct: 409 LGTAPSKEQLTIAGNNCPICHDEYATPVLLQCQHIFCEACVAKWFDREQTCPLCRAKLVD 468

Query: 66  DPAWRDGATSYFVQIF 81
           DPAWRDG+T+ F+Q+F
Sbjct: 469 DPAWRDGSTTNFIQLF 484

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91079492|ref|XP_968664.1| PREDICTED: similar to CG13605 CG13605-PA [Tribolium castaneum] gi|270003440|gb|EEZ99887.1| hypothetical protein TcasGA2_TC002671 [Tribolium castaneum]

 Score =  130 bits (326), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 50/76 (65%), Positives = 62/76 (81%)

Query: 6   LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD 65
           +G SP+KE +   G  CPICHD + +PV L C HIFCE+CVT WFDREQTCPLCRA +VD
Sbjct: 337 VGSSPSKEQIQTAGDHCPICHDNYDSPVLLQCRHIFCENCVTTWFDREQTCPLCRAKIVD 396

Query: 66  DPAWRDGATSYFVQIF 81
           DP+WRDG+TSYF+Q++
Sbjct: 397 DPSWRDGSTSYFIQLY 412

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242009781|ref|XP_002425661.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212509554|gb|EEB12923.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  126 bits (316), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 50/76 (65%), Positives = 60/76 (78%)

Query: 6   LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD 65
           LGV P+KE L   G  CPICHDE+  P+ L C H+FCE+CVT WFDREQTCPLCR  +VD
Sbjct: 417 LGVRPSKEQLDTAGSQCPICHDEYCFPILLQCRHVFCEACVTTWFDREQTCPLCRTKIVD 476

Query: 66  DPAWRDGATSYFVQIF 81
           DP+WRDGATS++ Q+F
Sbjct: 477 DPSWRDGATSFYSQLF 492

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328704294|ref|XP_003242447.1| PREDICTED: RING finger and transmembrane domain-containing protein 2-like [Acyrthosiphon pisum]

 Score =  125 bits (314), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 50/76 (65%), Positives = 62/76 (81%)

Query: 6   LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD 65
           LG +P+KE L   G  CPICHDE+ TPV L C HIFCE+CV KWFDREQTCP+CRA LVD
Sbjct: 399 LGTAPSKEQLTIAGNNCPICHDEYATPVLLQCEHIFCEACVAKWFDREQTCPICRANLVD 458

Query: 66  DPAWRDGATSYFVQIF 81
           +PAW+DG+T+ ++Q+F
Sbjct: 459 NPAWQDGSTTNYIQLF 474

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157124022|ref|XP_001654024.1| hypothetical protein AaeL_AAEL009719 [Aedes aegypti] gi|157124024|ref|XP_001654025.1| hypothetical protein AaeL_AAEL009719 [Aedes aegypti] gi|108874153|gb|EAT38378.1| AAEL009719-PB [Aedes aegypti] gi|108874154|gb|EAT38379.1| AAEL009719-PA [Aedes aegypti]

 Score =  122 bits (306), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 48/75 (64%), Positives = 58/75 (77%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           G  P+KE L   G  CPICHD F +PV L C HIFCE CV  WFDREQTCPLCRA +VDD
Sbjct: 618 GTIPSKEQLQACGGQCPICHDNFNSPVLLECNHIFCELCVGTWFDREQTCPLCRAKIVDD 677

Query: 67  PAWRDGATSYFVQIF 81
           P++RDGAT++F+Q++
Sbjct: 678 PSYRDGATTFFLQLY 692

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307183322|gb|EFN70191.1| Ring finger and transmembrane domain-containing protein 2 [Camponotus floridanus]

 Score =  120 bits (302), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 46/76 (60%), Positives = 63/76 (82%)

Query: 6   LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD 65
           LGVSP+KE L+  G IC ICH+E+ TPV+L C HIFCE+CV+ W DRE++CPLCRA++ D
Sbjct: 384 LGVSPSKEQLVASGGICAICHEEYTTPVRLHCKHIFCETCVSTWLDRERSCPLCRASITD 443

Query: 66  DPAWRDGATSYFVQIF 81
           DP +RDG T++F+Q++
Sbjct: 444 DPIYRDGHTTHFIQLY 459

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347972340|ref|XP_557438.4| AGAP004640-PA [Anopheles gambiae str. PEST] gi|347972342|ref|XP_003436880.1| AGAP004640-PB [Anopheles gambiae str. PEST] gi|333469296|gb|EAL40164.4| AGAP004640-PA [Anopheles gambiae str. PEST] gi|333469297|gb|EGK97243.1| AGAP004640-PB [Anopheles gambiae str. PEST]

 Score =  120 bits (300), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 48/75 (64%), Positives = 57/75 (76%)

Query: 7   GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
           G  PTKE L   G  C ICHD F +PV L C HIFCE CV  WFDREQTCPLCRA +VDD
Sbjct: 610 GTVPTKEQLQACGGQCSICHDNFNSPVLLECNHIFCELCVGTWFDREQTCPLCRAKIVDD 669

Query: 67  PAWRDGATSYFVQIF 81
           P++RDGAT++F+Q++
Sbjct: 670 PSYRDGATTFFLQLY 684

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322790174|gb|EFZ15173.1| hypothetical protein SINV_00016 [Solenopsis invicta]

 Score =  119 bits (298), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 46/76 (60%), Positives = 62/76 (81%)

Query: 6   LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD 65
           LGVSP+KE L+  G IC ICH+E+ TPV+L C HIFCE CV+ W DRE++CPLCRA++ D
Sbjct: 387 LGVSPSKEQLIASGGICAICHEEYTTPVRLHCKHIFCEMCVSTWLDRERSCPLCRASITD 446

Query: 66  DPAWRDGATSYFVQIF 81
           DP +RDG T++F+Q++
Sbjct: 447 DPIYRDGHTTHFIQLY 462

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198452503|ref|XP_001358810.2| GA12398 [Drosophila pseudoobscura pseudoobscura] gi|198131957|gb|EAL27953.2| GA12398 [Drosophila pseudoobscura pseudoobscura]

 Score =  119 bits (298), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/72 (61%), Positives = 55/72 (76%)

Query: 10  PTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 69
           PTKE L   G +CPICHD F TP+ L C HIFC+ CV  WF REQTCP+CRA + DDPAW
Sbjct: 603 PTKEELDAAGSVCPICHDTFNTPIILECGHIFCDECVQTWFKREQTCPMCRAKVSDDPAW 662

Query: 70  RDGATSYFVQIF 81
           +DG+T++F Q++
Sbjct: 663 QDGSTTFFHQLY 674

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195144928|ref|XP_002013448.1| GL24146 [Drosophila persimilis] gi|194102391|gb|EDW24434.1| GL24146 [Drosophila persimilis]

 Score =  119 bits (298), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/72 (61%), Positives = 55/72 (76%)

Query: 10  PTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 69
           PTKE L   G +CPICHD F TP+ L C HIFC+ CV  WF REQTCP+CRA + DDPAW
Sbjct: 596 PTKEELDAAGSVCPICHDTFNTPIILECGHIFCDECVQTWFKREQTCPMCRAKVSDDPAW 655

Query: 70  RDGATSYFVQIF 81
           +DG+T++F Q++
Sbjct: 656 QDGSTTFFHQLY 667

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	81
FB|FBgn0039150	669	CG13605 [Drosophila melanogast	0.888	0.107	0.597	7.8e-23
UNIPROTKB|F1P4I2	317	RNFT1 "Uncharacterized protein	0.925	0.236	0.5	2.5e-17
UNIPROTKB|J9P6W1	397	RNFT1 "Uncharacterized protein	0.925	0.188	0.5	3.8e-17
UNIPROTKB|F1MDV4	433	RNFT1 "Uncharacterized protein	0.925	0.173	0.513	4e-17
UNIPROTKB|Q5M7Z0	435	RNFT1 "RING finger and transme	0.925	0.172	0.513	4.1e-17
RGD|1562411	397	Rnft1 "ring finger protein, tr	0.925	0.188	0.5	6.4e-17
MGI|MGI:2442859	445	Rnft2 "ring finger protein, tr	0.925	0.168	0.473	1.2e-16
RGD|1560195	446	Rnft2 "ring finger protein, tr	0.925	0.168	0.473	1.2e-16
UNIPROTKB|F1MN99	449	RNFT2 "Uncharacterized protein	0.925	0.167	0.486	2.6e-16
ZFIN|ZDB-GENE-050522-168	443	rnft2 "ring finger protein, tr	0.777	0.142	0.546	3.2e-16

FB|FBgn0039150 CG13605 [Drosophila melanogaster (taxid:7227)]

 Score = 273 (101.2 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 43/72 (59%), Positives = 54/72 (75%)

Query:    10 PTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 69
             PTK+ L   G +CPICHD F TP  L C HIFC+ CV  WF REQTCP+CRA + DDPAW
Sbjct:   598 PTKDELDAAGALCPICHDAFNTPTVLECGHIFCDECVQTWFKREQTCPMCRAKVSDDPAW 657

Query:    70 RDGATSYFVQIF 81
             +DG+T++F Q++
Sbjct:   658 QDGSTTFFHQLY 669

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1P4I2 RNFT1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 212 (79.7 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 38/76 (50%), Positives = 49/76 (64%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV+ +K        IC ICH EF+ P+ L C H FCE C++ WF+RE+TCPLCR  + D 
Sbjct:   242 GVTASKRQCSESDDICSICHAEFQKPILLICQHTFCEECISLWFNREKTCPLCRTVISDH 301

Query:    67 P-AWRDGATSYFVQIF 81
                W+DGATS  +QIF
Sbjct:   302 VNKWKDGATSMRLQIF 317

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|J9P6W1 RNFT1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 215 (80.7 bits), Expect = 3.8e-17, P = 3.8e-17
 Identities = 38/76 (50%), Positives = 49/76 (64%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV+ +K     V  IC +C  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct:   322 GVAASKRQCSDVDDICSVCQAEFQKPILLICQHIFCEECITLWFNREKTCPLCRTVISDH 381

Query:    67 -PAWRDGATSYFVQIF 81
                W+DGATS   QI+
Sbjct:   382 INKWKDGATSSHFQIY 397

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1MDV4 RNFT1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 216 (81.1 bits), Expect = 4.0e-17, P = 4.0e-17
 Identities = 39/76 (51%), Positives = 49/76 (64%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV  +K     V  IC IC  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct:   358 GVPASKRQCSDVDDICSICQAEFQKPILLICQHIFCEECITLWFNREKTCPLCRTVISDH 417

Query:    67 -PAWRDGATSYFVQIF 81
                W+DGATS  +QI+
Sbjct:   418 INKWKDGATSSHLQIY 433

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q5M7Z0 RNFT1 "RING finger and transmembrane domain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 39/76 (51%), Positives = 50/76 (65%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV+ +K     V  IC IC  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct:   360 GVAASKRQCSDVDDICSICQAEFQKPILLICQHIFCEECMTLWFNREKTCPLCRTVISDH 419

Query:    67 -PAWRDGATSYFVQIF 81
                W+DGATS  +QI+
Sbjct:   420 INKWKDGATSSHLQIY 435

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

RGD|1562411 Rnft1 "ring finger protein, transmembrane 1" [Rattus norvegicus (taxid:10116)]

 Score = 213 (80.0 bits), Expect = 6.4e-17, P = 6.4e-17
 Identities = 38/76 (50%), Positives = 50/76 (65%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV  +K     +  ICPIC  EF+ PV L C HIFCE C+T WF+RE+TCPLCR  + + 
Sbjct:   322 GVPASKRQCSDMDGICPICQAEFQKPVLLFCQHIFCEECITLWFNREKTCPLCRTVISER 381

Query:    67 -PAWRDGATSYFVQIF 81
                W+DGATS  +Q++
Sbjct:   382 INKWKDGATSSHLQMY 397

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:2442859 Rnft2 "ring finger protein, transmembrane 2" [Mus musculus (taxid:10090)]

 Score = 212 (79.7 bits), Expect = 1.2e-16, P = 1.2e-16
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV  T +     G +C IC  EF+ P+ L C H+FCE C+  W DRE+TCPLCR+  VD 
Sbjct:   370 GVRATGQQCTEAGAVCAICQAEFRDPMILLCQHVFCEECLCLWLDRERTCPLCRSVAVDT 429

Query:    67 -PAWRDGATSYFVQIF 81
                W+DGATS  +Q++
Sbjct:   430 LRCWKDGATSAHLQVY 445

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|1560195 Rnft2 "ring finger protein, transmembrane 2" [Rattus norvegicus (taxid:10116)]

 Score = 212 (79.7 bits), Expect = 1.2e-16, P = 1.2e-16
 Identities = 36/76 (47%), Positives = 48/76 (63%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV  T +     G +C IC  EF+ P+ L C H+FCE C+  W DRE+TCPLCR+  VD 
Sbjct:   371 GVRATGQQCTEAGAVCAICQAEFRDPMILLCQHVFCEECLCLWLDRERTCPLCRSVAVDT 430

Query:    67 -PAWRDGATSYFVQIF 81
                W+DGATS  +Q++
Sbjct:   431 LRCWKDGATSAHLQVY 446

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1MN99 RNFT2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 209 (78.6 bits), Expect = 2.6e-16, P = 2.6e-16
 Identities = 37/76 (48%), Positives = 47/76 (61%)

Query:     7 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
             GV  T +     G IC IC  EF+ P+ L C H+FCE C+  W DRE+TCPLCR+  VD 
Sbjct:   374 GVRATGQQCTEAGDICAICQAEFREPLVLMCQHVFCEECLCLWLDRERTCPLCRSVAVDT 433

Query:    67 -PAWRDGATSYFVQIF 81
                W+DGATS   Q++
Sbjct:   434 LRCWKDGATSAHFQVY 449

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-050522-168 rnft2 "ring finger protein, transmembrane 2" [Danio rerio (taxid:7955)]

 Score = 208 (78.3 bits), Expect = 3.2e-16, P = 3.2e-16
 Identities = 35/64 (54%), Positives = 45/64 (70%)

Query:    19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA-WRDGATSYF 77
             G +C IC  EF+ PV L C H+FCE C+  WFDRE+TCPLCR+T+V+    W+DG TS  
Sbjct:   380 GDVCAICQAEFREPVALLCQHVFCEECLCLWFDRERTCPLCRSTVVETLRNWKDGTTSAH 439

Query:    78 VQIF 81
              QI+
Sbjct:   440 FQIY 443

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5M7Z0	RNFT1_HUMAN	No assigned EC number	0.5131	0.9259	0.1724	yes	N/A

EC Number Prediction by EFICAz Software

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	81
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	3e-10
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	3e-09
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	6e-09
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	2e-08
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-08
COG5574	271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	1e-06
smart00184	40	smart00184, RING, Ring finger	2e-06
COG5152	259	COG5152, COG5152, Uncharacterized conserved protei	4e-06
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	1e-05
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	6e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	9e-05
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-04
COG5222	427	COG5222, COG5222, Uncharacterized conserved protei	2e-04
pfam13445	55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	5e-04
PLN03208	193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	6e-04
TIGR00570	309	TIGR00570, cdk7, CDK-activating kinase assembly fa	0.001
smart00504	63	smart00504, Ubox, Modified RING finger domain	0.002
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	0.002
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	0.002
COG5220	314	COG5220, TFB3, Cdk activating kinase (CAK)/RNA pol	0.004

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

 Score = 54.2 bits (130), Expect = 3e-10
 Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 13/72 (18%)

Query: 8   VSPTKETLLGVGCICPICHDEF-------------KTPVQLTCCHIFCESCVTKWFDREQ 54
            + T+E L      C IC DE               TP +L C HI    C+  W +R+Q
Sbjct: 276 PTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ 335

Query: 55  TCPLCRATLVDD 66
           TCP+CR  ++ D
Sbjct: 336 TCPICRRPVIFD 347

Length = 491

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

 Score = 51.2 bits (122), Expect = 3e-09
 Identities = 18/41 (43%), Positives = 22/41 (53%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRAT 62
          C IC D F  PV  +C H FC  C+ +    +  CPLCRA 
Sbjct: 29 CHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAE 69

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|222279 pfam13639, zf-RING_2, Ring finger domain

 Score = 46.6 bits (111), Expect = 6e-09
 Identities = 22/43 (51%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 22 CPICHDEF---KTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
          CPIC DEF   +  V L C H+F + C+ KW     TCPLCRA
Sbjct: 3  CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

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

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 14/40 (35%), Positives = 19/40 (47%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
          C IC      P + TC H FC  C+ +    +  CP+CR 
Sbjct: 28 CRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCRE 67

Length = 391

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

 Score = 45.1 bits (107), Expect = 2e-08
 Identities = 23/44 (52%), Positives = 29/44 (65%), Gaps = 2/44 (4%)

Query: 22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ-TCPLCRATL 63
          CPIC +EF+ PV L  C H+FC SC+ KW    + TCPLCR  +
Sbjct: 2  CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 44.8 bits (106), Expect = 3e-08
 Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRA 61
           CPIC D  + PV LT C H+FC  C+ ++  ++  CP+CR 
Sbjct: 4  ECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 43.3 bits (102), Expect = 1e-06
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 22  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT--CPLCRA 61
           C +C +E + P    C H+FC SC+   + +++   CPLCRA
Sbjct: 218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRA 259

Length = 271

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

 Score = 39.8 bits (93), Expect = 2e-06
 Identities = 21/40 (52%), Positives = 26/40 (65%), Gaps = 2/40 (5%)

Query: 22 CPICHDEF-KTPVQLTCCHIFCESCVTKWFDRE-QTCPLC 59
          CPIC +E+ K PV L C H FC SC+ KW +    TCP+C
Sbjct: 1  CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 42.4 bits (99), Expect = 4e-06
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 21  ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
           +C IC  ++++PV   C H FC  C  + + +   C +C  
Sbjct: 198 LCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGK 238

Length = 259

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

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 37  CCHIFCESCVTKWFDREQTCPLCRATLV 64
           C H+FC  C+  W   + TCP+CR   +
Sbjct: 200 CNHVFCIECIDIWKKEKNTCPVCRTPFI 227

Length = 238

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

 Score = 38.8 bits (90), Expect = 6e-05
 Identities = 17/51 (33%), Positives = 19/51 (37%), Gaps = 4/51 (7%)

Query: 17  GVGCICPICHDEF---KTPVQLTCCHIFCESCVTKWF-DREQTCPLCRATL 63
             G  C IC   F        L C H F   CV KW       CP+CR  +
Sbjct: 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 38.5 bits (89), Expect = 9e-05
 Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 9/51 (17%)

Query: 22   CPIC------HD-EFKTPVQLTCCHIFCESCVTKWF--DREQTCPLCRATL 63
            C IC       D    +    TC + F   C+ KWF       CPLCR+ +
Sbjct: 1472 CAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522

Length = 1525

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

 Score = 35.5 bits (82), Expect = 1e-04
 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 22 CPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE-QTCPLC 59
          CPIC +E K PV +  C H+FC  C+  W +    TCPLC
Sbjct: 1  CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 22  CPICHDEFKTPVQLTCC-HIFCESCV-TKWFDREQTCPLC 59
           CP+CH   + P++  CC H FC+ C+ T   D +  CP C
Sbjct: 277 CPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNC 316

Length = 427

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

 Score = 34.2 bits (79), Expect = 5e-04
 Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 6/43 (13%)

Query: 21 ICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQT--CP 57
          +CPI  +        PV L C H++    + K         CP
Sbjct: 12 VCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCP 54

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

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

 Score = 35.8 bits (82), Expect = 6e-04
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 16/56 (28%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKW-------------FDREQ---TCPLCRA 61
          C IC D+ + PV   C H+FC  C+ KW             +D ++    CP+C++
Sbjct: 21 CNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKS 76

Length = 193

>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 15/61 (24%)

Query: 22 CPICH-DEFKTP-VQL---TCCHIFCESCVTKWFDR-EQTCPLC---------RATLVDD 66
          CP C   +++ P ++L    C H  CESCV   F R   +CP C         R  L +D
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFED 65

Query: 67 P 67
          P
Sbjct: 66 P 66

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) [DNA metabolism, DNA replication, recombination, and repair]. Length = 309

>gnl|CDD|128780 smart00504, Ubox, Modified RING finger domain

 Score = 33.0 bits (76), Expect = 0.002
 Identities = 13/46 (28%), Positives = 19/46 (41%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
          +CPI  +  K PV L     +  S + KW     T P+    L  +
Sbjct: 3  LCPISLEVMKDPVILPSGQTYERSAIEKWLLSHGTDPVTGQPLTHE 48

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination. Length = 63

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

 Score = 32.7 bits (75), Expect = 0.002
 Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 21 ICPICHDEFKTPVQLTCCH-IFCESCVTKWFDREQTCPLCRA 61
          +C IC +  +  V L C H   CE C  +    ++ CP+CR 
Sbjct: 4  LCVICLERPRNVVFLPCGHLCLCEECAKRLR-SKKKCPICRQ 44

Length = 49

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

 Score = 33.2 bits (76), Expect = 0.002
 Identities = 13/41 (31%), Positives = 17/41 (41%)

Query: 20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 60
          C       +    V   C H F   C+++W     TCPLCR
Sbjct: 33 CPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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|227545 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]

 Score = 33.4 bits (76), Expect = 0.004
 Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 7/43 (16%)

Query: 22 CPICH-DEFKTP-----VQLTCCHIFCESCVTKWFDREQT-CP 57
          CP+C  D +  P     +   C H  CESCV + F R    CP
Sbjct: 13 CPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCP 55

Length = 314

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	81
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.66
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.65
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.62
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.6
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.57
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.54
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.52
KOG0287|consensus	442		99.52
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	99.51
PHA02929	238	N1R/p28-like protein; Provisional	99.49
KOG0823|consensus	230		99.48
KOG0317|consensus	293		99.45
KOG0320|consensus	187		99.43
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	99.43
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.43
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.36
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	99.34
PF14634	44	zf-RING_5: zinc-RING finger domain	99.32
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.31
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.3
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.27
KOG0802|consensus	543		99.26
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.26
PHA02926	242	zinc finger-like protein; Provisional	99.23
KOG4628|consensus	348		99.19
KOG2177|consensus	386		99.16
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	99.11
KOG2164|consensus	513		99.04
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.96
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.92
KOG2660|consensus	331		98.92
KOG0311|consensus	381		98.91
KOG4159|consensus	398		98.9
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	98.89
KOG0978|consensus	698		98.84
COG5152	259	Uncharacterized conserved protein, contains RING a	98.71
KOG1734|consensus	328		98.63
KOG0824|consensus	324		98.63
KOG0297|consensus	391		98.57
KOG4265|consensus	349		98.54
KOG1813|consensus	313		98.48
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.42
KOG2879|consensus	298		98.38
KOG4172|consensus	62		98.37
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.35
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.33
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.32
KOG0828|consensus	636		98.31
KOG1039|consensus	344		98.23
KOG0804|consensus	493		98.21
KOG3039|consensus	303		98.19
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.13
COG5222	427	Uncharacterized conserved protein, contains RING Z	98.1
KOG0827|consensus	465		98.06
KOG1785|consensus	563		98.05
KOG1002|consensus	791		98.02
KOG4692|consensus	489		98.0
KOG2930|consensus	114		97.97
KOG1493|consensus	84		97.88
KOG1645|consensus	463		97.86
KOG0825|consensus	1134		97.8
KOG4367|consensus	699		97.74
KOG4185|consensus	296		97.73
PF04641	260	Rtf2: Rtf2 RING-finger	97.73
KOG4275|consensus	350		97.73
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.71
KOG0826|consensus	357		97.66
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.65
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.39
KOG1571|consensus	355		97.34
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	97.13
KOG1001|consensus	674		97.1
KOG2817|consensus	394		97.08
KOG1814|consensus	445		97.08
KOG3800|consensus	300		97.06
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	97.0
KOG1941|consensus	518		96.98
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.96
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	96.92
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.86
KOG3002|consensus	299		96.85
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.8
KOG4739|consensus	233		96.7
KOG1952|consensus	950		96.59
KOG1940|consensus	276		96.51
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	96.49
KOG2114|consensus	933		96.48
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.4
PHA03096	284	p28-like protein; Provisional	96.28
KOG4362|consensus	684		96.27
KOG3268|consensus	234		96.26
KOG3970|consensus	299		96.18
KOG1428|consensus	3738		96.12
KOG4445|consensus	368		96.03
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.02
KOG3113|consensus	293		95.98
PHA02862	156	5L protein; Provisional	95.84
KOG2932|consensus	389		95.56
KOG3161|consensus	861		95.36
KOG3039|consensus	303		95.11
KOG0298|consensus	1394		95.02
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	94.99
COG5109	396	Uncharacterized conserved protein, contains RING Z	94.39
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.17
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	93.97
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	93.58
KOG3579|consensus	352		93.42
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	93.31
KOG2034|consensus	911		93.16
KOG1815|consensus	444		93.07
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	92.88
KOG1812|consensus	384		92.56
KOG3899|consensus	381		91.64
KOG1100|consensus	207		91.56
KOG4718|consensus	235		91.28
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	91.14
KOG3053|consensus	293		90.79
KOG0309|consensus	1081		90.46
KOG1812|consensus	384		90.4
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	90.07
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	89.67
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	89.64
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	88.8
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	88.14
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	87.5
PLN02638	1079	cellulose synthase A (UDP-forming), catalytic subu	86.46
PF10497	105	zf-4CXXC_R1: Zinc-finger domain of monoamine-oxida	86.19
KOG2169|consensus	636		85.1
KOG2068|consensus	327		84.43
KOG2042|consensus	943		84.1
KOG1609|consensus	323		84.08
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	83.35
KOG0825|consensus	1134		82.14
PF14353	128	CpXC: CpXC protein	81.56
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	81.49
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	81.33
PLN02189	1040	cellulose synthase	80.92
KOG2979|consensus	262		80.84
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	80.39
cd00065	57	FYVE FYVE domain; Zinc-binding domain; targets pro	80.38

>smart00504 Ubox Modified RING finger domain

Probab=99.66  E-value=1.3e-16  Score=78.80  Aligned_cols=63  Identities=22%  Similarity=0.380  Sum_probs=56.2

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      .+.|+||.+.+.+|+.++|||+||+.||.+|+..+..||.|+.++......++..+.+.++.|
T Consensus         1 ~~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~~   63 (63)
T smart00504        1 EFLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQEW   63 (63)
T ss_pred             CcCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHhC
Confidence            368999999999999999999999999999999888999999999777788888777777654

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

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

Probab=99.65  E-value=1.1e-16  Score=73.36  Aligned_cols=38  Identities=50%  Similarity=1.233  Sum_probs=30.4

Q ss_pred             ccccccCCCCCeecCCCCcccHHHHHHHHhCC----CCCCCC
Q psy8828          22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDRE----QTCPLC   59 (81)
Q Consensus        22 C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~----~~CP~C   59 (81)
                      |+||++++.+|++++|||+||..||.+|.+..    ..||.|
T Consensus         1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999999999999999999999998843    468876

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.62  E-value=3.3e-16  Score=100.04  Aligned_cols=71  Identities=31%  Similarity=0.638  Sum_probs=61.5

Q ss_pred             CccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          11 TKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        11 ~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      .....++..+.|+||.+.+.+|++++|||+||..|+..|+.....||.|+..+....+..+..+.++++.|
T Consensus        18 ~~l~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~   88 (397)
T TIGR00599        18 PSLYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESF   88 (397)
T ss_pred             ccccccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHHHH
Confidence            33456678899999999999999999999999999999999888999999998877777788788877654

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

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.60  E-value=2.4e-15  Score=87.91  Aligned_cols=52  Identities=33%  Similarity=0.864  Sum_probs=44.4

Q ss_pred             CCCCccccccccCCCCCeecCCCCcccHHHHHHHHhC----------------CCCCCCCCCCCCCCc
Q psy8828          16 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR----------------EQTCPLCRATLVDDP   67 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~----------------~~~CP~C~~~~~~~~   67 (81)
                      ..+.+.|+||++.+.+|+.++|||.||..||.+|+..                ...||+|+..+....
T Consensus        15 ~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         15 SGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            3457899999999999999999999999999999742                258999999986543

>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=99.57  E-value=2.2e-15  Score=68.04  Aligned_cols=38  Identities=45%  Similarity=1.314  Sum_probs=33.5

Q ss_pred             ccccccCCCCC-eecCCCCcccHHHHHHHHhCCCCCCCC
Q psy8828          22 CPICHDEFKTP-VQLTCCHIFCESCVTKWFDREQTCPLC   59 (81)
Q Consensus        22 C~iC~~~~~~p-~~l~C~h~fc~~Cl~~~~~~~~~CP~C   59 (81)
                      |+||++.+.+| +.++|||+||.+|+.+|++.+..||.|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            79999999999 577999999999999999998899987

>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=99.54  E-value=1.8e-15  Score=69.97  Aligned_cols=40  Identities=48%  Similarity=1.299  Sum_probs=34.7

Q ss_pred             cccccccCCCC---CeecCCCCcccHHHHHHHHhCCCCCCCCC
Q psy8828          21 ICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCR   60 (81)
Q Consensus        21 ~C~iC~~~~~~---p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~   60 (81)
                      .|+||++.+..   .+.++|||.||.+||.+|++.+.+||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            69999999853   45679999999999999999999999996

...

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=99.52  E-value=1.1e-14  Score=69.02  Aligned_cols=46  Identities=37%  Similarity=1.003  Sum_probs=41.0

Q ss_pred             CccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      +..|.||++...+.+.+||||. ||..|+.+|+.....||+||+++.
T Consensus         2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4689999999999989999999 999999999999999999999874

...

>KOG0287|consensus

Probab=99.52  E-value=1.3e-15  Score=95.01  Aligned_cols=67  Identities=25%  Similarity=0.603  Sum_probs=60.2

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      .+...++|.||.++|..|+++||+|+||.-||..++.....||.|+.++.+..+..+..++.+++-|
T Consensus        19 ~lD~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~   85 (442)
T KOG0287|consen   19 TLDDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSL   85 (442)
T ss_pred             hhHHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHH
Confidence            3456789999999999999999999999999999999999999999999988888888888877654

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

Probab=99.51  E-value=6.3e-15  Score=74.88  Aligned_cols=65  Identities=22%  Similarity=0.446  Sum_probs=52.9

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      .+.+.|+|+.+++.+|+++++||+|.+.+|.+|+.. ...||.++.++....+.+|..+...++.|
T Consensus         2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~Lk~~I~~~   67 (73)
T PF04564_consen    2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRALKSAIEEW   67 (73)
T ss_dssp             SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHHHHHHHHH
T ss_pred             CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHHHHHHHHH
Confidence            357899999999999999999999999999999998 78999999999888888888888777654

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 ....

