Psyllid ID: psy3884

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----
Protein Sequence
MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHccccccccHHHHHccccccccccccccccEEEcccccccHHHHHHHHHccccccccccccccccccccccccccHHcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHcccccccccHHHHHHcccccEEEHHHcccccEcccccEccHHHHHHHHHHHccccccEEEEEccccccccccccEEEcc
Coil and Loop (DISEMBL)
MQAAKAWWKSFTKLLNNIqlgvsptketllgvgcicpichdefktpvqltcchifcescvtkwfdreqtcplcratlvddpawrdgatsYFVQIF
Flexible Loop (DISEMBL)
MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRAtlvddpawrdGATSYFVQIF
Low Complexity Region (SEG)
MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Disordered region (IsUnstruct)
****KAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI*
Disordered Region (DISOPRED)
******WWKSFTKLLN**************GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRAT************SYFVQIF
Disordered Region (DISEMBL)
MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Disordered Region (DISPRO)
MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF
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	95	2.2.26 [Sep-21-2011]
Q5M7Z0	435	RING finger and transmemb	yes	N/A	0.789	0.172	0.513	5e-17
Q3UF64	445	RING finger and transmemb	yes	N/A	0.915	0.195	0.431	6e-17
Q96EX2	444	RING finger and transmemb	no	N/A	0.915	0.195	0.443	2e-16
Q5RAG4	444	RING finger and transmemb	yes	N/A	0.915	0.195	0.431	2e-15
Q6NZ21	419	RING finger and transmemb	no	N/A	0.789	0.178	0.460	6e-15
Q9DCN7	395	RING finger and transmemb	no	N/A	0.789	0.189	0.486	2e-14
Q6NTV1	416	RING finger and transmemb	N/A	N/A	0.852	0.194	0.428	4e-14
Q28GL3	416	RING finger and transmemb	no	N/A	0.915	0.209	0.409	4e-14
Q9DBY1	612	E3 ubiquitin-protein liga	no	N/A	0.526	0.081	0.490	1e-07
Q9SK92	381	E3 ubiquitin-protein liga	no	N/A	0.494	0.123	0.431	1e-07

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

 Score = 86.3 bits (212), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 39/76 (51%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 21  GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
           GV+ +K     V  IC IC  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct: 360 GVAASKRQCSDVDDICSICQAEFQKPILLICQHIFCEECMTLWFNREKTCPLCRTVISDH 419

Query: 81  -PAWRDGATSYFVQIF 95
              W+DGATS  +QI+
Sbjct: 420 INKWKDGATSSHLQIY 435

Homo sapiens (taxid: 9606)

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

 Score = 86.3 bits (212), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 38/88 (43%), Positives = 52/88 (59%), Gaps = 1/88 (1%)

Query: 9   KSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ 68
           K+   L  +   GV  T +     G +C IC  EF+ P+ L C H+FCE C+  W DRE+
Sbjct: 358 KALKLLCTSQNYGVRATGQQCTEAGAVCAICQAEFRDPMILLCQHVFCEECLCLWLDRER 417

Query: 69  TCPLCRATLVDD-PAWRDGATSYFVQIF 95
           TCPLCR+  VD    W+DGATS  +Q++
Sbjct: 418 TCPLCRSVAVDTLRCWKDGATSAHLQVY 445

Mus musculus (taxid: 10090)

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

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/88 (44%), Positives = 51/88 (57%), Gaps = 1/88 (1%)

Query: 9   KSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ 68
           K+   L  +   GV  T +     G IC IC  EF+ P+ L C H+FCE C+  W DRE+
Sbjct: 357 KALKLLCTSQNYGVRATGQQCTEAGDICAICQAEFREPLILLCQHVFCEECLCLWLDRER 416

Query: 69  TCPLCRATLVDD-PAWRDGATSYFVQIF 95
           TCPLCR+  VD    W+DGATS   Q++
Sbjct: 417 TCPLCRSVAVDTLRCWKDGATSAHFQVY 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 = 80.9 bits (198), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 38/88 (43%), Positives = 50/88 (56%), Gaps = 1/88 (1%)

Query: 9   KSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ 68
           K+   L  +   GV  T +     G IC IC  EF+ P+ L C H+FCE C+  W DRE+
Sbjct: 357 KALKLLCTSQNYGVRATGQQCTEAGDICAICQAEFREPLILLCQHVFCEECLCLWLDRER 416

Query: 69  TCPLCRATLVDD-PAWRDGATSYFVQIF 95
           TCPL R+  VD    W+DGATS   Q++
Sbjct: 417 TCPLSRSVAVDTLRCWKDGATSAHFQVY 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: 21  GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
           G   +   +   G ICPIC  +FK P  L C HIFCE C+ +W ++E+TCPLCR  + D 
Sbjct: 344 GAPASPAQIREAGDICPICQADFKQPRVLVCQHIFCEECIAQWLNQERTCPLCRTVITDK 403

Query: 81  -PAWRDGATSYFVQIF 95
              W+DGATS  +QI+
Sbjct: 404 VHKWKDGATSAHLQIY 419

Danio rerio (taxid: 7955)

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

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/76 (48%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 21  GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD- 79
           GV  +K     +  IC IC  EF+ PV L C HIFCE C+T WF+RE+TCPLCR  + + 
Sbjct: 320 GVPASKRQCSDMDGICTICQAEFQKPVLLFCQHIFCEECITLWFNREKTCPLCRTVISEC 379

Query: 80  DPAWRDGATSYFVQIF 95
              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 = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 36/84 (42%), Positives = 52/84 (61%), Gaps = 3/84 (3%)

Query: 14  LLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLC 73
            L+    G + TK        +C IC  EF  P+ L C H+FCE C++ WF++E+TCPLC
Sbjct: 334 FLSQPNYGTTATKRQCSEADGMCAICQAEFTKPIALICQHVFCEECISSWFNKEKTCPLC 393

Query: 74  RATLVDDPA--WRDGATSYFVQIF 95
           R TL+ + +  W+DGATS  ++IF
Sbjct: 394 R-TLISNHSHKWKDGATSLQLRIF 416

Xenopus laevis (taxid: 8355)

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

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 36/88 (40%), Positives = 50/88 (56%), Gaps = 1/88 (1%)

Query: 9   KSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ 68
            S    L     G + TK     V  +C IC  EF  P+ L C H+FCE C++ WF++E+
Sbjct: 329 NSLRLFLTQPNYGAAATKSQCSEVDGMCAICQAEFIKPIVLVCQHVFCEECISLWFNKEK 388

Query: 69  TCPLCRATLVDDP-AWRDGATSYFVQIF 95
           TCPLCR  + +    W+DGATS  ++IF
Sbjct: 389 TCPLCRTVISNQSHKWKDGATSLQLRIF 416

Xenopus tropicalis (taxid: 8364)

>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: 25  TKETLLGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCR 74
           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|Q9SK92|ATL15_ARATH E3 ubiquitin-protein ligase ATL15 OS=Arabidopsis thaliana GN=ATL15 PE=1 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 4/51 (7%)

Query: 36  CPICHDEFKTPVQL----TCCHIFCESCVTKWFDREQTCPLCRATLVDDPA 82
           CP+C +EF+    L     CCH+F   C+  W   + TCPLCRA LV  P 
Sbjct: 118 CPVCLNEFEDDETLRLIPQCCHVFHPGCIDAWLRSQTTCPLCRANLVPVPG 168

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, UBC28 and UBC29 in vitro.

Arabidopsis thaliana (taxid: 3702)

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	95
328711386	484	PREDICTED: RING finger and transmembrane	1.0	0.196	0.652	3e-34
91079492	412	PREDICTED: similar to CG13605 CG13605-PA	1.0	0.230	0.6	3e-31
328704294	474	PREDICTED: RING finger and transmembrane	0.957	0.191	0.615	1e-30
242009781	492	conserved hypothetical protein [Pediculu	0.968	0.186	0.619	1e-30
347972340	684	AGAP004640-PA [Anopheles gambiae str. PE	0.915	0.127	0.609	1e-28
157124022	692	hypothetical protein AaeL_AAEL009719 [Ae	0.915	0.125	0.597	4e-28
307183322	459	Ring finger and transmembrane domain-con	0.873	0.180	0.590	1e-27
322790174	462	hypothetical protein SINV_00016 [Solenop	0.873	0.179	0.590	2e-27
198452503	674	GA12398 [Drosophila pseudoobscura pseudo	1.0	0.140	0.526	6e-27
195144928	667	GL24146 [Drosophila persimilis] gi|19410	1.0	0.142	0.526	6e-27

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

 Score =  148 bits (374), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 62/95 (65%), Positives = 72/95 (75%)

Query: 1   MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCV 60
           M   K WW +  KLL N+ LG +P+KE L   G  CPICHDE+ TPV L C HIFCE+CV
Sbjct: 390 MGCVKLWWTASYKLLQNVALGTAPSKEQLTIAGNNCPICHDEYATPVLLQCQHIFCEACV 449

Query: 61  TKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95
            KWFDREQTCPLCRA LVDDPAWRDG+T+ F+Q+F
Sbjct: 450 AKWFDREQTCPLCRAKLVDDPAWRDGSTTNFIQLF 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 =  139 bits (349), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 57/95 (60%), Positives = 71/95 (74%)

Query: 1   MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCV 60
           M   K    +F KLL N+ +G SP+KE +   G  CPICHD + +PV L C HIFCE+CV
Sbjct: 318 MSRMKLLKTAFFKLLQNVTVGSSPSKEQIQTAGDHCPICHDNYDSPVLLQCRHIFCENCV 377

Query: 61  TKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95
           T WFDREQTCPLCRA +VDDP+WRDG+TSYF+Q++
Sbjct: 378 TTWFDREQTCPLCRAKIVDDPSWRDGSTSYFIQLY 412

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

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 =  137 bits (344), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 56/91 (61%), Positives = 70/91 (76%)

Query: 5   KAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWF 64
           K W  +  KLL N+ LG +P+KE L   G  CPICHDE+ TPV L C HIFCE+CV KWF
Sbjct: 384 KLWRTALYKLLQNVALGTAPSKEQLTIAGNNCPICHDEYATPVLLQCEHIFCEACVAKWF 443

Query: 65  DREQTCPLCRATLVDDPAWRDGATSYFVQIF 95
           DREQTCP+CRA LVD+PAW+DG+T+ ++Q+F
Sbjct: 444 DREQTCPICRANLVDNPAWQDGSTTNYIQLF 474

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

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 =  136 bits (343), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/92 (61%), Positives = 70/92 (76%)

Query: 4   AKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKW 63
           A  + K+F KLL N+ LGV P+KE L   G  CPICHDE+  P+ L C H+FCE+CVT W
Sbjct: 401 ANHFMKAFLKLLRNVSLGVRPSKEQLDTAGSQCPICHDEYCFPILLQCRHVFCEACVTTW 460

Query: 64  FDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95
           FDREQTCPLCR  +VDDP+WRDGATS++ Q+F
Sbjct: 461 FDREQTCPLCRTKIVDDPSWRDGATSFYSQLF 492

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

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 =  130 bits (326), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/87 (60%), Positives = 63/87 (72%)

Query: 9   KSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ 68
           +SF KLL     G  PTKE L   G  C ICHD F +PV L C HIFCE CV  WFDREQ
Sbjct: 598 RSFVKLLQKTSYGTVPTKEQLQACGGQCSICHDNFNSPVLLECNHIFCELCVGTWFDREQ 657

Query: 69  TCPLCRATLVDDPAWRDGATSYFVQIF 95
           TCPLCRA +VDDP++RDGAT++F+Q++
Sbjct: 658 TCPLCRAKIVDDPSYRDGATTFFLQLY 684

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

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 =  128 bits (322), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 52/87 (59%), Positives = 63/87 (72%)

Query: 9   KSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ 68
           +S  KLL     G  P+KE L   G  CPICHD F +PV L C HIFCE CV  WFDREQ
Sbjct: 606 RSVIKLLQKTSYGTIPSKEQLQACGGQCPICHDNFNSPVLLECNHIFCELCVGTWFDREQ 665

Query: 69  TCPLCRATLVDDPAWRDGATSYFVQIF 95
           TCPLCRA +VDDP++RDGAT++F+Q++
Sbjct: 666 TCPLCRAKIVDDPSYRDGATTFFLQLY 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 =  127 bits (319), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 49/83 (59%), Positives = 67/83 (80%)

Query: 13  KLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPL 72
           KL  N+ LGVSP+KE L+  G IC ICH+E+ TPV+L C HIFCE+CV+ W DRE++CPL
Sbjct: 377 KLFQNVSLGVSPSKEQLVASGGICAICHEEYTTPVRLHCKHIFCETCVSTWLDRERSCPL 436

Query: 73  CRATLVDDPAWRDGATSYFVQIF 95
           CRA++ DDP +RDG T++F+Q++
Sbjct: 437 CRASITDDPIYRDGHTTHFIQLY 459

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  125 bits (315), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 49/83 (59%), Positives = 66/83 (79%)

Query: 13  KLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPL 72
           KL  N+ LGVSP+KE L+  G IC ICH+E+ TPV+L C HIFCE CV+ W DRE++CPL
Sbjct: 380 KLFQNVSLGVSPSKEQLIASGGICAICHEEYTTPVRLHCKHIFCEMCVSTWLDRERSCPL 439

Query: 73  CRATLVDDPAWRDGATSYFVQIF 95
           CRA++ DDP +RDG T++F+Q++
Sbjct: 440 CRASITDDPIYRDGHTTHFIQLY 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 =  124 bits (312), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 50/95 (52%), Positives = 64/95 (67%)

Query: 1   MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCV 60
           ++ AK+  KS      NI     PTKE L   G +CPICHD F TP+ L C HIFC+ CV
Sbjct: 580 VERAKSLHKSVVTFRRNIDSERPPTKEELDAAGSVCPICHDTFNTPIILECGHIFCDECV 639

Query: 61  TKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95
             WF REQTCP+CRA + DDPAW+DG+T++F Q++
Sbjct: 640 QTWFKREQTCPMCRAKVSDDPAWQDGSTTFFHQLY 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 =  124 bits (312), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 50/95 (52%), Positives = 64/95 (67%)

Query: 1   MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCV 60
           ++ AK+  KS      NI     PTKE L   G +CPICHD F TP+ L C HIFC+ CV
Sbjct: 573 VERAKSLHKSVVTFRRNIDSERPPTKEELDAAGSVCPICHDTFNTPIILECGHIFCDECV 632

Query: 61  TKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95
             WF REQTCP+CRA + DDPAW+DG+T++F Q++
Sbjct: 633 QTWFKREQTCPMCRAKVSDDPAWQDGSTTFFHQLY 667

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	95
FB|FBgn0039150	669	CG13605 [Drosophila melanogast	1.0	0.142	0.494	1.1e-23
UNIPROTKB|F1P4I2	317	RNFT1 "Uncharacterized protein	0.926	0.277	0.440	5.8e-18
UNIPROTKB|J9P6W1	397	RNFT1 "Uncharacterized protein	0.789	0.188	0.5	3.8e-17
UNIPROTKB|F1MDV4	433	RNFT1 "Uncharacterized protein	0.789	0.173	0.513	4e-17
UNIPROTKB|Q5M7Z0	435	RNFT1 "RING finger and transme	0.789	0.172	0.513	4.1e-17
ZFIN|ZDB-GENE-050522-168	443	rnft2 "ring finger protein, tr	0.915	0.196	0.443	4.3e-17
MGI|MGI:2442859	445	Rnft2 "ring finger protein, tr	0.873	0.186	0.470	5.6e-17
RGD|1560195	446	Rnft2 "ring finger protein, tr	0.873	0.186	0.470	5.6e-17
RGD|1562411	397	Rnft1 "ring finger protein, tr	0.789	0.188	0.5	6.4e-17
UNIPROTKB|F1MN99	449	RNFT2 "Uncharacterized protein	0.873	0.184	0.482	1.2e-16

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

 Score = 281 (104.0 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 47/95 (49%), Positives = 62/95 (65%)

Query:     1 MQAAKAWWKSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCV 60
             ++  K+  K+      NI     PTK+ L   G +CPICHD F TP  L C HIFC+ CV
Sbjct:   575 VERGKSLKKAIVTFRKNIDSERPPTKDELDAAGALCPICHDAFNTPTVLECGHIFCDECV 634

Query:    61 TKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF 95
               WF REQTCP+CRA + DDPAW+DG+T++F Q++
Sbjct:   635 QTWFKREQTCPMCRAKVSDDPAWQDGSTTFFHQLY 669

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 41/93 (44%), Positives = 56/93 (60%)

Query:     8 WKSFTKLLNNI----QLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKW 63
             W++F ++L         GV+ +K        IC ICH EF+ P+ L C H FCE C++ W
Sbjct:   225 WRNFRQVLRIFCTRPHYGVTASKRQCSESDDICSICHAEFQKPILLICQHTFCEECISLW 284

Query:    64 FDREQTCPLCRATLVDDP-AWRDGATSYFVQIF 95
             F+RE+TCPLCR  + D    W+DGATS  +QIF
Sbjct:   285 FNREKTCPLCRTVISDHVNKWKDGATSMRLQIF 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:    21 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
             GV+ +K     V  IC +C  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct:   322 GVAASKRQCSDVDDICSVCQAEFQKPILLICQHIFCEECITLWFNREKTCPLCRTVISDH 381

Query:    81 -PAWRDGATSYFVQIF 95
                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:    21 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
             GV  +K     V  IC IC  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct:   358 GVPASKRQCSDVDDICSICQAEFQKPILLICQHIFCEECITLWFNREKTCPLCRTVISDH 417

Query:    81 -PAWRDGATSYFVQIF 95
                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:    21 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
             GV+ +K     V  IC IC  EF+ P+ L C HIFCE C+T WF+RE+TCPLCR  + D 
Sbjct:   360 GVAASKRQCSDVDDICSICQAEFQKPILLICQHIFCEECMTLWFNREKTCPLCRTVISDH 419

Query:    81 -PAWRDGATSYFVQIF 95
                W+DGATS  +QI+
Sbjct:   420 INKWKDGATSSHLQIY 435

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

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

 Score = 216 (81.1 bits), Expect = 4.3e-17, P = 4.3e-17
 Identities = 39/88 (44%), Positives = 55/88 (62%)

Query:     9 KSFTKLLNNIQLGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ 68
             K+F  L ++   G+  + +     G +C IC  EF+ PV L C H+FCE C+  WFDRE+
Sbjct:   356 KAFIILCSSQNYGMRASAQQCGEAGDVCAICQAEFREPVALLCQHVFCEECLCLWFDRER 415

Query:    69 TCPLCRATLVDDPA-WRDGATSYFVQIF 95
             TCPLCR+T+V+    W+DG TS   QI+
Sbjct:   416 TCPLCRSTVVETLRNWKDGTTSAHFQIY 443

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 215 (80.7 bits), Expect = 5.6e-17, P = 5.6e-17
 Identities = 40/85 (47%), Positives = 52/85 (61%)

Query:    13 KLLNNIQ-LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCP 71
             KLL   Q  GV  T +     G +C IC  EF+ P+ L C H+FCE C+  W DRE+TCP
Sbjct:   361 KLLCTSQNYGVRATGQQCTEAGAVCAICQAEFRDPMILLCQHVFCEECLCLWLDRERTCP 420

Query:    72 LCRATLVDD-PAWRDGATSYFVQIF 95
             LCR+  VD    W+DGATS  +Q++
Sbjct:   421 LCRSVAVDTLRCWKDGATSAHLQVY 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 = 215 (80.7 bits), Expect = 5.6e-17, P = 5.6e-17
 Identities = 40/85 (47%), Positives = 52/85 (61%)

Query:    13 KLLNNIQ-LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCP 71
             KLL   Q  GV  T +     G +C IC  EF+ P+ L C H+FCE C+  W DRE+TCP
Sbjct:   362 KLLCTSQNYGVRATGQQCTEAGAVCAICQAEFRDPMILLCQHVFCEECLCLWLDRERTCP 421

Query:    72 LCRATLVDD-PAWRDGATSYFVQIF 95
             LCR+  VD    W+DGATS  +Q++
Sbjct:   422 LCRSVAVDTLRCWKDGATSAHLQVY 446

GO:0008270 "zinc ion binding" 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:    21 GVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
             GV  +K     +  ICPIC  EF+ PV L C HIFCE C+T WF+RE+TCPLCR  + + 
Sbjct:   322 GVPASKRQCSDMDGICPICQAEFQKPVLLFCQHIFCEECITLWFNREKTCPLCRTVISER 381

Query:    81 -PAWRDGATSYFVQIF 95
                W+DGATS  +Q++
Sbjct:   382 INKWKDGATSSHLQMY 397

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 212 (79.7 bits), Expect = 1.2e-16, P = 1.2e-16
 Identities = 41/85 (48%), Positives = 51/85 (60%)

Query:    13 KLLNNIQ-LGVSPTKETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCP 71
             KLL   Q  GV  T +     G IC IC  EF+ P+ L C H+FCE C+  W DRE+TCP
Sbjct:   365 KLLCTSQNYGVRATGQQCTEAGDICAICQAEFREPLVLMCQHVFCEECLCLWLDRERTCP 424

Query:    72 LCRATLVDD-PAWRDGATSYFVQIF 95
             LCR+  VD    W+DGATS   Q++
Sbjct:   425 LCRSVAVDTLRCWKDGATSAHFQVY 449

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5M7Z0	RNFT1_HUMAN	No assigned EC number	0.5131	0.7894	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!

---

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	95
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-10
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	7e-10
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	3e-09
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	6e-09
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	6e-09
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	4e-08
smart00184	40	smart00184, RING, Ring finger	3e-07
COG5574	271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	2e-06
COG5152	259	COG5152, COG5152, Uncharacterized conserved protei	6e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-05
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	5e-05
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	8e-05
COG5222	427	COG5222, COG5222, Uncharacterized conserved protei	2e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	2e-04
pfam13445	55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	3e-04
PLN03208	193	PLN03208, PLN03208, E3 ubiquitin-protein ligase RM	4e-04
pfam13920	49	pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RI	4e-04
TIGR00570	309	TIGR00570, cdk7, CDK-activating kinase assembly fa	0.002
smart00504	63	smart00504, Ubox, Modified RING finger domain	0.002
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	0.002

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

 Score = 54.2 bits (130), Expect = 4e-10
 Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 13/72 (18%)

Query: 22  VSPTKETLLGVGCICPICHDEF-------------KTPVQLTCCHIFCESCVTKWFDREQ 68
            + T+E L      C IC DE               TP +L C HI    C+  W +R+Q
Sbjct: 276 PTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ 335

Query: 69  TCPLCRATLVDD 80
           TCP+CR  ++ D
Sbjct: 336 TCPICRRPVIFD 347

Length = 491

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

 Score = 49.3 bits (118), Expect = 7e-10
 Identities = 22/43 (51%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 36 CPICHDEF---KTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75
          CPIC DEF   +  V L C H+F + C+ KW     TCPLCRA
Sbjct: 3  CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

>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 = 47.8 bits (114), Expect = 3e-09
 Identities = 23/44 (52%), Positives = 29/44 (65%), Gaps = 2/44 (4%)

Query: 36 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ-TCPLCRATL 77
          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 = 47.1 bits (112), Expect = 6e-09
 Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRA 75
           CPIC D  + PV LT C H+FC  C+ ++  ++  CP+CR 
Sbjct: 4  ECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 50.8 bits (121), Expect = 6e-09
 Identities = 18/41 (43%), Positives = 22/41 (53%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRAT 76
          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|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 48.5 bits (115), Expect = 4e-08
 Identities = 14/40 (35%), Positives = 19/40 (47%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75
          C IC      P + TC H FC  C+ +    +  CP+CR 
Sbjct: 28 CRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCRE 67

Length = 391

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

 Score = 42.5 bits (100), Expect = 3e-07
 Identities = 21/40 (52%), Positives = 26/40 (65%), Gaps = 2/40 (5%)

Query: 36 CPICHDEF-KTPVQLTCCHIFCESCVTKWFDRE-QTCPLC 73
          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|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 43.7 bits (103), Expect = 2e-06
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 36  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT--CPLCRA 75
           C +C +E + P    C H+FC SC+   + +++   CPLCRA
Sbjct: 218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRA 259

Length = 271

>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 = 6e-06
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 35  ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75
           +C IC  ++++PV   C H FC  C  + + +   C +C  
Sbjct: 198 LCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGK 238

Length = 259

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

 Score = 37.8 bits (88), Expect = 2e-05
 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 36 CPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE-QTCPLC 73
          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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 51  CCHIFCESCVTKWFDREQTCPLCRATLV 78
           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 = 39.2 bits (91), Expect = 8e-05
 Identities = 17/51 (33%), Positives = 19/51 (37%), Gaps = 4/51 (7%)

Query: 31  GVGCICPICHDEF---KTPVQLTCCHIFCESCVTKWF-DREQTCPLCRATL 77
             G  C IC   F        L C H F   CV KW       CP+CR  +
Sbjct: 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371

Length = 374

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

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 3/75 (4%)

Query: 2   QAAKAWWKSFTKLLNNIQL-GVSPTKETLLGVGCICPICHDEFKTPVQLTCC-HIFCESC 59
           Q     W+ + +    +        K     +   CP+CH   + P++  CC H FC+ C
Sbjct: 242 QPDVQSWEKYQQRTKAVAEIPDQVYKMQPPNISLKCPLCHCLLRNPMKTPCCGHTFCDEC 301

Query: 60  V-TKWFDREQTCPLC 73
           + T   D +  CP C
Sbjct: 302 IGTALLDSDFKCPNC 316

Length = 427

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

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 24/81 (29%), Positives = 30/81 (37%), Gaps = 21/81 (25%)

Query: 10   SFTKLL----NNIQLGVSPTKETLLGVGCICPIC------HD-EFKTPVQLTCCHIFCES 58
            SF  LL     NI    S  +E        C IC       D    +    TC + F   
Sbjct: 1450 SFMDLLGLWKKNIDEKFSGHEE--------CAICYSVLDMVDRSLPSKRCATCKNKFHTR 1501

Query: 59   CVTKWF--DREQTCPLCRATL 77
            C+ KWF       CPLCR+ +
Sbjct: 1502 CLYKWFASSARSNCPLCRSEI 1522

Length = 1525

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

 Score = 35.4 bits (82), Expect = 3e-04
 Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 6/43 (13%)

Query: 35 ICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQT--CP 71
          +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 = 37.0 bits (85), Expect = 4e-04
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 16/56 (28%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKW-------------FDREQ---TCPLCRA 75
          C IC D+ + PV   C H+FC  C+ KW             +D ++    CP+C++
Sbjct: 21 CNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKS 76

Length = 193

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

 Score = 34.7 bits (80), Expect = 4e-04
 Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 35 ICPICHDEFKTPVQLTCCH-IFCESCVTKWFDREQTCPLCRA 75
          +C IC +  +  V L C H   CE C  +    ++ CP+CR 
Sbjct: 4  LCVICLERPRNVVFLPCGHLCLCEECAKRLR-SKKKCPICRQ 44

Length = 49

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 15/61 (24%)

Query: 36 CPICH-DEFKTP-VQL---TCCHIFCESCVTKWFDR-EQTCPLC---------RATLVDD 80
          CP C   +++ P ++L    C H  CESCV   F R   +CP C         R  L +D
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFRVQLFED 65

Query: 81 P 81
          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 = 33.4 bits (77), Expect = 0.002
 Identities = 13/46 (28%), Positives = 19/46 (41%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
          +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|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 33.6 bits (77), Expect = 0.002
 Identities = 13/41 (31%), Positives = 17/41 (41%)

Query: 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 74
          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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	95
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.6
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.59
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.59
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.56
KOG0317|consensus	293		99.55
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.54
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.52
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.51
KOG0287|consensus	442		99.51
KOG0823|consensus	230		99.5
PHA02929	238	N1R/p28-like protein; Provisional	99.48
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	99.45
KOG0320|consensus	187		99.41
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.39
KOG4628|consensus	348		99.38
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.37
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	99.35
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.34
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.34
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	99.29
PF14634	44	zf-RING_5: zinc-RING finger domain	99.27
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.24
KOG0802|consensus	543		99.23
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	99.23
PHA02926	242	zinc finger-like protein; Provisional	99.22
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	99.19
KOG2164|consensus	513		99.19
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.16
KOG2177|consensus	386		99.05
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.05
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.94
KOG0978|consensus	698		98.93
KOG4159|consensus	398		98.84
KOG0311|consensus	381		98.79
KOG4265|consensus	349		98.78
KOG4172|consensus	62		98.76
KOG2879|consensus	298		98.71
KOG0824|consensus	324		98.69
COG5152	259	Uncharacterized conserved protein, contains RING a	98.69
KOG2660|consensus	331		98.62
KOG1734|consensus	328		98.56
KOG0828|consensus	636		98.54
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.52
KOG0804|consensus	493		98.44
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.43
KOG0297|consensus	391		98.43
KOG1813|consensus	313		98.42
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.42
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	98.32
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.28
COG5222	427	Uncharacterized conserved protein, contains RING Z	98.25
KOG1493|consensus	84		98.22
KOG1039|consensus	344		98.19
KOG0827|consensus	465		98.15
KOG4692|consensus	489		98.08
KOG2930|consensus	114		97.96
KOG1785|consensus	563		97.9
KOG4275|consensus	350		97.87
KOG3039|consensus	303		97.82
KOG0825|consensus	1134		97.79
KOG1002|consensus	791		97.77
KOG1645|consensus	463		97.74
PF04641	260	Rtf2: Rtf2 RING-finger	97.68
KOG0826|consensus	357		97.67
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	97.66
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.6
KOG4185|consensus	296		97.55
KOG1571|consensus	355		97.5
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.49
KOG4367|consensus	699		97.47
KOG1814|consensus	445		97.4
KOG1941|consensus	518		97.35
KOG2114|consensus	933		97.3
KOG1001|consensus	674		97.28
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.09
KOG4739|consensus	233		97.07
KOG2817|consensus	394		96.98
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.88
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	96.82
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	96.74
KOG4445|consensus	368		96.69
KOG3800|consensus	300		96.68
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	96.66
KOG1428|consensus	3738		96.65
KOG3002|consensus	299		96.53
KOG1952|consensus	950		96.52
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.52
KOG3970|consensus	299		96.51
KOG1940|consensus	276		96.39
KOG4362|consensus	684		96.26
KOG2932|consensus	389		96.25
KOG3268|consensus	234		96.21
PHA03096	284	p28-like protein; Provisional	96.16
PHA02862	156	5L protein; Provisional	96.09
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.89
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	95.74
KOG3113|consensus	293		95.64
KOG0298|consensus	1394		95.61
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.44
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	94.95
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.67
KOG1100|consensus	207		94.64
KOG3039|consensus	303		94.38
KOG3161|consensus	861		94.37
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	93.92
COG5109	396	Uncharacterized conserved protein, contains RING Z	93.85
KOG3899|consensus	381		92.8
KOG0309|consensus	1081		92.79
KOG3579|consensus	352		92.74
KOG2034|consensus	911		92.69
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	92.58
KOG1815|consensus	444		92.34
KOG1812|consensus	384		92.32
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	91.35
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	90.61
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	90.44
KOG1812|consensus	384		90.12
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	89.68
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	89.31
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	89.08
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	88.99
KOG4718|consensus	235		88.44
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	87.91
PF02318	118	FYVE_2: FYVE-type zinc finger; InterPro: IPR003315	87.87
KOG2068|consensus	327		87.68
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	86.94
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	86.73
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	85.05
KOG0827|consensus	465		84.64
KOG0802|consensus	543		83.26
KOG2169|consensus	636		83.14
KOG1609|consensus	323		81.95
KOG3053|consensus	293		81.56
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	80.51
KOG0825|consensus	1134		80.12

>smart00504 Ubox Modified RING finger domain

Probab=99.60  E-value=9.6e-16  Score=80.41  Aligned_cols=62  Identities=23%  Similarity=0.366  Sum_probs=55.4

Q ss_pred             cccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      ++.|+||.+.+.+|+.++|||+||..|+..|+..+..||.|+.++..++...+..+.+.++-
T Consensus         1 ~~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~~~l~~~i~~   62 (63)
T smart00504        1 EFLCPISLEVMKDPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPNLALKSAIQE   62 (63)
T ss_pred             CcCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeCHHHHHHHHh
Confidence            35899999999999999999999999999999988899999999988888888777776653

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=99.59  E-value=1.1e-15  Score=74.27  Aligned_cols=38  Identities=50%  Similarity=1.233  Sum_probs=30.6

Q ss_pred             ccccccCCCCCeecCCCCcchHHhHHHHhhCC----CCCCCC
Q psy3884          36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDRE----QTCPLC   73 (95)
Q Consensus        36 C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~----~~CP~C   73 (95)
                      |+||++.+.+|+.++|||+||..||.+|.+..    ..||.|
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            89999999999999999999999999998744    469987

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.59  E-value=2.2e-15  Score=93.83  Aligned_cols=52  Identities=33%  Similarity=0.870  Sum_probs=44.7

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhC----------------CCCCCCCCccCCCCcc
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR----------------EQTCPLCRATLVDDPA   82 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~----------------~~~CP~Cr~~~~~~~~   82 (95)
                      ...+.|+||++.+.+|++++|||.||..||..|+..                ...||+||..+.....
T Consensus        16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L   83 (193)
T PLN03208         16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL   83 (193)
T ss_pred             CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence            456899999999999999999999999999999742                2479999999976543

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.56  E-value=2.6e-15  Score=102.59  Aligned_cols=68  Identities=32%  Similarity=0.679  Sum_probs=60.0

Q ss_pred             ccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          28 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      ......+.|+||.+.+..|++++|||.||..|+..|+.....||.|+..+.......+..+.++++.|
T Consensus        21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~Lr~N~~L~~iVe~~   88 (397)
T TIGR00599        21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWLVSEIVESF   88 (397)
T ss_pred             cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccccCccchHHHHHHHHH
Confidence            34567789999999999999999999999999999999888999999999877777788888888765

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

>KOG0317|consensus

Probab=99.55  E-value=3.9e-15  Score=96.94  Aligned_cols=55  Identities=29%  Similarity=0.775  Sum_probs=49.2

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   83 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   83 (95)
                      ..+....|.+|++...+|..+||||.||..||..|......||+||..+...++.
T Consensus       235 i~~a~~kC~LCLe~~~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskvi  289 (293)
T KOG0317|consen  235 IPEATRKCSLCLENRSNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKVI  289 (293)
T ss_pred             CCCCCCceEEEecCCCCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCccee
Confidence            3445679999999999999999999999999999999999999999999877543

>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=1.5e-15  Score=74.57  Aligned_cols=40  Identities=48%  Similarity=1.299  Sum_probs=35.3

Q ss_pred             cccccccCCCC---CeecCCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884          35 ICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCR   74 (95)
Q Consensus        35 ~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr   74 (95)
                      .|+||++.+..   .+.++|||.||..|+.+|++.+.+||+||
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            79999999853   46789999999999999999999999997

...