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.49  E-value=3.9e-14  Score=85.55  Aligned_cols=49  Identities=29%  Similarity=0.866  Sum_probs=41.6

Q ss_pred             CCCccccccccCCCCC--------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTP--------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p--------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ....+|+||++.+.++        +.++|+|.||..||.+|+..+.+||+||..+..
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~  228 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFIS  228 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence            3467999999987653        345899999999999999999999999998753

>KOG0823|consensus

Probab=99.48  E-value=3e-14  Score=84.81  Aligned_cols=52  Identities=37%  Similarity=0.839  Sum_probs=45.5

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhC---CCCCCCCCCCCCCCcc
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR---EQTCPLCRATLVDDPA   68 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~---~~~CP~C~~~~~~~~~   68 (81)
                      ...+.|.||++.-++|+.+.|||.||-.||.+|+..   ++.||+|+..+....+
T Consensus        45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v   99 (230)
T KOG0823|consen   45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV   99 (230)
T ss_pred             CCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence            456899999999999999999999999999999983   4689999998866543

>KOG0317|consensus

Probab=99.45  E-value=7.6e-14  Score=85.31  Aligned_cols=54  Identities=30%  Similarity=0.800  Sum_probs=48.4

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcc
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   68 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~   68 (81)
                      ..+....|.+|++...+|.-+||||.||-.||..|......||+||..+.+.++
T Consensus       235 i~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  235 IPEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            345568999999999999999999999999999999999999999999877654

>KOG0320|consensus

Probab=99.43  E-value=1e-13  Score=79.73  Aligned_cols=50  Identities=30%  Similarity=0.815  Sum_probs=43.3

Q ss_pred             CCccccccccCCCCC--eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCc
Q psy8828          18 VGCICPICHDEFKTP--VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   67 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p--~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~   67 (81)
                      ..+.||||++.+.+.  +.+.|||.||..||++.++....||+|++.+....
T Consensus       130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~  181 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ  181 (187)
T ss_pred             cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence            457999999998874  45799999999999999999999999999776543

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

Probab=99.43  E-value=5.8e-15  Score=72.16  Aligned_cols=61  Identities=31%  Similarity=0.639  Sum_probs=34.1

Q ss_pred             CCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhh
Q psy8828          16 LGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFV   78 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~   78 (81)
                      +++.+.|++|.+.+.+|+.+ .|.|.||..|+.+.+.  ..||+|+.+....+...|+.+++++
T Consensus         4 le~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~NrqLd~~i   65 (65)
T PF14835_consen    4 LEELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQINRQLDSMI   65 (65)
T ss_dssp             HHHTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS----HHHHHHH
T ss_pred             HHHhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHhhhhhhccC
Confidence            34568999999999999865 8999999999977544  4599999999888888888887764

>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=99.43  E-value=1.3e-13  Score=62.66  Aligned_cols=38  Identities=50%  Similarity=1.378  Sum_probs=34.7

Q ss_pred             ccccccCCCCCe-ecCCCCcccHHHHHHHHh--CCCCCCCC
Q psy8828          22 CPICHDEFKTPV-QLTCCHIFCESCVTKWFD--REQTCPLC   59 (81)
Q Consensus        22 C~iC~~~~~~p~-~l~C~h~fc~~Cl~~~~~--~~~~CP~C   59 (81)
                      |+||++.+.++. .++|||.||..|+.+|++  ....||.|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            799999999999 789999999999999998  55789987

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

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

Probab=99.36  E-value=9.6e-13  Score=60.26  Aligned_cols=43  Identities=53%  Similarity=1.398  Sum_probs=37.0

Q ss_pred             cccccccCCCCCeec-CCCCcccHHHHHHHHhC-CCCCCCCCCCC
Q psy8828          21 ICPICHDEFKTPVQL-TCCHIFCESCVTKWFDR-EQTCPLCRATL   63 (81)
Q Consensus        21 ~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~   63 (81)
                      .|+||++.+.+++.+ +|||.||..|+.+|+.. ...||.|+..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            489999999777766 49999999999999987 77899998753

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

Probab=99.34  E-value=3.4e-13  Score=82.98  Aligned_cols=64  Identities=23%  Similarity=0.590  Sum_probs=52.6

Q ss_pred             CCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhh
Q psy8828          16 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ   79 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~   79 (81)
                      +...+.|.||.+.+..|..++|||+||.-||.+++.....||+|+.+........+.....+++
T Consensus        22 LDs~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr~~s~~~ei~e   85 (391)
T COG5432          22 LDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLRGSSGSREINE   85 (391)
T ss_pred             chhHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHhhhcccchhHHHHHH
Confidence            3456799999999999999999999999999999999999999999876655544444444443

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.32  E-value=1.9e-12  Score=59.75  Aligned_cols=41  Identities=39%  Similarity=1.081  Sum_probs=34.9

Q ss_pred             cccccccCC---CCCeecCCCCcccHHHHHHHHhCCCCCCCCCC
Q psy8828          21 ICPICHDEF---KTPVQLTCCHIFCESCVTKWFDREQTCPLCRA   61 (81)
Q Consensus        21 ~C~iC~~~~---~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~   61 (81)
                      .|++|.+.+   ..+..++|||+||..|+..+......||+|++
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            489999998   24667799999999999998866789999974

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

Probab=99.31  E-value=1.5e-12  Score=59.71  Aligned_cols=30  Identities=47%  Similarity=1.268  Sum_probs=21.2

Q ss_pred             ccccccCCCC----CeecCCCCcccHHHHHHHHhC
Q psy8828          22 CPICHDEFKT----PVQLTCCHIFCESCVTKWFDR   52 (81)
Q Consensus        22 C~iC~~~~~~----p~~l~C~h~fc~~Cl~~~~~~   52 (81)
                      |+||.+ +.+    |+.|+|||+||.+|+.++.+.
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~   34 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKK   34 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhc
Confidence            899999 777    899999999999999999883

>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=99.30  E-value=3e-12  Score=64.98  Aligned_cols=42  Identities=38%  Similarity=1.042  Sum_probs=34.3

Q ss_pred             CccccccccCCCCC------------e-ecCCCCcccHHHHHHHHhCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTP------------V-QLTCCHIFCESCVTKWFDREQTCPLCR   60 (81)
Q Consensus        19 ~~~C~iC~~~~~~p------------~-~l~C~h~fc~~Cl~~~~~~~~~CP~C~   60 (81)
                      +..|+||++.+.++            + ..+|||.||..||.+|++.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            34599999999432            2 238999999999999999999999997

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 ....

>smart00184 RING Ring finger

Probab=99.27  E-value=7.6e-12  Score=55.45  Aligned_cols=38  Identities=55%  Similarity=1.441  Sum_probs=34.1

Q ss_pred             ccccccCCCCCeecCCCCcccHHHHHHHHh-CCCCCCCC
Q psy8828          22 CPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLC   59 (81)
Q Consensus        22 C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C   59 (81)
                      |+||++....++.++|||.||..|+.+|+. ....||.|
T Consensus         1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999988888999999999999999998 55679986

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)

>KOG0802|consensus

Probab=99.26  E-value=2.4e-12  Score=85.59  Aligned_cols=54  Identities=44%  Similarity=0.968  Sum_probs=46.5

Q ss_pred             cCCCCccccccccCCCC-----CeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcc
Q psy8828          15 LLGVGCICPICHDEFKT-----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   68 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~-----p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~   68 (81)
                      .......|+||.+.+..     +.+++|+|.||..|+..|+++..+||.||..+.....
T Consensus       287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~~  345 (543)
T KOG0802|consen  287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDYVL  345 (543)
T ss_pred             hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhcccc
Confidence            34457799999999998     7899999999999999999999999999996554433

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

Probab=99.26  E-value=6.2e-12  Score=79.64  Aligned_cols=51  Identities=39%  Similarity=0.991  Sum_probs=43.3

Q ss_pred             ccCCCCccccccccCC-CC------------CeecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEF-KT------------PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~-~~------------p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      +...++..|.||++.+ ..            |+.+||||.+|..|++.|++++++||.||.++.
T Consensus       282 ql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         282 QLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             hhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            3445677999999984 33            478999999999999999999999999999853

>PHA02926 zinc finger-like protein; Provisional

Probab=99.23  E-value=8.3e-12  Score=74.33  Aligned_cols=49  Identities=29%  Similarity=0.803  Sum_probs=38.8

Q ss_pred             CCCccccccccCCCC---------CeecCCCCcccHHHHHHHHhCC------CCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKT---------PVQLTCCHIFCESCVTKWFDRE------QTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~---------p~~l~C~h~fc~~Cl~~~~~~~------~~CP~C~~~~~~   65 (81)
                      ..+.+|+||++...+         ++..+|+|.||..||..|....      ..||.||..+..
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            456899999998643         2345899999999999999742      469999998753

>KOG4628|consensus

Probab=99.19  E-value=1.4e-11  Score=77.73  Aligned_cols=47  Identities=28%  Similarity=0.862  Sum_probs=40.3

Q ss_pred             ccccccccCCCCC---eecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTP---VQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDD   66 (81)
Q Consensus        20 ~~C~iC~~~~~~p---~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~   66 (81)
                      ..|+||+|.|...   +.|||+|.||..||..|+.+. ..||+|+..+...
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence            5999999999875   356999999999999999977 4599999987553

>KOG2177|consensus

Probab=99.16  E-value=1.2e-11  Score=75.55  Aligned_cols=49  Identities=39%  Similarity=0.971  Sum_probs=43.0

Q ss_pred             cccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCC
Q psy8828          13 ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA   61 (81)
Q Consensus        13 ~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~   61 (81)
                      .....+.+.|+||++.+..|++++|||+||..|+..+......||.|+.
T Consensus         7 ~~~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    7 LEVLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hhhccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            3455678899999999999988899999999999998886678999994

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

Probab=99.11  E-value=4.6e-11  Score=72.56  Aligned_cols=52  Identities=33%  Similarity=0.772  Sum_probs=44.5

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHH-HHhCCC-CCCCCCCCCCCCcc
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTK-WFDREQ-TCPLCRATLVDDPA   68 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~-~~~~~~-~CP~C~~~~~~~~~   68 (81)
                      ..++.|+||++....|..++|||.||..||.. |-.+.. .||+||+......+
T Consensus       213 ~~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            45789999999999999999999999999998 877665 49999998765443

>KOG2164|consensus

Probab=99.04  E-value=1.7e-10  Score=75.35  Aligned_cols=49  Identities=35%  Similarity=0.954  Sum_probs=42.7

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCC-----CCCCCCCCCCCCCc
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-----QTCPLCRATLVDDP   67 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-----~~CP~C~~~~~~~~   67 (81)
                      ...||||++...-|..+.|||.||..||..++..+     ..||+|+..+...+
T Consensus       186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            78999999999999999999999999999988733     58999998876543

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.96  E-value=1.2e-09  Score=68.23  Aligned_cols=49  Identities=33%  Similarity=0.814  Sum_probs=37.9

Q ss_pred             CccccccccC-CCCCe---ec-CCCCcccHHHHHHHHh-CCCCCCCCCCCCCCCc
Q psy8828          19 GCICPICHDE-FKTPV---QL-TCCHIFCESCVTKWFD-REQTCPLCRATLVDDP   67 (81)
Q Consensus        19 ~~~C~iC~~~-~~~p~---~l-~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~~   67 (81)
                      +..||+|... +.+|.   .+ +|||.||..|+..++. ....||.|+..+....
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            4589999995 34443   22 7999999999999765 4568999999887654

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).

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

Probab=98.92  E-value=1.5e-09  Score=56.07  Aligned_cols=47  Identities=32%  Similarity=0.858  Sum_probs=37.2

Q ss_pred             CCccccccccCCCC------------Ceec-CCCCcccHHHHHHHHhC---CCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT------------PVQL-TCCHIFCESCVTKWFDR---EQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~------------p~~l-~C~h~fc~~Cl~~~~~~---~~~CP~C~~~~~   64 (81)
                      .+..|.||+..|..            |+.+ .|+|.||..||.+|+..   +..||.||++..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            46688888887763            3333 79999999999999984   369999998764

>KOG2660|consensus

Probab=98.92  E-value=3.4e-10  Score=70.63  Aligned_cols=54  Identities=26%  Similarity=0.713  Sum_probs=47.0

Q ss_pred             ccCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCc
Q psy8828          14 TLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDP   67 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~   67 (81)
                      ..+.....|.+|..++.++.++ .|.|+||+.||.+++.....||.|...+....
T Consensus        10 ~~~n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~   64 (331)
T KOG2660|consen   10 TELNPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKTH   64 (331)
T ss_pred             hhcccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCcc
Confidence            3455678999999999999876 79999999999999999999999988876543

>KOG0311|consensus

Probab=98.91  E-value=1.1e-10  Score=73.48  Aligned_cols=65  Identities=29%  Similarity=0.669  Sum_probs=51.8

Q ss_pred             ccCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHh-CCCCCCCCCCCCCCC-ccccCcccchhh
Q psy8828          14 TLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-REQTCPLCRATLVDD-PAWRDGATSYFV   78 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~-~~~~~~~~~~~~   78 (81)
                      ..+...+.|+||+++++..+++ .|+|.||.+||...+. .+..||.||+.+.+. .+..+.+++.++
T Consensus        38 ~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLi  105 (381)
T KOG0311|consen   38 AMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDPNFDALI  105 (381)
T ss_pred             HHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCccHHHHH
Confidence            3445678999999999998877 7999999999988777 568999999998764 555666665544

>KOG4159|consensus

Probab=98.90  E-value=8.1e-10  Score=71.14  Aligned_cols=52  Identities=35%  Similarity=0.816  Sum_probs=47.3

Q ss_pred             ccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      .....++.|.||...+..|+.+||||+||..||.+.+.....||.|+..+..
T Consensus        79 ~~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   79 EEIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             ccccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            3446789999999999999999999999999999988888999999999875

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

Probab=98.89  E-value=1.2e-09  Score=67.78  Aligned_cols=47  Identities=36%  Similarity=0.852  Sum_probs=40.0

Q ss_pred             CccccccccCCCCC---eecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTP---VQLTCCHIFCESCVTKWFD-REQTCPLCRATLVD   65 (81)
Q Consensus        19 ~~~C~iC~~~~~~p---~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~   65 (81)
                      ..+|+||++.+...   +.+||.|.||..|+.+|+. -+..||+|+.++++
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            46899999987642   4569999999999999998 56799999998864

>KOG0978|consensus

Probab=98.84  E-value=1.2e-09  Score=74.04  Aligned_cols=55  Identities=29%  Similarity=0.744  Sum_probs=46.8

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCCCccc
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPAW   69 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~~~~   69 (81)
                      ....-+.|++|..-..+.+++.|||.||..|+.+... +...||.|...|...++.
T Consensus       639 ~yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~  694 (698)
T KOG0978|consen  639 EYKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH  694 (698)
T ss_pred             HHHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence            3345689999999999999999999999999998777 668999999999876543

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

Probab=98.71  E-value=7e-09  Score=61.17  Aligned_cols=58  Identities=22%  Similarity=0.690  Sum_probs=47.1

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchh
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYF   77 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~   77 (81)
                      .+.|.||...|..|+.+.|||.||..|..+-.+....|-+|.+...-. .+....++.+
T Consensus       196 PF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~-f~V~~d~~km  253 (259)
T COG5152         196 PFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGR-FWVVSDLQKM  253 (259)
T ss_pred             ceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhccc-eeHHhhHHHH
Confidence            579999999999999999999999999999889999999998875432 3334444433

>KOG1734|consensus

Probab=98.63  E-value=8.1e-09  Score=63.29  Aligned_cols=52  Identities=27%  Similarity=0.740  Sum_probs=41.2

Q ss_pred             cCCCCccccccccCCCCC----------eecCCCCcccHHHHHHHHh--CCCCCCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTP----------VQLTCCHIFCESCVTKWFD--REQTCPLCRATLVDD   66 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p----------~~l~C~h~fc~~Cl~~~~~--~~~~CP~C~~~~~~~   66 (81)
                      .-.++..|+||...+...          .+++|+|+|+..||..|..  +.++||.|++.+...
T Consensus       220 khl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~  283 (328)
T KOG1734|consen  220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK  283 (328)
T ss_pred             CCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence            334667899999876543          3679999999999999976  568999998877543

>KOG0824|consensus

Probab=98.63  E-value=1.7e-08  Score=62.56  Aligned_cols=48  Identities=31%  Similarity=0.739  Sum_probs=42.1

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDD   66 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~   66 (81)
                      .-+|+||+....-|+.++|+|.||.-||+...... ..|++||.++.+.
T Consensus         7 ~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGNCPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCCcCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            34799999999999999999999999999877755 5699999998765

>KOG0297|consensus

Probab=98.57  E-value=5.8e-08  Score=62.76  Aligned_cols=52  Identities=38%  Similarity=0.924  Sum_probs=46.4

Q ss_pred             CCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCc
Q psy8828          16 LGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDP   67 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~   67 (81)
                      .++++.|++|...+.+|+.. .|||.||..|+..|+..+..||.|+..+....
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~   70 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAE   70 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhh
Confidence            56789999999999999984 99999999999999999999999988765543

>KOG4265|consensus

Probab=98.54  E-value=6.8e-08  Score=61.05  Aligned_cols=49  Identities=31%  Similarity=0.777  Sum_probs=44.0

Q ss_pred             CCCccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      +...+|-||+...++-+.+||.|. .|..|.+...-+...||+||+++..
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            457799999999999999999997 8999999887788999999999865

>KOG1813|consensus

Probab=98.48  E-value=4.7e-08  Score=60.50  Aligned_cols=47  Identities=32%  Similarity=0.725  Sum_probs=42.8

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      .+.|-||...|.+|+.+.|+|.||..|...-++.+..|++|.+.+..
T Consensus       241 Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  241 PFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             CccccccccccccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence            46799999999999999999999999999988889999999887643

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

Probab=98.42  E-value=1.5e-07  Score=45.54  Aligned_cols=42  Identities=26%  Similarity=0.715  Sum_probs=29.8

Q ss_pred             CCCccccccccCCCCCeec-CCCCcccHHHHHHHHh--CCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD--REQTCPL   58 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~--~~~~CP~   58 (81)
                      ...+.|||.+..+.+|+.- .|||+|-++.|..+++  ....||+
T Consensus         9 ~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            3467999999999999875 8999999999999994  3468997

>KOG2879|consensus

Probab=98.38  E-value=6.9e-07  Score=55.00  Aligned_cols=51  Identities=27%  Similarity=0.624  Sum_probs=42.2

Q ss_pred             cCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHh--CCCCCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD--REQTCPLCRATLVD   65 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~--~~~~CP~C~~~~~~   65 (81)
                      .-....+|++|.+....|.+. +|+|.||..|+.....  .+..||.|......
T Consensus       235 ~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  235 TGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             cccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            334567999999999999887 5999999999987665  45899999887753

>KOG4172|consensus

Probab=98.37  E-value=9.7e-08  Score=45.34  Aligned_cols=47  Identities=32%  Similarity=0.712  Sum_probs=39.8

Q ss_pred             CccccccccCCCCCeecCCCCc-ccHHHHHHHHh-CCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHI-FCESCVTKWFD-REQTCPLCRATLVD   65 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~-~~~~CP~C~~~~~~   65 (81)
                      ..+|.||.+...+.+...|||. .|.+|-.+.++ .+..||+||+++.+
T Consensus         7 ~dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            3689999999888888899996 89999988777 56799999998753

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

Probab=98.35  E-value=7.7e-08  Score=48.42  Aligned_cols=46  Identities=26%  Similarity=0.663  Sum_probs=22.9

Q ss_pred             CccccccccCCC-C---Ceec----CCCCcccHHHHHHHHhC---C--------CCCCCCCCCCC
Q psy8828          19 GCICPICHDEFK-T---PVQL----TCCHIFCESCVTKWFDR---E--------QTCPLCRATLV   64 (81)
Q Consensus        19 ~~~C~iC~~~~~-~---p~~l----~C~h~fc~~Cl~~~~~~---~--------~~CP~C~~~~~   64 (81)
                      +..|+||..... +   |...    .|+..||..||.+|+..   +        ..||.|++++.
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            468999999865 2   2222    69999999999999872   1        26999988764

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

Probab=98.33  E-value=4.8e-07  Score=46.09  Aligned_cols=46  Identities=35%  Similarity=0.834  Sum_probs=35.8

Q ss_pred             ccccccccCCCCC---------------eec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTP---------------VQL-TCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        20 ~~C~iC~~~~~~p---------------~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ..|+||+..+-++               +.. -|.|.|+..||.+|+.....||+++++...
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            4677777765431               112 599999999999999999999999987643

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

Probab=98.32  E-value=7.8e-07  Score=41.78  Aligned_cols=40  Identities=33%  Similarity=1.007  Sum_probs=30.5

Q ss_pred             ccccccc--CCCCCeecCCC-----CcccHHHHHHHHhC--CCCCCCCC
Q psy8828          21 ICPICHD--EFKTPVQLTCC-----HIFCESCVTKWFDR--EQTCPLCR   60 (81)
Q Consensus        21 ~C~iC~~--~~~~p~~l~C~-----h~fc~~Cl~~~~~~--~~~CP~C~   60 (81)
                      .|.||++  .-.++...||.     +.+|..|+.+|+..  +..||+|+
T Consensus         1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4889987  33456666875     77999999999974  45899984

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

Probab=98.31  E-value=4.1e-07  Score=59.93  Aligned_cols=49  Identities=31%  Similarity=0.724  Sum_probs=39.1

Q ss_pred             CCCccccccccCCCC-----------------CeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKT-----------------PVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~-----------------p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~   65 (81)
                      +....|+||+..+.-                 -+.+||.|.|+..|+.+|+. .+..||+||.+++.
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            445689999997642                 12359999999999999999 55699999998864

>KOG1039|consensus

Probab=98.23  E-value=8.1e-07  Score=56.58  Aligned_cols=47  Identities=30%  Similarity=0.817  Sum_probs=38.2

Q ss_pred             CCccccccccCCCCCe-----e---cCCCCcccHHHHHHHHh--C-----CCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPV-----Q---LTCCHIFCESCVTKWFD--R-----EQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~-----~---l~C~h~fc~~Cl~~~~~--~-----~~~CP~C~~~~~   64 (81)
                      .+..|.||++...+..     .   .+|.|.||..|+..|..  +     ...||.||....
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            4679999999877654     2   47999999999999984  3     478999998753

>KOG0804|consensus

Probab=98.21  E-value=9.1e-07  Score=57.63  Aligned_cols=48  Identities=31%  Similarity=0.816  Sum_probs=38.3

Q ss_pred             cCCCCccccccccCCCCCe----ecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTPV----QLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ...+.-.||||++.+.+.+    .+.|.|+|+..|+..|.  ..+||+||....
T Consensus       171 ~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  171 GLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             CcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            3345559999999998754    34899999999999994  478999987655

>KOG3039|consensus

Probab=98.19  E-value=1.8e-06  Score=52.66  Aligned_cols=53  Identities=21%  Similarity=0.417  Sum_probs=46.0

Q ss_pred             CCccccccccCCCCCee----cCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcccc
Q psy8828          18 VGCICPICHDEFKTPVQ----LTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWR   70 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~   70 (81)
                      ..+.||+|.+.+.+.+.    -+|||+|+.+|+++++.....||+|..++.+.++..
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~  276 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIG  276 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEe
Confidence            56899999999998543    389999999999999999999999999998775543

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

Probab=98.13  E-value=7.6e-07  Score=62.60  Aligned_cols=49  Identities=31%  Similarity=0.746  Sum_probs=37.7

Q ss_pred             CCCCccccccccCCC-CCee------cCCCCcccHHHHHHHHhC--CCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFK-TPVQ------LTCCHIFCESCVTKWFDR--EQTCPLCRATLV   64 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~-~p~~------l~C~h~fc~~Cl~~~~~~--~~~CP~C~~~~~   64 (81)
                      +....+|+||...+. ....      -.|.|.||..|+.+|.+.  +.+||+||..++
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            344568999999876 1122      259999999999999984  479999997764

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

Probab=98.10  E-value=2.1e-06  Score=53.80  Aligned_cols=42  Identities=31%  Similarity=0.912  Sum_probs=37.0

Q ss_pred             ccccccccCCCCCeec-CCCCcccHHHHHHHHh-CCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-REQTCPLCRA   61 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~-~~~~CP~C~~   61 (81)
                      +.|+.|..++.+|+.+ -|+|.||.+||...+. ..+.||.|..
T Consensus       275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            7999999999999998 5799999999997766 5589999954

>KOG0827|consensus

Probab=98.06  E-value=2.7e-06  Score=54.74  Aligned_cols=49  Identities=37%  Similarity=0.905  Sum_probs=36.4

Q ss_pred             ccccccccCCCCCeec----CCCCcccHHHHHHHHhC--C-CCCCCCCCCCCCCcc
Q psy8828          20 CICPICHDEFKTPVQL----TCCHIFCESCVTKWFDR--E-QTCPLCRATLVDDPA   68 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l----~C~h~fc~~Cl~~~~~~--~-~~CP~C~~~~~~~~~   68 (81)
                      ..|.||.+.+....-+    .|||+|+..|+..|+..  + ..||.|+-.+.....
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~   60 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHV   60 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceee
Confidence            4799997765543333    59999999999999983  3 589999855554433

>KOG1785|consensus

Probab=98.05  E-value=1.8e-06  Score=55.83  Aligned_cols=45  Identities=38%  Similarity=0.958  Sum_probs=38.0

Q ss_pred             cccccccCCCCCeecCCCCcccHHHHHHHHhC--CCCCCCCCCCCCC
Q psy8828          21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDR--EQTCPLCRATLVD   65 (81)
Q Consensus        21 ~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~--~~~CP~C~~~~~~   65 (81)
                      .|.||-+.-++-.+-||||..|..|+..|...  ...||+||..+.-
T Consensus       371 LCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG  417 (563)
T KOG1785|consen  371 LCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG  417 (563)
T ss_pred             HHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence            69999998777666699999999999999863  5899999988743

>KOG1002|consensus

Probab=98.02  E-value=3.5e-06  Score=56.29  Aligned_cols=50  Identities=30%  Similarity=0.782  Sum_probs=42.5

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHh-----CCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-----REQTCPLCRATLVDD   66 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-----~~~~CP~C~~~~~~~   66 (81)
                      .....|.+|.+.-++++...|.|.||+.|+.++..     .+.+||.|...+...
T Consensus       534 k~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiD  588 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSID  588 (791)
T ss_pred             cCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCcccccccccc
Confidence            34579999999999999999999999999988876     346999998887543

>KOG4692|consensus

Probab=98.00  E-value=3.7e-06  Score=53.69  Aligned_cols=49  Identities=29%  Similarity=0.674  Sum_probs=44.0

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      .++..||||..-..+.+..||+|.-|..||.+.+.+.+.|-.|+..+..
T Consensus       420 sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            4566899999999999999999999999999999999999999887653

>KOG2930|consensus

Probab=97.97  E-value=5.2e-06  Score=44.30  Aligned_cols=28  Identities=29%  Similarity=0.856  Sum_probs=25.6

Q ss_pred             CCCCcccHHHHHHHHhCCCCCCCCCCCC
Q psy8828          36 TCCHIFCESCVTKWFDREQTCPLCRATL   63 (81)
Q Consensus        36 ~C~h~fc~~Cl~~~~~~~~~CP~C~~~~   63 (81)
                      .|.|.|+.-||.+|++.+..||++.++-
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            5999999999999999999999997653

>KOG1493|consensus

Probab=97.88  E-value=3.6e-06  Score=42.62  Aligned_cols=45  Identities=36%  Similarity=0.925  Sum_probs=34.2

Q ss_pred             ccccccccCCCC------------Ceec-CCCCcccHHHHHHHHhC---CCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKT------------PVQL-TCCHIFCESCVTKWFDR---EQTCPLCRATLV   64 (81)
Q Consensus        20 ~~C~iC~~~~~~------------p~~l-~C~h~fc~~Cl~~~~~~---~~~CP~C~~~~~   64 (81)
                      ..|.||+-.|..            |..+ .|.|.|+..||.+|+..   ...||.||+...
T Consensus        21 e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   21 ETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            378888777653            3333 59999999999999873   368999998753

>KOG1645|consensus

Probab=97.86  E-value=4.8e-06  Score=53.88  Aligned_cols=48  Identities=40%  Similarity=1.063  Sum_probs=38.1

Q ss_pred             CccccccccCCCCC-----eecCCCCcccHHHHHHHHhCC--CCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTP-----VQLTCCHIFCESCVTKWFDRE--QTCPLCRATLVDD   66 (81)
Q Consensus        19 ~~~C~iC~~~~~~p-----~~l~C~h~fc~~Cl~~~~~~~--~~CP~C~~~~~~~   66 (81)
                      ...||||++.+.-+     +.+.|||.|-..||++|+.+.  ..||.|......+
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr   58 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKR   58 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHH
Confidence            46899999998765     345899999999999999743  5899997655443

>KOG0825|consensus

Probab=97.80  E-value=2.9e-06  Score=58.74  Aligned_cols=47  Identities=32%  Similarity=0.714  Sum_probs=36.1

Q ss_pred             ccccccccCCCCCe---ecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPV---QLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        20 ~~C~iC~~~~~~p~---~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ..|++|+..+.+..   ...|+|.||..|+..|.+...+||+||..+...
T Consensus       124 ~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  124 NQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            35666666554432   237999999999999999999999999987553

>KOG4367|consensus

Probab=97.74  E-value=1.8e-05  Score=51.95  Aligned_cols=36  Identities=25%  Similarity=0.782  Sum_probs=32.2

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR   52 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~   52 (81)
                      ++++.|+||...|.+|++++|+|..|+.|....+.+
T Consensus         2 eeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREPIILPCSHNLCQACARNILVQ   37 (699)
T ss_pred             cccccCceehhhccCceEeecccHHHHHHHHhhccc
Confidence            567899999999999999999999999999876653

>KOG4185|consensus

Probab=97.73  E-value=2.7e-05  Score=48.62  Aligned_cols=45  Identities=33%  Similarity=0.892  Sum_probs=37.4

Q ss_pred             CccccccccCCCC------CeecCCCCcccHHHHHHHHhCC-CCCCCCCCCC
Q psy8828          19 GCICPICHDEFKT------PVQLTCCHIFCESCVTKWFDRE-QTCPLCRATL   63 (81)
Q Consensus        19 ~~~C~iC~~~~~~------p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~   63 (81)
                      ...|-||.+.|..      |..+.|||++|..|+.+.+... ..||.||.+.
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            3578999988864      6777899999999999888754 5789999985

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.73  E-value=6.8e-05  Score=46.31  Aligned_cols=53  Identities=21%  Similarity=0.518  Sum_probs=41.7

Q ss_pred             CCCCccccccccCCCCCe----ecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccc
Q psy8828          16 LGVGCICPICHDEFKTPV----QLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   69 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~   69 (81)
                      ....+.|||....+....    ..+|||+|...++.+.- ....||+|..++...++.
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI  166 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDII  166 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEE
Confidence            456789999999985432    23999999999999884 467899999998766544

>KOG4275|consensus

Probab=97.73  E-value=3e-06  Score=52.79  Aligned_cols=42  Identities=36%  Similarity=0.880  Sum_probs=35.9

Q ss_pred             CccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ...|.||++...+-+.|+|||. -|.+|-.+.    ..||+||+.+.
T Consensus       300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcceEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence            5689999999999999999994 699998655    47999998754

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.71  E-value=2.7e-05  Score=37.16  Aligned_cols=46  Identities=26%  Similarity=0.627  Sum_probs=35.2

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ...|-.|...-...+.++|||..|..|..-  ++-+.||+|..++...
T Consensus         7 ~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~   52 (55)
T PF14447_consen    7 EQPCVFCGFVGTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFD   52 (55)
T ss_pred             ceeEEEccccccccccccccceeeccccCh--hhccCCCCCCCcccCC
Confidence            445666777666778899999999999753  2447899999988654

>KOG0826|consensus

Probab=97.66  E-value=5.2e-05  Score=47.99  Aligned_cols=49  Identities=20%  Similarity=0.511  Sum_probs=42.0

Q ss_pred             CCCCccccccccCCCCCeecC-CCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~-C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ..+...||+|+....+|..+. -|-+||..|+..++...+.||+-..+..
T Consensus       297 ~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~  346 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS  346 (357)
T ss_pred             CCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence            345579999999999998885 5999999999999999999998876654

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

Probab=97.65  E-value=5.6e-05  Score=35.21  Aligned_cols=42  Identities=26%  Similarity=0.774  Sum_probs=21.3

Q ss_pred             ccccccCCCCC--eec--CCCCcccHHHHHHHHh-CCCCCCCCCCCC
Q psy8828          22 CPICHDEFKTP--VQL--TCCHIFCESCVTKWFD-REQTCPLCRATL   63 (81)
Q Consensus        22 C~iC~~~~~~p--~~l--~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~   63 (81)
                      ||+|.+.+...  ...  +||...|..|..+.+. ....||-||++.
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            67888877321  122  6899999999999887 578999999864

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

Probab=97.39  E-value=0.00029  Score=45.25  Aligned_cols=53  Identities=23%  Similarity=0.573  Sum_probs=41.9

Q ss_pred             CccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHH--hCCCCCCCCCCCC
Q psy8828          11 TKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWF--DREQTCPLCRATL   63 (81)
Q Consensus        11 ~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~--~~~~~CP~C~~~~   63 (81)
                      +..+..++...|.||-+.+.-...+||+|..|.-|..+..  -..+.|++|+..-
T Consensus        53 SaddtDEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          53 SADDTDEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccccccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            3444556778999999987776788999999999987653  3778999998764

>KOG1571|consensus

Probab=97.34  E-value=0.00018  Score=45.97  Aligned_cols=45  Identities=31%  Similarity=0.702  Sum_probs=34.3

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      .....|.||.+..++.+.+||||.-|  |..-.. ....||+||..+.
T Consensus       303 ~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIR  347 (355)
T ss_pred             CCCCceEEecCCccceeeecCCcEEE--chHHHh-hCCCCchhHHHHH
Confidence            34568999999999999999999866  554332 2345999988764

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

Probab=97.13  E-value=0.00083  Score=30.59  Aligned_cols=38  Identities=24%  Similarity=0.743  Sum_probs=23.7

Q ss_pred             ccccccCCCCCeecC---CCCcccHHHHHHHHhCCC--CCCCC
Q psy8828          22 CPICHDEFKTPVQLT---CCHIFCESCVTKWFDREQ--TCPLC   59 (81)
Q Consensus        22 C~iC~~~~~~p~~l~---C~h~fc~~Cl~~~~~~~~--~CP~C   59 (81)
                      |.+|.++....+.-+   |+-.+|..|+..+++...  .||.|
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            678888888777654   988999999999988554  79977

; PDB: 3NW0_A 2CT0_A.