>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=99.52  E-value=7e-15  Score=70.41  Aligned_cols=38  Identities=45%  Similarity=1.314  Sum_probs=33.8

Q ss_pred             ccccccCCCCC-eecCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884          36 CPICHDEFKTP-VQLTCCHIFCESCVTKWFDREQTCPLC   73 (95)
Q Consensus        36 C~IC~~~~~~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~C   73 (95)
                      |+||++.+.+| +.++|||+||..|+.+|++.+..||.|
T Consensus         1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            89999999999 578999999999999999998899987

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

Probab=99.51  E-value=1.2e-14  Score=73.09  Aligned_cols=46  Identities=37%  Similarity=1.003  Sum_probs=41.2

Q ss_pred             cccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCC
Q psy3884          33 GCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      +..|.||++...+.+.+||||. ||..|+.+|+.....||+||+++.
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            4589999999999999999999 999999999999999999999875

...

>KOG0287|consensus

Probab=99.51  E-value=2.1e-15  Score=100.30  Aligned_cols=65  Identities=25%  Similarity=0.608  Sum_probs=60.3

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      .+.+.|.||.++|..|+++||+|+||.-||+.++..+..||.|+.++.+.+...+..++.++|.|
T Consensus        21 D~lLRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr~n~il~Eiv~S~   85 (442)
T KOG0287|consen   21 DDLLRCGICFEYFNIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLRNNRILDEIVKSL   85 (442)
T ss_pred             HHHHHHhHHHHHhcCceeccccchHHHHHHHHHhccCCCCCceecccchhhhhhhhHHHHHHHHH
Confidence            45679999999999999999999999999999999999999999999999888888888888865

>KOG0823|consensus

Probab=99.50  E-value=1.8e-14  Score=91.39  Aligned_cols=53  Identities=36%  Similarity=0.799  Sum_probs=46.4

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC---CCCCCCCCccCCCCcc
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR---EQTCPLCRATLVDDPA   82 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~~~~~   82 (95)
                      ....+.|.||++..++|+++.|||.||..||.+|+..   ...||+|+..+..+..
T Consensus        44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~v   99 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTV   99 (230)
T ss_pred             CCCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceE
Confidence            3467899999999999999999999999999999984   3578999999887743

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.48  E-value=4.7e-14  Score=90.90  Aligned_cols=47  Identities=30%  Similarity=0.897  Sum_probs=40.8

Q ss_pred             CcccccccccCCCCC--------eecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKTP--------VQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p--------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .+..|+||++.+.++        +.++|||.||..|+.+|+....+||+||.++.
T Consensus       173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            467999999987653        45589999999999999999999999999876

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

Probab=99.45  E-value=2.6e-14  Score=77.18  Aligned_cols=65  Identities=22%  Similarity=0.446  Sum_probs=53.2

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      .+.+.|||+.+.+.+|+++++||+|...+|..|+.. +..||.++.++...+..++..+.+.|+.|
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            467899999999999999999999999999999998 78999999999988888888887777654

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 ....

>KOG0320|consensus

Probab=99.41  E-value=1.4e-13  Score=84.36  Aligned_cols=52  Identities=31%  Similarity=0.816  Sum_probs=45.2

Q ss_pred             CcccccccccCCCC--CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884          32 VGCICPICHDEFKT--PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   83 (95)
Q Consensus        32 ~~~~C~IC~~~~~~--p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   83 (95)
                      ..+.||||++.+.+  |+.+.|||+||..||...++....||+|++.+..+.++
T Consensus       130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~~  183 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQFH  183 (187)
T ss_pred             cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhhhe
Confidence            45799999999886  45689999999999999999999999999988776543

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

Probab=99.39  E-value=4.9e-13  Score=90.08  Aligned_cols=53  Identities=40%  Similarity=0.983  Sum_probs=44.5

Q ss_pred             ccccCCCcccccccccCC-CC------------CeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          26 KETLLGVGCICPICHDEF-KT------------PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        26 ~~~~~~~~~~C~IC~~~~-~~------------p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .++...++..|.||++.+ ..            |..+||||.+|..|+..|++++.+||+||.++.
T Consensus       280 ~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         280 EEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             hhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            444456677999999983 33            478899999999999999999999999999953

>KOG4628|consensus

Probab=99.38  E-value=6.7e-13  Score=89.21  Aligned_cols=47  Identities=28%  Similarity=0.873  Sum_probs=41.0

Q ss_pred             ccccccccCCCCC---eecCCCCcchHHhHHHHhhCCC-CCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQ-TCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~   80 (95)
                      ..|+||++.|...   +++||+|.||..||.+|+.+.. .||+|+..+...
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            5999999999975   5789999999999999999875 599999977543

>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=99.37  E-value=3.9e-13  Score=64.85  Aligned_cols=38  Identities=50%  Similarity=1.378  Sum_probs=34.9

Q ss_pred             ccccccCCCCCe-ecCCCCcchHHhHHHHhh--CCCCCCCC
Q psy3884          36 CPICHDEFKTPV-QLTCCHIFCESCVTKWFD--REQTCPLC   73 (95)
Q Consensus        36 C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~--~~~~CP~C   73 (95)
                      |+||++.+.++. .++|||.||..|+.+|++  ....||.|
T Consensus         1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999999998 889999999999999998  55689987

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 ....

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

Probab=99.35  E-value=3.4e-13  Score=88.36  Aligned_cols=64  Identities=22%  Similarity=0.559  Sum_probs=53.6

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      ..+.|.||.+.+..|..++|||+||.-||..++..+..||+||.+...........+..++|.|
T Consensus        24 s~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~esrlr~~s~~~ei~es~   87 (391)
T COG5432          24 SMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCESRLRGSSGSREINESH   87 (391)
T ss_pred             hHHHhhhhhheeecceecccccchhHHHHHHHhcCCCCCccccccHHhhhcccchhHHHHHHhh
Confidence            4569999999999999999999999999999999999999999988766555555555555543

>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=99.34  E-value=1.2e-12  Score=63.64  Aligned_cols=43  Identities=53%  Similarity=1.388  Sum_probs=37.1

Q ss_pred             cccccccCCCCCeecC-CCCcchHHhHHHHhhC-CCCCCCCCccC
Q psy3884          35 ICPICHDEFKTPVQLT-CCHIFCESCVTKWFDR-EQTCPLCRATL   77 (95)
Q Consensus        35 ~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~   77 (95)
                      .|+||++.+..++.++ |||.||..|+..|+.. ...||.|+..+
T Consensus         1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            4899999997776665 9999999999999987 67899998754

>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=99.34  E-value=1.1e-12  Score=70.80  Aligned_cols=42  Identities=40%  Similarity=1.044  Sum_probs=34.5

Q ss_pred             cccccccccCCCCC-------------eecCCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884          33 GCICPICHDEFKTP-------------VQLTCCHIFCESCVTKWFDREQTCPLCR   74 (95)
Q Consensus        33 ~~~C~IC~~~~~~p-------------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr   74 (95)
                      ...|+||++.+.++             +..+|||.||..||.+|++.+.+||+||
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            34699999998432             3448999999999999999999999997

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 ....

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

Probab=99.29  E-value=5.1e-13  Score=69.36  Aligned_cols=59  Identities=29%  Similarity=0.595  Sum_probs=32.8

Q ss_pred             CcccccccccCCCCCee-cCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhh
Q psy3884          32 VGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFV   92 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~   92 (95)
                      ..+.|++|.+.+++|+. ..|.|.||..|+...+.  ..||+|+.+....+...+..++++|
T Consensus         6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~~NrqLd~~i   65 (65)
T PF14835_consen    6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQINRQLDSMI   65 (65)
T ss_dssp             HTTS-SSS-S--SS-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS----HHHHHHH
T ss_pred             HhcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHHhhhhhhccC
Confidence            45699999999999985 58999999999977544  4599999999999988888777664

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.27  E-value=4.7e-12  Score=62.03  Aligned_cols=41  Identities=39%  Similarity=1.060  Sum_probs=35.2

Q ss_pred             cccccccCCC---CCeecCCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884          35 ICPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRA   75 (95)
Q Consensus        35 ~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~   75 (95)
                      .|+||++.+.   .+.+++|||+||..|+..+......||+|++
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4899999982   4678899999999999998866789999974

>smart00184 RING Ring finger

Probab=99.24  E-value=1.2e-11  Score=58.19  Aligned_cols=38  Identities=55%  Similarity=1.441  Sum_probs=34.4

Q ss_pred             ccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCC
Q psy3884          36 CPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLC   73 (95)
Q Consensus        36 C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~C   73 (95)
                      |+||++....++.++|||.||..|+..|+. ....||.|
T Consensus         1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999988889999999999999999998 55679987

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

>KOG0802|consensus

Probab=99.23  E-value=5.6e-12  Score=89.77  Aligned_cols=52  Identities=46%  Similarity=1.024  Sum_probs=45.7

Q ss_pred             cCCCcccccccccCCCC-----CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          29 LLGVGCICPICHDEFKT-----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      .......|+||.+.+..     +.+++|||.||..|+..|+++..+||.||..+...
T Consensus       287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~  343 (543)
T KOG0802|consen  287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDY  343 (543)
T ss_pred             hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence            33457799999999998     78999999999999999999999999999965544

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

Probab=99.23  E-value=5.9e-12  Score=61.22  Aligned_cols=35  Identities=46%  Similarity=1.247  Sum_probs=22.2

Q ss_pred             ccccccCCCC----CeecCCCCcchHHhHHHHhhCC----CCCC
Q psy3884          36 CPICHDEFKT----PVQLTCCHIFCESCVTKWFDRE----QTCP   71 (95)
Q Consensus        36 C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~----~~CP   71 (95)
                      ||||.+ +.+    |++++|||+||..|+.++...+    ..||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 777    8999999999999999998733    3565

>PHA02926 zinc finger-like protein; Provisional

Probab=99.22  E-value=9.2e-12  Score=78.97  Aligned_cols=48  Identities=29%  Similarity=0.805  Sum_probs=38.3

Q ss_pred             CCcccccccccCCCC---------CeecCCCCcchHHhHHHHhhCC------CCCCCCCccCC
Q psy3884          31 GVGCICPICHDEFKT---------PVQLTCCHIFCESCVTKWFDRE------QTCPLCRATLV   78 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~---------p~~~~CgH~fc~~Ci~~~~~~~------~~CP~Cr~~~~   78 (95)
                      ..+.+|+||++...+         ++..+|+|.||..|+..|....      ..||+||..+.
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            356799999998633         2455899999999999999742      46999999865

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

Probab=99.19  E-value=9.5e-12  Score=80.43  Aligned_cols=51  Identities=33%  Similarity=0.829  Sum_probs=45.0

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHH-HhhCCCC-CCCCCccCCCCcc
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTK-WFDREQT-CPLCRATLVDDPA   82 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~-~~~~~~~-CP~Cr~~~~~~~~   82 (95)
                      .++.|+||++....|..++|||.||..||.. |-.+... ||+||+....+++
T Consensus       214 ~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            4678999999999999999999999999999 8877665 9999998876654

>KOG2164|consensus

Probab=99.19  E-value=1.1e-11  Score=86.12  Aligned_cols=50  Identities=34%  Similarity=0.927  Sum_probs=44.1

Q ss_pred             cccccccccCCCCCeecCCCCcchHHhHHHHhhCC-----CCCCCCCccCCCCcc
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-----QTCPLCRATLVDDPA   82 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-----~~CP~Cr~~~~~~~~   82 (95)
                      +..||||++...-|+.+.|||.||..||..++...     ..||+|+..+..++.
T Consensus       186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl  240 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDL  240 (513)
T ss_pred             CCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccce
Confidence            77999999999999999999999999999988743     589999999887544

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

Probab=99.16  E-value=2.2e-11  Score=80.32  Aligned_cols=48  Identities=35%  Similarity=0.823  Sum_probs=41.8

Q ss_pred             CcccccccccCCCCC---eecCCCCcchHHhHHHHhh-CCCCCCCCCccCCC
Q psy3884          32 VGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFD-REQTCPLCRATLVD   79 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~   79 (95)
                      ...+|+||++.+...   +++||.|.||..|+.+|+. ....||+||.+++.
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            446999999998753   6789999999999999998 56799999999874

>KOG2177|consensus

Probab=99.05  E-value=7.4e-11  Score=77.05  Aligned_cols=47  Identities=40%  Similarity=1.033  Sum_probs=41.6

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA   75 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~   75 (95)
                      ...+.+.|+||++.+..|.+++|||+||..|+..++.....||.||.
T Consensus         9 ~~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen    9 VLQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             hccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            34567899999999999989999999999999998875578999994

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

Probab=99.05  E-value=2.3e-10  Score=62.83  Aligned_cols=46  Identities=33%  Similarity=0.893  Sum_probs=36.6

Q ss_pred             cccccccccCCCC------------Ceec-CCCCcchHHhHHHHhhC---CCCCCCCCccCC
Q psy3884          33 GCICPICHDEFKT------------PVQL-TCCHIFCESCVTKWFDR---EQTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~~------------p~~~-~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~   78 (95)
                      +..|.||...|..            |.++ .|+|.||..||.+|+..   +..||+||++..
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            5688888887763            2322 79999999999999985   368999999865

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.94  E-value=9.4e-10  Score=73.20  Aligned_cols=49  Identities=33%  Similarity=0.814  Sum_probs=38.0

Q ss_pred             cccccccccC-CCCCe---ec-CCCCcchHHhHHHHhh-CCCCCCCCCccCCCCc
Q psy3884          33 GCICPICHDE-FKTPV---QL-TCCHIFCESCVTKWFD-REQTCPLCRATLVDDP   81 (95)
Q Consensus        33 ~~~C~IC~~~-~~~p~---~~-~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~   81 (95)
                      +..||+|... +.+|.   .+ +|||.||..|+...+. ....||.|+.++....
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            4589999985 33442   22 7999999999999664 4568999999988765

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).

>KOG0978|consensus

Probab=98.93  E-value=3.2e-10  Score=81.90  Aligned_cols=55  Identities=31%  Similarity=0.790  Sum_probs=48.2

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCcccc
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPAWR   84 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~~~   84 (95)
                      ....+.|++|....++.+++.|||.||..|+.+... +...||.|...|..+|+..
T Consensus       640 yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~  695 (698)
T KOG0978|consen  640 YKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHR  695 (698)
T ss_pred             HHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccc
Confidence            356789999999999999999999999999998776 6789999999999887643

>KOG4159|consensus

Probab=98.84  E-value=2.4e-09  Score=73.67  Aligned_cols=55  Identities=33%  Similarity=0.738  Sum_probs=48.6

Q ss_pred             ccccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          26 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        26 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      .+.....++.|.||+..+.+|+++||||.||..|+.+.+.....||.||.++...
T Consensus        77 ~~~~~~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   77 GPEEIRSEFECCVCSRALYPPVVTPCGHSFCLECLDRSLDQETECPLCRDELVEL  131 (398)
T ss_pred             cCccccchhhhhhhHhhcCCCccccccccccHHHHHHHhccCCCCcccccccccc
Confidence            3344478899999999999999999999999999999888889999999998863

>KOG0311|consensus

Probab=98.79  E-value=5.2e-10  Score=75.04  Aligned_cols=64  Identities=30%  Similarity=0.677  Sum_probs=50.2

Q ss_pred             cCCCcccccccccCCCCCeec-CCCCcchHHhHHHHhh-CCCCCCCCCccCCCC-ccccCCcchhhh
Q psy3884          29 LLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-REQTCPLCRATLVDD-PAWRDGATSYFV   92 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~-~~~~~~~~~~~~   92 (95)
                      .+...+.|+||++.++..+++ .|+|.||..||..-+. .++.||.||+.+... .+..|..++.+|
T Consensus        39 ~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~Dp~fdaLi  105 (381)
T KOG0311|consen   39 MFDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRIDPNFDALI  105 (381)
T ss_pred             HhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCCccHHHHH
Confidence            345678999999999988766 6999999999988776 457999999998876 444555555443

>KOG4265|consensus

Probab=98.78  E-value=4.5e-09  Score=70.66  Aligned_cols=50  Identities=30%  Similarity=0.735  Sum_probs=44.7

Q ss_pred             CCcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ....+|.||+...++-+++||.|. .|..|.....-++..||+||+++...
T Consensus       288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~l  338 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEEL  338 (349)
T ss_pred             cCCCeeEEEecCCcceEEecchhhehhHhHHHHHHHhhcCCCccccchHhh
Confidence            456799999999999999999998 89999998877889999999998653

>KOG4172|consensus

Probab=98.76  E-value=2e-09  Score=54.11  Aligned_cols=45  Identities=31%  Similarity=0.706  Sum_probs=39.5

Q ss_pred             ccccccccCCCCCeecCCCCc-chHHhHHHHhh-CCCCCCCCCccCC
Q psy3884          34 CICPICHDEFKTPVQLTCCHI-FCESCVTKWFD-REQTCPLCRATLV   78 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~-~~~~CP~Cr~~~~   78 (95)
                      .+|.||++...+.+...|||. +|..|..+.++ .+..||+||+++.
T Consensus         8 dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHPVDSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cceeeeccCcchHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            599999999888888899996 89999988776 5679999999875

>KOG2879|consensus

Probab=98.71  E-value=4.4e-08  Score=64.02  Aligned_cols=51  Identities=27%  Similarity=0.638  Sum_probs=42.0

Q ss_pred             ccCCCcccccccccCCCCCeec-CCCCcchHHhHHHHhh--CCCCCCCCCccCC
Q psy3884          28 TLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD--REQTCPLCRATLV   78 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~--~~~~CP~Cr~~~~   78 (95)
                      .....+.+|++|.+....|.++ +|||+||..|+..-..  ..+.||.|..+..
T Consensus       234 s~~t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  234 STGTSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             ccccCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            3345677999999999999766 5999999999987665  3479999988766

>KOG0824|consensus

Probab=98.69  E-value=8.2e-09  Score=68.14  Aligned_cols=48  Identities=31%  Similarity=0.739  Sum_probs=41.9

Q ss_pred             cccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCCC
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDD   80 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~   80 (95)
                      ...|+||+....-|+.++|+|.||.-||....... ..|++||.++.+.
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            34899999999999999999999999998766554 5699999999866

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

Probab=98.69  E-value=8.8e-09  Score=64.64  Aligned_cols=48  Identities=25%  Similarity=0.810  Sum_probs=42.8

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .-.+.|.||.+++..|+++.|||.||..|...-.+....|-+|.+...
T Consensus       194 ~IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         194 KIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             CCceeehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence            346799999999999999999999999999998888899999977543

>KOG2660|consensus

Probab=98.62  E-value=1.1e-08  Score=68.12  Aligned_cols=55  Identities=22%  Similarity=0.675  Sum_probs=46.3

Q ss_pred             CCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884          31 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   85 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   85 (95)
                      .....|.+|..++.++.++ .|-|+||.+||.+++.....||.|...+.......+
T Consensus        13 n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~pl~n   68 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKTHPLLN   68 (331)
T ss_pred             ccceehhhccceeecchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCcccccc
Confidence            3466999999999999655 799999999999999999999999888776643333

>KOG1734|consensus

Probab=98.56  E-value=3.7e-08  Score=64.37  Aligned_cols=61  Identities=25%  Similarity=0.638  Sum_probs=45.7

Q ss_pred             CCcccccCCCcccccccccCCCC----------CeecCCCCcchHHhHHHHhh--CCCCCCCCCccCCCCccc
Q psy3884          23 SPTKETLLGVGCICPICHDEFKT----------PVQLTCCHIFCESCVTKWFD--REQTCPLCRATLVDDPAW   83 (95)
Q Consensus        23 ~~~~~~~~~~~~~C~IC~~~~~~----------p~~~~CgH~fc~~Ci~~~~~--~~~~CP~Cr~~~~~~~~~   83 (95)
                      .........++..|+||...+..          -..++|+|+||..||+.|..  +..+||.|++.+..+..+
T Consensus       214 ~~glPtkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~rmf  286 (328)
T KOG1734|consen  214 PSGLPTKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKRMF  286 (328)
T ss_pred             CCCCCCCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHhhhc
Confidence            33444444567799999987653          35779999999999999986  446999999887655433

>KOG0828|consensus

Probab=98.54  E-value=4.4e-08  Score=68.53  Aligned_cols=50  Identities=30%  Similarity=0.722  Sum_probs=40.4

Q ss_pred             CCCcccccccccCCCC-----------------CeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCC
Q psy3884          30 LGVGCICPICHDEFKT-----------------PVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVD   79 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~-----------------p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~   79 (95)
                      .+....|+||+..+.-                 -..+||.|.||..|+..|+. ..-.||+||.+++.
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            4556799999987642                 14559999999999999999 44599999999874

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

Probab=98.52  E-value=8.2e-08  Score=51.87  Aligned_cols=30  Identities=40%  Similarity=0.944  Sum_probs=27.6

Q ss_pred             CCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          50 TCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      .|.|.||..||.+|+.....||++|+++..
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            599999999999999999999999998753

>KOG0804|consensus

Probab=98.44  E-value=1.3e-07  Score=65.43  Aligned_cols=46  Identities=30%  Similarity=0.868  Sum_probs=38.0

Q ss_pred             CCcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          31 GVGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ....+||||++.+...    +.+.|.|+||..|+..|.  ..+||+||....
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            3456999999999875    355899999999999995  478999988665

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

Probab=98.43  E-value=8.8e-08  Score=71.44  Aligned_cols=76  Identities=24%  Similarity=0.504  Sum_probs=49.4

Q ss_pred             hHHHHHHHHHHHHhhccCCCCC-------cccccCCCcccccccccCCC-C----C--eecCCCCcchHHhHHHHhhC--
Q psy3884           3 AAKAWWKSFTKLLNNIQLGVSP-------TKETLLGVGCICPICHDEFK-T----P--VQLTCCHIFCESCVTKWFDR--   66 (95)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~C~IC~~~~~-~----p--~~~~CgH~fc~~Ci~~~~~~--   66 (95)
                      +.+.|..+.+..+.........       ..........+|+||...+. -    |  .-..|.|.||..|+.+|+..  
T Consensus      1432 ~wkswI~~~q~~~~~~ngs~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~ 1511 (1525)
T COG5219        1432 GWKSWINLRQNEMIKKNGSFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA 1511 (1525)
T ss_pred             HHHHHHHHHHHHHHhccchHHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC
Confidence            3456666655555443321111       12223445679999998765 1    2  23369999999999999984  


Q ss_pred             CCCCCCCCccCC
Q psy3884          67 EQTCPLCRATLV   78 (95)
Q Consensus        67 ~~~CP~Cr~~~~   78 (95)
                      +.+||+||.+++
T Consensus      1512 ~s~CPlCRseit 1523 (1525)
T COG5219        1512 RSNCPLCRSEIT 1523 (1525)
T ss_pred             CCCCCccccccc
Confidence            468999998775

>KOG0297|consensus

Probab=98.43  E-value=1.2e-07  Score=65.50  Aligned_cols=54  Identities=37%  Similarity=0.885  Sum_probs=47.5

Q ss_pred             CCCcccccccccCCCCCee-cCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884          30 LGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   83 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   83 (95)
                      ....+.|++|...+.+|+. +.|||.||..|+..|+..+..||.|+.++......
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             CcccccCccccccccCCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            4567899999999999988 49999999999999999999999998887765443

>KOG1813|consensus

Probab=98.42  E-value=7.4e-08  Score=63.54  Aligned_cols=49  Identities=31%  Similarity=0.678  Sum_probs=43.5

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      .-.+.|-||...|.+|+++.|||.||..|...-++....|++|.+....
T Consensus       239 ~~Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  239 LLPFKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             cCCccccccccccccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence            3456899999999999999999999999999988888999999876543

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

Probab=98.42  E-value=3.8e-08  Score=52.66  Aligned_cols=46  Identities=26%  Similarity=0.663  Sum_probs=23.2

Q ss_pred             cccccccccCCC-C---Ceec----CCCCcchHHhHHHHhhC---C--------CCCCCCCccCC
Q psy3884          33 GCICPICHDEFK-T---PVQL----TCCHIFCESCVTKWFDR---E--------QTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~-~---p~~~----~CgH~fc~~Ci~~~~~~---~--------~~CP~Cr~~~~   78 (95)
                      +..|+||++... .   |...    .|+..||..|+.+|+..   .        ..||.|+.++.
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            458999999865 2   2222    69999999999999862   1        36999998875

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

Probab=98.32  E-value=3.5e-07  Score=47.01  Aligned_cols=41  Identities=29%  Similarity=0.788  Sum_probs=29.2

Q ss_pred             CcccccccccCCCCCeec-CCCCcchHHhHHHHhhC--CCCCCC
Q psy3884          32 VGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDR--EQTCPL   72 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~--~~~CP~   72 (95)
                      ..+.|||.+..+.+|++. .|||+|-+..|..++.+  ...||.
T Consensus        10 ~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            457999999999999865 89999999999999943  457997

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

Probab=98.28  E-value=9.6e-07  Score=44.03  Aligned_cols=40  Identities=33%  Similarity=1.001  Sum_probs=31.3

Q ss_pred             ccccccc--CCCCCeecCCC-----CcchHHhHHHHhhCC--CCCCCCC
Q psy3884          35 ICPICHD--EFKTPVQLTCC-----HIFCESCVTKWFDRE--QTCPLCR   74 (95)
Q Consensus        35 ~C~IC~~--~~~~p~~~~Cg-----H~fc~~Ci~~~~~~~--~~CP~Cr   74 (95)
                      .|.||++  ...++.+.||.     |.+|..|+.+|+..+  ..||+|+
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            4889997  33456777885     789999999999744  5899984

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

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

Probab=98.25  E-value=2.1e-06  Score=57.14  Aligned_cols=43  Identities=30%  Similarity=0.894  Sum_probs=37.0

Q ss_pred             cccccccccCCCCCeec-CCCCcchHHhHHHHhh-CCCCCCCCCc
Q psy3884          33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-REQTCPLCRA   75 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-~~~~CP~Cr~   75 (95)
                      .+.|+.|..++.+|+.+ .|+|.||..||...+. ..+.||.|..
T Consensus       274 ~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             cccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            47999999999999988 5899999999986655 5689999944

>KOG1493|consensus

Probab=98.22  E-value=2.5e-07  Score=49.61  Aligned_cols=45  Identities=36%  Similarity=0.925  Sum_probs=34.4

Q ss_pred             ccccccccCCCC------------Ceec-CCCCcchHHhHHHHhh---CCCCCCCCCccCC
Q psy3884          34 CICPICHDEFKT------------PVQL-TCCHIFCESCVTKWFD---REQTCPLCRATLV   78 (95)
Q Consensus        34 ~~C~IC~~~~~~------------p~~~-~CgH~fc~~Ci~~~~~---~~~~CP~Cr~~~~   78 (95)
                      ..|.||.-.|..            |.++ .|.|.|+..||.+|+.   .+..||+||+.+.
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            378888776653            2333 5999999999999997   3468999999764

>KOG1039|consensus

Probab=98.19  E-value=1e-06  Score=59.90  Aligned_cols=48  Identities=29%  Similarity=0.803  Sum_probs=38.6

Q ss_pred             CCcccccccccCCCCCe-----e---cCCCCcchHHhHHHHhh--C-----CCCCCCCCccCC
Q psy3884          31 GVGCICPICHDEFKTPV-----Q---LTCCHIFCESCVTKWFD--R-----EQTCPLCRATLV   78 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~-----~---~~CgH~fc~~Ci~~~~~--~-----~~~CP~Cr~~~~   78 (95)
                      ..+.+|.||++......     .   .+|.|.||..|+..|..  +     .+.||.||.+..
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            34679999999877653     2   46999999999999983  4     478999998754

>KOG0827|consensus

Probab=98.15  E-value=1.3e-06  Score=59.81  Aligned_cols=50  Identities=34%  Similarity=0.801  Sum_probs=36.7

Q ss_pred             ccccccccCCCCC----eecCCCCcchHHhHHHHhhCC---CCCCCCCccCCCCccc
Q psy3884          34 CICPICHDEFKTP----VQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDDPAW   83 (95)
Q Consensus        34 ~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~   83 (95)
                      ..|.||.+.+.+.    .+-.|||+||..|+..|+...   ..||+|+-.+..+.++
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~r~~~   61 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQERHVA   61 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccceeee
Confidence            4899995554432    233599999999999999843   5899999666655544

>KOG4692|consensus

Probab=98.08  E-value=4.3e-06  Score=56.83  Aligned_cols=48  Identities=27%  Similarity=0.656  Sum_probs=43.8

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .++..||||..-..+.+..||+|.-|+.||.+.+.+.+.|-.|+..+.
T Consensus       420 sEd~lCpICyA~pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  420 SEDNLCPICYAGPINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             cccccCcceecccchhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence            356699999999999999999999999999999999999999988765

>KOG2930|consensus

Probab=97.96  E-value=5e-06  Score=47.09  Aligned_cols=28  Identities=29%  Similarity=0.856  Sum_probs=25.8

Q ss_pred             CCCCcchHHhHHHHhhCCCCCCCCCccC
Q psy3884          50 TCCHIFCESCVTKWFDREQTCPLCRATL   77 (95)
Q Consensus        50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   77 (95)
                      .|.|.||..||.+|++....||++.++-
T Consensus        80 ~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   80 VCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             ecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            5999999999999999999999997754

>KOG1785|consensus

Probab=97.90  E-value=5.3e-06  Score=57.22  Aligned_cols=47  Identities=36%  Similarity=0.896  Sum_probs=39.8

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhhC--CCCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDR--EQTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~--~~~CP~Cr~~~~~~   80 (95)
                      ..|-||.+.-++-.+-||||..|..|+..|...  ...||.||.++...
T Consensus       370 eLCKICaendKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGt  418 (563)
T KOG1785|consen  370 ELCKICAENDKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGT  418 (563)
T ss_pred             HHHHHhhccCCCcccccccchHHHHHHHhhcccCCCCCCCceeeEeccc
Confidence            479999998777777799999999999999853  57999999988644

>KOG4275|consensus

Probab=97.87  E-value=5.3e-06  Score=55.00  Aligned_cols=42  Identities=36%  Similarity=0.876  Sum_probs=35.5

Q ss_pred             cccccccccCCCCCeecCCCC-cchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          33 GCICPICHDEFKTPVQLTCCH-IFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH-~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ...|.||++...+-+.++||| +-|..|-.+    ...||+||+.+.
T Consensus       300 ~~LC~ICmDaP~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPRDCVFLECGHMVTCTKCGKR----MNECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCcceEEeecCcEEeehhhccc----cccCchHHHHHH
Confidence            569999999999999999999 479999754    348999998654

>KOG3039|consensus

Probab=97.82  E-value=2.1e-05  Score=51.11  Aligned_cols=54  Identities=22%  Similarity=0.397  Sum_probs=47.1

Q ss_pred             CcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884          32 VGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   85 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   85 (95)
                      ..+.||+|.+.+.+.    +.-+|||+|+..|+.+++.....||+|..++.++++...
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~L  277 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGL  277 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEee
Confidence            567999999999985    333999999999999999999999999999999877543

>KOG0825|consensus

Probab=97.79  E-value=3.4e-06  Score=62.20  Aligned_cols=49  Identities=31%  Similarity=0.657  Sum_probs=38.3

Q ss_pred             cccccccccCCCCC---eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          33 GCICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        33 ~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ...|++|+..+.+.   ...+|+|.||..|+..|.....+||+||..|..-.
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~  174 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVK  174 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheee
Confidence            34677777655543   24479999999999999999999999999886543