>KOG1001|consensus

Probab=97.10  E-value=0.00012  Score=50.56  Aligned_cols=48  Identities=33%  Similarity=0.771  Sum_probs=39.7

Q ss_pred             ccccccccCCCCCeecCCCCcccHHHHHHHHhCC--CCCCCCCCCCCCCcc
Q psy8828          20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE--QTCPLCRATLVDDPA   68 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~--~~CP~C~~~~~~~~~   68 (81)
                      ..|.+|.+ ...++.++|+|.||.+|+.......  ..||.|+..+.....
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l  504 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL  504 (674)
T ss_pred             cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence            79999999 7778888999999999999887743  479999887755433

>KOG2817|consensus

Probab=97.08  E-value=0.00055  Score=44.36  Aligned_cols=49  Identities=20%  Similarity=0.558  Sum_probs=38.5

Q ss_pred             cCCCCccccccccCCC---CCeecCCCCcccHHHHHHHHhCC---CCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATL   63 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~---~p~~l~C~h~fc~~Cl~~~~~~~---~~CP~C~~~~   63 (81)
                      .....|.|||=.+.-.   .|+.+.|||+.+.+-+.+..++.   ..||.|-...
T Consensus       330 ~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  330 HFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             cccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            3456789999777544   38899999999999999987743   6899995543

>KOG1814|consensus

Probab=97.08  E-value=0.00016  Score=47.05  Aligned_cols=48  Identities=29%  Similarity=0.665  Sum_probs=35.5

Q ss_pred             cCCCCccccccccCCCCC---eecCCCCcccHHHHHHHHh--------CCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFD--------REQTCPLCRAT   62 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p---~~l~C~h~fc~~Cl~~~~~--------~~~~CP~C~~~   62 (81)
                      .....+.|.||++.....   +.+||+|.||+.|+..+..        +...||.+...
T Consensus       180 F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  180 FVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             HHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            345568999999986542   4569999999999999876        22478775443

>KOG3800|consensus

Probab=97.06  E-value=0.00063  Score=42.53  Aligned_cols=46  Identities=35%  Similarity=0.860  Sum_probs=35.2

Q ss_pred             cccccccC-CCCCee----cCCCCcccHHHHHHHHh-CCCCCCCCCCCCCCC
Q psy8828          21 ICPICHDE-FKTPVQ----LTCCHIFCESCVTKWFD-REQTCPLCRATLVDD   66 (81)
Q Consensus        21 ~C~iC~~~-~~~p~~----l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~   66 (81)
                      .||+|... |.+|-.    -+|+|..|.+|+.+.+. ....||.|...+...
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~   53 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKN   53 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhc
Confidence            58888875 445421    28999999999999887 457999998877654

>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=97.00  E-value=0.00028  Score=32.64  Aligned_cols=42  Identities=29%  Similarity=0.768  Sum_probs=25.5

Q ss_pred             ccccccCCCCCeecCCC-CcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        22 C~iC~~~~~~p~~l~C~-h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      |.-|.-.  +.-.+.|. |..|..|+...+..+..||+|..+++.
T Consensus         5 CKsCWf~--~k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen    5 CKSCWFA--NKGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             --SS-S----SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             Chhhhhc--CCCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            4444433  33355776 788999999999999999999998864

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.

>KOG1941|consensus

Probab=96.98  E-value=0.00025  Score=46.14  Aligned_cols=44  Identities=27%  Similarity=0.759  Sum_probs=34.9

Q ss_pred             CCccccccccCCCC-Ce---ecCCCCcccHHHHHHHHhCC--CCCCCCCC
Q psy8828          18 VGCICPICHDEFKT-PV---QLTCCHIFCESCVTKWFDRE--QTCPLCRA   61 (81)
Q Consensus        18 ~~~~C~iC~~~~~~-p~---~l~C~h~fc~~Cl~~~~~~~--~~CP~C~~   61 (81)
                      -++-|..|.+.+-. +-   -+||.|.||..|+.+++.++  .+||.|++
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            35689999987643 22   35999999999999999855  68999984

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.96  E-value=0.0017  Score=37.43  Aligned_cols=49  Identities=24%  Similarity=0.643  Sum_probs=35.5

Q ss_pred             CCCCccccccccCCCCCeecCCCC-----cccHHHHHHHHhC--CCCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTPVQLTCCH-----IFCESCVTKWFDR--EQTCPLCRATLVD   65 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~C~h-----~fc~~Cl~~~~~~--~~~CP~C~~~~~~   65 (81)
                      ...+..|-||.+...+ ..-||..     ..|.+|+.+|+..  ...|+.|+.+...
T Consensus         5 s~~~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          5 SLMDKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            3455689999988542 3346543     3499999999984  4689999988643

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

Probab=96.92  E-value=0.0015  Score=36.60  Aligned_cols=49  Identities=20%  Similarity=0.567  Sum_probs=40.5

Q ss_pred             CCccccccccCCCCCeec-C---CCCcccHHHHHHHHhC---CCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQL-T---CCHIFCESCVTKWFDR---EQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l-~---C~h~fc~~Cl~~~~~~---~~~CP~C~~~~~~~   66 (81)
                      ...+|.||.+...+...| |   ||-..|..|--..++.   ...||+|+..+...
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence            457999999998888877 2   8999999999877773   47999999888664

>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=96.86  E-value=0.0004  Score=37.08  Aligned_cols=32  Identities=22%  Similarity=0.613  Sum_probs=26.1

Q ss_pred             CCCCccccccccCCCCCeec--CCCCcccHHHHH
Q psy8828          16 LGVGCICPICHDEFKTPVQL--TCCHIFCESCVT   47 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~   47 (81)
                      +.+...|++|...+.+....  ||||.||..|+.
T Consensus        75 i~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            34566899999999876543  999999999975

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

>KOG3002|consensus

Probab=96.85  E-value=0.0011  Score=41.96  Aligned_cols=47  Identities=28%  Similarity=0.609  Sum_probs=37.7

Q ss_pred             CCCCccccccccCCCCCee-cCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~-l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ..+.+.||||.+.+..|+. -.=||..|..|-.   +....||.|+.++..
T Consensus        45 ~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             chhhccCchhhccCcccceecCCCcEehhhhhh---hhcccCCcccccccc
Confidence            3456899999999999863 3568999999975   356789999998874

>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=96.80  E-value=0.0022  Score=36.97  Aligned_cols=34  Identities=24%  Similarity=0.616  Sum_probs=25.6

Q ss_pred             CCccccccccCCCCCeecC------------CCCcc-cHHHHHHHHh
Q psy8828          18 VGCICPICHDEFKTPVQLT------------CCHIF-CESCVTKWFD   51 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~------------C~h~f-c~~Cl~~~~~   51 (81)
                      ++..||||++...+++.|-            |+..| +..||.++.+
T Consensus         1 ed~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            3568999999999999873            44332 6789988754

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.

>KOG4739|consensus

Probab=96.70  E-value=0.00048  Score=41.96  Aligned_cols=44  Identities=30%  Similarity=0.739  Sum_probs=29.5

Q ss_pred             cccccccCCC-CCe-ecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          21 ICPICHDEFK-TPV-QLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        21 ~C~iC~~~~~-~p~-~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      .|..|..... ++. .+.|+|+||..|...-  ....||.|++.+...
T Consensus         5 hCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~ir~i   50 (233)
T KOG4739|consen    5 HCNKCFRFPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSIRII   50 (233)
T ss_pred             EeccccccCCCCceeeeechhhhhhhhcccC--Cccccccccceeeee
Confidence            4666655433 233 4589999999998532  223899999986543

>KOG1952|consensus

Probab=96.59  E-value=0.0013  Score=46.40  Aligned_cols=46  Identities=28%  Similarity=0.799  Sum_probs=35.4

Q ss_pred             CCCccccccccCCCCCeec----CCCCcccHHHHHHHHhC-------CCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL----TCCHIFCESCVTKWFDR-------EQTCPLCRAT   62 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l----~C~h~fc~~Cl~~~~~~-------~~~CP~C~~~   62 (81)
                      ...++|.||.+.+.....+    .|-|+|+..||.+|...       ...||.|+..
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            4567999999987653222    58899999999999872       3589999843

>KOG1940|consensus

Probab=96.51  E-value=0.0018  Score=40.41  Aligned_cols=42  Identities=29%  Similarity=0.686  Sum_probs=35.4

Q ss_pred             ccccccccCCCC----CeecCCCCcccHHHHHHHHhCCCCCCCCCC
Q psy8828          20 CICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRA   61 (81)
Q Consensus        20 ~~C~iC~~~~~~----p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~   61 (81)
                      ..||||.+.+..    +..++|||..+..|+......+.+||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            459999997654    456799999999999988887799999988

>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=96.49  E-value=0.0014  Score=30.73  Aligned_cols=42  Identities=24%  Similarity=0.729  Sum_probs=21.0

Q ss_pred             ccccccccCCCCCeec-CCCCcccHHHHHHHHh-----CCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-----REQTCPLCRAT   62 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~-----~~~~CP~C~~~   62 (81)
                      +.||+....+..|++- .|.|.-|.+- ..|+.     ....||+|.++
T Consensus         3 L~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence            6899999999999876 8999866432 22332     34689999763

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.

>KOG2114|consensus

Probab=96.48  E-value=0.0018  Score=45.69  Aligned_cols=41  Identities=29%  Similarity=0.844  Sum_probs=34.8

Q ss_pred             ccccccccCCCCCee-cCCCCcccHHHHHHHHhCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATL   63 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~-l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~   63 (81)
                      -.|..|...+.-|.. -.|||.||..|+.   .+...||.|+...
T Consensus       841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  841 SKCSACEGTLDLPFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeecccCCccccceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            489999999999865 4999999999998   4667999997744

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.40  E-value=0.0038  Score=40.22  Aligned_cols=46  Identities=24%  Similarity=0.674  Sum_probs=34.5

Q ss_pred             cccccccCCCCC--e--ecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCCC
Q psy8828          21 ICPICHDEFKTP--V--QLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDD   66 (81)
Q Consensus        21 ~C~iC~~~~~~p--~--~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~~   66 (81)
                      -||+|++.+...  -  -.+||...|+.|.....+. +..||.||....+.
T Consensus        16 ~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          16 YCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             cCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            499999987632  1  2378999999998766553 57899999876554

>PHA03096 p28-like protein; Provisional

Probab=96.28  E-value=0.003  Score=39.70  Aligned_cols=42  Identities=29%  Similarity=0.542  Sum_probs=29.8

Q ss_pred             ccccccccCCCCC--------eecCCCCcccHHHHHHHHhCC---CCCCCCCC
Q psy8828          20 CICPICHDEFKTP--------VQLTCCHIFCESCVTKWFDRE---QTCPLCRA   61 (81)
Q Consensus        20 ~~C~iC~~~~~~p--------~~l~C~h~fc~~Cl~~~~~~~---~~CP~C~~   61 (81)
                      ..|.||++.....        +.-.|.|.||..|+..|...+   ..||.|+.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            5799999976532        222799999999999998733   34444433

>KOG4362|consensus

Probab=96.27  E-value=0.00079  Score=46.44  Aligned_cols=49  Identities=35%  Similarity=0.809  Sum_probs=39.9

Q ss_pred             CCccccccccCCCCCeecCCCCcccHHHHHHHHhC---CCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR---EQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~---~~~CP~C~~~~~~~   66 (81)
                      ..++|+||...+.+|+.+.|.|.||..|+...+..   ...||+|+..+...
T Consensus        20 k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~   71 (684)
T KOG4362|consen   20 KILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR   71 (684)
T ss_pred             hhccCCceeEEeeccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence            45799999999999999999999999999865552   45799998665443

>KOG3268|consensus

Probab=96.26  E-value=0.0047  Score=36.42  Aligned_cols=44  Identities=25%  Similarity=0.686  Sum_probs=30.9

Q ss_pred             cccccccCCCCCee-------cCCCCcccHHHHHHHHhC------C-----CCCCCCCCCCC
Q psy8828          21 ICPICHDEFKTPVQ-------LTCCHIFCESCVTKWFDR------E-----QTCPLCRATLV   64 (81)
Q Consensus        21 ~C~iC~~~~~~p~~-------l~C~h~fc~~Cl~~~~~~------~-----~~CP~C~~~~~   64 (81)
                      .|.||..+--+..+       ..||..|+.-|+..|++.      +     ..||.|..++.
T Consensus       167 ~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia  228 (234)
T KOG3268|consen  167 ACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA  228 (234)
T ss_pred             cccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence            45566554333221       369999999999999972      2     37999988764

>KOG3970|consensus

Probab=96.18  E-value=0.0068  Score=37.00  Aligned_cols=47  Identities=21%  Similarity=0.627  Sum_probs=37.4

Q ss_pred             ccccccccCCCC--CeecCCCCcccHHHHHHHHhC--------CCCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKT--PVQLTCCHIFCESCVTKWFDR--------EQTCPLCRATLVDD   66 (81)
Q Consensus        20 ~~C~iC~~~~~~--p~~l~C~h~fc~~Cl~~~~~~--------~~~CP~C~~~~~~~   66 (81)
                      --|.+|...+.+  .+.+-|-|.|+-+|+.+|...        ...||.|..++...
T Consensus        51 pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   51 PNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            478899988875  456799999999999999762        35899998876543

>KOG1428|consensus

Probab=96.12  E-value=0.0047  Score=46.58  Aligned_cols=51  Identities=27%  Similarity=0.705  Sum_probs=38.6

Q ss_pred             cCCCCccccccccCCC---CCeecCCCCcccHHHHHHHHhCC----------CCCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDRE----------QTCPLCRATLVD   65 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~---~p~~l~C~h~fc~~Cl~~~~~~~----------~~CP~C~~~~~~   65 (81)
                      ....+..|-||+..--   ..+++.|+|.|+..|..+.+++.          ..||+|..++..
T Consensus      3482 kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            3445678999988643   24678999999999998776643          389999888754

>KOG4445|consensus

Probab=96.03  E-value=0.0021  Score=40.61  Aligned_cols=49  Identities=24%  Similarity=0.632  Sum_probs=37.4

Q ss_pred             CCccccccccCCCCC---eecCCCCcccHHHHHHHHh-----------------------CCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFD-----------------------REQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p---~~l~C~h~fc~~Cl~~~~~-----------------------~~~~CP~C~~~~~~~   66 (81)
                      ....|.||+--|.+.   +.++|.|.|+..|+.+++.                       ....||+|+..+...
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            345899998877653   3569999999999988874                       113799999988654

>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=96.02  E-value=0.004  Score=34.99  Aligned_cols=35  Identities=29%  Similarity=0.709  Sum_probs=26.8

Q ss_pred             CccccccccCCCC--Cee-cCCC------CcccHHHHHHHHhCC
Q psy8828          19 GCICPICHDEFKT--PVQ-LTCC------HIFCESCVTKWFDRE   53 (81)
Q Consensus        19 ~~~C~iC~~~~~~--p~~-l~C~------h~fc~~Cl~~~~~~~   53 (81)
                      ..+|.||++.+.+  .++ ++||      |.||.+|+.+|....
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~   69 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRER   69 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhc
Confidence            5799999999887  543 3554      679999999995433

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.

>KOG3113|consensus

Probab=95.98  E-value=0.0082  Score=37.15  Aligned_cols=55  Identities=20%  Similarity=0.395  Sum_probs=41.0

Q ss_pred             CCCCccccccccCCCCCe----ecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCc
Q psy8828          16 LGVGCICPICHDEFKTPV----QLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDG   72 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~   72 (81)
                      ....+.|||-.-.+....    ..+|||+|-..-+.+.  ....|++|++.+...+.....
T Consensus       108 ~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvlN  166 (293)
T KOG3113|consen  108 QRARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIVLN  166 (293)
T ss_pred             ccceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEeeC
Confidence            356789999877766543    3489999999888765  468999999998776554433

>PHA02862 5L protein; Provisional

Probab=95.84  E-value=0.012  Score=33.51  Aligned_cols=45  Identities=24%  Similarity=0.616  Sum_probs=33.5

Q ss_pred             ccccccccCCCCCeecCCC-----CcccHHHHHHHHhC--CCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQLTCC-----HIFCESCVTKWFDR--EQTCPLCRATLVD   65 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l~C~-----h~fc~~Cl~~~~~~--~~~CP~C~~~~~~   65 (81)
                      ..|-||.+.-.+. .-||.     ...|++|+.+|+..  ...|+.|+.+...
T Consensus         3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            4688999986544 34654     34699999999984  4689999988743

>KOG2932|consensus

Probab=95.56  E-value=0.0066  Score=38.64  Aligned_cols=42  Identities=29%  Similarity=0.811  Sum_probs=28.5

Q ss_pred             ccccccccCCCC-CeecCCCCcccHHHHHHHHhCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKT-PVQLTCCHIFCESCVTKWFDREQTCPLCRATL   63 (81)
Q Consensus        20 ~~C~iC~~~~~~-p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~   63 (81)
                      ..|--|-..+.. ...++|.|+||.+|...  ...+.||.|...+
T Consensus        91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIAIYGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCcceeeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            355556554433 34569999999999752  3467899996554

>KOG3161|consensus

Probab=95.36  E-value=0.0043  Score=42.87  Aligned_cols=41  Identities=34%  Similarity=0.837  Sum_probs=31.3

Q ss_pred             cCCCCccccccccCCC----CCeecCCCCcccHHHHHHHHhCCCCCC
Q psy8828          15 LLGVGCICPICHDEFK----TPVQLTCCHIFCESCVTKWFDREQTCP   57 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~----~p~~l~C~h~fc~~Cl~~~~~~~~~CP   57 (81)
                      .+.+.+.|+||...+.    .|+.+.|||+.|..|+.....  ..||
T Consensus         7 ~w~~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp   51 (861)
T KOG3161|consen    7 KWVLLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP   51 (861)
T ss_pred             hhHHHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC
Confidence            3445678999977765    478889999999999987644  4555

>KOG3039|consensus

Probab=95.11  E-value=0.027  Score=34.92  Aligned_cols=36  Identities=11%  Similarity=0.180  Sum_probs=30.9

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHH
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWF   50 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~   50 (81)
                      .+.+..-|.+|+....+|++.+=||.|+++||.+++
T Consensus        39 siK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~i   74 (303)
T KOG3039|consen   39 SIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYI   74 (303)
T ss_pred             ccCCcceeeeecccccCCccCCCCeeeeHHHHHHHH
Confidence            334456789999999999999999999999998775

>KOG0298|consensus

Probab=95.02  E-value=0.0046  Score=45.44  Aligned_cols=48  Identities=27%  Similarity=0.642  Sum_probs=40.8

Q ss_pred             CCccccccccCCC-CCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFK-TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~-~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ....|.||.+.+. ...+..|||.+|..|...|+..+..||.|+....+
T Consensus      1152 ~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~~d 1200 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKSIKGD 1200 (1394)
T ss_pred             cccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhhhhhh
Confidence            4468999999998 45677999999999999999999999999755443

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

Probab=94.99  E-value=0.013  Score=27.11  Aligned_cols=38  Identities=26%  Similarity=0.834  Sum_probs=23.1

Q ss_pred             ccccccCCCC--CeecCCCC-----cccHHHHHHHHh--CCCCCCCC
Q psy8828          22 CPICHDEFKT--PVQLTCCH-----IFCESCVTKWFD--REQTCPLC   59 (81)
Q Consensus        22 C~iC~~~~~~--p~~l~C~h-----~fc~~Cl~~~~~--~~~~CP~C   59 (81)
                      |-||++.-.+  +.+.||.-     ..|.+|+.+|+.  .+..|++|
T Consensus         1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            5577776443  35557642     469999999998  45678776

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

Probab=94.39  E-value=0.045  Score=35.09  Aligned_cols=49  Identities=22%  Similarity=0.522  Sum_probs=37.2

Q ss_pred             cCCCCccccccccCCC---CCeecCCCCcccHHHHHHHHhC---CCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDR---EQTCPLCRATL   63 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~---~p~~l~C~h~fc~~Cl~~~~~~---~~~CP~C~~~~   63 (81)
                      .....+.||+=.+.-.   .|+.+.|||+.-.+-+....+.   ++.||.|-...
T Consensus       332 hfHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~~  386 (396)
T COG5109         332 HFHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEMS  386 (396)
T ss_pred             cccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcch
Confidence            4566789998666543   3788999999999999887764   36899995543

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

Probab=94.17  E-value=0.044  Score=35.63  Aligned_cols=30  Identities=37%  Similarity=0.976  Sum_probs=22.5

Q ss_pred             CCCcccHHHHHHHHh-------------CCCCCCCCCCCCCCC
Q psy8828          37 CCHIFCESCVTKWFD-------------REQTCPLCRATLVDD   66 (81)
Q Consensus        37 C~h~fc~~Cl~~~~~-------------~~~~CP~C~~~~~~~   66 (81)
                      |....|.+|+-+|+.             ++..||+||+.+-..
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil  353 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL  353 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence            455679999998876             234899999987543

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

>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=93.97  E-value=0.015  Score=35.88  Aligned_cols=47  Identities=38%  Similarity=0.992  Sum_probs=34.3

Q ss_pred             CccccccccC-CCCC-ee-c--C-CCCcccHHHHHHHHhCC-CCCC--CCCCCCCC
Q psy8828          19 GCICPICHDE-FKTP-VQ-L--T-CCHIFCESCVTKWFDRE-QTCP--LCRATLVD   65 (81)
Q Consensus        19 ~~~C~iC~~~-~~~p-~~-l--~-C~h~fc~~Cl~~~~~~~-~~CP--~C~~~~~~   65 (81)
                      +..||+|... +-+| +. +  | |-|..|.+|+.+.+... ..||  -|.+.+..
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILRK   65 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILRK   65 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHHH
Confidence            4589999976 4444 22 2  4 99999999999998854 6898  57665543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=93.58  E-value=0.098  Score=24.96  Aligned_cols=31  Identities=29%  Similarity=0.835  Sum_probs=24.5

Q ss_pred             CccccccccCC--CCCeec--CCCCcccHHHHHHH
Q psy8828          19 GCICPICHDEF--KTPVQL--TCCHIFCESCVTKW   49 (81)
Q Consensus        19 ~~~C~iC~~~~--~~p~~l--~C~h~fc~~Cl~~~   49 (81)
                      .-.|++|.+.+  .+.++.  .||-.++++|..+.
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~   39 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA   39 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence            45799999999  555554  79999999998653

>KOG3579|consensus

Probab=93.42  E-value=0.12  Score=32.68  Aligned_cols=36  Identities=22%  Similarity=0.681  Sum_probs=29.9

Q ss_pred             CCCccccccccCCCCCeecCC----CCcccHHHHHHHHhC
Q psy8828          17 GVGCICPICHDEFKTPVQLTC----CHIFCESCVTKWFDR   52 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C----~h~fc~~Cl~~~~~~   52 (81)
                      ...+.|-+|.+.+++-..+.|    .|.||..|-.+.++.
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~  305 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQ  305 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHh
Confidence            345899999999999877766    699999999888773

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.31  E-value=0.056  Score=27.28  Aligned_cols=33  Identities=27%  Similarity=0.626  Sum_probs=24.5

Q ss_pred             CCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccC
Q psy8828          37 CCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   71 (81)
Q Consensus        37 C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~   71 (81)
                      =.++||.+|.+..+.  ..||.|...+...+..+.
T Consensus        27 fEcTFCadCae~~l~--g~CPnCGGelv~RP~RPa   59 (84)
T COG3813          27 FECTFCADCAENRLH--GLCPNCGGELVARPIRPA   59 (84)
T ss_pred             EeeehhHhHHHHhhc--CcCCCCCchhhcCcCChH
Confidence            357999999986544  789999888866555443

>KOG2034|consensus

Probab=93.16  E-value=0.054  Score=38.79  Aligned_cols=37  Identities=22%  Similarity=0.489  Sum_probs=28.2

Q ss_pred             cCCCCccccccccCCCC-Cee-cCCCCcccHHHHHHHHh
Q psy8828          15 LLGVGCICPICHDEFKT-PVQ-LTCCHIFCESCVTKWFD   51 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~-p~~-l~C~h~fc~~Cl~~~~~   51 (81)
                      .++....|.+|...+.. |-. -+|||.|+.+|+.+...
T Consensus       813 v~ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  813 VLEPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             EecCccchHHhcchhhcCcceeeeccchHHHHHHHHHHH
Confidence            34566789999987654 443 39999999999987653

>KOG1815|consensus

Probab=93.07  E-value=0.08  Score=35.25  Aligned_cols=34  Identities=29%  Similarity=0.744  Sum_probs=29.1

Q ss_pred             CCccccccccCCCC-CeecCCCCcccHHHHHHHHh
Q psy8828          18 VGCICPICHDEFKT-PVQLTCCHIFCESCVTKWFD   51 (81)
Q Consensus        18 ~~~~C~iC~~~~~~-p~~l~C~h~fc~~Cl~~~~~   51 (81)
                      ....|.||.+.+.. ...+.|||.||..|+..++.
T Consensus        69 ~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~  103 (444)
T KOG1815|consen   69 GDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLG  103 (444)
T ss_pred             ccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhh
Confidence            45789999999885 55669999999999999887

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

Probab=92.88  E-value=0.18  Score=24.18  Aligned_cols=45  Identities=24%  Similarity=0.646  Sum_probs=29.4

Q ss_pred             cccccccCCCCC----eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCc
Q psy8828          21 ICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   67 (81)
Q Consensus        21 ~C~iC~~~~~~p----~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~   67 (81)
                      .|-.|-..+...    .+-+=..+||.+|....+  ...||.|...+..++
T Consensus         7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~RP   55 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVRRP   55 (57)
T ss_pred             CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccccCC
Confidence            355555554432    222333589999998876  478999988876543

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

>KOG1812|consensus

Probab=92.56  E-value=0.061  Score=35.28  Aligned_cols=33  Identities=33%  Similarity=0.674  Sum_probs=24.9

Q ss_pred             CccccccccCCCCC-e---ecCCCCcccHHHHHHHHh
Q psy8828          19 GCICPICHDEFKTP-V---QLTCCHIFCESCVTKWFD   51 (81)
Q Consensus        19 ~~~C~iC~~~~~~p-~---~l~C~h~fc~~Cl~~~~~   51 (81)
                      ...|.||......+ .   ...|+|.||.+|+.++..
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE  182 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence            56899999433322 1   347999999999998877

>KOG3899|consensus

Probab=91.64  E-value=0.14  Score=32.67  Aligned_cols=30  Identities=30%  Similarity=0.850  Sum_probs=22.8

Q ss_pred             CCCcccHHHHHHHHh-------------CCCCCCCCCCCCCCC
Q psy8828          37 CCHIFCESCVTKWFD-------------REQTCPLCRATLVDD   66 (81)
Q Consensus        37 C~h~fc~~Cl~~~~~-------------~~~~CP~C~~~~~~~   66 (81)
                      |....|.+|+-+|+.             ++..||.||+.+-..
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~  367 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR  367 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence            556779999988865             345899999987543

>KOG1100|consensus

Probab=91.56  E-value=0.082  Score=31.90  Aligned_cols=39  Identities=31%  Similarity=0.781  Sum_probs=28.9

Q ss_pred             ccccccCCCCCeecCCCC-cccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          22 CPICHDEFKTPVQLTCCH-IFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        22 C~iC~~~~~~p~~l~C~h-~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      |-.|.+.-..-..+||.| .+|..|-..    -..||+|+....
T Consensus       161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~  200 (207)
T KOG1100|consen  161 CRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKT  200 (207)
T ss_pred             ceecCcCCceEEeecccceEeccccccc----CccCCCCcChhh
Confidence            888888766655669998 589988643    356999977654

>KOG4718|consensus

Probab=91.28  E-value=0.12  Score=31.35  Aligned_cols=42  Identities=21%  Similarity=0.675  Sum_probs=35.9

Q ss_pred             ccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRA   61 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~   61 (81)
                      ..|.+|..+....+.. .|+-.++..|+.+++++...||.|.-
T Consensus       182 k~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d  224 (235)
T KOG4718|consen  182 KNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGD  224 (235)
T ss_pred             HHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence            4899999988777655 78888999999999999999999944

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

Probab=91.14  E-value=0.15  Score=25.23  Aligned_cols=12  Identities=42%  Similarity=1.450  Sum_probs=8.8

Q ss_pred             cccHHHHHHHHh
Q psy8828          40 IFCESCVTKWFD   51 (81)
Q Consensus        40 ~fc~~Cl~~~~~   51 (81)
                      .||+.||.+|..
T Consensus        11 gFCRNCLskWy~   22 (68)
T PF06844_consen   11 GFCRNCLSKWYR   22 (68)
T ss_dssp             S--HHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            499999999986

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

>KOG3053|consensus

Probab=90.79  E-value=0.21  Score=31.19  Aligned_cols=50  Identities=22%  Similarity=0.604  Sum_probs=35.6

Q ss_pred             cCCCCccccccccCCCCCeec----CC-----CCcccHHHHHHHHhCC--------CCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTPVQL----TC-----CHIFCESCVTKWFDRE--------QTCPLCRATLV   64 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l----~C-----~h~fc~~Cl~~~~~~~--------~~CP~C~~~~~   64 (81)
                      ..+.+..|-||+..=++....    ||     .|-.|..|+.+|....        -.||.|+....
T Consensus        16 ~~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   16 NQELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             ccccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            344566899999987664332    54     3568999999998732        37999988753

>KOG0309|consensus

Probab=90.46  E-value=0.19  Score=35.89  Aligned_cols=39  Identities=33%  Similarity=0.761  Sum_probs=28.3

Q ss_pred             ccccccccCCCCCe--ecCCCCcccHHHHHHHHhCCCCCCC
Q psy8828          20 CICPICHDEFKTPV--QLTCCHIFCESCVTKWFDREQTCPL   58 (81)
Q Consensus        20 ~~C~iC~~~~~~p~--~l~C~h~fc~~Cl~~~~~~~~~CP~   58 (81)
                      +.|.+|--......  ...|+|..+.+|..+|++....||.
T Consensus      1029 ~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1029 FQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            45666554433322  2379999999999999998888887

>KOG1812|consensus

Probab=90.40  E-value=0.14  Score=33.64  Aligned_cols=41  Identities=27%  Similarity=0.636  Sum_probs=31.2

Q ss_pred             CccccccccCCCC-----CeecCCCCcccHHHHHHHHhCCCCCCCC
Q psy8828          19 GCICPICHDEFKT-----PVQLTCCHIFCESCVTKWFDREQTCPLC   59 (81)
Q Consensus        19 ~~~C~iC~~~~~~-----p~~l~C~h~fc~~Cl~~~~~~~~~CP~C   59 (81)
                      ...|+.|...+..     .++-.|||.||..|...|...+..|..|
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence            4589999887653     3444799999999999998877666443

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

Probab=90.07  E-value=0.19  Score=20.28  Aligned_cols=8  Identities=50%  Similarity=1.244  Sum_probs=4.1

Q ss_pred             ccccccCC
Q psy8828          22 CPICHDEF   29 (81)
Q Consensus        22 C~iC~~~~   29 (81)
                      ||-|...+
T Consensus         3 CP~C~~~V   10 (26)
T PF10571_consen    3 CPECGAEV   10 (26)
T ss_pred             CCCCcCCc
Confidence            55555544

Several members are annotated as putative helicases.

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

Probab=89.67  E-value=0.44  Score=34.45  Aligned_cols=51  Identities=20%  Similarity=0.505  Sum_probs=36.3

Q ss_pred             CCCccccccccCC--CCCeecCCCCc-----ccHHHHHHHHhC--CCCCCCCCCCCCCCc
Q psy8828          17 GVGCICPICHDEF--KTPVQLTCCHI-----FCESCVTKWFDR--EQTCPLCRATLVDDP   67 (81)
Q Consensus        17 ~~~~~C~iC~~~~--~~p~~l~C~h~-----fc~~Cl~~~~~~--~~~CP~C~~~~~~~~   67 (81)
                      ++...|.||...-  .+|..-||..+     .|++|+.+|+..  ...|-.|+.++.-.+
T Consensus        10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            3446899998753  34544476542     599999999984  468999998875443

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

Probab=89.64  E-value=0.0077  Score=30.20  Aligned_cols=40  Identities=33%  Similarity=0.795  Sum_probs=20.9

Q ss_pred             ccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      +.||.|...+...    =++.+|..|-..+ .....||.|.+++.
T Consensus         2 ~~CP~C~~~L~~~----~~~~~C~~C~~~~-~~~a~CPdC~~~Le   41 (70)
T PF07191_consen    2 NTCPKCQQELEWQ----GGHYHCEACQKDY-KKEAFCPDCGQPLE   41 (70)
T ss_dssp             -B-SSS-SBEEEE----TTEEEETTT--EE-EEEEE-TTT-SB-E
T ss_pred             CcCCCCCCccEEe----CCEEECccccccc-eecccCCCcccHHH
Confidence            4789998875421    2677788887643 33457899988764

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

>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A

Probab=88.80  E-value=0.82  Score=23.45  Aligned_cols=48  Identities=29%  Similarity=0.668  Sum_probs=19.2

Q ss_pred             CCccccccccCCCC----Ceec---CCCCcccHHHHHHH-HhCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT----PVQL---TCCHIFCESCVTKW-FDREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~~----p~~l---~C~h~fc~~Cl~~~-~~~~~~CP~C~~~~~~   65 (81)
                      ..-.|.||.+.+--    .+.+   .|+-..|+.|.+-- ...++.||.|+.....
T Consensus         8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr   63 (80)
T PF14569_consen    8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKR   63 (80)
T ss_dssp             SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B---
T ss_pred             CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCccc
Confidence            34579999987542    1222   57777899999633 3367899999877643

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=88.14  E-value=0.054  Score=21.26  Aligned_cols=6  Identities=50%  Similarity=1.353  Sum_probs=2.5

Q ss_pred             CCCCCC
Q psy8828          55 TCPLCR   60 (81)
Q Consensus        55 ~CP~C~   60 (81)
                      .||.|.
T Consensus        15 fC~~CG   20 (23)
T PF13240_consen   15 FCPNCG   20 (23)
T ss_pred             chhhhC
Confidence            344443

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

Probab=87.50  E-value=0.6  Score=24.63  Aligned_cols=40  Identities=23%  Similarity=0.788  Sum_probs=28.9

Q ss_pred             ccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcc
Q psy8828          20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   68 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~   68 (81)
                      ..|-||...+..+     |+.||..|..    ....|..|.+.+.+...
T Consensus        45 ~~C~~CK~~v~q~-----g~~YCq~CAY----kkGiCamCGKki~dtk~   84 (90)
T PF10235_consen   45 SKCKICKTKVHQP-----GAKYCQTCAY----KKGICAMCGKKILDTKN   84 (90)
T ss_pred             ccccccccccccC-----CCccChhhhc----ccCcccccCCeeccccc
Confidence            3687887765542     7889999975    34689999998865433

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

>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit

Probab=86.46  E-value=1.7  Score=32.32  Aligned_cols=47  Identities=28%  Similarity=0.705  Sum_probs=33.4

Q ss_pred             CCccccccccCCCCC----eec---CCCCcccHHHHH-HHHhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTP----VQL---TCCHIFCESCVT-KWFDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p----~~l---~C~h~fc~~Cl~-~~~~~~~~CP~C~~~~~   64 (81)
                      ..-.|.||.+.+-..    ..+   .|+--.|+.|.+ +....++.||.|+....
T Consensus        16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYk   70 (1079)
T PLN02638         16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYK   70 (1079)
T ss_pred             CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchh
Confidence            345899999986531    122   678789999995 33336789999988765

>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression

Probab=86.19  E-value=1.8  Score=23.35  Aligned_cols=25  Identities=28%  Similarity=0.805  Sum_probs=18.7

Q ss_pred             CCcccHHHHHHHHh---------CCCCCCCCCCC
Q psy8828          38 CHIFCESCVTKWFD---------REQTCPLCRAT   62 (81)
Q Consensus        38 ~h~fc~~Cl~~~~~---------~~~~CP~C~~~   62 (81)
                      .-.||..||.....         ....||.|+..
T Consensus        37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi   70 (105)
T PF10497_consen   37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI   70 (105)
T ss_pred             cceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence            66799999976654         33579998774

This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].

>KOG2169|consensus

Probab=85.10  E-value=0.95  Score=31.77  Aligned_cols=66  Identities=24%  Similarity=0.399  Sum_probs=42.1

Q ss_pred             ccCCCCccccccccCCCCCee-cCCCCcccHHHHHHHHh----CCCCCCCCCCCCCCCccccCcccchhhh
Q psy8828          14 TLLGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFD----REQTCPLCRATLVDDPAWRDGATSYFVQ   79 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~-l~C~h~fc~~Cl~~~~~----~~~~CP~C~~~~~~~~~~~~~~~~~~~~   79 (81)
                      ......+.|+|....+.-|.. ..|.|.-|.+-+.-...    ....||+|.+......+..+..+.++++
T Consensus       301 t~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l~iD~~~~~iL~  371 (636)
T KOG2169|consen  301 TSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGLIIDGYFLNILQ  371 (636)
T ss_pred             ccceeEecCCcccceeecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccchhhhHHHHHHHh
Confidence            344556789988877666544 37888777665432211    2368999988877666666655555443

>KOG2068|consensus

Probab=84.43  E-value=1.3  Score=28.68  Aligned_cols=46  Identities=26%  Similarity=0.594  Sum_probs=35.7

Q ss_pred             ccccccccCCCC--Cee--cCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKT--PVQ--LTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        20 ~~C~iC~~~~~~--p~~--l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      -.|++|.+....  ...  .+|++..|..|+.........||.|+++...
T Consensus       250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~  299 (327)
T KOG2068|consen  250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYER  299 (327)
T ss_pred             CCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCcccc
Confidence            589999997632  122  3788888999999888889999999977643

>KOG2042|consensus

Probab=84.10  E-value=1.3  Score=32.45  Aligned_cols=63  Identities=16%  Similarity=0.154  Sum_probs=51.7

Q ss_pred             CCCccccccccCCCCCeecC-CCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhh
Q psy8828          17 GVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ   79 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~-C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~   79 (81)
                      .+.+.=|+-.....+|+.+| -+++.++.=+.+++....+=|+||.++......++..+..-++
T Consensus       868 pdef~DPlm~Tlm~dPV~LP~Srv~vDRsti~rhlLs~~tdPFNR~pLt~d~v~pn~eLK~kI~  931 (943)
T KOG2042|consen  868 PDEFLDPLMSTLMSDPVVLPSSRVTVDRSTIERHLLSDCTDPFNREPLTEDMVSPNEELKAKIR  931 (943)
T ss_pred             chhhhCccccccCCCCccCCcccccccHHHHHHHHhcCCCCccccccCchhhcCCCHHHHHHHH
Confidence            34556677778889999998 8899999999999998888899999999887777766655554

>KOG1609|consensus

Probab=84.08  E-value=1.5  Score=27.45  Aligned_cols=46  Identities=35%  Similarity=0.870  Sum_probs=33.7

Q ss_pred             CccccccccCCCC----CeecCCC-----CcccHHHHHHHHh--CCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKT----PVQLTCC-----HIFCESCVTKWFD--REQTCPLCRATLV   64 (81)
Q Consensus        19 ~~~C~iC~~~~~~----p~~l~C~-----h~fc~~Cl~~~~~--~~~~CP~C~~~~~   64 (81)
                      ...|-||......    +...||.     ...++.|+..|..  .+..|..|.....
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            4679999996543    3455653     3458999999998  5678999987654

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

Probab=83.35  E-value=0.13  Score=32.35  Aligned_cols=46  Identities=26%  Similarity=0.494  Sum_probs=22.7

Q ss_pred             CCccccccccCCCCCeecCC---C--CcccHHHHHHHHhCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTC---C--HIFCESCVTKWFDREQTCPLCRATL   63 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C---~--h~fc~~Cl~~~~~~~~~CP~C~~~~   63 (81)
                      ..-.||||.....-.+...=   |  +.+|.-|-..|.-....||.|...-
T Consensus       171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~  221 (290)
T PF04216_consen  171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTD  221 (290)
T ss_dssp             T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---S
T ss_pred             cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCC
Confidence            34689999997654444322   3  5679999999988889999997653

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

>KOG0825|consensus

Probab=82.14  E-value=1.9  Score=31.40  Aligned_cols=46  Identities=17%  Similarity=0.392  Sum_probs=32.6

Q ss_pred             CCccccccccCCCCCe----ecC---CCCcccHHHHHHHHhC------CCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPV----QLT---CCHIFCESCVTKWFDR------EQTCPLCRATL   63 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~----~l~---C~h~fc~~Cl~~~~~~------~~~CP~C~~~~   63 (81)
                      +...|.+|...+.+++    ..+   |+|.+|..||..|..+      .-.|++|..-+
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            4467888887777632    234   9999999999999872      24567775544

>PF14353 CpXC: CpXC protein

Probab=81.56  E-value=1.5  Score=24.23  Aligned_cols=46  Identities=26%  Similarity=0.346  Sum_probs=25.5

Q ss_pred             ccccccccCCCCCeecCCCCcccHHHHHHHHhCC---CCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVD   65 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~---~~CP~C~~~~~~   65 (81)
                      +.||-|...+.-.+-..-.-..-.+-..+.+..+   .+||.|++.+..
T Consensus         2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~   50 (128)
T PF14353_consen    2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL   50 (128)
T ss_pred             cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence            5788888877654332221111223334444433   589999887643

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=81.49  E-value=0.33  Score=31.07  Aligned_cols=45  Identities=20%  Similarity=0.548  Sum_probs=32.5

Q ss_pred             CCccccccccCCCCCeec----CCC--CcccHHHHHHHHhCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQL----TCC--HIFCESCVTKWFDREQTCPLCRAT   62 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l----~C~--h~fc~~Cl~~~~~~~~~CP~C~~~   62 (81)
                      ..-.||||.....-.++.    .=|  +.+|.-|-.+|.-....||.|...
T Consensus       183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~  233 (305)
T TIGR01562       183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES  233 (305)
T ss_pred             CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence            345899999976543322    123  456888989998889999999764

The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=81.33  E-value=1.4  Score=18.58  Aligned_cols=11  Identities=36%  Similarity=0.911  Sum_probs=7.3

Q ss_pred             CCCCCCCCCCC
Q psy8828          52 REQTCPLCRAT   62 (81)
Q Consensus        52 ~~~~CP~C~~~   62 (81)
                      ....||.|..+
T Consensus        16 ~~~~CP~Cg~~   26 (33)
T cd00350          16 APWVCPVCGAP   26 (33)
T ss_pred             CCCcCcCCCCc
Confidence            34578888653

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PLN02189 cellulose synthase

Probab=80.92  E-value=1.6  Score=32.40  Aligned_cols=46  Identities=28%  Similarity=0.692  Sum_probs=32.6

Q ss_pred             CccccccccCCCCC----eec---CCCCcccHHHHHHH-HhCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTP----VQL---TCCHIFCESCVTKW-FDREQTCPLCRATLV   64 (81)
Q Consensus        19 ~~~C~iC~~~~~~p----~~l---~C~h~fc~~Cl~~~-~~~~~~CP~C~~~~~   64 (81)
                      ...|.||.+.+...    ..+   .|+--.|+.|.+-- ...++.||.|+....
T Consensus        34 ~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~   87 (1040)
T PLN02189         34 GQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYK   87 (1040)
T ss_pred             CccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchh
Confidence            34899999986521    222   57778899999532 235689999988765

>KOG2979|consensus

Probab=80.84  E-value=1  Score=28.22  Aligned_cols=43  Identities=19%  Similarity=0.393  Sum_probs=35.2

Q ss_pred             ccccccccCCCCCeec-CCCCcccHHHHHHHHhC--CCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQL-TCCHIFCESCVTKWFDR--EQTCPLCRAT   62 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~--~~~CP~C~~~   62 (81)
                      +.||+-...+.+|++- .|||.|=++-+..++..  ...||+-+..
T Consensus       177 ~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~~~~~i~CPv~gC~  222 (262)
T KOG2979|consen  177 NRDPISKKPIVNPVISKKCGHVYDRDSIMQILCDEITIRCPVLGCE  222 (262)
T ss_pred             ccCchhhhhhhchhhhcCcCcchhhhhHHHHhccCceeecccccCC
Confidence            5899988888898754 89999999999998886  4678885444

>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=80.39  E-value=2  Score=20.26  Aligned_cols=25  Identities=28%  Similarity=0.740  Sum_probs=12.7

Q ss_pred             CCCCcccHHHHHHHHhCCCCCCCCC
Q psy8828          36 TCCHIFCESCVTKWFDREQTCPLCR   60 (81)
Q Consensus        36 ~C~h~fc~~Cl~~~~~~~~~CP~C~   60 (81)
                      .|++.||.+|=.=.-+.-..||-|.
T Consensus        26 ~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen   26 KCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             TTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CCCCccccCcChhhhccccCCcCCC
Confidence            5889999999532222335788773

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.

>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;

Probab=80.38  E-value=1.5  Score=20.44  Aligned_cols=29  Identities=28%  Similarity=0.653  Sum_probs=19.9

Q ss_pred             cccccccCCCCCe----ecCCCCcccHHHHHHH
Q psy8828          21 ICPICHDEFKTPV----QLTCCHIFCESCVTKW   49 (81)
Q Consensus        21 ~C~iC~~~~~~p~----~l~C~h~fc~~Cl~~~   49 (81)
                      .|.+|...|..-.    -..||+.||.+|....
T Consensus         4 ~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~   36 (57)
T cd00065           4 SCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNR   36 (57)
T ss_pred             cCcccCccccCCccccccCcCcCCcChHHcCCe
Confidence            5777877655321    1279999999998644

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	81
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		8e-07
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		3e-05
4ayc_A	138	Rnf8 Ring Domain Structure Length = 138		3e-05
4epo_C	149	Crystal Structure Of Rnf8 Bound To The Ubc13MMS2 HE		3e-05
2ecn_A	70	Solution Structure Of The Ring Domain Of The Human		1e-04
1jm7_A	112	Solution Structure Of The Brca1/bard1 Ring-domain H		2e-04
2ecj_A	58	Solution Structure Of The Ring Domain Of The Human		4e-04
1chc_A	68	Structure Of The C3hc4 Domain By 1h-Nuclear Magneti		4e-04

>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 = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 4/64 (6%)
Query: 4  GQLGVSPTKETLLGVGCICPICHDEF---KTPVQLTCCHIFCESCVTKWFDREQTCPLCR 60
          G  G S T+E + G G  CP+C +++   ++  QL C H+F +SC+  W ++  +CP+CR
Sbjct: 1  GSSGSSGTEEHV-GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 59
Query: 61 ATLV 64
           +L 
Sbjct: 60 KSLT 63

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          C IC + F   V L C H FC  C+ +W  R+  CP+CR  +
Sbjct: 56 CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDI 97

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          C IC + F   V L C H FC  C+ +W  R+  CP+CR  +
Sbjct: 56 CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDI 97

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 22  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
           C IC + F   V L C H FC  C+ +W  R+  CP+CR  +
Sbjct: 67  CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring Finger Protein 141 Length = 70

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 64
          C IC D  +  + L C H FC+ C+ KW DR + CP+CR  + 
Sbjct: 18 CCICMD-GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMT 59

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ---TCPLCRATLVDDPAWRDGATSYFV 78
          CPIC +  K PV   C HIFC+ C+ K  ++++    CPLC+  +           S  V
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLV 83
Query: 79 Q 79
          +
Sbjct: 84 E 84

>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human Tripartite Motif-Containing Protein 39 Length = 58

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 4  GQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWF---DREQTCPLC 59
          G  G S   E L  V   C +C +  K PV + C H FC++C+T+W+   +R+  CP+C
Sbjct: 1  GSSGSSGALENL-QVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58

>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic Resonance Spectroscopy; A New Structural Class Of Zinc- Finger Length = 68

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 22 CPIC-HDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          CPIC  D     + L C H FC  C+T+W  +  TCPLC+  +
Sbjct: 8  CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	81
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-15
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	7e-15
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	7e-15
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	1e-14
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-13
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-12
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	3e-12
1z6u_A	150	NP95-like ring finger protein isoform B; structura	3e-12
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	4e-12
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	4e-12
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	5e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	6e-12
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	9e-12
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-11
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	6e-11
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	1e-10
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	1e-10
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-10
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	4e-10
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	4e-10
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	7e-10
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	1e-09
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	1e-09
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-09
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	3e-09
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	4e-09
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	4e-09
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	4e-09
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	5e-09
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	7e-09
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	1e-08
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	1e-08
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	2e-08
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	2e-08
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	2e-08
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	5e-08
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	9e-08
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-07
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	2e-07
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-07
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	2e-07
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-07
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	4e-07
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	6e-07
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	7e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	9e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	2e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	8e-05
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	3e-06
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	4e-06
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	1e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-05
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-04
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	1e-04
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-04
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	5e-04
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	5e-04
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	8e-04

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

 Score = 65.8 bits (160), Expect = 1e-15
 Identities = 17/46 (36%), Positives = 23/46 (50%)

Query: 22  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 67
           C IC + F   V L C H FC  C+ +W  R+  CP+CR  +    
Sbjct: 67  CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKT 112

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

 Score = 61.8 bits (150), Expect = 7e-15
 Identities = 17/45 (37%), Positives = 21/45 (46%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
          C IC      PV L C H+FC  CV       + C LCR  + +D
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED 62

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

 Score = 62.2 bits (151), Expect = 7e-15
 Identities = 16/40 (40%), Positives = 19/40 (47%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
          C IC   F+ PV   C H FCESC  + F     C +C  
Sbjct: 18 CFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQ 57

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

 Score = 61.3 bits (149), Expect = 1e-14
 Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 4  GQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          G  G S   + L      C IC D     + L C H FC+ C+ KW DR + CP+CR  +
Sbjct: 1  GSSGSSGRVKQL-TDEEECCICMDGRA-DLILPCAHSFCQKCIDKWSDRHRNCPICRLQM 58

Query: 64 VDD 66
             
Sbjct: 59 TGA 61

>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 = 62.1 bits (150), Expect = 3e-13
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 22  CPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATL 63
           C IC +  K      C H+ C SC+T W + E Q CP CR  +
Sbjct: 335 CKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 57.1 bits (138), Expect = 1e-12
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 63
           C IC + F   + +  C H +C  C+ K+   +  CP C  T+
Sbjct: 24 RCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

>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 = 56.1 bits (135), Expect = 3e-12
 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ-TCPLCRATL 63
          C IC ++ +       C  + C SC+ +W   ++  CP CRA L
Sbjct: 25 CFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

>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 = 56.9 bits (137), Expect = 3e-12
 Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 22  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATLVDDPA 68
           C  C +    PV   C H  C+ C+ + F  +  +CP CR  L  +  
Sbjct: 81  CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYI 128

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

 Score = 54.8 bits (132), Expect = 4e-12
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 63
          +C IC         +T C H FC+SC+ + F     CP C   +
Sbjct: 17 LCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

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

 Score = 54.7 bits (132), Expect = 4e-12
 Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRA 61
          CPIC ++         C H FC  C+T+W  +  TCPLC+ 
Sbjct: 8  CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKV 48

>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 = 55.6 bits (134), Expect = 5e-12
 Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 63
          +C +C   F     +  C H FC++C+ ++ +  + CP+C   +
Sbjct: 17 MCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 54.1 bits (130), Expect = 6e-12
 Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 7/49 (14%)

Query: 22 CPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          CPIC D +          V   C H+FC  C+        TCP CR  +
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 54.0 bits (130), Expect = 9e-12
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ--TCPLCRATLVDDPA 68
          C IC D     V + CC + +C+ C+          TCP C    V   A
Sbjct: 18 CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 67

>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 = 55.0 bits (132), Expect = 1e-11
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 22  CPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPAWR 70
           C  C +    P+   C H  C+ C+ + F  +  +CP CR  L    A +
Sbjct: 55  CICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQ 104

>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 = 52.5 bits (126), Expect = 3e-11
 Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 7/49 (14%)

Query: 22 CPICHDEFKTPVQ-------LTCCHIFCESCVTKWFDREQTCPLCRATL 63
          CPIC D +   VQ         C H+FC  C+        TCP CR  +
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

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

 Score = 51.7 bits (124), Expect = 6e-11
 Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 7/49 (14%)

Query: 22 CPICHDEFKTPVQ-------LTCCHIFCESCVTKWFDREQTCPLCRATL 63
          CPIC D +   VQ         C H+FC  C+        TCP CR  +
Sbjct: 6  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

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

 Score = 52.0 bits (125), Expect = 1e-10
 Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 3/44 (6%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ---TCPLCRAT 62
          CPIC +  K PV   C HIFC+ C+ K  ++++    CPLC+  
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

>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 = 52.1 bits (125), Expect = 1e-10
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWF-DREQTCPLCRATLVDDPAWRD 71
           CPIC    +  VQ  C H FC++C+ K   D    CP+    L+++  + D
Sbjct: 20 ECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD 71

>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 = 50.5 bits (121), Expect = 2e-10
 Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 13 ETLLGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA 68
          E  +G G  CP+C +++    +  QL C H+F +SC+  W ++  +CP+CR +L     
Sbjct: 9  EEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT 67

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

 Score = 49.8 bits (119), Expect = 4e-10
 Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWF-DREQTCPLCRATLVDD 66
           C  CH    +P Q  C H FCESC+          C  C+ ++V D
Sbjct: 17 KCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKD 63

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

 Score = 50.1 bits (120), Expect = 4e-10
 Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 3/49 (6%)

Query: 22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDR--EQTCPLCRATLVDDP 67
          C IC D     V + CC + +C+ C+        E TCP C    V   
Sbjct: 16 CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD 64

>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 = 50.3 bits (120), Expect = 7e-10
 Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 22 CPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRAT 62
          C  C +  + PV L  C HIFC +CV+        CP+C   
Sbjct: 25 CSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTP 64

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

 Score = 49.3 bits (118), Expect = 1e-09
 Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 3/45 (6%)

Query: 22 CPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          CPIC  E+       +L C H F + CV+ W  +  TCP+CR   
Sbjct: 43 CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 87

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

 Score = 49.7 bits (118), Expect = 1e-09
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 1/48 (2%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDP 67
          +C  C +  + P Q  C H +C  C+        Q C  C    + + 
Sbjct: 33 LCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEE 80

>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 = 49.1 bits (117), Expect = 2e-09
 Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATL 63
          C C IC +    PV L C H  C+ C     ++    CP CR  +
Sbjct: 16 CQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV 60

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

 Score = 48.8 bits (116), Expect = 3e-09
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATL 63
           C IC      PV+ +C H+FC  C+ +        CP CR   
Sbjct: 25 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

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

 Score = 47.4 bits (113), Expect = 4e-09
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 6/48 (12%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT------CPLCRAT 62
           CPIC +  K PV   C H FC +C+T  ++  +       CP+CR  
Sbjct: 21 TCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVP 68

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

 Score = 47.3 bits (113), Expect = 4e-09
 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 7/48 (14%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT-------CPLCRAT 62
          CPIC +    P+ L C H  C +C+T       T       CP+C  +
Sbjct: 15 CPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGIS 62

>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 = 49.2 bits (117), Expect = 4e-09
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 21  ICPICHDEFKTPVQLTCC-HIFCESCVTK-WFDREQTCPLCRATLV 64
           +CPIC D  K  +    C H FC  C+        + CP CR  LV
Sbjct: 56  MCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 101

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

 Score = 47.0 bits (112), Expect = 5e-09
 Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 3/45 (6%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT---CPLCRAT 62
          ICPIC D  + PV + C H FC  C+T+  +       CPLC+ +
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTS 66

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

 Score = 46.7 bits (111), Expect = 7e-09
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 22 CPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 67
          C +C ++FK         C H F   C+ KW +  + CPLC   ++   
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA 66

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

 Score = 46.5 bits (111), Expect = 1e-08
 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 6/48 (12%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT------CPLCRAT 62
           CPIC +    P+ L C H FC++C+T    +         CP+CR +
Sbjct: 21 TCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRIS 68

>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 Length = 968

 Score = 48.6 bits (115), Expect = 1e-08
 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 1/47 (2%)

Query: 21  ICPICHDEFKTPVQLTCCHIFCE-SCVTKWFDREQTCPLCRATLVDD 66
           + P+ +   K PV L    +  + S +      + T P  R  L  +
Sbjct: 893 LDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLE 939

>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 = 44.9 bits (107), Expect = 2e-08
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 22 CPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          CPIC ++  T       L C H+   +C  +       CPLC    
Sbjct: 8  CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

>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 = 48.0 bits (113), Expect = 2e-08
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 5/48 (10%)

Query: 21  ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQT--CPL--CRATL 63
            CPI    ++ P+    C H+F    +  +     T  CP   C   +
Sbjct: 183 TCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVV 230