>KOG1002|consensus

Probab=97.77  E-value=1.4e-05  Score=56.88  Aligned_cols=50  Identities=30%  Similarity=0.782  Sum_probs=42.8

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhh-----CCCCCCCCCccCCCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-----REQTCPLCRATLVDD   80 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~~~~~   80 (95)
                      .....|.+|.+.-.+++...|.|.||..|+..+..     .+-+||.|...+..+
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            45669999999999999999999999999988876     336899998887654

>KOG1645|consensus

Probab=97.74  E-value=1.3e-05  Score=55.22  Aligned_cols=50  Identities=38%  Similarity=1.020  Sum_probs=39.5

Q ss_pred             CcccccccccCCCCC-----eecCCCCcchHHhHHHHhhCC--CCCCCCCccCCCCc
Q psy3884          32 VGCICPICHDEFKTP-----VQLTCCHIFCESCVTKWFDRE--QTCPLCRATLVDDP   81 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p-----~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~   81 (95)
                      ....||||++.+.-+     +.+.|||.|-..|+.+|+.+.  ..||.|......+.
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~katkr~   59 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKATKRQ   59 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhHHHH
Confidence            356899999998765     456899999999999999632  58999976655443

>PF04641 Rtf2: Rtf2 RING-finger

Probab=97.68  E-value=7.4e-05  Score=49.24  Aligned_cols=56  Identities=20%  Similarity=0.469  Sum_probs=44.4

Q ss_pred             CCCcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCC
Q psy3884          30 LGVGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDG   86 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   86 (95)
                      ....+.|||....+...    ...+|||+|...++...- ....||+|..++...++....
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~~~DiI~Ln  169 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFTEEDIIPLN  169 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccccCCEEEec
Confidence            35678999999998653    234999999999998873 466899999999988776543

>KOG0826|consensus

Probab=97.67  E-value=3.6e-05  Score=51.79  Aligned_cols=50  Identities=22%  Similarity=0.527  Sum_probs=42.1

Q ss_pred             cCCCcccccccccCCCCCeecC-CCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          29 LLGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ...+...||+|.....+|.++. -|-+||..|+..++...+.||+-..+..
T Consensus       296 l~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~  346 (357)
T KOG0826|consen  296 LPPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS  346 (357)
T ss_pred             CCCccccChhHHhccCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence            3456779999999999997775 5999999999999999999998765543

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=97.66  E-value=3e-05  Score=39.19  Aligned_cols=47  Identities=26%  Similarity=0.609  Sum_probs=36.7

Q ss_pred             cccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ...|-.|...-...++++|||..|..|..-  .+-+.||.|..++...+
T Consensus         7 ~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~--~rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    7 EQPCVFCGFVGTKGTVLPCGHLICDNCFPG--ERYNGCPFCGTPFEFDD   53 (55)
T ss_pred             ceeEEEccccccccccccccceeeccccCh--hhccCCCCCCCcccCCC
Confidence            346677777767788999999999999754  35578999999887554

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

Probab=97.60  E-value=6.2e-05  Score=37.19  Aligned_cols=42  Identities=26%  Similarity=0.774  Sum_probs=21.5

Q ss_pred             ccccccCCCCC--eec--CCCCcchHHhHHHHhh-CCCCCCCCCccC
Q psy3884          36 CPICHDEFKTP--VQL--TCCHIFCESCVTKWFD-REQTCPLCRATL   77 (95)
Q Consensus        36 C~IC~~~~~~p--~~~--~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~   77 (95)
                      ||+|.+.+...  ...  +||...|..|...... ....||.||.+.
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            68888887432  233  6899999999998886 578999999874

>KOG4185|consensus

Probab=97.55  E-value=7e-05  Score=49.94  Aligned_cols=45  Identities=33%  Similarity=0.892  Sum_probs=37.4

Q ss_pred             cccccccccCCCC------CeecCCCCcchHHhHHHHhhCC-CCCCCCCccC
Q psy3884          33 GCICPICHDEFKT------PVQLTCCHIFCESCVTKWFDRE-QTCPLCRATL   77 (95)
Q Consensus        33 ~~~C~IC~~~~~~------p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~   77 (95)
                      ...|-||-+.|..      |..+.|||++|..|+...+... ..||.||.+.
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            4589999988764      6788899999999999887755 4789999984

>KOG1571|consensus

Probab=97.50  E-value=6.5e-05  Score=51.07  Aligned_cols=47  Identities=32%  Similarity=0.707  Sum_probs=35.6

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .......|.||.+...+.+.+||||.-|  |..-. +....||+||+.+.
T Consensus       301 ~~~~p~lcVVcl~e~~~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  301 ELPQPDLCVVCLDEPKSAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             ccCCCCceEEecCCccceeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            3456679999999999999999999855  54322 33355999998765

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

Probab=97.49  E-value=0.00011  Score=50.01  Aligned_cols=52  Identities=23%  Similarity=0.607  Sum_probs=41.9

Q ss_pred             ccccCCCcccccccccCCCCCeecCCCCcchHHhHHHH--hhCCCCCCCCCccC
Q psy3884          26 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKW--FDREQTCPLCRATL   77 (95)
Q Consensus        26 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~--~~~~~~CP~Cr~~~   77 (95)
                      ..+...+...|.||.+-+.-..++||+|..|.-|..+.  +-..+.||.||..-
T Consensus        54 addtDEen~~C~ICA~~~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          54 ADDTDEENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccccccccceeEEecCCceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            33344566799999999988889999999999998764  34678999999864

>KOG4367|consensus

Probab=97.47  E-value=7.1e-05  Score=52.43  Aligned_cols=35  Identities=26%  Similarity=0.790  Sum_probs=31.5

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhh
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD   65 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~   65 (95)
                      ++++.|+||...|.+|++++|+|..|..|....+.
T Consensus         2 eeelkc~vc~~f~~epiil~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    2 EEELKCPVCGSFYREPIILPCSHNLCQACARNILV   36 (699)
T ss_pred             cccccCceehhhccCceEeecccHHHHHHHHhhcc
Confidence            35789999999999999999999999999987654

>KOG1814|consensus

Probab=97.40  E-value=4.8e-05  Score=52.58  Aligned_cols=39  Identities=33%  Similarity=0.770  Sum_probs=31.8

Q ss_pred             cccCCCcccccccccCCCCC---eecCCCCcchHHhHHHHhh
Q psy3884          27 ETLLGVGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFD   65 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~   65 (95)
                      ..+....+.|.||++.....   +.+||+|+||..|+..++.
T Consensus       178 ~~F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  178 EKFVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFT  219 (445)
T ss_pred             HHHHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHH
Confidence            33455678999999987763   5779999999999999886

>KOG1941|consensus

Probab=97.35  E-value=6.4e-05  Score=51.87  Aligned_cols=44  Identities=27%  Similarity=0.762  Sum_probs=36.2

Q ss_pred             CcccccccccCCCC-C---eecCCCCcchHHhHHHHhhCC--CCCCCCCc
Q psy3884          32 VGCICPICHDEFKT-P---VQLTCCHIFCESCVTKWFDRE--QTCPLCRA   75 (95)
Q Consensus        32 ~~~~C~IC~~~~~~-p---~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~   75 (95)
                      -++.|..|.+.+-. +   -.+||.|+||..|+..++.++  .+||.||+
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            46799999998753 2   467999999999999998755  68999984

>KOG2114|consensus

Probab=97.30  E-value=0.00033  Score=52.30  Aligned_cols=41  Identities=29%  Similarity=0.865  Sum_probs=35.1

Q ss_pred             ccccccccCCCCCe-ecCCCCcchHHhHHHHhhCCCCCCCCCccC
Q psy3884          34 CICPICHDEFKTPV-QLTCCHIFCESCVTKWFDREQTCPLCRATL   77 (95)
Q Consensus        34 ~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   77 (95)
                      -.|..|...+.-|. ...|||.||..|+.   .....||.|+...
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            49999999999884 66999999999997   4668999998743

>KOG1001|consensus

Probab=97.28  E-value=6.8e-05  Score=55.18  Aligned_cols=52  Identities=31%  Similarity=0.707  Sum_probs=42.8

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhhCC--CCCCCCCccCCCCccccCC
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE--QTCPLCRATLVDDPAWRDG   86 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~~~~~~   86 (95)
                      ..|.+|.+ ...+++++|||.||..|+...+...  ..||.||..+.....+...
T Consensus       455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~s~~  508 (674)
T KOG1001|consen  455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLLSAN  508 (674)
T ss_pred             cccccccc-cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHhhcc
Confidence            79999999 7788899999999999999887743  4799999988766555443

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

Probab=97.09  E-value=0.00035  Score=39.69  Aligned_cols=32  Identities=22%  Similarity=0.626  Sum_probs=26.2

Q ss_pred             CCCcccccccccCCCCCe--ecCCCCcchHHhHH
Q psy3884          30 LGVGCICPICHDEFKTPV--QLTCCHIFCESCVT   61 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~--~~~CgH~fc~~Ci~   61 (95)
                      ......|++|...+.+..  +.||||.||..|+.
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            345668999999998764  55999999999974

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 [].

>KOG4739|consensus

Probab=97.07  E-value=0.00029  Score=45.61  Aligned_cols=44  Identities=30%  Similarity=0.739  Sum_probs=30.8

Q ss_pred             cccccccCCC-CC-eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          35 ICPICHDEFK-TP-VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        35 ~C~IC~~~~~-~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      .|..|..... .+ ..+.|+|+||..|...-  ....||+|++++...
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            5777766544 23 46699999999998532  223899999986543

>KOG2817|consensus

Probab=96.98  E-value=0.00056  Score=47.18  Aligned_cols=49  Identities=20%  Similarity=0.558  Sum_probs=38.1

Q ss_pred             cCCCcccccccccCCC---CCeecCCCCcchHHhHHHHhhCC---CCCCCCCccC
Q psy3884          29 LLGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATL   77 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~   77 (95)
                      .....+.|||=.+.-.   .|+.+.|||+.+..-+.+..++.   +.||.|-...
T Consensus       330 ~fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  330 HFHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             cccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            3567789999665433   47899999999999999988754   5899995543

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

Probab=96.88  E-value=0.0017  Score=31.39  Aligned_cols=38  Identities=24%  Similarity=0.743  Sum_probs=23.3

Q ss_pred             ccccccCCCCCeecC---CCCcchHHhHHHHhhCCC--CCCCC
Q psy3884          36 CPICHDEFKTPVQLT---CCHIFCESCVTKWFDREQ--TCPLC   73 (95)
Q Consensus        36 C~IC~~~~~~p~~~~---CgH~fc~~Ci~~~~~~~~--~CP~C   73 (95)
                      |.+|.+.....+.=+   |+-.+|..|+..++....  .||.|
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            667888877765544   888999999999998654  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=96.82  E-value=0.0021  Score=39.32  Aligned_cols=33  Identities=24%  Similarity=0.570  Sum_probs=24.6

Q ss_pred             cccccccccCCCCCeecC------------CCCc-chHHhHHHHhh
Q psy3884          33 GCICPICHDEFKTPVQLT------------CCHI-FCESCVTKWFD   65 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~------------CgH~-fc~~Ci~~~~~   65 (95)
                      +..||||++...++|.|-            |+.. -|..|+.++-+
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            458999999999998874            4432 36788887653

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.

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

Probab=96.74  E-value=0.0021  Score=38.21  Aligned_cols=50  Identities=20%  Similarity=0.561  Sum_probs=40.8

Q ss_pred             CcccccccccCCCCCeec----CCCCcchHHhHHHHhh---CCCCCCCCCccCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQL----TCCHIFCESCVTKWFD---REQTCPLCRATLVDDP   81 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~----~CgH~fc~~Ci~~~~~---~~~~CP~Cr~~~~~~~   81 (95)
                      ...+|.||.+...+...+    -||-..|.-|....++   -...||.|+.++....
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            356999999998888777    3999999999987766   3468999999887553

>KOG4445|consensus

Probab=96.69  E-value=0.00043  Score=46.37  Aligned_cols=49  Identities=27%  Similarity=0.680  Sum_probs=37.7

Q ss_pred             CcccccccccCCCC-C--eecCCCCcchHHhHHHHhh-----------------------CCCCCCCCCccCCCC
Q psy3884          32 VGCICPICHDEFKT-P--VQLTCCHIFCESCVTKWFD-----------------------REQTCPLCRATLVDD   80 (95)
Q Consensus        32 ~~~~C~IC~~~~~~-p--~~~~CgH~fc~~Ci~~~~~-----------------------~~~~CP~Cr~~~~~~   80 (95)
                      ....|.||+--|.. +  .+++|-|.||..|+.+++.                       ....||+||..+...
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            34589999877764 3  5779999999999988774                       113799999998755

>KOG3800|consensus

Probab=96.68  E-value=0.0018  Score=43.10  Aligned_cols=46  Identities=35%  Similarity=0.882  Sum_probs=34.8

Q ss_pred             cccccccC-CCCC----eecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCC
Q psy3884          35 ICPICHDE-FKTP----VQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDD   80 (95)
Q Consensus        35 ~C~IC~~~-~~~p----~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~   80 (95)
                      .||+|... +.+|    .+-+|||..|.+|+...+.. ...||.|...+...
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            58999865 3455    12289999999999998874 57999998776544

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

Probab=96.66  E-value=0.00069  Score=33.21  Aligned_cols=35  Identities=29%  Similarity=0.776  Sum_probs=24.4

Q ss_pred             CCeecCCC-CcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          45 TPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        45 ~p~~~~Cg-H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      +.-.+.|. |..|..|+...+..+..||+|..+++.
T Consensus        12 ~k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   12 NKGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             CCCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            33456676 888999999999999999999998874

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.

>KOG1428|consensus

Probab=96.65  E-value=0.0015  Score=52.06  Aligned_cols=49  Identities=29%  Similarity=0.768  Sum_probs=37.9

Q ss_pred             CCcccccccccCCCC---CeecCCCCcchHHhHHHHhhCC----------CCCCCCCccCCC
Q psy3884          31 GVGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDRE----------QTCPLCRATLVD   79 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~----------~~CP~Cr~~~~~   79 (95)
                      ..+..|.||+..--.   .+.+.|+|.||..|.+..+++.          ..||+|..++..
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            456699999975432   3788999999999998777643          389999988764

>KOG3002|consensus

Probab=96.53  E-value=0.0021  Score=43.29  Aligned_cols=48  Identities=29%  Similarity=0.624  Sum_probs=37.9

Q ss_pred             cCCCcccccccccCCCCCee-cCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          29 LLGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      ...+.+.||||.+.+..|+. -.=||..|..|-.   +....||.||.++..
T Consensus        44 ~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   44 LDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             cchhhccCchhhccCcccceecCCCcEehhhhhh---hhcccCCcccccccc
Confidence            34567899999999998842 2457999999975   356789999999883

>KOG1952|consensus

Probab=96.52  E-value=0.0042  Score=46.72  Aligned_cols=47  Identities=28%  Similarity=0.740  Sum_probs=36.0

Q ss_pred             CCCcccccccccCCCCCe-ec---CCCCcchHHhHHHHhhC-------CCCCCCCCcc
Q psy3884          30 LGVGCICPICHDEFKTPV-QL---TCCHIFCESCVTKWFDR-------EQTCPLCRAT   76 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~-~~---~CgH~fc~~Ci~~~~~~-------~~~CP~Cr~~   76 (95)
                      ....++|.||.+.+.... +.   .|-|+||..||.+|...       ...||.|+..
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv  245 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSV  245 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccch
Confidence            346679999999987532 22   57799999999999863       2589999843

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.52  E-value=0.0046  Score=37.89  Aligned_cols=48  Identities=25%  Similarity=0.654  Sum_probs=35.2

Q ss_pred             CCcccccccccCCCCCeecCCCC-----cchHHhHHHHhhCC--CCCCCCCccCCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCH-----IFCESCVTKWFDRE--QTCPLCRATLVD   79 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH-----~fc~~Ci~~~~~~~--~~CP~Cr~~~~~   79 (95)
                      ..+..|-||.+... +..-||.-     ..|.+|+.+|+..+  ..|+.|+.++.-
T Consensus         6 ~~~~~CRIC~~~~~-~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i   60 (162)
T PHA02825          6 LMDKCCWICKDEYD-VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNI   60 (162)
T ss_pred             CCCCeeEecCCCCC-CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEE
Confidence            34559999998854 33446653     24999999999854  689999998753

>KOG3970|consensus

Probab=96.51  E-value=0.0031  Score=40.82  Aligned_cols=47  Identities=21%  Similarity=0.609  Sum_probs=37.9