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

 Score = 44.7 bits (106), Expect = 2e-08
 Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 3/40 (7%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
          C  C  E K P  L C H  C  C+         CP+C+A
Sbjct: 9  CQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQA 45

>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.20A {Homo sapiens} Length = 170

 Score = 46.2 bits (109), Expect = 5e-08
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRD 71
           CPIC    +  VQ  C H FC++C+ K        CP+    L+++  + D
Sbjct: 20 ECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD 71

>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 Length = 100

 Score = 44.3 bits (105), Expect = 9e-08
 Identities = 11/46 (23%), Positives = 16/46 (34%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
            P+       PV+L    I   S + +      T P  R TL + 
Sbjct: 31 RDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTES 76

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

 Score = 43.2 bits (102), Expect = 2e-07
 Identities = 15/46 (32%), Positives = 17/46 (36%), Gaps = 7/46 (15%)

Query: 22 CPICHDEFK----TPVQLTCCHIFCESCVTKWFDREQ---TCPLCR 60
          CPIC + F      P  L C H  C  C+ K          CP C 
Sbjct: 18 CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus} Length = 85

 Score = 43.1 bits (102), Expect = 2e-07
 Identities = 9/46 (19%), Positives = 15/46 (32%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
            P+       PV+L    +   S + +      T P  R  L + 
Sbjct: 16 RDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTES 61

>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 = 42.7 bits (101), Expect = 2e-07
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 22 CPICHDEFKTPV---QLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 67
          C IC    +      +L C H+F + CV +W    + CP+CR  +    
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQL 65

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

 Score = 42.3 bits (100), Expect = 2e-07
 Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 3/42 (7%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLC 59
           C +C +  K PV + C H FC++C+T+W++   R+  CP+C
Sbjct: 17 SCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58

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

 Score = 42.3 bits (100), Expect = 3e-07
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 22 CPICHDEFKTPV---QLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA 68
          C +C  +F++      L C H F   CV KW    +TCP+CRA       
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPSSG 75

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

 Score = 42.0 bits (99), Expect = 4e-07
 Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT---CPLC 59
          ICPIC D  + PV + C H FC  C+T+  +       CPLC
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A Length = 61

 Score = 41.6 bits (98), Expect = 6e-07
 Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 63
          +C I     + PV       IF +S + ++       P+    L
Sbjct: 5  LCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL 48

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

 Score = 41.8 bits (98), Expect = 7e-07
 Identities = 15/47 (31%), Positives = 19/47 (40%), Gaps = 4/47 (8%)

Query: 22 CPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 64
          C  C  E K      V   C H F   C++ W  +   CPLC+   V
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWV 75

>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 = 41.5 bits (97), Expect = 9e-07
 Identities = 13/48 (27%), Positives = 15/48 (31%), Gaps = 3/48 (6%)

Query: 22 CPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQ--TCPLCRATLVDD 66
          C ICH          TC       CV K+F       CP C      +
Sbjct: 18 CNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE 65

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

 Score = 41.7 bits (97), Expect = 2e-06
 Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 7/49 (14%)

Query: 22 CPICHDEFK-------TPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 63
          CPIC D +          V   C H+FC  C+        TCP CR  +
Sbjct: 10 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58

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

 Score = 37.5 bits (86), Expect = 8e-05
 Identities = 17/51 (33%), Positives = 21/51 (41%), Gaps = 7/51 (13%)

Query: 20  CICPICHDEFKTPVQ-------LTCCHIFCESCVTKWFDREQTCPLCRATL 63
             CPIC D +   VQ         C H+FC  C+        TCP CR  +
Sbjct: 73  VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123

>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 Length = 98

 Score = 40.1 bits (94), Expect = 3e-06
 Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 1/47 (2%)

Query: 21 ICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDD 66
          + PI       PV L +       S + +    +QT P  R+ L  D
Sbjct: 24 LDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD 70

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

 Score = 39.1 bits (92), Expect = 4e-06
 Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 22 CPICHDEFKTPVQL----TCCHIFCESCVTKWFDREQTCPLCRATLV 64
          C +C  E +   +      C H F   CV  W     TCPLCR T+V
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 94

 Score = 39.2 bits (91), Expect = 1e-05
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 15/63 (23%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ------TCP--------LCRATLVD 65
           CPI  +E K PV+   C H + E  + +  +  Q       CP        + ++ L+ 
Sbjct: 9  TCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQ 68

Query: 66 DPA 68
          D A
Sbjct: 69 DEA 71

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

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 15/50 (30%), Positives = 17/50 (34%), Gaps = 3/50 (6%)

Query: 20  CICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDR--EQTCPLCRATLVDD 66
            IC ICH          TC       CV K+F    E  CP C      +
Sbjct: 181 KICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE 230

>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 = 36.8 bits (84), Expect = 1e-04
 Identities = 11/36 (30%), Positives = 14/36 (38%)

Query: 25  CHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 60
              E  T     C H F   C+++W    Q CPL  
Sbjct: 72  ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 65

 Score = 35.7 bits (82), Expect = 1e-04
 Identities = 17/48 (35%), Positives = 17/48 (35%), Gaps = 6/48 (12%)

Query: 22 CPICHDEFKTPVQL-----TCCHIFCESCVTKWFDREQ-TCPLCRATL 63
          CP C         L      C H  CESCV   F R    CP C   L
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

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

 Score = 37.1 bits (85), Expect = 2e-04
 Identities = 12/61 (19%), Positives = 16/61 (26%), Gaps = 19/61 (31%)

Query: 22  CPICHDEF--------KTPVQLTCCHIFCESCVTKWFDREQ-----------TCPLCRAT 62
           C IC             +     C       C+ +WF                CP C+A 
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAK 370

Query: 63  L 63
           L
Sbjct: 371 L 371

>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 = 35.6 bits (81), Expect = 2e-04
 Identities = 11/36 (30%), Positives = 14/36 (38%)

Query: 25 CHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 60
             E  T     C H F   C+++W    Q CPL  
Sbjct: 61 ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

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

 Score = 34.3 bits (78), Expect = 5e-04
 Identities = 15/52 (28%), Positives = 20/52 (38%), Gaps = 5/52 (9%)

Query: 22 CPICHDEF----KTPVQLTCCHIFCESCVTKWFDREQT-CPLCRATLVDDPA 68
          CP+C +            TC +  C  C  +    E   CP CR    +DPA
Sbjct: 14 CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA 65

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2 Length = 78

 Score = 34.1 bits (79), Expect = 5e-04
 Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDD 66
           CPI  +  K PV ++    +  S + KW D   +TCP  + TL+  
Sbjct: 10 RCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA 56

>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 = 34.4 bits (78), Expect = 8e-04
 Identities = 10/64 (15%), Positives = 15/64 (23%), Gaps = 23/64 (35%)

Query: 22 CPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDREQ-----TCPL 58
          C IC ++                          C H F   C+   +          CP 
Sbjct: 28 CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPS 87

Query: 59 CRAT 62
          C+  
Sbjct: 88 CKTI 91

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	81
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.84
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.83
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.83
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.81
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.81
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.8
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.8
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.79
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.79
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.78
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.77
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.77
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.77
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.77
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.75
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.75
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.75
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.75
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.74
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.74
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.74
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.74
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.73
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.73
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.71
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.71
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.71
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.71
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.7
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.7
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.7
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.69
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.68
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.68
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.67
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.67
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.66
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.66
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.66
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.65
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.65
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.65
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.64
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.64
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.64
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.63
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.63
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.62
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.61
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.6
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.6
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.59
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.51
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.49
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.49
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.48
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.46
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.44
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.44
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.41
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.38
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.36
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.35
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.33
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.28
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.25
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.16
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	99.15
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.9
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.72
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.7
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	98.23
3nw0_A	238	Non-structural maintenance of chromosomes element	98.08
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.75
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.45
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	96.85
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	95.94
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	95.87
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	95.73
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	94.45
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	93.72
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	92.39
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	92.13
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	91.64
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	91.11
3mjh_B	34	Early endosome antigen 1; protein-zinc finger comp	90.92
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	90.62
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	89.69
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	89.6
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	89.09
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	89.0
2o35_A	105	Hypothetical protein DUF1244; helix bundle, struct	88.62
3fyb_A	104	Protein of unknown function (DUF1244); hydrocar de	88.56
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	88.13
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	88.03
1wem_A	76	Death associated transcription factor 1; structura	88.0
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	87.95
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	87.15
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	86.98
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	86.63
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	86.34
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	86.23
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	85.58
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	85.41
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	85.08
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	85.05
3zyq_A	226	Hepatocyte growth factor-regulated tyrosine kinas	84.29
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	84.18
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	83.95
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	83.81
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	83.69
2cor_A	79	Pinch protein; LIM domain, particularly interestin	83.3
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	83.12
1z60_A	59	TFIIH basal transcription factor complex P44 subun	82.87
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	82.62
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	82.17
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	81.6
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	81.14
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	80.97
2co8_A	82	NEDD9 interacting protein with calponin homology a	80.74
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	80.22

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

Probab=99.84  E-value=1.2e-20  Score=97.13  Aligned_cols=75  Identities=25%  Similarity=0.599  Sum_probs=62.0

Q ss_pred             CCCCCCCccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhC------CCCCCCCCCCCCCCccccCcccchhh
Q psy8828           5 QLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR------EQTCPLCRATLVDDPAWRDGATSYFV   78 (81)
Q Consensus         5 ~~~~~~~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~------~~~CP~C~~~~~~~~~~~~~~~~~~~   78 (81)
                      +.+.+....+.+.+.+.|+||++.+.+|+.++|||+||..|+..|+..      ...||.|+..+......++..+.+++
T Consensus         5 ~~~~~~~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~l~~~v   84 (85)
T 2ecw_A            5 SSGMASSVLEMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNLHVANIV   84 (85)
T ss_dssp             CCCCCCCCCCCCCTTTSCTTTCSCCSSCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEECSCCCSSC
T ss_pred             cccchHHHHHhCccCCCCcCCChhhCcceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCcCHHHHHhh
Confidence            334444555667788999999999999999999999999999999986      67999999999877777777777665


Q ss_pred             h
Q psy8828          79 Q   79 (81)
Q Consensus        79 ~   79 (81)
                      +
T Consensus        85 e   85 (85)
T 2ecw_A           85 E   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

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

Probab=99.83  E-value=1.4e-20  Score=96.80  Aligned_cols=76  Identities=26%  Similarity=0.643  Sum_probs=62.5

Q ss_pred             CCCCCCCCccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhC------CCCCCCCCCCCCCCccccCcccchh
Q psy8828           4 GQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR------EQTCPLCRATLVDDPAWRDGATSYF   77 (81)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~------~~~CP~C~~~~~~~~~~~~~~~~~~   77 (81)
                      ++.+.+......+.+.+.|+||++.+.+|+.++|||+||..|+..|+..      ...||.|+..+......++..+.++
T Consensus         4 ~~~~~~~~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~l~~~   83 (85)
T 2ecv_A            4 GSSGMASGILVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRHVANI   83 (85)
T ss_dssp             CCCCCCCCCCCCCCCCCCCTTTCSCCSSCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCSCCCCCC
T ss_pred             ccccchHHHHHHccCCCCCCCCCcccCCceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCccHHHHHh
Confidence            3344444555667788999999999999999999999999999999876      6899999999987777777777766


Q ss_pred             hh
Q psy8828          78 VQ   79 (81)
Q Consensus        78 ~~   79 (81)
                      ++
T Consensus        84 ve   85 (85)
T 2ecv_A           84 VE   85 (85)
T ss_dssp             CC
T ss_pred             hC
Confidence            53

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

Probab=99.83  E-value=5.7e-21  Score=97.26  Aligned_cols=67  Identities=22%  Similarity=0.434  Sum_probs=58.9

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ...+.+.|+||++.+.+|+.++|||+||..||.+|+.. ...||.|+..+......+|..+.+.++.|
T Consensus         4 ~~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n~~l~~~i~~~   71 (78)
T 1t1h_A            4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLKSLIALW   71 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECTTTHHHHHHH
T ss_pred             CCcccCCCCCccccccCCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccCHHHHHHHHHH
Confidence            35678899999999999999999999999999999986 78999999999877777888888777654

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

Probab=99.81  E-value=1.5e-20  Score=98.35  Aligned_cols=71  Identities=23%  Similarity=0.490  Sum_probs=57.1

Q ss_pred             CCccccCCCCccccccccCCCCCeecC-CCCcccHHHHHHHHhC--CCCCCCCCCCCC-CCccccCcccchhhhc
Q psy8828          10 PTKETLLGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDR--EQTCPLCRATLV-DDPAWRDGATSYFVQI   80 (81)
Q Consensus        10 ~~~~~~~~~~~~C~iC~~~~~~p~~l~-C~h~fc~~Cl~~~~~~--~~~CP~C~~~~~-~~~~~~~~~~~~~~~~   80 (81)
                      .+....+.+.+.|+||++.+.+|++++ |||+||..||.+|+..  ...||.|+..+. ......|..+.++++.
T Consensus         4 ~~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~~~~n~~l~~~i~~   78 (92)
T 3ztg_A            4 GSEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVNN   78 (92)
T ss_dssp             SSSCCCCCTTTEETTTTEECSSCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCTTSCEECHHHHHHHHH
T ss_pred             CcccccCCcCCCCCCCChhhcCceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCccccCcCHHHHHHHHH
Confidence            344556678899999999999999999 9999999999999874  369999999973 4456667666666553

>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=99.81  E-value=4.9e-20  Score=97.61  Aligned_cols=68  Identities=19%  Similarity=0.150  Sum_probs=60.5

Q ss_pred             ccCCCCccccccccCCCCCeecCCC-CcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~-h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ....+.+.||||++++.+|++++|| |+||+.||.+|+.....||+|+.++....+.+|..+.+.++.|
T Consensus        17 ~~~p~~~~CpI~~~~m~dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn~~Lk~~I~~~   85 (98)
T 1wgm_A           17 ADACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNTELKEKIQRW   85 (98)
T ss_dssp             CSCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECHHHHHHHHHH
T ss_pred             hcCcHhcCCcCccccccCCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEcHHHHHHHHHH
Confidence            3456789999999999999999999 9999999999999888999999999888888888888777654

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

Probab=99.80  E-value=1.5e-20  Score=95.74  Aligned_cols=67  Identities=22%  Similarity=0.549  Sum_probs=57.2

Q ss_pred             ccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhC-------CCCCCCCCCCCCCCccccCcccchhh
Q psy8828          12 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-------EQTCPLCRATLVDDPAWRDGATSYFV   78 (81)
Q Consensus        12 ~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~-------~~~CP~C~~~~~~~~~~~~~~~~~~~   78 (81)
                      ..+.+++.+.|+||++.+.+|+.++|||+||..|+.+|+..       ...||.||..+.......|..+.+++
T Consensus         5 ~~~~~~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~lv   78 (79)
T 2egp_A            5 SSGNVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQANQHLANIV   78 (79)
T ss_dssp             SSCCCCCCCEETTTTEECSSCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGTCSSSCCCC
T ss_pred             hHhhcccCCCCcCCCcccCCeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCcCHHHHHhh
Confidence            34456678899999999999999999999999999999886       57899999999877777777776665

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

Probab=99.80  E-value=1.6e-19  Score=90.74  Aligned_cols=61  Identities=25%  Similarity=0.603  Sum_probs=52.4

Q ss_pred             CCCccccCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccc
Q psy8828           9 SPTKETLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   69 (81)
Q Consensus         9 ~~~~~~~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~   69 (81)
                      +....+.+++.+.|+||++.+.+|+.+ +|||+||..||.+|+..+..||+||+.+...+..
T Consensus         5 ~~~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A            5 SSGNLSELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             CCCCCCCCCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSC
T ss_pred             chhhHhhcCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccc
Confidence            344555667889999999999999987 9999999999999999889999999998765443

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

Probab=99.79  E-value=4.6e-20  Score=95.49  Aligned_cols=68  Identities=15%  Similarity=0.099  Sum_probs=60.1

Q ss_pred             ccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ....+.+.|+||++.+.+|++++|||+||+.||.+|+....+||+|+.++....+.+|..+.+.++.|
T Consensus         9 ~~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn~~L~~~i~~~   76 (85)
T 2kr4_A            9 SDAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPVPELKEQIQAW   76 (85)
T ss_dssp             TTCCTTTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHHHHH
T ss_pred             hcCchheECcccCchhcCCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchHHHHHHHHHHH
Confidence            34567899999999999999999999999999999999888999999999877788888887777654

>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=99.79  E-value=1.3e-19  Score=96.29  Aligned_cols=67  Identities=18%  Similarity=0.113  Sum_probs=60.0

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ...+.+.||||++++.+|++++|||+||+.||.+|+.....||.|+.++....+.+|..+.+.++.|
T Consensus        25 ~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn~~Lk~~I~~~   91 (100)
T 2kre_A           25 DAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVPELKEQIQAW   91 (100)
T ss_dssp             SCSTTTBCTTTCSBCSSEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEECHHHHHHHHHH
T ss_pred             cCcHhhCCcCccCcccCCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceECHHHHHHHHHH
Confidence            4467899999999999999999999999999999999889999999999888888888887777654

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

Probab=99.78  E-value=2.1e-20  Score=98.98  Aligned_cols=67  Identities=21%  Similarity=0.542  Sum_probs=56.6

Q ss_pred             ccCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhc
Q psy8828          14 TLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   80 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~   80 (81)
                      +.+.+.+.|+||++.+.+|+.+ +|||+||..|+.+|+..+..||.|+..+.......|..+.++++.
T Consensus        17 ~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~~i~~   84 (99)
T 2y43_A           17 KTIDDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNNRILDELVKS   84 (99)
T ss_dssp             HHHHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECHHHHHHHHH
T ss_pred             HhCCCCCCcccCChhhCCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCCcCHHHHHHHHH
Confidence            3345678999999999999988 899999999999999988999999999887666667766666553

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

Probab=99.77  E-value=4.9e-19  Score=90.68  Aligned_cols=53  Identities=30%  Similarity=0.666  Sum_probs=47.7

Q ss_pred             ccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          12 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        12 ~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ..+...+.+.|+||++.+.+|++++|||+||..|+.+|+.....||+|+..+.
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A            8 GSEEEEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CSSCCCCCSBCSSSCSBCCSEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CcccCCCCCCCcCCCchhcCeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            33455667899999999999999999999999999999998899999999986

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

Probab=99.77  E-value=1.5e-18  Score=87.16  Aligned_cols=56  Identities=34%  Similarity=0.757  Sum_probs=48.3

Q ss_pred             ccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHh---CCCCCCCCCCCCCCCc
Q psy8828          12 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLCRATLVDDP   67 (81)
Q Consensus        12 ~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~---~~~~CP~C~~~~~~~~   67 (81)
                      ....+.+.+.|+||++.+.+|+.++|||+||..|+.+|+.   ....||+||+.+....
T Consensus        13 ~~~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           13 FVNKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCCCCCBCTTTCSBCSSEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             HHHhCccCCEeccCCcccCCeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            3455677899999999999999999999999999999997   4568999999986543

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

Probab=99.77  E-value=1e-18  Score=86.39  Aligned_cols=56  Identities=29%  Similarity=0.622  Sum_probs=48.5

Q ss_pred             ccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCCCc
Q psy8828          12 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDP   67 (81)
Q Consensus        12 ~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~~   67 (81)
                      ......+.+.|+||++.+.+|+.++|||+||..|+.+|+. ....||.|++.+....
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A            8 FVKTVEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             SCCSCCCCEECTTTCCEESSCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             hhhcCCcCCCCCCCChHhcCeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            3445567899999999999999999999999999999995 5679999999987654

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

Probab=99.77  E-value=8.2e-19  Score=88.55  Aligned_cols=56  Identities=23%  Similarity=0.628  Sum_probs=48.1

Q ss_pred             CCccccCCCCccccccccCCCCCeecC-CCCcccHHHHHHHHhCC--CCCCCCCCCCCC
Q psy8828          10 PTKETLLGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE--QTCPLCRATLVD   65 (81)
Q Consensus        10 ~~~~~~~~~~~~C~iC~~~~~~p~~l~-C~h~fc~~Cl~~~~~~~--~~CP~C~~~~~~   65 (81)
                      ....+.+.+.+.|+||++.+.+|+.++ |||+||..||.+|+..+  ..||+||+.+..
T Consensus         6 ~~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A            6 SGEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CSCCCCSCGGGSCSSSCCCCTTCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             ccccccCCCCCCCcCCChHHhCCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            334456677899999999999999999 99999999999999854  689999998654

>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=99.75  E-value=4.1e-20  Score=98.16  Aligned_cols=65  Identities=22%  Similarity=0.498  Sum_probs=54.8

Q ss_pred             ccCCCCccccccccCCCCCee-cCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCCccccCcccchhh
Q psy8828          14 TLLGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFV   78 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~-l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~~~~~~~~~~~~~   78 (81)
                      ..+.+.+.|+||++.+.+|+. ++|||+||..||.+|+... ..||.||.++....+..+..+..+.
T Consensus        17 ~~l~~~~~C~IC~~~~~~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~i~   83 (100)
T 3lrq_A           17 ESIAEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRWAEEVT   83 (100)
T ss_dssp             HHHHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECTTHHHHH
T ss_pred             ccCCCCCCCccCCccccCccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHhhHHHHHHH
Confidence            445667899999999999999 8999999999999999977 7999999999776666666555544

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

Probab=99.75  E-value=1.3e-18  Score=87.12  Aligned_cols=53  Identities=32%  Similarity=0.589  Sum_probs=47.3

Q ss_pred             ccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ....+.+.|+||++.+.+++.++|||.||..|+.+|+.....||+||..+...
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           10 APSLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             CSSSSCCBCSSSSSBCSSEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             ccCCCCCCCccCCcccCCCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            34456789999999999999999999999999999999889999999988643

>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=99.75  E-value=5.5e-19  Score=96.84  Aligned_cols=64  Identities=20%  Similarity=0.481  Sum_probs=53.3

Q ss_pred             CCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCC-CccccCcccchhhh
Q psy8828          16 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVD-DPAWRDGATSYFVQ   79 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~-~~~~~~~~~~~~~~   79 (81)
                      +.+.+.|+||++.+.+|+.++|||+||..||.+|+... ..||.||..+.. .....|..+.++++
T Consensus        49 ~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~n~~l~~~i~  114 (124)
T 3fl2_A           49 VEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQTVLN  114 (124)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTCCCCCCHHHHHHHH
T ss_pred             CccCCCCCcCChHHcCcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCCCCCCCCCHHHHHHHH
Confidence            34568999999999999999999999999999999854 599999999976 45566666666554

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

Probab=99.75  E-value=4.1e-18  Score=88.15  Aligned_cols=57  Identities=28%  Similarity=0.637  Sum_probs=48.8

Q ss_pred             CCccccCCCCccccccccCCCC----CeecCCCCcccHHHHHHHHhCC---CCCCCCCCCCCCC
Q psy8828          10 PTKETLLGVGCICPICHDEFKT----PVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDD   66 (81)
Q Consensus        10 ~~~~~~~~~~~~C~iC~~~~~~----p~~l~C~h~fc~~Cl~~~~~~~---~~CP~C~~~~~~~   66 (81)
                      ....+...+.+.|+||++.+.+    |+.++|||+||..|+.+|+..+   ..||.||..+...
T Consensus         6 ~~~~~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A            6 SGNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCSCCCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             ccChhhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            3344566778899999999998    8999999999999999999865   7999999987654

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

Probab=99.74  E-value=7.4e-18  Score=82.52  Aligned_cols=49  Identities=39%  Similarity=0.813  Sum_probs=42.9

Q ss_pred             CccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHh---CCCCCCCC
Q psy8828          11 TKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLC   59 (81)
Q Consensus        11 ~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~---~~~~CP~C   59 (81)
                      ...+.+++.+.|+||++.+.+|+.++|||+||..||.+|+.   ....||+|
T Consensus        12 ~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           12 QFVNKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCCCCCBCTTTCSBCSSCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             HHHHhCccCCCCCcCCchhCCeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            34456678899999999999999999999999999999998   45689987

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

Probab=99.74  E-value=4.5e-18  Score=86.43  Aligned_cols=61  Identities=31%  Similarity=0.897  Sum_probs=50.1

Q ss_pred             CccccCCCCccccccccCCCCC---eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccC
Q psy8828          11 TKETLLGVGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   71 (81)
Q Consensus        11 ~~~~~~~~~~~C~iC~~~~~~p---~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~   71 (81)
                      ...+...+...|+||++.+.++   +.++|+|.||..||.+|+..+..||+||+.+.......+
T Consensus         7 ~~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (78)
T 2ect_A            7 GTEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN   70 (78)
T ss_dssp             CCCTTSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCC
T ss_pred             CCcccCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCC
Confidence            3444556778999999999866   446999999999999999988999999999877655443

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

Probab=99.74  E-value=1.8e-18  Score=85.83  Aligned_cols=54  Identities=30%  Similarity=0.729  Sum_probs=46.8

Q ss_pred             ccccCCCCccccccccCCCCC-------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          12 KETLLGVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        12 ~~~~~~~~~~C~iC~~~~~~p-------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ......+...|+||++.+.++       +.++|||.||..||.+|+..+..||+||..+..
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A            8 TGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cccCCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            344556788999999999876       778999999999999999988999999998754

>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=99.74  E-value=1.1e-18  Score=94.95  Aligned_cols=68  Identities=25%  Similarity=0.550  Sum_probs=56.2

Q ss_pred             CccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCC-CCCCCCCCCCCCccccCcccchhh
Q psy8828          11 TKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATLVDDPAWRDGATSYFV   78 (81)
Q Consensus        11 ~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~-~CP~C~~~~~~~~~~~~~~~~~~~   78 (81)
                      .....+.+.+.|+||++.+.+|+.++|||+||..||.+|+..+. .||.||..+......++..+.+.+
T Consensus        10 ~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~l~~~i   78 (118)
T 3hct_A           10 EFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREI   78 (118)
T ss_dssp             CBSSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHH
T ss_pred             hhccCCCCCCCCCcCChhhcCeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhcccCHHHHHHH
Confidence            34556778899999999999999999999999999999998654 999999998776666665554444

>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=99.73  E-value=7.6e-19  Score=94.26  Aligned_cols=65  Identities=23%  Similarity=0.644  Sum_probs=53.2

Q ss_pred             ccCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCC----ccccCcccchhh
Q psy8828          14 TLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDD----PAWRDGATSYFV   78 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~----~~~~~~~~~~~~   78 (81)
                      +.+.+.+.|+||++.+.+|+.+ +|||+||..||..|+..+..||.|+..+...    ....+..+.+++
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~l~~n~~l~~~i   79 (108)
T 2ckl_A           10 TELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIV   79 (108)
T ss_dssp             HHHGGGTBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSSCGGGGEEECHHHHHHH
T ss_pred             hccCCcCCCccCChHHhCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCccccccCcccccCcCHHHHHHH
Confidence            4456788999999999999998 9999999999999999989999999998754    333444444443

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

Probab=99.73  E-value=2.1e-18  Score=86.15  Aligned_cols=54  Identities=30%  Similarity=0.734  Sum_probs=47.1

Q ss_pred             CCCCccccccccCCCCC-------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccc
Q psy8828          16 LGVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   69 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p-------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~   69 (81)
                      ..+.+.|+||++.+.++       +.++|||+||..|+.+|+..+..||+||+.+......
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhhee
Confidence            34677999999999887       7889999999999999999889999999998765443

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

Probab=99.71  E-value=4.5e-18  Score=94.76  Aligned_cols=50  Identities=34%  Similarity=0.928  Sum_probs=45.7

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ++.+.|+||++.+.+|+.++|||+||..||.+|+..+..||.||+++...
T Consensus        51 ~~~~~C~iC~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           51 ENELQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHHSBCTTTCSBCSSEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cccCCCcccCcccCCceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            34578999999999999999999999999999999999999999998653

>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=99.71  E-value=8.9e-18  Score=90.33  Aligned_cols=63  Identities=32%  Similarity=0.704  Sum_probs=52.9

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC---CCCCCCCCCCCCCccccCcccchhhh
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDDPAWRDGATSYFVQ   79 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~---~~CP~C~~~~~~~~~~~~~~~~~~~~   79 (81)
                      .+.+.|+||++.+.+|+.++|||+||..|+.+|+...   ..||.|+..+.......+..+.++++
T Consensus        19 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~~~~l~~~~~   84 (112)
T 1jm7_A           19 QKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVE   84 (112)
T ss_dssp             HHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCCSSSHHHH
T ss_pred             cCCCCCcccChhhcCeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCccHHHHHHHH
Confidence            4567999999999999999999999999999999865   48999999998776666666555544

>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=99.71  E-value=7e-18  Score=95.23  Aligned_cols=65  Identities=23%  Similarity=0.596  Sum_probs=54.0

Q ss_pred             CCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCC-ccccCcccchhhhc
Q psy8828          16 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDD-PAWRDGATSYFVQI   80 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~-~~~~~~~~~~~~~~   80 (81)
                      +.+.+.|+||++.+.+|++++|||+||..||.+|+... ..||+||..+... ....|..+.++++.
T Consensus        75 l~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~l~~n~~l~~lv~~  141 (150)
T 1z6u_A           75 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIMIPNEILQTLLDL  141 (150)
T ss_dssp             HHHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTCCCCBCHHHHHHHHH
T ss_pred             CccCCEeecCChhhcCCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCCCCCCCCHHHHHHHHH
Confidence            34567999999999999999999999999999999865 4899999999876 55566666666543

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

Probab=99.71  E-value=2.4e-17  Score=79.30  Aligned_cols=49  Identities=37%  Similarity=1.016  Sum_probs=42.1

Q ss_pred             CccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHh---CCCCCCCC
Q psy8828          11 TKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLC   59 (81)
Q Consensus        11 ~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~---~~~~CP~C   59 (81)
                      ...+...+.+.|+||++.+.+|+.++|||+||..||.+|+.   ....||+|
T Consensus         7 ~~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A            7 GALENLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCSSCSCCCCBCSSSCCBCSSCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             hHhhccccCCCCccCCcccCccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            44455667889999999999999999999999999999954   55789987

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

Probab=99.70  E-value=3.2e-17  Score=82.47  Aligned_cols=55  Identities=31%  Similarity=0.818  Sum_probs=46.4

Q ss_pred             ccccCCCCccccccccCCCCCeec---CCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          12 KETLLGVGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        12 ~~~~~~~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ..........|+||++.+.++..+   +|+|.||..||.+|+..+..||+||+.+...
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A            8 KVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCCCCCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             ccccCCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            344556678999999999876544   9999999999999999888999999998654

>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=99.70  E-value=7.8e-19  Score=95.10  Aligned_cols=52  Identities=29%  Similarity=0.754  Sum_probs=45.7

Q ss_pred             ccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVD   65 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~   65 (81)
                      ....+.+.|+||++.+.+|+.++|||+||..||.+|+.. ...||.||..+..
T Consensus        10 ~~~~~~~~C~iC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           10 IPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CCCHHHHBCTTTCSBCSSCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             cCCCCCCCCccCCcccCceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            344567899999999999999999999999999999876 5789999998753

>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=99.70  E-value=2.1e-19  Score=97.71  Aligned_cols=65  Identities=26%  Similarity=0.519  Sum_probs=54.8

Q ss_pred             cccCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhh
Q psy8828          13 ETLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ   79 (81)
Q Consensus        13 ~~~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~   79 (81)
                      ...+.+.+.|+||++.+.+|+.+ +|||+||..||..|+.  ..||.|+..+.......+..+.++++
T Consensus        16 ~~~l~~~~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~n~~l~~l~~   81 (117)
T 1jm7_B           16 LDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINRQLDSMIQ   81 (117)
T ss_dssp             HHHHHHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCCHHHHHHHH
T ss_pred             HHhchhCCCCCCCChHhhCccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccccccccHHHHHHHH
Confidence            34456788999999999999999 9999999999999987  78999999987666666766666654

>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=99.69  E-value=5.2e-18  Score=89.17  Aligned_cols=65  Identities=26%  Similarity=0.540  Sum_probs=54.4

Q ss_pred             CCCCccccccccCCCCCeecC-CCCcccHHHHHHHHhCC------CCCCC--CCCC-CCCCccccCcccchhhhc
Q psy8828          16 LGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE------QTCPL--CRAT-LVDDPAWRDGATSYFVQI   80 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~-C~h~fc~~Cl~~~~~~~------~~CP~--C~~~-~~~~~~~~~~~~~~~~~~   80 (81)
                      ..+.+.||||++++.+|++++ |||+||+.||.+|+..+      ..||+  |+.. +....+.+|..+.+.++.
T Consensus         4 ~~~~~~CPI~~~~~~dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~pn~~L~~~I~~   78 (94)
T 2yu4_A            4 GSSGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQDEALRRAIEN   78 (94)
T ss_dssp             CSSCCBCTTTCSBCSSEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEECHHHHHHHHH
T ss_pred             CCcEeECcCcCchhcCCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcCCHHHHHHHHH
Confidence            456789999999999999996 99999999999999753      58999  8876 766677778777777654

>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=9.6e-17  Score=79.74  Aligned_cols=53  Identities=28%  Similarity=0.727  Sum_probs=44.6

Q ss_pred             ccCCCCccccccccCCCC---CeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~---p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ........|+||++.+..   ++.++|||.||..||.+|+..+..||+||..+...
T Consensus         9 ~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A            9 TEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             CSTTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CcCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            344566799999998853   46789999999999999999888999999988653

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

Probab=99.68  E-value=1.2e-17  Score=81.77  Aligned_cols=51  Identities=31%  Similarity=0.801  Sum_probs=45.1

Q ss_pred             CCccccccccCCCCC-------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcc
Q psy8828          18 VGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   68 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p-------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~   68 (81)
                      +.+.|+||++.+.++       +.++|||.||..|+.+|+..+..||.||+.+.....
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   59 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   59 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccce
Confidence            467899999999876       678999999999999999999999999999876543

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

Probab=99.67  E-value=5.6e-17  Score=77.32  Aligned_cols=48  Identities=40%  Similarity=0.884  Sum_probs=42.5

Q ss_pred             CCCccccccccCCCC---CeecC-CCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKT---PVQLT-CCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~---p~~l~-C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ++...|+||++.+.+   ++.++ |||.||..|+.+|++.+..||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            456789999999987   66776 9999999999999999999999998764

>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=99.67  E-value=2.5e-17  Score=99.81  Aligned_cols=67  Identities=12%  Similarity=0.122  Sum_probs=57.4

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ...+.+.|+||++.+.+|++++|||+||+.||.+|+..+ ..||+|+.++....+.+|..+.+.++.|
T Consensus       204 ~~~~~~~c~i~~~~~~dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n~~l~~~i~~~  271 (281)
T 2c2l_A          204 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAF  271 (281)
T ss_dssp             CCCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHHHHHHHHHH
T ss_pred             CCCcccCCcCcCCHhcCCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCcccHHHHHHHHHH
Confidence            345678999999999999999999999999999999854 4599999999877788888877776643

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

Probab=99.66  E-value=2.5e-17  Score=82.08  Aligned_cols=53  Identities=36%  Similarity=0.842  Sum_probs=46.8

Q ss_pred             cccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          13 ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        13 ~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      .....+...|+||++.+.+ +.++|||.||..|+.+|+.....||+||..+...
T Consensus         9 ~~~~~~~~~C~IC~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (70)
T 2ecn_A            9 VKQLTDEEECCICMDGRAD-LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGA   61 (70)
T ss_dssp             CCCCCCCCCCSSSCCSCCS-EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCC
T ss_pred             hhcCCCCCCCeeCCcCccC-cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCC
Confidence            3445667899999999999 8899999999999999999899999999988754

>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=99.66  E-value=1.4e-17  Score=95.00  Aligned_cols=62  Identities=29%  Similarity=0.693  Sum_probs=49.8

Q ss_pred             CCCccccccccCCCCCeec-CCCCcccHHHHHHHHhC-CCCCCCCCCCCCCC-ccccCcccchhh
Q psy8828          17 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDR-EQTCPLCRATLVDD-PAWRDGATSYFV   78 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~~-~~~~~~~~~~~~   78 (81)
                      .+.+.|+||++.+.+|+.+ +|||+||..||.+|+.. ...||.|+..+... ....+..+.+++
T Consensus        52 ~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~l~~~~~l~~~i  116 (165)
T 2ckl_B           52 HSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALI  116 (165)
T ss_dssp             HHHHBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCSGGGEEECHHHHHHH
T ss_pred             CCCCCCcccChHhhCcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCCcccCCcCHHHHHHH
Confidence            4557999999999999988 99999999999999996 68899999998543 334444444444

>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=99.66  E-value=3.6e-17  Score=93.68  Aligned_cols=68  Identities=25%  Similarity=0.537  Sum_probs=55.3

Q ss_pred             CCccccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCCccccCcccchh
Q psy8828          10 PTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYF   77 (81)
Q Consensus        10 ~~~~~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~~~~~~~~~~~~   77 (81)
                      ......+.+.+.|+||++.+.+|++++|||+||..|+.+|+..+ ..||.||..+......++..+.+.
T Consensus         9 ~~~~~~~~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~   77 (170)
T 3hcs_A            9 VEFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKRE   77 (170)
T ss_dssp             SEESSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHH
T ss_pred             hhhccCCCCCCCCCCCChhhcCcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhhhHHHHHH
Confidence            33455677889999999999999999999999999999999854 499999999877655555444433

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

Probab=99.65  E-value=6.3e-17  Score=81.67  Aligned_cols=51  Identities=33%  Similarity=0.803  Sum_probs=44.7

Q ss_pred             CCCCccccccccCCCCC---eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p---~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ..+...|+||++.+.++   +.++|+|.||..||.+|+..+..||+||+.+...
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            34567999999999887   6679999999999999999889999999988653

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

Probab=99.65  E-value=1.3e-16  Score=83.27  Aligned_cols=49  Identities=37%  Similarity=0.981  Sum_probs=43.5

Q ss_pred             CCCccccccccCCCC---CeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~---p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      .+...|+||++.+.+   ++.++|||.||..||.+|+..+..||+||..+..
T Consensus        38 ~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           38 GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            456789999999887   6678999999999999999999999999998764

>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=99.65  E-value=1.2e-16  Score=76.12  Aligned_cols=47  Identities=28%  Similarity=0.704  Sum_probs=41.6

Q ss_pred             CCccccccccCCCC----CeecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~----p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      +...|+||++.+.+    ++.++|||.||..|+.+|+..+..||+||+.+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            45689999999866    667799999999999999998899999998764

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

Probab=99.64  E-value=1.9e-16  Score=77.87  Aligned_cols=51  Identities=33%  Similarity=0.753  Sum_probs=42.6

Q ss_pred             CCcccccccc-CCCCC----eecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCCCcc
Q psy8828          18 VGCICPICHD-EFKTP----VQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPA   68 (81)
Q Consensus        18 ~~~~C~iC~~-~~~~p----~~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~~~~   68 (81)
                      +++.|+||++ .+.+|    +.++|||+||..|+.+|+.+ ...||.|++.+.....
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   58 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccc
Confidence            3578999999 88888    45799999999999999664 4689999999876544

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

Probab=99.64  E-value=1.4e-16  Score=78.86  Aligned_cols=48  Identities=38%  Similarity=0.993  Sum_probs=43.4

Q ss_pred             CCccccccccCCCCC-eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTP-VQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p-~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ....|+||++.+.++ +.++|||.||..|+.+|+..+..||.||..+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccCCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            456899999999997 677999999999999999988999999998864

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

Probab=99.64  E-value=9.2e-17  Score=92.75  Aligned_cols=68  Identities=13%  Similarity=0.128  Sum_probs=58.4

Q ss_pred             ccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ....+.+.||||++++.+|++++|||+||+.||.+|+..+ .+||+|+.++....+.+|..+.+.++.|
T Consensus       101 ~~ip~~f~CPI~~elm~DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN~~Lk~~Ie~~  169 (179)
T 2f42_A          101 REIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMKEVIDAF  169 (179)
T ss_dssp             CCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECHHHHHHHHHH
T ss_pred             cCCcHhhcccCccccCCCCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcchHHHHHHHHHH
Confidence            3456789999999999999999999999999999999853 4699999999877788888887777643

>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=99.63  E-value=6.6e-17  Score=87.57  Aligned_cols=54  Identities=26%  Similarity=0.659  Sum_probs=47.2

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCCCcc
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPA   68 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~~~~   68 (81)
                      .+.+.+.|+||++.+.+|+.++|||+||..||.+|+.. ...||.|+..+.....
T Consensus        19 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   73 (116)
T 1rmd_A           19 HFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (116)
T ss_dssp             HHHHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             hccCCCCCCCCCcHhcCcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhc
Confidence            34557899999999999999999999999999999986 6799999999876543

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

Probab=99.63  E-value=1.4e-16  Score=87.51  Aligned_cols=52  Identities=31%  Similarity=0.782  Sum_probs=46.6

Q ss_pred             CCCccccccccCCCCC-------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcc
Q psy8828          17 GVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   68 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p-------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~   68 (81)
                      .+.+.|+||++.+.+|       +.++|||+||..||.+|+..+..||+|++.+.....
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            4578999999999988       888999999999999999999999999999876543

>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=99.62  E-value=4e-17  Score=91.32  Aligned_cols=51  Identities=25%  Similarity=0.680  Sum_probs=45.2

Q ss_pred             ccCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLV   64 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~   64 (81)
                      ..+++.+.|+||++.+.+|++++|||+||..||.+|+... ..||.||.++.
T Consensus        26 ~~l~~~~~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           26 TKLEAKYLCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             GGCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             ccCCcCcCCCCCChhhcCcEECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            3456789999999999999999999999999999999865 48999998753

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

Probab=99.61  E-value=8.3e-16  Score=78.72  Aligned_cols=49  Identities=29%  Similarity=0.710  Sum_probs=41.5

Q ss_pred             CCccccccccCCCC--------------Ceec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT--------------PVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~--------------p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ++..|+||++.+.+              ++.+ +|+|.||..||.+|+..+.+||+||+++...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            46689999999976              3444 5999999999999999999999999987643

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

Probab=99.60  E-value=3.5e-16  Score=75.03  Aligned_cols=47  Identities=30%  Similarity=0.636  Sum_probs=41.3

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      .+.+.|+||++.+.+|+.++|||+||..|+..   ....||+||+.+...
T Consensus         4 ~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~---~~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBCCSCSTTSCCSBTTTCSS---SSSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCCeEEcCCCCcccHHHHcc---CCCCCCcCCcEeecC
Confidence            45789999999999999999999999999976   457899999988654

>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=99.60  E-value=1.6e-15  Score=81.76  Aligned_cols=49  Identities=22%  Similarity=0.561  Sum_probs=41.2

Q ss_pred             CCccccccccCCCCCe------------------ecCCCCcccHHHHHHHH-----hCCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPV------------------QLTCCHIFCESCVTKWF-----DREQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~------------------~l~C~h~fc~~Cl~~~~-----~~~~~CP~C~~~~~~~   66 (81)
                      .+..|+||++.|.++.                  .++|+|.||..||.+|+     ..+..||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4468999999997654                  57999999999999999     4567999999988654

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

Probab=99.59  E-value=3.9e-15  Score=75.76  Aligned_cols=53  Identities=23%  Similarity=0.558  Sum_probs=42.3

Q ss_pred             cCCCCccccccccCCC--CCeecC--CCCcccHHHHHHHHh-CCCCCCCCCCCCCCCc
Q psy8828          15 LLGVGCICPICHDEFK--TPVQLT--CCHIFCESCVTKWFD-REQTCPLCRATLVDDP   67 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~--~p~~l~--C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~~   67 (81)
                      .+++.+.|+||++.+.  ++..++  |||+||..|+.+++. ....||.||+++....
T Consensus         7 ~~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            7 AKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             ccccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            3567789999999884  344555  999999999999875 4578999999987653

>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=99.51  E-value=1.6e-14  Score=77.28  Aligned_cols=47  Identities=28%  Similarity=0.615  Sum_probs=41.0

Q ss_pred             CCccccccccCCCCC------------------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p------------------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      +...|+||++.+.++                  +.++|+|.||..||.+|+..+.+||+||+.+.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            456899999998865                  33699999999999999999999999999864

>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=99.49  E-value=4.4e-15  Score=89.77  Aligned_cols=65  Identities=20%  Similarity=0.452  Sum_probs=55.1

Q ss_pred             CCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCC--CCCCC--CCCCCCCCccccCcccchhhhc
Q psy8828          16 LGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDRE--QTCPL--CRATLVDDPAWRDGATSYFVQI   80 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~--~~CP~--C~~~~~~~~~~~~~~~~~~~~~   80 (81)
                      ....+.||||++.+.+|++. .|||+||+.||..|+..+  ..||+  |++.+....+.+|..+.++++.
T Consensus       178 ~~~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN~~L~~lve~  247 (267)
T 3htk_C          178 GKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPIMELRCKI  247 (267)
T ss_dssp             SBCCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEECHHHHHHHHH
T ss_pred             CceeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcCHHHHHHHHH
Confidence            35678999999999999985 999999999999998854  57999  9999887777778777766653

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

Probab=99.49  E-value=4.7e-15  Score=81.37  Aligned_cols=53  Identities=30%  Similarity=0.740  Sum_probs=46.2

Q ss_pred             CCCCccccccccCCCCC-------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcc
Q psy8828          16 LGVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   68 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p-------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~   68 (81)
                      ..+...|+||++.+.++       +.++|||.||..|+.+|+..+..||+||..+....+
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~  128 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY  128 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGE
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcc
Confidence            35678999999998876       778999999999999999999999999999876543

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

Probab=99.48  E-value=1.1e-15  Score=77.03  Aligned_cols=46  Identities=28%  Similarity=0.689  Sum_probs=41.0

Q ss_pred             CCCCccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      +++.+.|+||++.+.+++.++|||. ||..|+.+|    ..||+||+.+..
T Consensus        21 ~~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           21 LQEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             CccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            3456799999999999999999999 999999887    789999998754

>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=99.46  E-value=4.1e-14  Score=69.47  Aligned_cols=47  Identities=28%  Similarity=0.605  Sum_probs=42.6

Q ss_pred             CCccccccccCCCCCeec--CCCCc-ccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQL--TCCHI-FCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l--~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ++..|+||++...+++.+  ||||. ||..|+.+|...+..||+||+++.
T Consensus         7 ~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSCEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCCEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            456899999999999877  99999 899999999998899999999875

>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=99.44  E-value=5.4e-14  Score=68.82  Aligned_cols=47  Identities=17%  Similarity=0.527  Sum_probs=42.3

Q ss_pred             CCccccccccCCCCCeec--CCCCc-ccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQL--TCCHI-FCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l--~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ....|+||++...+++.+  ||||. ||..|+.+|...+..||+||+++.
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             cCCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            355899999999998877  99998 999999999988889999999875

>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=99.44  E-value=9.9e-14  Score=87.90  Aligned_cols=49  Identities=33%  Similarity=0.808  Sum_probs=44.4

Q ss_pred             CCccccccccCCCCCeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~   66 (81)
                      ....|+||++.+.+|+.++|||.||..|+..|+. ....||.||..+...
T Consensus       331 ~~~~C~ICle~~~~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          331 TFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSSBCTTTSSSBCCEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCCccCcCCCCeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            3479999999999999999999999999999998 778999999988653

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

Probab=99.41  E-value=2e-14  Score=72.52  Aligned_cols=45  Identities=27%  Similarity=0.679  Sum_probs=39.5

Q ss_pred             CCCccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ++...|+||++.+.+++.++|||. ||..|+.+    ...||+||.++..
T Consensus        23 ~~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           23 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCCcCCCCCCCEEEecCCCHHHHHHHhhC----CCCCccCCceecC
Confidence            445789999999999999999999 99999964    3789999998865

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=99.38  E-value=1.8e-13  Score=66.62  Aligned_cols=54  Identities=17%  Similarity=0.203  Sum_probs=47.4

Q ss_pred             CccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCc
Q psy8828          19 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDG   72 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~   72 (81)
                      .+.|+|+++.+.+|+.+ ++||+|++.+|.+|+..+..||+.++++...++.++.
T Consensus         3 ~~~CpIs~~~m~dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip~~   57 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIV   57 (61)
T ss_dssp             -CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECC
T ss_pred             eEEecCCCCCCCCCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEECc
Confidence            47899999999999999 9999999999999999878899999998776665544

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

Probab=99.36  E-value=8.9e-13  Score=65.37  Aligned_cols=48  Identities=29%  Similarity=0.640  Sum_probs=41.3

Q ss_pred             ccCCCCccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ....+...|.||++...+++.+||||. ||..|+..    ...||+||..+..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           10 PSEENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CSCCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             ccCCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            344457899999999999999999999 99999984    3789999998865

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

Probab=99.35  E-value=1.1e-12  Score=66.96  Aligned_cols=50  Identities=28%  Similarity=0.778  Sum_probs=41.2

Q ss_pred             CCCccccccccCCC--CCeecCCC-----CcccHHHHHHHHhCC--CCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFK--TPVQLTCC-----HIFCESCVTKWFDRE--QTCPLCRATLVDD   66 (81)
Q Consensus        17 ~~~~~C~iC~~~~~--~p~~l~C~-----h~fc~~Cl~~~~~~~--~~CP~C~~~~~~~   66 (81)
                      .+...|.||++.+.  +++++||.     |.||..||.+|+..+  ..||+|+..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            34568999998874  46777996     999999999999854  5999999998654

>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=99.33  E-value=1.4e-13  Score=74.78  Aligned_cols=48  Identities=27%  Similarity=0.571  Sum_probs=0.8

Q ss_pred             CCccccccccCCCCCe------------------ecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPV------------------QLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~------------------~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      +...|+||++.+.++.                  .++|+|.||..||.+|+..+..||+||+++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            3468999999987631                  24899999999999999999999999998643

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

Probab=99.28  E-value=1.9e-11  Score=61.41  Aligned_cols=51  Identities=27%  Similarity=0.537  Sum_probs=42.3

Q ss_pred             cCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCC--CCCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDRE--QTCPLCRATLVD   65 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~--~~CP~C~~~~~~   65 (81)
                      ..+....|+||.+.+...... .|+|.|+..||.+|++.+  .+||.|+.....
T Consensus        11 y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~   64 (74)
T 2ct0_A           11 YPDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH   64 (74)
T ss_dssp             CSSSSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCS
T ss_pred             ccCCCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCC
Confidence            334556899999999876544 899999999999999976  899999988653

>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=99.25  E-value=1e-12  Score=66.84  Aligned_cols=47  Identities=32%  Similarity=0.764  Sum_probs=40.6

Q ss_pred             cCCCCccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      .+++...|+||++.+.+++.+||||. ||..|+..|    ..||+||..+..
T Consensus        14 ~l~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   61 (79)
T 2yho_A           14 KLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEH   61 (79)
T ss_dssp             HHHHHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE
T ss_pred             cCCCCCEeEEeCcccCcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhC
Confidence            33456789999999999999999999 999999866    489999998764

>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=99.16  E-value=1.7e-11  Score=64.03  Aligned_cols=48  Identities=25%  Similarity=0.679  Sum_probs=38.9

Q ss_pred             CCccccccccCCCCCeec---CCCCcccHHHHHHHHhC--------CCCCCC--CCCC--CCC
Q psy8828          18 VGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFDR--------EQTCPL--CRAT--LVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~~--------~~~CP~--C~~~--~~~   65 (81)
                      +.+.|+||++.+..+..+   +|||.||..|+..++..        ...||.  |+..  +..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            467899999999887554   79999999999998762        247999  9888  543

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

Probab=99.15  E-value=5.4e-12  Score=79.14  Aligned_cols=45  Identities=27%  Similarity=0.778  Sum_probs=40.5

Q ss_pred             CCCccccccccCCCCCeecCCCCc-ccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~-fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ++...|+||++.+.+|+.+||||. ||..|+..|    ..||.||.++..
T Consensus       293 ~~~~~C~IC~~~~~~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSBCCEEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             cCCCCCCccCCcCCceEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            456899999999999999999999 999999877    789999998754

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

Probab=98.90  E-value=2.9e-09  Score=51.39  Aligned_cols=47  Identities=23%  Similarity=0.600  Sum_probs=38.4

Q ss_pred             CCccccccccCCCCCeecCCC--C---cccHHHHHHHHh--CCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTCC--H---IFCESCVTKWFD--REQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~--h---~fc~~Cl~~~~~--~~~~CP~C~~~~~   64 (81)
                      +...|.||++...++..+||.  +   .||..||.+|+.  .+..||+|+..+.
T Consensus         5 ~~~~CrIC~~~~~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCEeEEeecCCCCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            456899999887777767865  4   799999999987  3678999998875

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

Probab=98.72  E-value=2.5e-09  Score=67.03  Aligned_cols=49  Identities=27%  Similarity=0.651  Sum_probs=38.6

Q ss_pred             CCCccccccccCCCC----Cee----cCCCCcccHHHHHHHHhCC-----------CCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKT----PVQ----LTCCHIFCESCVTKWFDRE-----------QTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~----p~~----l~C~h~fc~~Cl~~~~~~~-----------~~CP~C~~~~~~   65 (81)
                      +....|+||++.+.+    |..    ..|+|.||..||.+|++..           ..||.|++++..
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCc
Confidence            456799999999876    211    3699999999999999731           479999998753

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

Probab=98.70  E-value=1.7e-08  Score=52.93  Aligned_cols=45  Identities=24%  Similarity=0.630  Sum_probs=36.7

Q ss_pred             cccccccCCCC-CeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCC
Q psy8828          21 ICPICHDEFKT-PVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVD   65 (81)
Q Consensus        21 ~C~iC~~~~~~-p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~   65 (81)
                      .|++|.-.+.. ...+||+|.||.+|+..|.+ +.+.||.|+.++..
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~r   49 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQR   49 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeee
Confidence            57888777665 34669999999999999986 56899999998764

>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=98.23  E-value=7.3e-07  Score=61.96  Aligned_cols=67  Identities=16%  Similarity=0.114  Sum_probs=59.5

Q ss_pred             cCCCCccccccccCCCCCeecCCC-CcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~-h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ...+.+.|||-.+.+.+|++++-| ++|=+..|.+|+..+.+||.-+.++......+|..+...++.|
T Consensus       887 ~iP~~F~cPIs~~lM~DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN~~Lk~~I~~w  954 (968)
T 3m62_A          887 DVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILCF  954 (968)
T ss_dssp             CSCGGGBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECHHHHHHHHHH
T ss_pred             CCcHHhCCcchhhHHhCCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcccccccHHHHHHHHHH
Confidence            446789999999999999999998 6999999999999889999999999887888888888777654

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

Probab=98.08  E-value=6e-06  Score=49.52  Aligned_cols=47  Identities=30%  Similarity=0.598  Sum_probs=39.3

Q ss_pred             CccccccccCCCCCeec-CCCCcccHHHHHHHHhCC--CCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDRE--QTCPLCRATLVD   65 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~--~~CP~C~~~~~~   65 (81)
                      ...|.+|.+.....+.- .|++.||..|+..|++..  ..||.|+.....
T Consensus       180 i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~  229 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH  229 (238)
T ss_dssp             CCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCS
T ss_pred             CCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Confidence            56899999998877666 499999999999998754  599999887543

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

Probab=97.75  E-value=1.9e-05  Score=41.16  Aligned_cols=32  Identities=22%  Similarity=0.729  Sum_probs=26.9

Q ss_pred             CCccccccccC-CCCCee--cCCCCcccHHHHHHH
Q psy8828          18 VGCICPICHDE-FKTPVQ--LTCCHIFCESCVTKW   49 (81)
Q Consensus        18 ~~~~C~iC~~~-~~~p~~--l~C~h~fc~~Cl~~~   49 (81)
                      +++.|+||.+. +.+++.  +.|+|+||..|+..+
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            45789999975 567777  799999999999983

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=96.85  E-value=0.0052  Score=30.94  Aligned_cols=35  Identities=26%  Similarity=0.665  Sum_probs=28.9

Q ss_pred             CCCccccccccCCCCCeecCC----CCcccHHHHHHHHh
Q psy8828          17 GVGCICPICHDEFKTPVQLTC----CHIFCESCVTKWFD   51 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C----~h~fc~~Cl~~~~~   51 (81)
                      ...+.|.+|.+.+++...+.|    .|.||..|-...++
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk   51 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   51 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHH
Confidence            456799999999998765544    69999999988877

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

Probab=95.94  E-value=0.019  Score=27.73  Aligned_cols=45  Identities=24%  Similarity=0.448  Sum_probs=31.6

Q ss_pred             CCCccccccccCCCCCeec--CCCCcccHHHHHHHHh----CCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRATL   63 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~~~~~----~~~~CP~C~~~~   63 (81)
                      .....|.||.+.  ..+++  .|...||..|+..-+.    ....|+.|....
T Consensus        10 ~~~~~C~vC~~~--~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           10 APGARCGVCGDG--TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CTTCCCTTTSCC--TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCcCCCCCC--CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            345579999864  22333  7889999999976655    346899997643

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

Probab=95.87  E-value=0.008  Score=38.21  Aligned_cols=61  Identities=18%  Similarity=0.338  Sum_probs=42.7

Q ss_pred             CCccccccccCCCCCeec-CCCCcccHH--HHHHHHh--CCCCCCCCCCCCCCCccccCcccchhh
Q psy8828          18 VGCICPICHDEFKTPVQL-TCCHIFCES--CVTKWFD--REQTCPLCRATLVDDPAWRDGATSYFV   78 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l-~C~h~fc~~--Cl~~~~~--~~~~CP~C~~~~~~~~~~~~~~~~~~~   78 (81)
                      -.+.||+-...+..|+.- .|.|.-|.+  -+.....  ....||+|.+.+....+..+..+..++
T Consensus       248 vSL~CPlS~~ri~~PvRg~~C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~dL~ID~~~~~IL  313 (371)
T 3i2d_A          248 MSLQCPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDIL  313 (371)
T ss_dssp             EESBCTTTSSBCSSEEEETTCCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGGGEEEBHHHHHHH
T ss_pred             EeecCCCccccccccCcCCcCCCcceECHHHHHHHhhcCCceeCCCCCcccCHHHeeEcHHHHHHH
Confidence            347999999999999865 899985533  3333332  457999999988766666665554444

>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=95.73  E-value=0.01  Score=37.57  Aligned_cols=61  Identities=21%  Similarity=0.486  Sum_probs=42.5

Q ss_pred             CCccccccccCCCCCeec-CCCCccc--HHHHHHHHh--CCCCCCCCCCCCCCCccccCcccchhh
Q psy8828          18 VGCICPICHDEFKTPVQL-TCCHIFC--ESCVTKWFD--REQTCPLCRATLVDDPAWRDGATSYFV   78 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l-~C~h~fc--~~Cl~~~~~--~~~~CP~C~~~~~~~~~~~~~~~~~~~   78 (81)
                      -.+.||+-...+..|+.- .|.|.-|  ..-+.....  ....||+|.+.+....+..+..+..++
T Consensus       214 vSL~CPlS~~ri~~P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~dL~ID~~~~~IL  279 (360)
T 4fo9_A          214 VSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYESLILDGLFMEIL  279 (360)
T ss_dssp             EESBCTTTCSBCSSEEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGGGEEEBHHHHHHH
T ss_pred             EeeeCCCccceeccCCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCcccCHHHeEEcHHHHHHH
Confidence            357899999999999865 8999844  433333333  457999999988766666655544443

>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=94.45  E-value=0.22  Score=25.45  Aligned_cols=47  Identities=26%  Similarity=0.605  Sum_probs=33.8

Q ss_pred             CCccccccccCCCC----Ceec---CCCCcccHHHHHHH-HhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT----PVQL---TCCHIFCESCVTKW-FDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~----p~~l---~C~h~fc~~Cl~~~-~~~~~~CP~C~~~~~   64 (81)
                      ..-.|.||-+.+-.    ...+   .|+-..|+.|++-- ...+..||.|+..+.
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYk   69 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccc
Confidence            34589999997532    1223   57778899999743 346789999988875

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

Probab=93.72  E-value=0.31  Score=24.72  Aligned_cols=35  Identities=14%  Similarity=0.450  Sum_probs=24.7

Q ss_pred             ccCCCCccccccccCCCCCeec---CCCCcccHHHHHHH
Q psy8828          14 TLLGVGCICPICHDEFKTPVQL---TCCHIFCESCVTKW   49 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~   49 (81)
                      +....+..|.||...-.+ ..+   -|+..||..|+.+.
T Consensus        10 e~~~~D~~C~VC~~~t~~-~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           10 EPVVNDEMCDVCEVWTAE-SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCSCCCTTTCCCCSS-CCSSCSSSSSCCCHHHHHHH
T ss_pred             cCCCCCcccCcccccccc-ceeccccccccccHhhcccc
Confidence            344467789999854322 333   47899999999986

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=92.39  E-value=0.15  Score=23.97  Aligned_cols=43  Identities=21%  Similarity=0.580  Sum_probs=29.8