Q ss_pred             ccccccccCCCCC--eecCCCCcchHHhHHHHhh--------CCCCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTP--VQLTCCHIFCESCVTKWFD--------REQTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~~--------~~~~CP~Cr~~~~~~   80 (95)
                      -.|..|...+...  +.+-|-|.||..|+..|..        ....||.|..++...
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            3789998888754  6789999999999999875        235899998887654

>KOG1940|consensus

Probab=96.39  E-value=0.0023  Score=42.59  Aligned_cols=42  Identities=29%  Similarity=0.686  Sum_probs=35.5

Q ss_pred             ccccccccCCCC----CeecCCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884          34 CICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRA   75 (95)
Q Consensus        34 ~~C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~   75 (95)
                      ..||||.+.+..    +..++|||..+..|+......+..||+|.+
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            359999987653    567799999999999988877799999987

>KOG4362|consensus

Probab=96.26  E-value=0.00093  Score=49.13  Aligned_cols=49  Identities=35%  Similarity=0.809  Sum_probs=40.5

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhhC---CCCCCCCCccCCCC
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR---EQTCPLCRATLVDD   80 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~---~~~CP~Cr~~~~~~   80 (95)
                      ..++|+||...+..|+.+.|-|.||..|+...+..   ...||+|+..+...
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            35699999999999999999999999999866553   45899998766544

>KOG2932|consensus

Probab=96.25  E-value=0.0021  Score=43.38  Aligned_cols=42  Identities=29%  Similarity=0.809  Sum_probs=30.4

Q ss_pred             cccccccCCCC-CeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          35 ICPICHDEFKT-PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        35 ~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .|--|--.+.. ...++|.|+||.+|...  ...+.||.|-..+.
T Consensus        92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   92 FCDRCDFPIAIYGRMIPCKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             eecccCCcceeeecccccchhhhhhhhhc--CccccCcCcccHHH
Confidence            56666555443 46779999999999864  34678999966554

>KOG3268|consensus

Probab=96.21  E-value=0.0043  Score=38.83  Aligned_cols=47  Identities=23%  Similarity=0.622  Sum_probs=33.1

Q ss_pred             ccccccccCCCCCe-------ecCCCCcchHHhHHHHhhC------C-----CCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTPV-------QLTCCHIFCESCVTKWFDR------E-----QTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p~-------~~~CgH~fc~~Ci~~~~~~------~-----~~CP~Cr~~~~~~   80 (95)
                      ..|.||..+--+..       -+.||..||.-|+..|++.      +     ..||.|..++..+
T Consensus       166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            35666665543322       2369999999999999972      1     4799998887644

>PHA03096 p28-like protein; Provisional

Probab=96.16  E-value=0.0034  Score=42.05  Aligned_cols=42  Identities=29%  Similarity=0.542  Sum_probs=29.9

Q ss_pred             ccccccccCCCCC--------eecCCCCcchHHhHHHHhhCC---CCCCCCCc
Q psy3884          34 CICPICHDEFKTP--------VQLTCCHIFCESCVTKWFDRE---QTCPLCRA   75 (95)
Q Consensus        34 ~~C~IC~~~~~~p--------~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~   75 (95)
                      ..|.||++.....        ....|.|.||..|+..|....   ..||.||.
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            4899999876532        233699999999999998733   34555443

>PHA02862 5L protein; Provisional

Probab=96.09  E-value=0.0083  Score=36.28  Aligned_cols=46  Identities=24%  Similarity=0.585  Sum_probs=34.6

Q ss_pred             ccccccccCCCCCeecCCCC-----cchHHhHHHHhhCC--CCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTPVQLTCCH-----IFCESCVTKWFDRE--QTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH-----~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~   80 (95)
                      ..|-||.+.-.+. .-||.-     ..|..|+.+|+..+  ..|+.|+.++.-+
T Consensus         3 diCWIC~~~~~e~-~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          3 DICWICNDVCDER-NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CEEEEecCcCCCC-cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            4799999886544 456653     36999999999844  5899999987544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.89  E-value=0.0069  Score=41.50  Aligned_cols=49  Identities=22%  Similarity=0.598  Sum_probs=35.4

Q ss_pred             cccccccccCCCCC----eecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCc
Q psy3884          33 GCICPICHDEFKTP----VQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDP   81 (95)
Q Consensus        33 ~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~   81 (95)
                      +..||.|++.+...    .--+||-..|..|.....+ -+..||.||....++.
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            33699999987642    2237898889888865544 3479999999877653

>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=95.74  E-value=0.0077  Score=29.96  Aligned_cols=43  Identities=23%  Similarity=0.716  Sum_probs=21.3

Q ss_pred             cccccccccCCCCCeec-CCCCcchHHhHHHHhh-----CCCCCCCCCcc
Q psy3884          33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFD-----REQTCPLCRAT   76 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~   76 (95)
                      .+.|||....+..|+.. .|.|.-|.+- ..|+.     ....||+|.++
T Consensus         2 sL~CPls~~~i~~P~Rg~~C~H~~CFDl-~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    2 SLRCPLSFQRIRIPVRGKNCKHLQCFDL-ESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             ESB-TTTSSB-SSEEEETT--SS--EEH-HHHHHHHHHS---B-TTT---
T ss_pred             eeeCCCCCCEEEeCccCCcCcccceECH-HHHHHHhhccCCeECcCCcCc
Confidence            35899999999999755 8999866432 23332     33579999764

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.

>KOG3113|consensus

Probab=95.64  E-value=0.012  Score=38.72  Aligned_cols=62  Identities=21%  Similarity=0.359  Sum_probs=46.0

Q ss_pred             CCCcccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhh
Q psy3884          30 LGVGCICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      ....+.|||-.-.+..-    ...+|||+|-..-+.+.  ....|++|.+.+...+.........-++
T Consensus       108 ~~a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dvIvlNg~~E~~d  173 (293)
T KOG3113|consen  108 QRARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDVIVLNGTEEDVD  173 (293)
T ss_pred             ccceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCeEeeCCCHHHHH
Confidence            35678999987777654    34489999998877654  4689999999999888776655554443

>KOG0298|consensus

Probab=95.61  E-value=0.0068  Score=47.45  Aligned_cols=46  Identities=26%  Similarity=0.678  Sum_probs=40.3

Q ss_pred             CCcccccccccCCC-CCeecCCCCcchHHhHHHHhhCCCCCCCCCcc
Q psy3884          31 GVGCICPICHDEFK-TPVQLTCCHIFCESCVTKWFDREQTCPLCRAT   76 (95)
Q Consensus        31 ~~~~~C~IC~~~~~-~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~   76 (95)
                      .....|.||.+.+. ...+..|||.+|..|...|+..+..||.|...
T Consensus      1151 ~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1151 SGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             hcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence            35569999999998 45688999999999999999999999999743

>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=95.44  E-value=0.0098  Score=35.52  Aligned_cols=33  Identities=30%  Similarity=0.741  Sum_probs=26.2

Q ss_pred             cccccccccCCCC--C-eecCCC------CcchHHhHHHHhh
Q psy3884          33 GCICPICHDEFKT--P-VQLTCC------HIFCESCVTKWFD   65 (95)
Q Consensus        33 ~~~C~IC~~~~~~--p-~~~~Cg------H~fc~~Ci~~~~~   65 (95)
                      ..+|.||++.+.+  . +.++||      |.||..|+.+|-.
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            5599999999887  4 344666      5699999999954

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.

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

Probab=94.95  E-value=0.018  Score=28.26  Aligned_cols=38  Identities=26%  Similarity=0.834  Sum_probs=23.9

Q ss_pred             ccccccCCCC--CeecCCCC-----cchHHhHHHHhh--CCCCCCCC
Q psy3884          36 CPICHDEFKT--PVQLTCCH-----IFCESCVTKWFD--REQTCPLC   73 (95)
Q Consensus        36 C~IC~~~~~~--p~~~~CgH-----~fc~~Ci~~~~~--~~~~CP~C   73 (95)
                      |-||++.-.+  +.+.||+-     ..|..|+.+|+.  ....|++|
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            5688876543  45667652     469999999998  44678876

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

Probab=94.67  E-value=0.026  Score=38.99  Aligned_cols=31  Identities=35%  Similarity=0.937  Sum_probs=23.7

Q ss_pred             CCCcchHHhHHHHhh-------------CCCCCCCCCccCCCCc
Q psy3884          51 CCHIFCESCVTKWFD-------------REQTCPLCRATLVDDP   81 (95)
Q Consensus        51 CgH~fc~~Ci~~~~~-------------~~~~CP~Cr~~~~~~~   81 (95)
                      |....|.+|+-+|+.             +...||.||+.+...|
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCilD  354 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCILD  354 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceeee
Confidence            556679999999885             2247999999987544

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

>KOG1100|consensus

Probab=94.64  E-value=0.019  Score=36.78  Aligned_cols=40  Identities=30%  Similarity=0.798  Sum_probs=30.8

Q ss_pred             ccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          36 CPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        36 C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      |-.|.+.-..-..+||.|. +|..|-..    -..||+|+.+...
T Consensus       161 Cr~C~~~~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGEREATVLLLPCRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcCCceEEeecccceEeccccccc----CccCCCCcChhhc
Confidence            8899888766667799985 89999642    4569999876543

>KOG3039|consensus

Probab=94.38  E-value=0.041  Score=36.25  Aligned_cols=36  Identities=11%  Similarity=0.162  Sum_probs=31.2

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhh
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD   65 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~   65 (95)
                      +..-..|..|+....+|++++=||.|+..||.+++.
T Consensus        40 iK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~il   75 (303)
T KOG3039|consen   40 IKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYIL   75 (303)
T ss_pred             cCCcceeeeecccccCCccCCCCeeeeHHHHHHHHH
Confidence            344558899999999999999999999999988763

>KOG3161|consensus

Probab=94.37  E-value=0.014  Score=43.06  Aligned_cols=38  Identities=37%  Similarity=0.956  Sum_probs=30.0

Q ss_pred             CcccccccccCCC----CCeecCCCCcchHHhHHHHhhCCCCCC
Q psy3884          32 VGCICPICHDEFK----TPVQLTCCHIFCESCVTKWFDREQTCP   71 (95)
Q Consensus        32 ~~~~C~IC~~~~~----~p~~~~CgH~fc~~Ci~~~~~~~~~CP   71 (95)
                      ..+.|+||...|.    .|+.+.|||+.|..|+.....  .+||
T Consensus        10 ~~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~lyn--~scp   51 (861)
T KOG3161|consen   10 LLLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLYN--ASCP   51 (861)
T ss_pred             HHhhchHHHHHHHHHhcCcccccccchHHHHHHHhHhh--ccCC
Confidence            4568999987765    478889999999999987544  4566

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

Probab=93.92  E-value=0.08  Score=26.90  Aligned_cols=46  Identities=26%  Similarity=0.748  Sum_probs=31.6

Q ss_pred             cccccccCCCCCe--ecCCC--CcchHHhHHHHhhCCCCCCCCCccCCCCcc
Q psy3884          35 ICPICHDEFKTPV--QLTCC--HIFCESCVTKWFDREQTCPLCRATLVDDPA   82 (95)
Q Consensus        35 ~C~IC~~~~~~p~--~~~Cg--H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   82 (95)
                      .|-.|-..+....  ..-|.  .+||..|....+  ...||.|...+..++.
T Consensus         7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l--~~~CPNCgGelv~RP~   56 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYICSFECTFCADCAETML--NGVCPNCGGELVRRPR   56 (57)
T ss_pred             CccccCCCCCCCCCcceEEeEeCcccHHHHHHHh--cCcCcCCCCccccCCC
Confidence            5666666655322  22344  479999998765  5789999998876653

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

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

Probab=93.85  E-value=0.055  Score=36.84  Aligned_cols=47  Identities=23%  Similarity=0.565  Sum_probs=35.3

Q ss_pred             CCCcccccccccCCC---CCeecCCCCcchHHhHHHHhhCC---CCCCCCCcc
Q psy3884          30 LGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDRE---QTCPLCRAT   76 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~---~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~   76 (95)
                      ...-+.||+=.+.-.   .|+.+.|||+.-..-+....+++   +.||.|...
T Consensus       333 fHs~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP~~  385 (396)
T COG5109         333 FHSLFICPVLKELCTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCPEM  385 (396)
T ss_pred             ccceeeccccHhhhcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCCcc
Confidence            456679998665433   47899999999998888776644   689999543

>KOG3899|consensus

Probab=92.80  E-value=0.062  Score=36.26  Aligned_cols=31  Identities=29%  Similarity=0.815  Sum_probs=24.2

Q ss_pred             CCCcchHHhHHHHhh-------------CCCCCCCCCccCCCCc
Q psy3884          51 CCHIFCESCVTKWFD-------------REQTCPLCRATLVDDP   81 (95)
Q Consensus        51 CgH~fc~~Ci~~~~~-------------~~~~CP~Cr~~~~~~~   81 (95)
                      |....|.+|+-+|+.             ++..||+||+.+...+
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            566789999988874             3458999999987554

>KOG0309|consensus

Probab=92.79  E-value=0.071  Score=40.27  Aligned_cols=38  Identities=34%  Similarity=0.798  Sum_probs=27.0

Q ss_pred             cccccccCCCCC--eecCCCCcchHHhHHHHhhCCCCCCC
Q psy3884          35 ICPICHDEFKTP--VQLTCCHIFCESCVTKWFDREQTCPL   72 (95)
Q Consensus        35 ~C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~~~~~~CP~   72 (95)
                      .|.||--.....  +-..|||+.|.+|...|+.....||.
T Consensus      1030 ~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1030 QCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeeEeeEeeccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            344444333332  23369999999999999999889984

>KOG3579|consensus

Probab=92.74  E-value=0.11  Score=35.02  Aligned_cols=37  Identities=22%  Similarity=0.678  Sum_probs=30.5

Q ss_pred             CCcccccccccCCCCCeecCC----CCcchHHhHHHHhhCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTC----CHIFCESCVTKWFDRE   67 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~C----gH~fc~~Ci~~~~~~~   67 (95)
                      ...+.|.+|.+.+++-..+.|    .|.||..|-++.++++
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Q  306 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQ  306 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhh
Confidence            345899999999999877766    5899999999888743

>KOG2034|consensus

Probab=92.69  E-value=0.12  Score=39.47  Aligned_cols=35  Identities=23%  Similarity=0.528  Sum_probs=27.5

Q ss_pred             CCCcccccccccCCCC-C-eecCCCCcchHHhHHHHh
Q psy3884          30 LGVGCICPICHDEFKT-P-VQLTCCHIFCESCVTKWF   64 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~-p-~~~~CgH~fc~~Ci~~~~   64 (95)
                      ......|.+|...+.. | .+.+|||.||..|+.+..
T Consensus       814 ~ep~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             ecCccchHHhcchhhcCcceeeeccchHHHHHHHHHH
Confidence            3456699999987654 4 566999999999997654

>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=92.58  E-value=0.071  Score=35.03  Aligned_cols=45  Identities=38%  Similarity=0.977  Sum_probs=33.1

Q ss_pred             cccccccccCC-CCC-eec---C-CCCcchHHhHHHHhhCC-CCCC--CCCccC
Q psy3884          33 GCICPICHDEF-KTP-VQL---T-CCHIFCESCVTKWFDRE-QTCP--LCRATL   77 (95)
Q Consensus        33 ~~~C~IC~~~~-~~p-~~~---~-CgH~fc~~Ci~~~~~~~-~~CP--~Cr~~~   77 (95)
                      +..||||..+. -+| +.+   | |-|.+|.+|+.+.+... ..||  -|.+-+
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL   63 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL   63 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence            44899999753 355 222   4 99999999999988754 6899  675543

>KOG1815|consensus

Probab=92.34  E-value=0.1  Score=37.06  Aligned_cols=35  Identities=29%  Similarity=0.712  Sum_probs=29.8

Q ss_pred             CCcccccccccCCCC-CeecCCCCcchHHhHHHHhh
Q psy3884          31 GVGCICPICHDEFKT-PVQLTCCHIFCESCVTKWFD   65 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~   65 (95)
                      .....|.||.+.+.. ...+.|||.||..|...++.
T Consensus        68 ~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~  103 (444)
T KOG1815|consen   68 KGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLG  103 (444)
T ss_pred             CccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhh
Confidence            345799999999885 56779999999999999886

>KOG1812|consensus

Probab=92.32  E-value=0.059  Score=37.65  Aligned_cols=48  Identities=29%  Similarity=0.733  Sum_probs=32.3

Q ss_pred             cccccccc-cCCCCC---eecCCCCcchHHhHHHHhhCC------CCCCC--CCccCCCC
Q psy3884          33 GCICPICH-DEFKTP---VQLTCCHIFCESCVTKWFDRE------QTCPL--CRATLVDD   80 (95)
Q Consensus        33 ~~~C~IC~-~~~~~p---~~~~CgH~fc~~Ci~~~~~~~------~~CP~--Cr~~~~~~   80 (95)
                      ...|.||. +.....   .+..|+|.||..|+.+++...      ..||.  |...++..
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~~~~~C~~~~C~~~l~~~  205 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSGTVIRCPHDGCESRLTLE  205 (384)
T ss_pred             cccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccCCCccCCCCCCCccCCHH
Confidence            56899999 443331   245799999999999888732      36763  54444433

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.35  E-value=0.12  Score=27.66  Aligned_cols=33  Identities=27%  Similarity=0.626  Sum_probs=25.4

Q ss_pred             CCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884          51 CCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   85 (95)
Q Consensus        51 CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   85 (95)
                      =.++||..|....+  +..||.|...+..+++.+.
T Consensus        27 fEcTFCadCae~~l--~g~CPnCGGelv~RP~RPa   59 (84)
T COG3813          27 FECTFCADCAENRL--HGLCPNCGGELVARPIRPA   59 (84)
T ss_pred             EeeehhHhHHHHhh--cCcCCCCCchhhcCcCChH
Confidence            34789999997643  5789999998887766543

>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=90.61  E-value=0.054  Score=36.27  Aligned_cols=46  Identities=26%  Similarity=0.494  Sum_probs=23.2

Q ss_pred             CcccccccccCCCCCeecCC---C--CcchHHhHHHHhhCCCCCCCCCccC
Q psy3884          32 VGCICPICHDEFKTPVQLTC---C--HIFCESCVTKWFDREQTCPLCRATL   77 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~C---g--H~fc~~Ci~~~~~~~~~CP~Cr~~~   77 (95)
                      ....||||.....-.++..=   |  +.+|.-|-..|--....||.|...-
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            34699999997665444432   3  5689999999988889999996653

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.