Q ss_pred             CCCccccccccCCCCCeec--CCCCcccHHHHHHHHh----CCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRA   61 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~~~~~----~~~~CP~C~~   61 (81)
                      .....|.+|.+.  ..+++  .|...||..|+..-+.    ....||.|..
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            345689999874  23333  7888999999986433    3468998854

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.13  E-value=0.12  Score=23.30  Aligned_cols=41  Identities=22%  Similarity=0.561  Sum_probs=26.6

Q ss_pred             cccccccCCCCCeec---CCCCcccHHHHHHHHh----CCCCCCCCCC
Q psy8828          21 ICPICHDEFKTPVQL---TCCHIFCESCVTKWFD----REQTCPLCRA   61 (81)
Q Consensus        21 ~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~----~~~~CP~C~~   61 (81)
                      .|.||...-.....+   .|...||..|+..-+.    ....||.|..
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            477887654332233   6888999999964333    2357888854

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=91.64  E-value=0.067  Score=26.15  Aligned_cols=48  Identities=21%  Similarity=0.409  Sum_probs=32.4

Q ss_pred             CCCccccccccCCCCCeec---CCCCcccHHHHHHHHh----CCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFD----REQTCPLCRATLV   64 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~----~~~~CP~C~~~~~   64 (81)
                      .+...|++|.........+   .|...||..|+..-..    ....||.|...+.
T Consensus        16 ~~~~~C~~C~~~~~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           16 NQIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             CEEECBTTTTBCCSSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCCcCCCCCCCCCCCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            3446799998876543233   6888999999964332    2467999966543

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=91.11  E-value=0.17  Score=25.70  Aligned_cols=30  Identities=23%  Similarity=0.620  Sum_probs=21.6

Q ss_pred             CccccccccCCCCCe----ecCCCCcccHHHHHH
Q psy8828          19 GCICPICHDEFKTPV----QLTCCHIFCESCVTK   48 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~~   48 (81)
                      ...|.+|...|.--.    -..||..||..|...
T Consensus        20 ~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~   53 (90)
T 3t7l_A           20 APNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNR   53 (90)
T ss_dssp             CCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCE
T ss_pred             CCcCcCCCCcccchhhCccccCCCCEECCcccCC
Confidence            457999998775321    127999999999753

>3mjh_B Early endosome antigen 1; protein-zinc finger complex, beta BETA alpha fold, beta HAIR RAB5A GTPase, EEA1, protein transport; HET: GTP; 2.03A {Homo sapiens}

Probab=90.92  E-value=0.016  Score=24.40  Aligned_cols=16  Identities=31%  Similarity=0.746  Sum_probs=11.1

Q ss_pred             CCccccccccCCCCCe
Q psy8828          18 VGCICPICHDEFKTPV   33 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~   33 (81)
                      +.+.||+|+..+..+.
T Consensus         4 EGFiCP~C~~~l~s~~   19 (34)
T 3mjh_B            4 EGFICPQCMKSLGSAD   19 (34)
T ss_dssp             EEEECTTTCCEESSHH
T ss_pred             cccCCcHHHHHcCCHH
Confidence            3578888887776653

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=90.62  E-value=0.34  Score=25.69  Aligned_cols=47  Identities=11%  Similarity=0.162  Sum_probs=35.5

Q ss_pred             ccccccccCCCC---CeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        20 ~~C~iC~~~~~~---p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      +.|..|...+.+   .....=|..||..|..+.+.....|..|..++...
T Consensus        33 F~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~   82 (122)
T 1m3v_A           33 LKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGG   82 (122)
T ss_dssp             HCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCE
T ss_pred             CCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCch
Confidence            688999888863   23345677899999988776555899998888653

>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=89.69  E-value=0.9  Score=22.01  Aligned_cols=44  Identities=23%  Similarity=0.499  Sum_probs=28.4

Q ss_pred             CCCccccccccCCCCCeec--C--CC-CcccHHHHHHHHh----CCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL--T--CC-HIFCESCVTKWFD----REQTCPLCRATL   63 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l--~--C~-h~fc~~Cl~~~~~----~~~~CP~C~~~~   63 (81)
                      .+...| +|.......++.  .  |. ..||..|+.  +.    ....||.|....
T Consensus        14 ~~~~~C-~C~~~~~g~MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~   66 (71)
T 1wen_A           14 NEPTYC-LCHQVSYGEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQES   66 (71)
T ss_dssp             TSCCCS-TTCCCSCSSEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCS
T ss_pred             CCCCEE-ECCCCCCCCEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCccc
Confidence            345677 898865443332  3  55 589999996  22    346899996543

>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=89.60  E-value=0.25  Score=24.03  Aligned_cols=29  Identities=24%  Similarity=0.637  Sum_probs=21.2

Q ss_pred             CccccccccCCCCCee----cCCCCcccHHHHH
Q psy8828          19 GCICPICHDEFKTPVQ----LTCCHIFCESCVT   47 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~   47 (81)
                      ...|.+|...|.--..    -.||..||..|..
T Consensus        11 ~~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~   43 (73)
T 1vfy_A           11 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSS   43 (73)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSC
T ss_pred             CCcccCCCCccCCccccccCCCCCEEEcccccC
Confidence            3589999988763221    2799999999864

>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=89.09  E-value=0.14  Score=27.57  Aligned_cols=43  Identities=26%  Similarity=0.633  Sum_probs=25.8

Q ss_pred             CCccccccccCCCCCe----ecCCCCcccHHHHHHHHhCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPV----QLTCCHIFCESCVTKWFDREQTCPLCR   60 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~~~~~~~~~CP~C~   60 (81)
                      +...|..|...|.--.    -..||..||..|..........|-.|.
T Consensus        18 ~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~   64 (120)
T 1y02_A           18 LEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   64 (120)
T ss_dssp             --CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             ccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHH
Confidence            3458999998876421    127999999999754433344565553

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=89.00  E-value=0.69  Score=22.40  Aligned_cols=39  Identities=15%  Similarity=0.198  Sum_probs=28.6

Q ss_pred             CCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ....|+.|.+.+...++..-+..||..|+        .|-.|+..+.
T Consensus        14 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF--------~C~~C~~~L~   52 (79)
T 1x62_A           14 KLPMCDKCGTGIVGVFVKLRDRHRHPECY--------VCTDCGTNLK   52 (79)
T ss_dssp             CCCCCSSSCCCCCSSCEECSSCEECTTTT--------SCSSSCCCHH
T ss_pred             CCCccccCCCCccCcEEEECcceeCcCcC--------eeCCCCCCCC
Confidence            45589999998877655566777777764        5888887764

>2o35_A Hypothetical protein DUF1244; helix bundle, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.12A {Sinorhizobium meliloti} SCOP: a.293.1.1

Probab=88.62  E-value=0.2  Score=26.10  Aligned_cols=12  Identities=33%  Similarity=1.384  Sum_probs=10.8

Q ss_pred             cccHHHHHHHHh
Q psy8828          40 IFCESCVTKWFD   51 (81)
Q Consensus        40 ~fc~~Cl~~~~~   51 (81)
                      .||+.||.+|..
T Consensus        42 GFCRNCLskWy~   53 (105)
T 2o35_A           42 GFCRNCLSNWYR   53 (105)
T ss_dssp             SCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            499999999986

>3fyb_A Protein of unknown function (DUF1244); hydrocar degrading, structural genomics, PSI-2; HET: PEG; 1.80A {Alcanivorax borkumensis SK2}

Probab=88.56  E-value=0.21  Score=26.03  Aligned_cols=12  Identities=42%  Similarity=1.284  Sum_probs=10.8

Q ss_pred             cccHHHHHHHHh
Q psy8828          40 IFCESCVTKWFD   51 (81)
Q Consensus        40 ~fc~~Cl~~~~~   51 (81)
                      .||+.||.+|..
T Consensus        41 GFCRNCLskWy~   52 (104)
T 3fyb_A           41 DFCRNCLAKWLM   52 (104)
T ss_dssp             SCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            499999999986

>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=88.13  E-value=0.17  Score=23.81  Aligned_cols=44  Identities=23%  Similarity=0.490  Sum_probs=29.0

Q ss_pred             CCCccccccccCCCCCeec--CCCCcccHHHHHHHHh----CCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRAT   62 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~~~~~----~~~~CP~C~~~   62 (81)
                      .....|.+|.+.  ..+++  .|...||..|+..-+.    ....||.|...
T Consensus         7 ~~~~~C~vC~~~--g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   56 (61)
T 1mm2_A            7 HHMEFCRVCKDG--GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SSCSSCTTTCCC--SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCCCcCCCCCCC--CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCc
Confidence            345679999863  22222  6888899999875333    34579999654

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=88.03  E-value=0.23  Score=23.94  Aligned_cols=59  Identities=19%  Similarity=0.291  Sum_probs=28.3

Q ss_pred             CCCCCCCCCCCccccCCCCccccccccCCCCCeec---CCCCcccHHHHHHHHh---CCCCCCCCC
Q psy8828           1 MLGGQLGVSPTKETLLGVGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFD---REQTCPLCR   60 (81)
Q Consensus         1 m~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~---~~~~CP~C~   60 (81)
                      |+.+...++........+...| ||.........+   .|..-|+..|+.--..   ....||.|+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~C-iC~~~~~~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~   65 (68)
T 3o70_A            1 MHHHHHHSSGRENLYFQGLVTC-FCMKPFAGRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCR   65 (68)
T ss_dssp             -------------CTTTTCCCS-TTCCCCTTCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHH
T ss_pred             CcccccCCcccccCCCCCceEe-ECCCcCCCCCEEECCCCCccccccccCcCcccCCCcEECCCCC
Confidence            4445545555555555667788 998876654344   5777788888742111   234566663

>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=88.00  E-value=1.4  Score=21.40  Aligned_cols=46  Identities=22%  Similarity=0.477  Sum_probs=30.3

Q ss_pred             CCCccccccccCCCCCeec---CCCCcccHHHHHH----H-----HhCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQL---TCCHIFCESCVTK----W-----FDREQTCPLCRATL   63 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~----~-----~~~~~~CP~C~~~~   63 (81)
                      .....| +|.........+   .|..-||..|+.-    .     ......||.|+...
T Consensus        14 ~~~~~C-~C~~~~~~~~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~   71 (76)
T 1wem_A           14 PNALYC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             TTCCCS-TTCCCCCSSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CCCCEE-ECCCccCCCCEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCcc
Confidence            345677 899877643333   6888899999841    1     12467899986543

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=87.95  E-value=0.14  Score=25.96  Aligned_cols=47  Identities=15%  Similarity=0.453  Sum_probs=32.2

Q ss_pred             CCCccccccccCCC---CCeec--CCCCcccHHHHHHHHh--------CCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFK---TPVQL--TCCHIFCESCVTKWFD--------REQTCPLCRATL   63 (81)
Q Consensus        17 ~~~~~C~iC~~~~~---~p~~l--~C~h~fc~~Cl~~~~~--------~~~~CP~C~~~~   63 (81)
                      +....|.+|...-.   +.+++  .|...||..|+..-+.        ....|+.|....
T Consensus        14 e~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~   73 (88)
T 1wev_A           14 EMGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQM   73 (88)
T ss_dssp             HHCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHH
T ss_pred             CCCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchh
Confidence            45678999998643   34444  7888999999875332        346888886544

>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=87.15  E-value=0.044  Score=28.11  Aligned_cols=46  Identities=20%  Similarity=0.356  Sum_probs=28.1

Q ss_pred             CCCCccccccccCCCCCeec---CCCCcccHHHHHHHHh----CCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFD----REQTCPLCRA   61 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~----~~~~CP~C~~   61 (81)
                      ..+...|.||...-....++   .|...||..|+.+-+.    ....||.|..
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            34556799998764322222   6777788888763332    2356888754

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=86.98  E-value=0.19  Score=25.93  Aligned_cols=44  Identities=16%  Similarity=0.260  Sum_probs=29.5

Q ss_pred             CCccccccccCCCCCeec---CCCCcccHHHHHHHHh---CCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFD---REQTCPLCRAT   62 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~---~~~~CP~C~~~   62 (81)
                      +...| ||.........+   .|...|+..|+..-..   ....||.|+..
T Consensus        27 d~vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           27 DVTRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             CBCCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             CCEEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            44577 888776555444   6788899999854222   23689999643

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=86.63  E-value=1.9  Score=21.31  Aligned_cols=41  Identities=17%  Similarity=0.268  Sum_probs=30.1

Q ss_pred             CCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ....|..|.+.+...++..-+..||.+|        +.|-.|+..+...
T Consensus        24 ~~~~C~~C~~~I~~~~~~a~~~~~H~~C--------F~C~~C~~~L~~~   64 (89)
T 1x64_A           24 RMPLCDKCGSGIVGAVVKARDKYRHPEC--------FVCADCNLNLKQK   64 (89)
T ss_dssp             SCCBCTTTCCBCCSCCEESSSCEECTTT--------CCCSSSCCCTTTS
T ss_pred             cCCCcccCCCEecccEEEECCceECccC--------CEecCCCCCCCCC
Confidence            4458999999888755556677777766        4588898887653

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=86.34  E-value=0.43  Score=23.82  Aligned_cols=31  Identities=26%  Similarity=0.562  Sum_probs=22.4

Q ss_pred             CCccccccccCCCCCee----cCCCCcccHHHHHH
Q psy8828          18 VGCICPICHDEFKTPVQ----LTCCHIFCESCVTK   48 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~~   48 (81)
                      +...|.+|...|.--..    -.||..||..|...
T Consensus        20 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~   54 (84)
T 1z2q_A           20 DAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRH   54 (84)
T ss_dssp             TCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCC
T ss_pred             CCCCCcCcCCccccchhcccccCCCcEEChHHhCC
Confidence            34589999998764221    27999999999753

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=86.23  E-value=0.44  Score=23.67  Aligned_cols=30  Identities=33%  Similarity=0.893  Sum_probs=21.9

Q ss_pred             CccccccccCCCCCee----cCCCCcccHHHHHH
Q psy8828          19 GCICPICHDEFKTPVQ----LTCCHIFCESCVTK   48 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~~   48 (81)
                      ...|.+|...|.--..    -.||..||..|...
T Consensus        19 ~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~   52 (82)
T 2yw8_A           19 ATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSN   52 (82)
T ss_dssp             CCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCE
T ss_pred             CCcccCcCCcccCccccccCCCCCCEEChHHhCC
Confidence            3479999998763221    27999999999753

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=85.58  E-value=0.81  Score=24.26  Aligned_cols=48  Identities=13%  Similarity=0.333  Sum_probs=34.6

Q ss_pred             CCccccccccCCCC---CeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~~---p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      +-+.|..|...+..   +....=|..||..|..+.......|..|.+++..
T Consensus        28 ~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~   78 (131)
T 2xjy_A           28 DCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRA   78 (131)
T ss_dssp             TTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECT
T ss_pred             HHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCc
Confidence            44788899888853   3344567789999988766544478888887754

>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=85.41  E-value=0.35  Score=26.08  Aligned_cols=28  Identities=32%  Similarity=0.755  Sum_probs=20.8

Q ss_pred             ccccccccCCCCCe----ecCCCCcccHHHHH
Q psy8828          20 CICPICHDEFKTPV----QLTCCHIFCESCVT   47 (81)
Q Consensus        20 ~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~   47 (81)
                      ..|.+|...|.--.    --.||+.||..|..
T Consensus        70 ~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~  101 (125)
T 1joc_A           70 QNCMACGKGFSVTVRRHHCRQCGNIFCAECSA  101 (125)
T ss_dssp             CBCTTTCCBCCSSSCCEECTTTCCEECGGGSC
T ss_pred             CCCcCcCCccccccccccCCCCCeEEChHHhC
Confidence            47999999876321    12799999999964

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=85.08  E-value=2.8  Score=21.91  Aligned_cols=43  Identities=19%  Similarity=0.281  Sum_probs=25.7

Q ss_pred             CCccccccccCCC-------CCeec--CCCCcccHHHHHH-------HHhCCCCCCCCC
Q psy8828          18 VGCICPICHDEFK-------TPVQL--TCCHIFCESCVTK-------WFDREQTCPLCR   60 (81)
Q Consensus        18 ~~~~C~iC~~~~~-------~p~~l--~C~h~fc~~Cl~~-------~~~~~~~CP~C~   60 (81)
                      ....|.+|...-.       +..+.  .|+..||..|+..       .......||.|+
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            4557888876521       12222  7999999999941       122445666663

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=85.05  E-value=0.47  Score=23.67  Aligned_cols=29  Identities=24%  Similarity=0.591  Sum_probs=21.0

Q ss_pred             CccccccccCCCCCee----cCCCCcccHHHHH
Q psy8828          19 GCICPICHDEFKTPVQ----LTCCHIFCESCVT   47 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~   47 (81)
                      ...|.+|...|.--..    ..||..||..|..
T Consensus        14 ~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~   46 (84)
T 1x4u_A           14 FGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCS   46 (84)
T ss_dssp             CSSCSSSCCCCCSSSCCEECSSSCCEECTTTSC
T ss_pred             CCcCcCcCCccccchhhhhhcCCCcEEChhhcC
Confidence            3579999998753211    2799999999854

>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate; signaling; 1.48A {Homo sapiens} PDB: 4avx_A*

Probab=84.29  E-value=0.66  Score=27.39  Aligned_cols=31  Identities=26%  Similarity=0.554  Sum_probs=22.3

Q ss_pred             CCCccccccccCCCCCe----ecCCCCcccHHHHH
Q psy8828          17 GVGCICPICHDEFKTPV----QLTCCHIFCESCVT   47 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~   47 (81)
                      .+...|.+|...|.--.    -..||..||..|-.
T Consensus       162 ~~~~~C~~C~~~F~~~~RrhHCR~CG~v~C~~Cs~  196 (226)
T 3zyq_A          162 VDAEECHRCRVQFGVMTRKHHCRACGQIFCGKCSS  196 (226)
T ss_dssp             CCCSBCTTTCCBCBTTBCCEECTTTCCEECTTTCC
T ss_pred             ccCCCCcCcCCCCCccccccccCCCcCEeChhhcC
Confidence            34568999998776322    12799999999864

>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=84.18  E-value=0.59  Score=23.63  Aligned_cols=29  Identities=24%  Similarity=0.620  Sum_probs=20.0

Q ss_pred             CccccccccCCCCCee----cCCCCcccHHHHH
Q psy8828          19 GCICPICHDEFKTPVQ----LTCCHIFCESCVT   47 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~   47 (81)
                      ...|.+|...|.--..    ..||..||..|..
T Consensus         9 ~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~   41 (88)
T 1wfk_A            9 ESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLS   41 (88)
T ss_dssp             CSBCTTTCCBCCSSSCEEECSSSCCEEETTTSC
T ss_pred             CCCCcCcCCcccCccccccCCCCCCEEChhHcC
Confidence            3478899887653211    2689999888864

>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=83.95  E-value=2.6  Score=20.60  Aligned_cols=47  Identities=26%  Similarity=0.514  Sum_probs=29.9

Q ss_pred             CCccccccccCCC-CCeec---CCCCcccHHHHHHH---H--hCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFK-TPVQL---TCCHIFCESCVTKW---F--DREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~-~p~~l---~C~h~fc~~Cl~~~---~--~~~~~CP~C~~~~~~   65 (81)
                      +...| +|..... ....+   .|..-||..|+.--   .  .....||.|+.....
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~~   66 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP   66 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCS
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccCC
Confidence            34466 8988764 22223   68888999999411   1  145789999776533

>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=83.81  E-value=0.55  Score=27.49  Aligned_cols=31  Identities=29%  Similarity=0.735  Sum_probs=22.0

Q ss_pred             CCCccccccccCCCCCe----ecCCCCcccHHHHH
Q psy8828          17 GVGCICPICHDEFKTPV----QLTCCHIFCESCVT   47 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~----~l~C~h~fc~~Cl~   47 (81)
                      .+...|.+|...|.--.    --.||+.||..|..
T Consensus       159 ~~~~~C~~C~~~F~~~~rrhhCr~CG~v~C~~Cs~  193 (220)
T 1dvp_A          159 ADGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTA  193 (220)
T ss_dssp             CCCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSC
T ss_pred             CCCCccCCCCCccCCcccccccCCcCCEEChHHhC
Confidence            34578999998875321    12799999998864

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=83.69  E-value=2.6  Score=23.28  Aligned_cols=42  Identities=19%  Similarity=0.603  Sum_probs=28.8

Q ss_pred             CCccccccccCCCCCeec--CCCCcccHHHHHHHHh-----------CCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD-----------REQTCPLCRA   61 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~~~~~-----------~~~~CP~C~~   61 (81)
                      .+..|.+|.+-=.  ...  .|-..||..||.+-+.           ....||.|..
T Consensus        62 ~~d~C~vC~~GG~--LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           62 MDEQCRWCAEGGN--LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             CBCSCSSSCCCSS--EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCeecccCCCCc--EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            3457888877422  222  7889999999986542           3468999964

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=83.30  E-value=2  Score=20.79  Aligned_cols=40  Identities=20%  Similarity=0.379  Sum_probs=27.4

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ...|+.|...+....+..-+..||..|        +.|..|+.++...
T Consensus        15 ~~~C~~C~~~I~~~~v~a~~~~~H~~C--------F~C~~C~~~L~~~   54 (79)
T 2cor_A           15 KYICQKCHAIIDEQPLIFKNDPYHPDH--------FNCANCGKELTAD   54 (79)
T ss_dssp             CCBCTTTCCBCCSCCCCCSSSCCCTTT--------SBCSSSCCBCCTT
T ss_pred             CCCCccCCCEecceEEEECcceeCCCC--------CEeCCCCCccCCC
Confidence            457888988877655445566666655        4588888877644

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=83.12  E-value=1.4  Score=22.41  Aligned_cols=47  Identities=26%  Similarity=0.542  Sum_probs=32.1

Q ss_pred             ccCCCCccccccccCCCCCeec--CCCCcccHHHHHHHHh----CCCCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRAT   62 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~~~~~----~~~~CP~C~~~   62 (81)
                      ........|.+|.+.-  ...+  .|...|+..|+.+-+.    ....||.|...
T Consensus        20 ~~d~n~~~C~vC~~~g--~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           20 TLDDSATICRVCQKPG--DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSSSSCCSSSCSSS--CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             ccCCCCCcCcCcCCCC--CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            3344567899999752  2222  6888999999976544    34689999654

>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=82.87  E-value=1.2  Score=20.95  Aligned_cols=40  Identities=30%  Similarity=0.702  Sum_probs=26.9

Q ss_pred             ccccccccCCCCCeec---CCCCcccHHHHHHHHhCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQL---TCCHIFCESCVTKWFDREQTCPLC   59 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~~~~~CP~C   59 (81)
                      ..|-.|...+.+....   .|++.||.+|=.=.-..-..||-|
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            3588888888654422   689999999953222233578877

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=82.62  E-value=2.5  Score=22.97  Aligned_cols=44  Identities=18%  Similarity=0.526  Sum_probs=27.8

Q ss_pred             CCccccccccCCCCCeecCCCCcccHHHHHHHH-----------hCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWF-----------DREQTCPLCRA   61 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~-----------~~~~~CP~C~~   61 (81)
                      .+..|.+|.+-=.-..--.|-..||.+||.+-+           .....|+.|..
T Consensus        56 ~~~~C~vC~dGG~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           56 MDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             CBSSCTTTCCCSEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCcCeecCCCCeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            345688887642210011688999999998642           13468999944

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=82.17  E-value=2.5  Score=20.40  Aligned_cols=47  Identities=19%  Similarity=0.457  Sum_probs=29.7

Q ss_pred             ccCCCCccccccccCC---CCCeec--CCCCcccHHHHHHHHh--CCCCCCCCC
Q psy8828          14 TLLGVGCICPICHDEF---KTPVQL--TCCHIFCESCVTKWFD--REQTCPLCR   60 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~---~~p~~l--~C~h~fc~~Cl~~~~~--~~~~CP~C~   60 (81)
                      ....+...|.||.+.-   .+.+++  .|...|+..|+..-..  ....||.|.
T Consensus        11 ~~~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~   64 (71)
T 2ku3_A           11 SLIDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCL   64 (71)
T ss_dssp             CCCCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHH
T ss_pred             cCCCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCc
Confidence            3445567899998763   223333  7888999999863222  235677664

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=81.60  E-value=0.52  Score=24.81  Aligned_cols=31  Identities=16%  Similarity=0.503  Sum_probs=19.5

Q ss_pred             CCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          31 TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        31 ~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      .+.-..||+.|.     .-+.....||.|+..-...
T Consensus        67 p~~C~~CG~~F~-----~~~~kPsrCP~CkSe~Ie~   97 (105)
T 2gmg_A           67 PAQCRKCGFVFK-----AEINIPSRCPKCKSEWIEE   97 (105)
T ss_dssp             CCBBTTTCCBCC-----CCSSCCSSCSSSCCCCBCC
T ss_pred             CcChhhCcCeec-----ccCCCCCCCcCCCCCccCC
Confidence            344457999981     1123447899998875543

>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=81.14  E-value=0.39  Score=25.12  Aligned_cols=42  Identities=21%  Similarity=0.519  Sum_probs=26.7

Q ss_pred             CCccccccccCCCC-Ceec--CCCCcccHHHHHHHHh----CCCCCCCC
Q psy8828          18 VGCICPICHDEFKT-PVQL--TCCHIFCESCVTKWFD----REQTCPLC   59 (81)
Q Consensus        18 ~~~~C~iC~~~~~~-p~~l--~C~h~fc~~Cl~~~~~----~~~~CP~C   59 (81)
                      ++..|.+|.+.-.. ..+.  .|+..||..|+.....    ....||.|
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C   54 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPEC   54 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTT
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCccccccccCccCCcC
Confidence            45689999876432 2222  7889999999975443    23455554

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A

Probab=80.97  E-value=4  Score=22.65  Aligned_cols=46  Identities=17%  Similarity=0.377  Sum_probs=31.7

Q ss_pred             CCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      +-+.|..|...+.......=|..||..|..+...  ..|..|...+..
T Consensus        32 ~CF~C~~C~~~L~~~~f~~~g~~yC~~~y~~~f~--~~C~~C~~~I~~   77 (169)
T 2rgt_A           32 KCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFG--TKCAACQLGIPP   77 (169)
T ss_dssp             TTSBCTTTCCBCCSCCEESSSCEECHHHHHHHHS--CBCTTTCCBCCT
T ss_pred             ccCccCCCCCcCCCCCcccCCeeeeccccccccc--ccccccccccCC
Confidence            4478888988877644445677899999876543  567777666543

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=80.74  E-value=3.5  Score=19.99  Aligned_cols=43  Identities=30%  Similarity=0.612  Sum_probs=28.0

Q ss_pred             CCCCccccccccCCCCC-eecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTP-VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   66 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p-~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~   66 (81)
                      ......|+.|.+.+... .+..-+..||..|        +.|-.|+..+...
T Consensus        12 ~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~C--------F~C~~C~~~L~~~   55 (82)
T 2co8_A           12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSC--------FRCHTCEATLWPG   55 (82)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTT--------CBCSSSCCBCCTT
T ss_pred             CCCCCCCcccCCCcccceEEEECCCeeCCCc--------CEEcCCCCCcCCC
Confidence            34456899999987543 3334556677666        4588887777553

>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*

Probab=80.22  E-value=2.7  Score=27.01  Aligned_cols=42  Identities=24%  Similarity=0.657  Sum_probs=28.2

Q ss_pred             CccccccccCCCCCeec----CCCCcccHHHHHHHHh----------CCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQL----TCCHIFCESCVTKWFD----------REQTCPLCRAT   62 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l----~C~h~fc~~Cl~~~~~----------~~~~CP~C~~~   62 (81)
                      +..|.+|-+--.  +.+    .|...||.+||.+.+.          ....|-.|...
T Consensus        93 ~~yCr~C~~Gg~--l~~Cdn~~C~r~FC~~Ci~~n~g~~~~~~i~~~d~W~Cf~C~p~  148 (386)
T 2pv0_B           93 QSYCSICCSGET--LLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPS  148 (386)
T ss_dssp             BCSCTTTCCCSS--CEECCSTTCCCEECHHHHHHHTCTTHHHHHHHCSSCCCTTTSSC
T ss_pred             cccceEcCCCCe--EEEeCCCCCCcchHHHHHHHhcChhHHHHhhccCCceEEEcCCc
Confidence            446777766421  111    6889999999998874          23689888543

---

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	81
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	6e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-10
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	3e-10
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-09
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-09
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	4e-07
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	7e-07
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-05
d1wgma_	98	g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Hu	8e-05
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	3e-04
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	7e-04
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	0.001
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	0.002

>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 = 50.8 bits (121), Expect = 6e-11
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATL 63
          +C IC +  K      C H+ C SC+T W +   Q CP CR  +
Sbjct: 25 LCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 49.9 bits (119), Expect = 1e-10
 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 22 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 63
          CPIC ++         C H FC  C+T+W  +  TCPLC+  +
Sbjct: 8  CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.5 bits (118), Expect = 3e-10
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATL 63
           C IC      PV+ +C H+FC  C+ +        CP CR   
Sbjct: 25 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

>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 = 49.3 bits (117), Expect = 4e-10
 Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 22 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ---TCPLCRATL 63
          CPIC +  K PV   C HIFC+ C+ K  ++++    CPLC+  +
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 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 = 47.2 bits (112), Expect = 1e-09
 Identities = 14/49 (28%), Positives = 17/49 (34%), Gaps = 3/49 (6%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 69
           C  C  E K P  L C H  C  C+         CP+C+A        
Sbjct: 8  RCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGADT 53

>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 = 46.8 bits (111), Expect = 2e-09
 Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 22 CPICHDEFK---TPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLV 64
          C +C  E +       L  C H F   CV  W     TCPLCR T+V
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>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 = 41.3 bits (96), Expect = 4e-07
 Identities = 11/42 (26%), Positives = 14/42 (33%)

Query: 20 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 61
                  E  T     C H F   C+++W    Q CPL   
Sbjct: 40 ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 40.4 bits (94), Expect = 7e-07
 Identities = 10/40 (25%), Positives = 15/40 (37%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 60
           CPI  +  K PV ++    +  S + KW D         
Sbjct: 10 RCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKS 49

>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 = 2e-05
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 3/62 (4%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ 79
           C  C +  + PV L  C HIFC +CV+        CP+C           +      +Q
Sbjct: 24 RCSRCTNILREPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDLKINRQLDSMIQ 81

Query: 80 IF 81
          + 
Sbjct: 82 LC 83

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]} Length = 98

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]

 Score = 35.6 bits (81), Expect = 8e-05
 Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 21 ICPICHDEFKTPVQLTCCHIFCE-SCVTKWFDREQTCPLCR 60
          + PI       PV L    +  + S + +    +QT P  R
Sbjct: 24 LDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNR 64