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=90.44  E-value=0.48  Score=23.96  Aligned_cols=30  Identities=33%  Similarity=0.950  Sum_probs=23.6

Q ss_pred             cccccccccCCC--CCeec--CCCCcchHHhHHH
Q psy3884          33 GCICPICHDEFK--TPVQL--TCCHIFCESCVTK   62 (95)
Q Consensus        33 ~~~C~IC~~~~~--~p~~~--~CgH~fc~~Ci~~   62 (95)
                      ...|++|.+.|.  +.++.  .||-.+|+.|...
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            458999999994  45544  6999999999753

>KOG1812|consensus

Probab=90.12  E-value=0.16  Score=35.54  Aligned_cols=41  Identities=27%  Similarity=0.636  Sum_probs=30.8

Q ss_pred             cccccccccCCCC-----CeecCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884          33 GCICPICHDEFKT-----PVQLTCCHIFCESCVTKWFDREQTCPLC   73 (95)
Q Consensus        33 ~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~~~~CP~C   73 (95)
                      -..||.|...+..     .++-.|||.||+.|...|...+..|..|
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence            3489999887653     2333699999999999998877766544

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

Probab=89.68  E-value=0.0097  Score=31.66  Aligned_cols=40  Identities=33%  Similarity=0.803  Sum_probs=21.6

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      +.||.|...+...    =|+.+|..|-.. +.....||.|.+++.
T Consensus         2 ~~CP~C~~~L~~~----~~~~~C~~C~~~-~~~~a~CPdC~~~Le   41 (70)
T PF07191_consen    2 NTCPKCQQELEWQ----GGHYHCEACQKD-YKKEAFCPDCGQPLE   41 (70)
T ss_dssp             -B-SSS-SBEEEE----TTEEEETTT--E-EEEEEE-TTT-SB-E
T ss_pred             CcCCCCCCccEEe----CCEEECcccccc-ceecccCCCcccHHH
Confidence            5799998875421    167778888754 234567999988875

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

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

Probab=89.31  E-value=0.22  Score=21.33  Aligned_cols=10  Identities=40%  Similarity=0.956  Sum_probs=5.1

Q ss_pred             cccccccCCC
Q psy3884          35 ICPICHDEFK   44 (95)
Q Consensus        35 ~C~IC~~~~~   44 (95)
                      .||-|...+.
T Consensus         2 ~CP~C~~~V~   11 (26)
T PF10571_consen    2 TCPECGAEVP   11 (26)
T ss_pred             cCCCCcCCch
Confidence            3555555543

Several members are annotated as putative helicases.

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

Probab=89.08  E-value=0.54  Score=36.10  Aligned_cols=53  Identities=19%  Similarity=0.492  Sum_probs=38.5

Q ss_pred             CCcccccccccCCC--CCeecCCCCc-----chHHhHHHHhhCC--CCCCCCCccCCCCccc
Q psy3884          31 GVGCICPICHDEFK--TPVQLTCCHI-----FCESCVTKWFDRE--QTCPLCRATLVDDPAW   83 (95)
Q Consensus        31 ~~~~~C~IC~~~~~--~p~~~~CgH~-----fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~~~   83 (95)
                      .+...|.||...-.  +|..-||.-+     .|..|+.+|+..+  ..|-+|..++.-++++
T Consensus        10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY   71 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIY   71 (1175)
T ss_pred             ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeec
Confidence            34569999986543  4555577643     6999999999854  5899999887655443

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

Probab=88.99  E-value=0.44  Score=26.66  Aligned_cols=42  Identities=21%  Similarity=0.804  Sum_probs=31.3

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCcccc
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWR   84 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   84 (95)
                      ..|.||......+     ||.||..|..    ....|.+|...+.+...+.
T Consensus        45 ~~C~~CK~~v~q~-----g~~YCq~CAY----kkGiCamCGKki~dtk~yk   86 (90)
T PF10235_consen   45 SKCKICKTKVHQP-----GAKYCQTCAY----KKGICAMCGKKILDTKNYK   86 (90)
T ss_pred             ccccccccccccC-----CCccChhhhc----ccCcccccCCeeccccccc
Confidence            4788888865543     7889999974    4578999999886654443

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 [].

>KOG4718|consensus

Probab=88.44  E-value=0.28  Score=31.63  Aligned_cols=43  Identities=21%  Similarity=0.625  Sum_probs=35.0

Q ss_pred             cccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCc
Q psy3884          33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRA   75 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~   75 (95)
                      ...|.+|.......+.- .||-.++..|+..++.+...||.|.-
T Consensus       181 lk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d  224 (235)
T KOG4718|consen  181 LKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGD  224 (235)
T ss_pred             HHHHhHhHHHhheeeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence            35899999987765433 67778999999999999999999943

>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=87.91  E-value=0.74  Score=22.99  Aligned_cols=25  Identities=28%  Similarity=0.740  Sum_probs=13.3

Q ss_pred             CCCCcchHHhHHHHhhCCCCCCCCC
Q psy3884          50 TCCHIFCESCVTKWFDREQTCPLCR   74 (95)
Q Consensus        50 ~CgH~fc~~Ci~~~~~~~~~CP~Cr   74 (95)
                      .|++.||.+|=.-.-+.-..||-|.
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            5889999999432223346899884

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.

>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A

Probab=87.87  E-value=0.92  Score=26.40  Aligned_cols=43  Identities=23%  Similarity=0.508  Sum_probs=24.2

Q ss_pred             cccccccccCCC---CC--eecCCCCcchHHhHHHHhh-CCCCCCCCCc
Q psy3884          33 GCICPICHDEFK---TP--VQLTCCHIFCESCVTKWFD-REQTCPLCRA   75 (95)
Q Consensus        33 ~~~C~IC~~~~~---~p--~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~   75 (95)
                      ...|.+|...|.   +.  .-..|+|.+|..|-..-.. ....|.+|.+
T Consensus        54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k  102 (118)
T PF02318_consen   54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK  102 (118)
T ss_dssp             CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred             CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence            449999988653   22  3347999999988643111 1125666643

The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.

>KOG2068|consensus

Probab=87.68  E-value=0.61  Score=31.96  Aligned_cols=48  Identities=25%  Similarity=0.618  Sum_probs=37.3

Q ss_pred             cccccccccCCCC--C--eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          33 GCICPICHDEFKT--P--VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        33 ~~~C~IC~~~~~~--p--~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ...|+||.+....  .  .-.+||+..|..|+......+..||.||.+....
T Consensus       249 ~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~~~  300 (327)
T KOG2068|consen  249 PPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYERN  300 (327)
T ss_pred             CCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccccC
Confidence            3689999997642  2  2337899999999988888889999999776543

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=86.94  E-value=0.36  Score=32.80  Aligned_cols=45  Identities=20%  Similarity=0.548  Sum_probs=33.3

Q ss_pred             CcccccccccCCCCCeec----CCC--CcchHHhHHHHhhCCCCCCCCCcc
Q psy3884          32 VGCICPICHDEFKTPVQL----TCC--HIFCESCVTKWFDREQTCPLCRAT   76 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~----~Cg--H~fc~~Ci~~~~~~~~~CP~Cr~~   76 (95)
                      ....||||.....-.++.    .=|  +.+|.-|-..|-.....||.|...
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            345999999986544322    233  457899999998888999999764

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).

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=86.73  E-value=0.52  Score=32.14  Aligned_cols=44  Identities=23%  Similarity=0.591  Sum_probs=33.1

Q ss_pred             CcccccccccCCCCCee-c--CCC--CcchHHhHHHHhhCCCCCCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQ-L--TCC--HIFCESCVTKWFDREQTCPLCRA   75 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~-~--~Cg--H~fc~~Ci~~~~~~~~~CP~Cr~   75 (95)
                      ....||||.....-.++ +  .=|  +.+|.-|-..|--....||.|..
T Consensus       186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~  234 (309)
T PRK03564        186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ  234 (309)
T ss_pred             CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence            45699999998654432 1  233  45789999999888899999975

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

Probab=85.05  E-value=0.59  Score=24.55  Aligned_cols=12  Identities=42%  Similarity=1.450  Sum_probs=8.7

Q ss_pred             cchHHhHHHHhh
Q psy3884          54 IFCESCVTKWFD   65 (95)
Q Consensus        54 ~fc~~Ci~~~~~   65 (95)
                      .||+.|+.+|..
T Consensus        11 gFCRNCLskWy~   22 (68)
T PF06844_consen   11 GFCRNCLSKWYR   22 (68)
T ss_dssp             S--HHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            499999999985

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

>KOG0827|consensus

Probab=84.64  E-value=0.047  Score=38.11  Aligned_cols=47  Identities=26%  Similarity=0.639  Sum_probs=39.6

Q ss_pred             ccccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ..|+||...++.-    ..+.|||.++..|+..|+.....||.|+..++..
T Consensus       197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            3789999887653    4568999999999999999888999999988754

>KOG0802|consensus

Probab=83.26  E-value=0.91  Score=33.15  Aligned_cols=52  Identities=27%  Similarity=0.675  Sum_probs=39.6

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCcccc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWR   84 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   84 (95)
                      .......|.+|.... ....++|.   +..|+..|......||.|+..+..++...
T Consensus       475 l~~~~~~~~~~~~~~-~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~  526 (543)
T KOG0802|consen  475 LREPNDVCAICYQEM-SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDDFLS  526 (543)
T ss_pred             hhcccCcchHHHHHH-Hhcccccc---chhHHHhhhhhccccCCCchhhhcccccC
Confidence            334556899999988 55666777   57888899999999999988877664433

>KOG2169|consensus

Probab=83.14  E-value=1.2  Score=33.20  Aligned_cols=67  Identities=24%  Similarity=0.380  Sum_probs=43.4

Q ss_pred             cccCCCcccccccccCCCCCe-ecCCCCcchHHhHHHHhh----CCCCCCCCCccCCCCccccCCcchhhhh
Q psy3884          27 ETLLGVGCICPICHDEFKTPV-QLTCCHIFCESCVTKWFD----REQTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~----~~~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      .......+.|+|....+.-|. -..|.|.-|.+-..-.-.    ....||+|.+....+....|..+..+++
T Consensus       300 tt~~~vSL~CPl~~~Rm~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l~iD~~~~~iL~  371 (636)
T KOG2169|consen  300 TTSLRVSLNCPLSKMRMSLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGLIIDGYFLNILQ  371 (636)
T ss_pred             eccceeEecCCcccceeecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccchhhhHHHHHHHh
Confidence            334456789999988877764 457888766554422111    2248999998888776666655555443

>KOG1609|consensus

Probab=81.95  E-value=1.5  Score=29.32  Aligned_cols=46  Identities=35%  Similarity=0.870  Sum_probs=34.3

Q ss_pred             cccccccccCCCC----CeecCCC-----CcchHHhHHHHhh--CCCCCCCCCccCC
Q psy3884          33 GCICPICHDEFKT----PVQLTCC-----HIFCESCVTKWFD--REQTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~~----p~~~~Cg-----H~fc~~Ci~~~~~--~~~~CP~Cr~~~~   78 (95)
                      ...|-||......    +...||.     ...|..|+..|..  +...|..|...+.
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            4689999986543    3556664     2369999999998  5678999987654

>KOG3053|consensus

Probab=81.56  E-value=1.1  Score=29.87  Aligned_cols=47  Identities=23%  Similarity=0.663  Sum_probs=33.5

Q ss_pred             CcccccccccCCCCCee----cCCC-----CcchHHhHHHHhhCC--------CCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKTPVQ----LTCC-----HIFCESCVTKWFDRE--------QTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~----~~Cg-----H~fc~~Ci~~~~~~~--------~~CP~Cr~~~~   78 (95)
                      .+-.|=||+..-++...    -||.     |=.|..|+..|+...        -.||.|+.+..
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            44589999988765432    2654     337999999999622        37999998753

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

Probab=80.51  E-value=1.9  Score=19.15  Aligned_cols=35  Identities=20%  Similarity=0.482  Sum_probs=20.6

Q ss_pred             ccccccCCCCC--eecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          36 CPICHDEFKTP--VQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        36 C~IC~~~~~~p--~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      |+.|.+.+...  ....=+..||..|        +.|..|+.++.
T Consensus         2 C~~C~~~i~~~~~~~~~~~~~~H~~C--------f~C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELVLRALGKVWHPEC--------FKCSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEEEEeCCccccccC--------CCCcccCCcCc
Confidence            66777766653  2333456666666        34777766553

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

>KOG0825|consensus

Probab=80.12  E-value=1.5  Score=33.71  Aligned_cols=46  Identities=15%  Similarity=0.352  Sum_probs=31.7

Q ss_pred             CcccccccccCCCCC----eecC---CCCcchHHhHHHHhhC------CCCCCCCCccC
Q psy3884          32 VGCICPICHDEFKTP----VQLT---CCHIFCESCVTKWFDR------EQTCPLCRATL   77 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p----~~~~---CgH~fc~~Ci~~~~~~------~~~CP~Cr~~~   77 (95)
                      ....|.+|...+.++    -..+   |+|.||..||..|..+      .-.|+.|..-|
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            445777777776663    2334   9999999999999863      23567775544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	95
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-06
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
1chc_A	68	Structure Of The C3hc4 Domain By 1h-Nuclear Magneti		4e-04
2ecj_A	58	Solution Structure Of The Ring Domain Of The Human		9e-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 = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 38/61 (62%), Gaps = 4/61 (6%)
Query: 21 GVSPTKETLLGVGCICPICHDEF---KTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          G S T+E + G G  CP+C +++   ++  QL C H+F +SC+  W ++  +CP+CR +L
Sbjct: 4  GSSGTEEHV-GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62
Query: 78 V 78
Sbjct: 63 T 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: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          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: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          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: 36  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
           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: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78
          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 = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ---TCPLCRATLVDDPAWRDGATSYFV 92
          CPIC +  K PV   C HIFC+ C+ K  ++++    CPLC+  +           S  V
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLV 83
Query: 93 Q 93
          +
Sbjct: 84 E 84

>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 = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 36 CPIC-HDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          CPIC  D     + L C H FC  C+T+W  +  TCPLC+  +
Sbjct: 8  CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV 50

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

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKW---FDREQTCPLC 73
          L V   C +C +  K PV + C H FC++C+T+W    +R+  CP+C
Sbjct: 12 LQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	95
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	9e-16
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	1e-15
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	3e-15
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-15
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	5e-13
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-13
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	8e-13
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-12
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-12
1z6u_A	150	NP95-like ring finger protein isoform B; structura	2e-12
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-12
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	2e-12
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	5e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	9e-12
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	2e-11
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	2e-11
2ect_A	78	Ring finger protein 126; metal binding protein, st	3e-11
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	4e-11
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	7e-11
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-10
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	2e-10
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	4e-10
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	4e-10
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	5e-10
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	8e-10
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	1e-09
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	1e-09
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	1e-09
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	1e-09
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-09
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	3e-09
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	4e-09
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-09
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	7e-09
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	4e-08
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	5e-08
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	6e-08
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	7e-08
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	9e-08
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	1e-07
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	2e-07
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	2e-07
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	3e-07
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	3e-07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	4e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	3e-05
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	8e-07
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-06
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	6e-06
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	9e-06
3nw0_A	238	Non-structural maintenance of chromosomes element	2e-05
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	4e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	1e-04
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-04
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	3e-04
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-04
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	5e-04
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	6e-04