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 1e-04
 Identities = 15/48 (31%), Positives = 16/48 (33%), Gaps = 6/48 (12%)

Query: 22 CPICHDEFKTP-----VQLTCCHIFCESCVTKWFD-REQTCPLCRATL 63
          CP C            +   C H  CESCV   F      CP C   L
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 33.2 bits (75), Expect = 3e-04
 Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)

Query: 21 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 63
          +C I     + PV       IF +S + ++       P+    L
Sbjct: 2  LCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL 45

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.4 bits (73), Expect = 7e-04
 Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 5/50 (10%)

Query: 22 CPICHDEF----KTPVQLTCCHIFCESCVTKWFDREQT-CPLCRATLVDD 66
          CP+C +            TC +  C  C  +    E   CP CR    +D
Sbjct: 3  CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 31.8 bits (71), Expect = 0.001
 Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 7/49 (14%)

Query: 21 ICPICHDEFKTP-----VQLTCCHIFCESCVTKWFDREQ--TCPLCRAT 62
          +C IC++E                    SC++ W    +   C +C   
Sbjct: 8  VCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>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 = 32.3 bits (72), Expect = 0.002
 Identities = 7/32 (21%), Positives = 10/32 (31%), Gaps = 5/32 (15%)

Query: 35 LTCCHIFCESCVTKWFDREQ-----TCPLCRA 61
            C H F   C+   +          CP C+ 
Sbjct: 59 TKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT 90

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	81
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.81
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.8
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.79
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.75
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.74
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.72
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.72
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.69
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.68
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.68
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.63
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.61
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.49
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.48
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.36
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.85
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	96.22
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.12
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.09
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	95.0
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	94.99
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	91.86
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	91.45
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	91.13
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	91.03
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	91.02
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	90.16
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	89.41
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	87.19
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	86.93
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	86.26
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	85.2
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	85.1
d2epqa1	32	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	84.68
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	84.25
d1wfha_	64	Zinc finger A20 and AN1 domains containing protein	83.29
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	83.24
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	82.58
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	82.14
d1wfpa_	74	Zinc finger A20 and AN1 domains containing protein	81.8

>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=99.81  E-value=1.3e-20  Score=94.92  Aligned_cols=67  Identities=22%  Similarity=0.428  Sum_probs=59.2

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC-CCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~-~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ...+++.|+||++++.+|++++|||+||+.||.+|+..+ ..||.|+.++....+.+|..+.+.++.|
T Consensus         4 eiP~~l~CpIc~~~m~dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN~~L~~~I~~~   71 (78)
T d1t1ha_           4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLKSLIALW   71 (78)
T ss_dssp             CCSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECTTTHHHHHHH
T ss_pred             CCCccCCCcCcCchhhCceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccccchHHHHHHHHHH
Confidence            356789999999999999999999999999999999854 6799999999888788888888887754

>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=99.80  E-value=8.5e-21  Score=96.04  Aligned_cols=67  Identities=10%  Similarity=0.094  Sum_probs=58.1

Q ss_pred             cCCCCccccccccCCCCCeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ...+.+.|+||++++.+|++++|||+||+.||.+|+. .+..||.|+.++....+.+|..+.+.++.|
T Consensus         3 eiP~~l~CpIc~~l~~dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN~~L~~~I~~~   70 (80)
T d2c2la2           3 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAF   70 (80)
T ss_dssp             CCCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHHHHHHHHHH
T ss_pred             CCCccccCcCcCchhhhhcccCCcCeecHHHHHHHHhcCCccCCCccccccccccccHHHHHHHHHHH
Confidence            3467899999999999999999999999999999987 456899999998877778888887777654

>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=99.79  E-value=5e-20  Score=97.06  Aligned_cols=64  Identities=31%  Similarity=0.707  Sum_probs=53.7

Q ss_pred             CCCCccccccccCCCCCeecCCCCcccHHHHHHHHhCC---CCCCCCCCCCCCCccccCcccchhhh
Q psy8828          16 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDDPAWRDGATSYFVQ   79 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~---~~CP~C~~~~~~~~~~~~~~~~~~~~   79 (81)
                      +++.+.|+||++.+.+|++++|||+||..||.+|+...   ..||.||.++.......+..+.++++
T Consensus        18 l~~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~~ve   84 (103)
T d1jm7a_          18 MQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVE   84 (103)
T ss_dssp             HHHHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCCSSSHHHH
T ss_pred             cccCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcCHHHHHHHH
Confidence            34567899999999999999999999999999998754   48999999998776777766666554

>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=99.75  E-value=1.3e-19  Score=92.53  Aligned_cols=52  Identities=27%  Similarity=0.685  Sum_probs=45.4

Q ss_pred             CCCccccccccCCCCCeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCCCcc
Q psy8828          17 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPA   68 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~~~   68 (81)
                      .+.+.|+||++.+.+|++++|||+||..||.+|++ ++..||.||.++...++
T Consensus        21 ~~~l~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l   73 (86)
T d1rmda2          21 VKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL   73 (86)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             ccCcCCccCCcchhcceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhc
Confidence            35579999999999999999999999999999987 55689999999875543

>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=99.74  E-value=2.1e-18  Score=90.05  Aligned_cols=67  Identities=19%  Similarity=0.149  Sum_probs=59.1

Q ss_pred             cCCCCccccccccCCCCCeecCCC-CcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhcC
Q psy8828          15 LLGVGCICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   81 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l~C~-h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~y   81 (81)
                      ...+.|.||||.+++.+|++++|+ |+||+.||.+|+..+..||.|++++....+.+|..+...++.|
T Consensus        18 ~~P~~f~CPI~~~lm~dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN~~Lr~~I~~~   85 (98)
T d1wgma_          18 DACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNTELKEKIQRW   85 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECHHHHHHHHHH
T ss_pred             CCcHHhCCcCchhHHHHHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhcchHHHHHHHHHH
Confidence            445689999999999999999877 5899999999999999999999999888888888888877654

>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=99.72  E-value=5.1e-18  Score=85.48  Aligned_cols=48  Identities=33%  Similarity=0.825  Sum_probs=43.1

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHh-CCCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDD   66 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~-~~~~CP~C~~~~~~~   66 (81)
                      ...|+||++.+.+++.++|||.||..||.+|+. ++..||+||..+...
T Consensus        23 ~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~   71 (79)
T d1fbva4          23 FQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT   71 (79)
T ss_dssp             TTBCTTTSSSBCCEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCC
T ss_pred             CCCCccCCCcCCCeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCC
Confidence            357999999999999999999999999999997 457899999998754

>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=99.72  E-value=2.1e-20  Score=97.61  Aligned_cols=65  Identities=26%  Similarity=0.547  Sum_probs=54.0

Q ss_pred             ccCCCCccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCccccCcccchhhhc
Q psy8828          14 TLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   80 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~~~~~~~~~~~   80 (81)
                      ..+.+.+.|+||++.+.+|+.+ +|||+||..||.+|+.  ..||.|+.++.......+..+..+++.
T Consensus        17 ~~l~~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~n~~l~~lv~~   82 (97)
T d1jm7b_          17 DRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINRQLDSMIQL   82 (97)
T ss_dssp             HHHHHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCCHHHHHHHHH
T ss_pred             HhhhhcCCCccCCchhhcCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhCcccHHHHHHHHH
Confidence            3445678999999999999976 8999999999999975  459999999887777777777776654

>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=99.72  E-value=8.4e-19  Score=83.18  Aligned_cols=51  Identities=18%  Similarity=0.270  Sum_probs=45.5

Q ss_pred             ccccccccCCCCCeec-CCCCcccHHHHHHHHhCCCCCCCCCCCCCCCcccc
Q psy8828          20 CICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWR   70 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~~~~   70 (81)
                      +.|+||++.+.+|+.+ .|||+||++||.+|+.++..||+||+++...++.+
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLip   52 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE   52 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEE
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhcee
Confidence            4799999999999988 59999999999999999999999999987665543

>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=99.69  E-value=5.9e-18  Score=83.06  Aligned_cols=47  Identities=36%  Similarity=0.966  Sum_probs=41.9

Q ss_pred             CccccccccCCCCCee-cCCCCcccHHHHHHHHhCCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVD   65 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~-l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~   65 (81)
                      ...|+||++.+.++.. ++|||+||.+|+.+|++.+..||+||.++..
T Consensus         5 ~d~C~IC~~~~~~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCSCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCccCCcCccCCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            4579999999988755 6999999999999999999999999998754

>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=99.68  E-value=1.7e-17  Score=78.28  Aligned_cols=49  Identities=39%  Similarity=0.870  Sum_probs=41.5

Q ss_pred             CCCCccccccccCCCCC---eec-CCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          16 LGVGCICPICHDEFKTP---VQL-TCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        16 ~~~~~~C~iC~~~~~~p---~~l-~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      .+++..|+||++.+.+.   +.+ +|+|.||..|+.+|++.+..||+||+++.
T Consensus         2 ~ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            34567899999999753   344 69999999999999999999999998763

>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=99.68  E-value=5.1e-18  Score=80.34  Aligned_cols=47  Identities=30%  Similarity=0.653  Sum_probs=40.9

Q ss_pred             CCccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCCCCc
Q psy8828          18 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   67 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~~~~   67 (81)
                      +.+.|+||++.+.+|++++|||+||..|+.+|   +..||.||+++....
T Consensus         5 ~~l~C~IC~~~~~~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           5 QFLRCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCBCCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCCcccCcccCCCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            45799999999999999999999999999653   568999999987643

>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=99.63  E-value=7.9e-17  Score=78.31  Aligned_cols=49  Identities=35%  Similarity=0.702  Sum_probs=39.1

Q ss_pred             CCccccccccCCCC-C----eecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT-P----VQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~-p----~~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~~   66 (81)
                      ++..||||++.+.. +    +.++|||.||.+||.+|+.. +..||.||+++...
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            45789999986532 1    34589999999999999864 56899999998654

>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=99.61  E-value=2.1e-16  Score=73.68  Aligned_cols=46  Identities=24%  Similarity=0.647  Sum_probs=38.1

Q ss_pred             ccccccccCCCCC----eecCCCCcccHHHHHHHHhC-CCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTP----VQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVD   65 (81)
Q Consensus        20 ~~C~iC~~~~~~p----~~l~C~h~fc~~Cl~~~~~~-~~~CP~C~~~~~~   65 (81)
                      ++|+||++.+...    +.++|||.||..|+.+|+.. +..||+||+++.+
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            4799999988642    34589999999999999985 4579999998864

>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=99.49  E-value=1.5e-14  Score=73.86  Aligned_cols=47  Identities=28%  Similarity=0.615  Sum_probs=38.9

Q ss_pred             CCccccccccCCCCC------------------eecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p------------------~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      ....|+||++.+.++                  +.++|||.||..||.+|++.+.+||+||.++.
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            345699998876542                  34589999999999999999999999999864

>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=99.48  E-value=2.3e-14  Score=76.10  Aligned_cols=49  Identities=20%  Similarity=0.510  Sum_probs=38.7

Q ss_pred             CCccccccccCCCCC------------------eecCCCCcccHHHHHHHHhC-----CCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDR-----EQTCPLCRATLVDD   66 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p------------------~~l~C~h~fc~~Cl~~~~~~-----~~~CP~C~~~~~~~   66 (81)
                      .+..|+||++.+..+                  ..++|+|.||..||..|+..     +.+||+||..+...
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            356799999987542                  34689999999999999973     24799999987543

>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=99.36  E-value=3.7e-13  Score=64.05  Aligned_cols=49  Identities=22%  Similarity=0.586  Sum_probs=40.0

Q ss_pred             CCCccccccccCCCCCeecCC-----CCcccHHHHHHHHh--CCCCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTPVQLTC-----CHIFCESCVTKWFD--REQTCPLCRATLVD   65 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p~~l~C-----~h~fc~~Cl~~~~~--~~~~CP~C~~~~~~   65 (81)
                      ++...|+||++.+.++...+|     +|.||..||.+|+.  ++.+||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            456689999998887766654     59999999999986  55789999998753

>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=98.85  E-value=7e-10  Score=56.55  Aligned_cols=43  Identities=23%  Similarity=0.655  Sum_probs=32.8

Q ss_pred             CccccccccCCCC---CeecCCCCcccHHHHHHHHhC-----C---CCCCCCCC
Q psy8828          19 GCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDR-----E---QTCPLCRA   61 (81)
Q Consensus        19 ~~~C~iC~~~~~~---p~~l~C~h~fc~~Cl~~~~~~-----~---~~CP~C~~   61 (81)
                      ...|+||++.+..   +..++|+|.||.+|+..|+..     .   ..||.|+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            4589999998754   334589999999999999861     1   26998643

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.22  E-value=0.0059  Score=28.77  Aligned_cols=33  Identities=27%  Similarity=0.734  Sum_probs=27.6

Q ss_pred             CccccccccCCCCCeecCC----CCcccHHHHHHHHh
Q psy8828          19 GCICPICHDEFKTPVQLTC----CHIFCESCVTKWFD   51 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C----~h~fc~~Cl~~~~~   51 (81)
                      .+.|.+|.+.+++...+.|    +|.||..|-...++
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik   44 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   44 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHH
Confidence            4789999999998765544    69999999988876

>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=95.12  E-value=0.028  Score=27.16  Aligned_cols=36  Identities=14%  Similarity=0.520  Sum_probs=26.8

Q ss_pred             ccCCCCccccccccCCCCCeecC---CCCcccHHHHHHHH
Q psy8828          14 TLLGVGCICPICHDEFKTPVQLT---CCHIFCESCVTKWF   50 (81)
Q Consensus        14 ~~~~~~~~C~iC~~~~~~p~~l~---C~h~fc~~Cl~~~~   50 (81)
                      +....+..|.|| +.+.....+|   |+..||..|+.+.-
T Consensus        10 e~v~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~g   48 (89)
T d1wila_          10 EPVVNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRMG   48 (89)
T ss_dssp             CCCCCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHHT
T ss_pred             cCCCcCcccccc-CcccccceecceeecchhhHHHHHHhc
Confidence            345567799999 6666555555   68899999999873

>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=95.09  E-value=0.0066  Score=26.52  Aligned_cols=41  Identities=22%  Similarity=0.561  Sum_probs=28.0

Q ss_pred             cccccccCCCCCeec---CCCCcccHHHHHHHHh----CCCCCCCCCC
Q psy8828          21 ICPICHDEFKTPVQL---TCCHIFCESCVTKWFD----REQTCPLCRA   61 (81)
Q Consensus        21 ~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~----~~~~CP~C~~   61 (81)
                      .|.||...-.....+   .|...||..|+..-+.    ....||.|+.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            578887654433333   7889999999976544    2357888864

>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=95.00  E-value=0.02  Score=26.90  Aligned_cols=47  Identities=21%  Similarity=0.487  Sum_probs=30.7

Q ss_pred             cCCCCccccccccCCCCCeec---CCCCcccHHHHH----HH-----HhCCCCCCCCCCC
Q psy8828          15 LLGVGCICPICHDEFKTPVQL---TCCHIFCESCVT----KW-----FDREQTCPLCRAT   62 (81)
Q Consensus        15 ~~~~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~----~~-----~~~~~~CP~C~~~   62 (81)
                      ...+...| ||.....+...+   .|.-.||..|+.    ..     ......||.|+..
T Consensus        12 ~d~~~~~C-iC~~~~~~~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          12 YDPNALYC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCTTCCCS-TTCCCCCSSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             cCCCcCEE-ECCCccCCCeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            33445668 898776654444   688899999982    11     1235799999544

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.99  E-value=0.07  Score=25.88  Aligned_cols=48  Identities=25%  Similarity=0.632  Sum_probs=34.5

Q ss_pred             CCccccccccCCCC----Ceec---CCCCcccHHHHH-HHHhCCCCCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKT----PVQL---TCCHIFCESCVT-KWFDREQTCPLCRATLVD   65 (81)
Q Consensus        18 ~~~~C~iC~~~~~~----p~~l---~C~h~fc~~Cl~-~~~~~~~~CP~C~~~~~~   65 (81)
                      ..-.|.||-+.+-.    ...+   .|+-..|+.|.+ +....++.||.|+.....
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhh
Confidence            45689999997542    1223   577788999996 333467899999888754

>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=91.86  E-value=0.1  Score=24.31  Aligned_cols=43  Identities=26%  Similarity=0.497  Sum_probs=26.3

Q ss_pred             CCccccccccCCCCCee-c---CCC-CcccHHHHHHHHh---CCCCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQ-L---TCC-HIFCESCVTKWFD---REQTCPLCRAT   62 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~-l---~C~-h~fc~~Cl~~~~~---~~~~CP~C~~~   62 (81)
                      +...| ||........+ .   .|- ..||..|+. ...   ....||.|+..
T Consensus        15 e~~~C-iC~~~~~~~~i~c~~~~C~~~wfH~~Cvg-l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          15 EPTYC-LCNQVSYGEMIGCDNEQCPIEWFHFSCVS-LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             SCCCS-TTCCCCCSSEECCSCTTCSCCCEETTTTT-CSSCCSSCCCCTTTSSC
T ss_pred             CCCEE-EeCCCCCCCEEEEECCCCCCcCccCccCC-CCcCCCCcEECcCCccc
Confidence            34456 89986544433 3   243 469999984 211   34689999654

>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=91.45  E-value=0.057  Score=25.25  Aligned_cols=30  Identities=30%  Similarity=0.797  Sum_probs=21.3

Q ss_pred             CCccccccccCCCCCee----cCCCCcccHHHHH
Q psy8828          18 VGCICPICHDEFKTPVQ----LTCCHIFCESCVT   47 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~   47 (81)
                      +...|.+|...|.--..    ..||+.||.+|..
T Consensus        12 ~~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~   45 (72)
T d1dvpa2          12 DGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTA   45 (72)
T ss_dssp             CCSBCTTTCCBCCSSSCCEECTTTCCEECSTTSC
T ss_pred             cCCccccCCCcccCccccccccccCCeeChhhhC
Confidence            44579999987753211    2799999999864

>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=91.13  E-value=0.066  Score=24.74  Aligned_cols=43  Identities=23%  Similarity=0.594  Sum_probs=28.9

Q ss_pred             CccccccccCCCCCeec--CCCCcccHHHHHHHHh----CCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRATL   63 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~~~~~----~~~~CP~C~~~~   63 (81)
                      ...|.+|.+.  ..+++  .|...||..|+...+.    ....||.|+...
T Consensus         7 c~~C~~C~~~--~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQKP--GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCSS--SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCc--CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            4467788753  22222  7899999999986544    235899996544

>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=91.03  E-value=0.13  Score=23.09  Aligned_cols=42  Identities=29%  Similarity=0.637  Sum_probs=28.8

Q ss_pred             CCccccccccCCCCCeec---CCCCcccHHHHHHHHhCCCCCCCC
Q psy8828          18 VGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFDREQTCPLC   59 (81)
Q Consensus        18 ~~~~C~iC~~~~~~p~~l---~C~h~fc~~Cl~~~~~~~~~CP~C   59 (81)
                      ....|--|+..+.+....   .|++.||.+|=.=.-..-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCCceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            345788888888766443   689999999954222233578876

>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=91.02  E-value=0.28  Score=22.93  Aligned_cols=45  Identities=24%  Similarity=0.521  Sum_probs=28.8

Q ss_pred             CCCccccccccCCCCC--eec---CCCCcccHHHHHH----HHh-----CCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTP--VQL---TCCHIFCESCVTK----WFD-----REQTCPLCRAT   62 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p--~~l---~C~h~fc~~Cl~~----~~~-----~~~~CP~C~~~   62 (81)
                      .+...| ||.......  +..   .|..-||..|+.-    ...     ....||.|+..
T Consensus        14 ~~~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T d1wewa_          14 EIKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCc
Confidence            345678 899876553  334   3888999999831    101     13689988654

>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=90.16  E-value=0.065  Score=25.43  Aligned_cols=12  Identities=33%  Similarity=1.384  Sum_probs=10.7

Q ss_pred             cccHHHHHHHHh
Q psy8828          40 IFCESCVTKWFD   51 (81)
Q Consensus        40 ~fc~~Cl~~~~~   51 (81)
                      .||+.|+.+|..
T Consensus        39 GFCRNCLskWy~   50 (79)
T d2o35a1          39 GFCRNCLSNWYR   50 (79)
T ss_dssp             SCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            499999999986

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.41  E-value=0.046  Score=26.34  Aligned_cols=47  Identities=15%  Similarity=0.470  Sum_probs=30.6

Q ss_pred             CCCccccccccCCCCC--eec---CCCCcccHHHHHH-----HHh---CCCCCCCCCCCC
Q psy8828          17 GVGCICPICHDEFKTP--VQL---TCCHIFCESCVTK-----WFD---REQTCPLCRATL   63 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~p--~~l---~C~h~fc~~Cl~~-----~~~---~~~~CP~C~~~~   63 (81)
                      +..+.|.||.......  .++   .|...||..|+..     ...   ....||.|....
T Consensus        14 ~~~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~   73 (88)
T d1weva_          14 EMGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQM   73 (88)
T ss_dssp             HHCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHH
T ss_pred             cCcCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchH
Confidence            3457899998754321  223   7888999999752     122   246899996543

>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=87.19  E-value=0.22  Score=22.75  Aligned_cols=28  Identities=25%  Similarity=0.655  Sum_probs=20.0

Q ss_pred             ccccccccCCCCCee----cCCCCcccHHHHH
Q psy8828          20 CICPICHDEFKTPVQ----LTCCHIFCESCVT   47 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~   47 (81)
                      ..|.+|...|.--..    -.||..||..|..
T Consensus         6 ~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~   37 (67)
T d1vfya_           6 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSS   37 (67)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSC
T ss_pred             cccccCCCcccCcccccccccCCCEecccccC
Confidence            469999987753211    1699999999963

>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=86.93  E-value=0.0091  Score=26.32  Aligned_cols=38  Identities=29%  Similarity=0.771  Sum_probs=20.8

Q ss_pred             ccccccCCCCCee----cCCCCcccHHHHHHHHhCCCCCCCC
Q psy8828          22 CPICHDEFKTPVQ----LTCCHIFCESCVTKWFDREQTCPLC   59 (81)
Q Consensus        22 C~iC~~~~~~p~~----l~C~h~fc~~Cl~~~~~~~~~CP~C   59 (81)
                      |.+|...|..-..    -.||..||.+|..........|..|
T Consensus         3 C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C   44 (51)
T d1y02a2           3 CKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLC   44 (51)
T ss_dssp             CTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHH
T ss_pred             ccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhH
Confidence            6667766653211    2699999999965332223344444

>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=86.26  E-value=0.081  Score=23.71  Aligned_cols=41  Identities=24%  Similarity=0.582  Sum_probs=27.1

Q ss_pred             ccccccccCCCCCeec--CCCCcccHHHHHHHHh----CCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRAT   62 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l--~C~h~fc~~Cl~~~~~----~~~~CP~C~~~   62 (81)
                      ..|.+|.+.  ..++.  .|...||..|+...+.    ....||.|+..
T Consensus        10 ~~C~~C~~~--g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_          10 EFCRVCKDG--GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SSCTTTCCC--SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCCcCCCCC--CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            469999863  22222  6888999999864433    24589999654

>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=85.20  E-value=0.18  Score=22.82  Aligned_cols=28  Identities=32%  Similarity=0.801  Sum_probs=20.0

Q ss_pred             ccccccccCCCCCee----cCCCCcccHHHHH
Q psy8828          20 CICPICHDEFKTPVQ----LTCCHIFCESCVT   47 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~----l~C~h~fc~~Cl~   47 (81)
                      ..|.+|...|.--..    -.||..||..|..
T Consensus         9 ~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~   40 (64)
T d1joca1           9 QNCMACGKGFSVTVRRHHCRQCGNIFCAECSA   40 (64)
T ss_dssp             CBCTTTCCBCCSSSCCEECTTTCCEECGGGSC
T ss_pred             CcCcCcCCcccCCccccchhhhCCeecccccC
Confidence            468899887653221    2799999999964

>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=85.10  E-value=0.97  Score=20.97  Aligned_cols=45  Identities=24%  Similarity=0.557  Sum_probs=28.9

Q ss_pred             ccccccccCCCCC-eec---CCCCcccHHHHH---HHHh--CCCCCCCCCCCCCC
Q psy8828          20 CICPICHDEFKTP-VQL---TCCHIFCESCVT---KWFD--REQTCPLCRATLVD   65 (81)
Q Consensus        20 ~~C~iC~~~~~~p-~~l---~C~h~fc~~Cl~---~~~~--~~~~CP~C~~~~~~   65 (81)
                      .-| ||....... ..+   .|..-||..|+.   .-..  ....||.|+.....
T Consensus        13 v~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~gp   66 (79)
T d1wepa_          13 VYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP   66 (79)
T ss_dssp             CCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCS
T ss_pred             eEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcCC
Confidence            345 898865432 233   688899999984   2112  24799999876543

>d2epqa1 g.37.1.1 (A:380-411) PATZ1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: PATZ1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.68  E-value=0.13  Score=19.69  Aligned_cols=12  Identities=42%  Similarity=0.971  Sum_probs=7.1

Q ss_pred             CccccccccCCC
Q psy8828          19 GCICPICHDEFK   30 (81)
Q Consensus        19 ~~~C~iC~~~~~   30 (81)
                      .+.||||...|.
T Consensus         3 p~~cpic~qrfk   14 (32)
T d2epqa1           3 PYSCPVCGLRFK   14 (32)
T ss_dssp             SSEETTTTEECS
T ss_pred             CcccchHHHHhh
Confidence            356666666554

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=84.25  E-value=0.18  Score=19.21  Aligned_cols=28  Identities=18%  Similarity=0.571  Sum_probs=19.7

Q ss_pred             ccccccccCCCCCeec-CCCCcccHHHHH
Q psy8828          20 CICPICHDEFKTPVQL-TCCHIFCESCVT   47 (81)
Q Consensus        20 ~~C~iC~~~~~~p~~l-~C~h~fc~~Cl~   47 (81)
                      ++|+.|...++..... .=|..||..|.-
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cya   29 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYA   29 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeee
Confidence            4688888877765443 567788888864

>d1wfha_ g.80.1.1 (A:) Zinc finger A20 and AN1 domains containing protein At2g36320 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: Zinc finger A20 and AN1 domains containing protein At2g36320
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=83.29  E-value=1.2  Score=20.13  Aligned_cols=29  Identities=21%  Similarity=0.456  Sum_probs=21.0

Q ss_pred             CCCccccccccCCCC-CeecCCCCcccHHH
Q psy8828          17 GVGCICPICHDEFKT-PVQLTCCHIFCESC   45 (81)
Q Consensus        17 ~~~~~C~iC~~~~~~-p~~l~C~h~fc~~C   45 (81)
                      ....+|..|..-+.- +..-.||+.||..-
T Consensus        13 ~k~~RC~~C~KKl~l~~~~CrCg~~FC~~H   42 (64)
T d1wfha_          13 QRPNRCTVCRKRVGLTGFMCRCGTTFCGSH   42 (64)
T ss_dssp             SSCCCCTTTCCCCCTTCEECSSSCEECTTT
T ss_pred             CCCCcChhhCCCccceeeeccCCCEehhhc
Confidence            345689999986543 45568999999753

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=83.24  E-value=0.0059  Score=28.71  Aligned_cols=41  Identities=27%  Similarity=0.586  Sum_probs=25.4

Q ss_pred             CccccccccCCCCCeecCCCCcccHHHHHHHHhCCCCCCCCCCCCC
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   64 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~Cl~~~~~~~~~CP~C~~~~~   64 (81)
                      .+.||.|...+..    .=++.+|..|-..+ .....||.|++++.
T Consensus         2 ~~~CP~C~~eL~~----~~~~~~C~~C~~~~-~~~a~CPdC~~~Le   42 (71)
T d2jnea1           2 ELHCPQCQHVLDQ----DNGHARCRSCGEFI-EMKALCPDCHQPLQ   42 (71)
T ss_dssp             CCBCSSSCSBEEE----ETTEEEETTTCCEE-EEEEECTTTCSBCE
T ss_pred             CCcCCCccCcccc----cCCCEehhhhhhhh-eeEEeCCccccHHH
Confidence            3579999887553    12556666664332 22356899988764

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.58  E-value=0.21  Score=20.00  Aligned_cols=27  Identities=11%  Similarity=0.290  Sum_probs=20.5

Q ss_pred             CccccccccCCCCCeecCCCCcccHHH
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESC   45 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~C   45 (81)
                      ...|.+|...+.+.+.-..|..|+-.|
T Consensus         8 lEkC~~C~~~I~driLrA~Gk~yHP~C   34 (35)
T d2dloa1           8 LEKCATCSQPILDRILRAMGKAYHPGC   34 (35)
T ss_dssp             CCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             HHHHHHhchHHHHHHHHHhCCCCCCCC
Confidence            447999999988887777777776554

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.14  E-value=0.15  Score=21.25  Aligned_cols=27  Identities=19%  Similarity=0.388  Sum_probs=22.3

Q ss_pred             CccccccccCCCCCeecCCCCcccHHH
Q psy8828          19 GCICPICHDEFKTPVQLTCCHIFCESC   45 (81)
Q Consensus        19 ~~~C~iC~~~~~~p~~l~C~h~fc~~C   45 (81)
                      ...|..|.+.+.-++...=+|.|+..|
T Consensus        15 G~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          15 GTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             CcccccccCEeeeeeeEecCcccCCCC
Confidence            458999999999888877778888665

>d1wfpa_ g.80.1.1 (A:) Zinc finger A20 and AN1 domains containing protein At1g12440 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: Zinc finger A20 and AN1 domains containing protein At1g12440
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=81.80  E-value=1.6  Score=20.34  Aligned_cols=28  Identities=18%  Similarity=0.516  Sum_probs=19.9

Q ss_pred             CCccccccccCCCC-CeecCCCCcccHHH
Q psy8828          18 VGCICPICHDEFKT-PVQLTCCHIFCESC   45 (81)
Q Consensus        18 ~~~~C~iC~~~~~~-p~~l~C~h~fc~~C   45 (81)
                      ...+|.+|..-+.- ...-.|++.||...
T Consensus        24 kk~RC~~C~KKl~l~~~~CrCg~~FC~~H   52 (74)
T d1wfpa_          24 TATRCLSCNKKVGVTGFKCRCGSTFCGTH   52 (74)
T ss_dssp             CCCBCSSSCCBCTTTCEECTTSCEECTTT
T ss_pred             CCCcChhcCCccCCCceecCCCChhhhcc
Confidence            35689999976543 24448999999754