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

 Score = 64.5 bits (157), Expect = 9e-16
 Identities = 17/45 (37%), Positives = 21/45 (46%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
          C IC      PV L C H+FC  CV       + C LCR  + +D
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED 62

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

 Score = 66.6 bits (162), Expect = 1e-15
 Identities = 17/46 (36%), Positives = 23/46 (50%)

Query: 36  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81
           C IC + F   V L C H FC  C+ +W  R+  CP+CR  +    
Sbjct: 67  CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKT 112

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

 Score = 63.2 bits (154), Expect = 3e-15
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
          C IC D     + L C H FC+ C+ KW DR + CP+CR  +   
Sbjct: 18 CCICMDGRA-DLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGA 61

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

 Score = 63.3 bits (154), Expect = 3e-15
 Identities = 16/40 (40%), Positives = 19/40 (47%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75
          C IC   F+ PV   C H FCESC  + F     C +C  
Sbjct: 18 CFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQ 57

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

 Score = 58.6 bits (142), Expect = 5e-13
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 77
           C IC + F   + +  C H +C  C+ K+   +  CP C  T+
Sbjct: 24 RCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

>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 = 61.7 bits (149), Expect = 5e-13
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 36  CPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATL 77
           C IC +  K      C H+ C SC+T W + E Q CP CR  +
Sbjct: 335 CKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 57.1 bits (138), Expect = 8e-13
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 77
          +C IC         +T C H FC+SC+ + F     CP C   +
Sbjct: 17 LCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

>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 = 57.2 bits (138), Expect = 1e-12
 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 36 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ-TCPLCRATL 77
          C IC ++ +       C  + C SC+ +W   ++  CP CRA L
Sbjct: 25 CFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 56.3 bits (136), Expect = 2e-12
 Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 36 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRA 75
          CPIC ++         C H FC  C+T+W  +  TCPLC+ 
Sbjct: 8  CPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKV 48

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

 Score = 56.1 bits (135), Expect = 2e-12
 Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 7/49 (14%)

Query: 36 CPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          CPIC D +          V   C H+FC  C+        TCP CR  +
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

>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 = 58.1 bits (140), Expect = 2e-12
 Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 36  CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATLVDDPA 82
           C  C +    PV   C H  C+ C+ + F  +  +CP CR  L  +  
Sbjct: 81  CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYI 128

>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 = 56.3 bits (136), Expect = 2e-12
 Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 36 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ--TCPLCRATLVDDPA 82
          C IC D     V + CC + +C+ C+          TCP C    V   A
Sbjct: 18 CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 67

>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 = 56.8 bits (137), Expect = 2e-12
 Identities = 11/44 (25%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 77
          +C +C   F     +  C H FC++C+ ++ +  + CP+C   +
Sbjct: 17 MCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 56.5 bits (136), Expect = 5e-12
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 36  CPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPAWR 84
           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 = 54.5 bits (131), Expect = 9e-12
 Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 7/49 (14%)

Query: 36 CPICHDEFKTPVQ-------LTCCHIFCESCVTKWFDREQTCPLCRATL 77
          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 = 53.6 bits (129), Expect = 2e-11
 Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 7/49 (14%)

Query: 36 CPICHDEFKTPVQ-------LTCCHIFCESCVTKWFDREQTCPLCRATL 77
          CPIC D +   VQ         C H+FC  C+        TCP CR  +
Sbjct: 6  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

>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 = 54.8 bits (132), Expect = 2e-11
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWF-DREQTCPLCRATLVDDPAWRD 85
           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 = 53.2 bits (128), Expect = 3e-11
 Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 27 ETLLGVGCICPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA 82
          E  +G G  CP+C +++    +  QL C H+F +SC+  W ++  +CP+CR +L     
Sbjct: 9  EEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT 67

>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 = 53.6 bits (129), Expect = 4e-11
 Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 3/44 (6%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ---TCPLCRAT 76
          CPIC +  K PV   C HIFC+ C+ K  ++++    CPLC+  
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67

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

 Score = 52.1 bits (125), Expect = 7e-11
 Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWF-DREQTCPLCRATLVDD 80
           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 = 51.7 bits (124), Expect = 2e-10
 Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 3/49 (6%)

Query: 36 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDR--EQTCPLCRATLVDDP 81
          C IC D     V + CC + +C+ C+        E TCP C    V   
Sbjct: 16 CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD 64

>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 = 52.4 bits (125), Expect = 2e-10
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 1/48 (2%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDP 81
          +C  C +  + P Q  C H +C  C+        Q C  C    + + 
Sbjct: 33 LCSACRNVLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEE 80

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

 Score = 50.8 bits (122), Expect = 4e-10
 Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 3/45 (6%)

Query: 36 CPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          CPIC  E+       +L C H F + CV+ W  +  TCP+CR   
Sbjct: 43 CPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF 87

>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 = 51.4 bits (123), Expect = 4e-10
 Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 36 CPICHDEFKTPVQLT-CCHIFCESCVTKWFDREQTCPLCRAT 76
          C  C +  + PV L  C HIFC +CV+        CP+C   
Sbjct: 25 CSRCTNILREPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTP 64

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

 Score = 51.1 bits (122), Expect = 5e-10
 Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)

Query: 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATL 77
          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 = 50.7 bits (121), Expect = 8e-10
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATL 77
           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 = 49.3 bits (118), Expect = 1e-09
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 6/48 (12%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT------CPLCRAT 76
           CPIC +  K PV   C H FC +C+T  ++  +       CP+CR  
Sbjct: 21 TCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVP 68

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

 Score = 48.9 bits (117), Expect = 1e-09
 Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 3/45 (6%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT---CPLCRAT 76
          ICPIC D  + PV + C H FC  C+T+  +       CPLC+ +
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTS 66

>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 = 50.7 bits (121), Expect = 1e-09
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 35  ICPICHDEFKTPVQLTCC-HIFCESCVTK-WFDREQTCPLCRATLV 78
           +CPIC D  K  +    C H FC  C+        + CP CR  LV
Sbjct: 56  MCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLV 101

>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 = 48.8 bits (117), Expect = 1e-09
 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 7/48 (14%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT-------CPLCRAT 76
          CPIC +    P+ L C H  C +C+T       T       CP+C  +
Sbjct: 15 CPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGIS 62

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

 Score = 48.6 bits (116), Expect = 2e-09
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 36 CPICHDEFK---TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81
          C +C ++FK         C H F   C+ KW +  + CPLC   ++   
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA 66

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

 Score = 47.4 bits (113), Expect = 3e-09
 Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 3/40 (7%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75
          C  C  E K P  L C H  C  C+         CP+C+A
Sbjct: 9  CQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQA 45

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

 Score = 48.0 bits (115), Expect = 4e-09
 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 6/48 (12%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT------CPLCRAT 76
           CPIC +    P+ L C H FC++C+T    +         CP+CR +
Sbjct: 21 TCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRIS 68

>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 = 47.3 bits (113), Expect = 4e-09
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 36 CPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          CPIC ++  T       L C H+   +C  +       CPLC    
Sbjct: 8  CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

>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 = 49.3 bits (117), Expect = 7e-09
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRD 85
           CPIC    +  VQ  C H FC++C+ K        CP+    L+++  + D
Sbjct: 20 ECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD 71

>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 = 4e-08
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 5/48 (10%)

Query: 35  ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQT--CPL--CRATL 77
            CPI    ++ P+    C H+F    +  +     T  CP   C   +
Sbjct: 183 TCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVV 230

>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 = 47.8 bits (113), Expect = 5e-08
 Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 1/47 (2%)

Query: 35  ICPICHDEFKTPVQLTCCHIFCE-SCVTKWFDREQTCPLCRATLVDD 80
           + P+ +   K PV L    +  + S +      + T P  R  L  +
Sbjct: 893 LDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLE 939

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

 Score = 45.1 bits (107), Expect = 6e-08
 Identities = 15/46 (32%), Positives = 17/46 (36%), Gaps = 7/46 (15%)

Query: 36 CPICHDEFK----TPVQLTCCHIFCESCVTKWFDREQ---TCPLCR 74
          CPIC + F      P  L C H  C  C+ K          CP C 
Sbjct: 18 CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63

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

 Score = 44.2 bits (105), Expect = 7e-08
 Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 3/42 (7%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLC 73
           C +C +  K PV + C H FC++C+T+W++   R+  CP+C
Sbjct: 17 SCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58

>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 = 44.3 bits (105), Expect = 9e-08
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 36 CPICHDEFKTPV---QLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP 81
          C IC    +      +L C H+F + CV +W    + CP+CR  +    
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQL 65

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

 Score = 43.9 bits (104), Expect = 1e-07
 Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQT---CPLC 73
          ICPIC D  + PV + C H FC  C+T+  +       CPLC
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63

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

 Score = 43.5 bits (103), Expect = 2e-07
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 36 CPICHDEFKTPV---QLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA 82
          C +C  +F++      L C H F   CV KW    +TCP+CRA       
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPSSG 75

>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 = 43.9 bits (104), Expect = 2e-07
 Identities = 11/46 (23%), Positives = 16/46 (34%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
            P+       PV+L    I   S + +      T P  R TL + 
Sbjct: 31 RDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTES 76

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

 Score = 42.7 bits (101), Expect = 3e-07
 Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 77
          +C I     + PV       IF +S + ++       P+    L
Sbjct: 5  LCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL 48

>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 = 3e-07
 Identities = 9/46 (19%), Positives = 15/46 (32%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
            P+       PV+L    +   S + +      T P  R  L + 
Sbjct: 16 RDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTES 61

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

 Score = 42.6 bits (100), Expect = 4e-07
 Identities = 13/48 (27%), Positives = 15/48 (31%), Gaps = 3/48 (6%)

Query: 36 CPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQ--TCPLCRATLVDD 80
          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 = 43.6 bits (102), Expect = 5e-07
 Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 7/49 (14%)

Query: 36 CPICHDEFK-------TPVQLTCCHIFCESCVTKWFDREQTCPLCRATL 77
          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 = 39.0 bits (90), Expect = 3e-05
 Identities = 17/51 (33%), Positives = 21/51 (41%), Gaps = 7/51 (13%)

Query: 34  CICPICHDEFKTPVQ-------LTCCHIFCESCVTKWFDREQTCPLCRATL 77
             CPIC D +   VQ         C H+FC  C+        TCP CR  +
Sbjct: 73  VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123

>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 = 8e-07
 Identities = 15/47 (31%), Positives = 19/47 (40%), Gaps = 4/47 (8%)

Query: 36 CPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV 78
          C  C  E K      V   C H F   C++ W  +   CPLC+   V
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWV 75

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

 Score = 41.0 bits (97), Expect = 1e-06
 Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 36 CPICHDEFKTPVQL----TCCHIFCESCVTKWFDREQTCPLCRATLV 78
          C +C  E +   +      C H F   CV  W     TCPLCR T+V
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>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 = 6e-06
 Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 1/47 (2%)

Query: 35 ICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDD 80
          + PI       PV L +       S + +    +QT P  R+ L  D
Sbjct: 24 LDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD 70

>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 = 39.6 bits (92), Expect = 9e-06
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 15/63 (23%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQ------TCP--------LCRATLVD 79
           CPI  +E K PV+   C H + E  + +  +  Q       CP        + ++ L+ 
Sbjct: 9  TCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQ 68

Query: 80 DPA 82
          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 = 2e-05
 Identities = 15/50 (30%), Positives = 17/50 (34%), Gaps = 3/50 (6%)

Query: 34  CICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDR--EQTCPLCRATLVDD 80
            IC ICH          TC       CV K+F    E  CP C      +
Sbjct: 181 KICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE 230

>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 = 37.2 bits (86), Expect = 4e-05
 Identities = 17/48 (35%), Positives = 17/48 (35%), Gaps = 6/48 (12%)

Query: 36 CPICHDEFKTPVQL-----TCCHIFCESCVTKWFDREQ-TCPLCRATL 77
          CP C         L      C H  CESCV   F R    CP C   L
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

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

 Score = 36.2 bits (83), Expect = 1e-04
 Identities = 15/52 (28%), Positives = 20/52 (38%), Gaps = 5/52 (9%)

Query: 36 CPICHDEF----KTPVQLTCCHIFCESCVTKWFDREQT-CPLCRATLVDDPA 82
          CP+C +            TC +  C  C  +    E   CP CR    +DPA
Sbjct: 14 CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA 65

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

 Score = 36.4 bits (83), Expect = 2e-04
 Identities = 10/64 (15%), Positives = 15/64 (23%), Gaps = 23/64 (35%)

Query: 36 CPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDREQ-----TCPL 72
          C IC ++                          C H F   C+   +          CP 
Sbjct: 28 CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPS 87

Query: 73 CRAT 76
          C+  
Sbjct: 88 CKTI 91

>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 = 36.4 bits (83), Expect = 3e-04
 Identities = 11/36 (30%), Positives = 14/36 (38%)

Query: 39  CHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 74
              E  T     C H F   C+++W    Q CPL  
Sbjct: 72  ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 36.8 bits (84), Expect = 3e-04
 Identities = 12/61 (19%), Positives = 16/61 (26%), Gaps = 19/61 (31%)

Query: 36  CPICHDEF--------KTPVQLTCCHIFCESCVTKWFDREQ-----------TCPLCRAT 76
           C IC             +     C       C+ +WF                CP C+A 
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAK 370

Query: 77  L 77
           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 = 5e-04
 Identities = 11/36 (30%), Positives = 14/36 (38%)

Query: 39 CHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 74
             E  T     C H F   C+++W    Q CPL  
Sbjct: 61 ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 34.5 bits (80), Expect = 6e-04
 Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDD 80
           CPI  +  K PV ++    +  S + KW D   +TCP  + TL+  
Sbjct: 10 RCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA 56

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	95
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.8
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.78
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.77
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.77
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.76
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.76
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.76
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.74
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.74
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.74
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.73
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.73
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.73
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.73
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.72
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.72
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.71
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.7
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.7
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.7
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.7
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.69
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.69
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.69
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.68
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.68
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.67
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.67
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.67
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.66
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.66
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.66
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.65
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.65
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.64
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.64
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.63
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.63
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.63
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.62
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.62
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.61
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.61
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.61
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.6
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.59
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.59
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.58
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.58
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.56
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.56
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.55
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.51
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.47
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.47
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.45
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.45
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.44
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	99.44
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.38
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.35
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.35
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.34
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	99.31
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.29
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.25
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	99.14
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.09
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.87
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.83
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.77
3nw0_A	238	Non-structural maintenance of chromosomes element	98.07
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	98.06
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.49
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.13
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	96.52
3i2d_A	371	E3 SUMO-protein ligase SIZ1; signal transduction,	94.75
4fo9_A	360	E3 SUMO-protein ligase PIAS2; E3 ligase, pinit dom	94.55
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	94.18
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	93.39
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	89.57
1z60_A	59	TFIIH basal transcription factor complex P44 subun	89.49
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	89.18
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	88.65
3mjh_B	34	Early endosome antigen 1; protein-zinc finger comp	88.48
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	88.11
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	87.91
1zbd_B	134	Rabphilin-3A; G protein, effector, RABCDR, synapti	87.8
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	87.78
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	87.13
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	86.93
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	86.89
3mpx_A	434	FYVE, rhogef and PH domain-containing protein 5; s	86.87
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	86.63
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	86.6
2cor_A	79	Pinch protein; LIM domain, particularly interestin	86.1
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	85.71
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	85.03
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	84.61
2zet_C	153	Melanophilin; complex, GTP-binding protein, GTPase	84.49
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	84.48
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	84.44
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	84.26
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	83.99
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	83.82
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	83.68
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	83.25
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	82.8
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	82.78
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	82.51
2co8_A	82	NEDD9 interacting protein with calponin homology a	82.49
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	82.39
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	81.47
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	81.18
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	81.11
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	80.92
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	80.55
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	80.35

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

Probab=99.80  E-value=4.1e-20  Score=100.09  Aligned_cols=66  Identities=23%  Similarity=0.455  Sum_probs=59.0

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      ..+.+.|+||++.+.+|++++|||+||..|+..|+.. ...||.||.++...+..++..+.++++.|
T Consensus         5 ~~~~~~C~IC~~~~~~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n~~l~~~i~~~   71 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLKSLIALW   71 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECTTTHHHHHHH
T ss_pred             CcccCCCCCccccccCCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccCHHHHHHHHHH
Confidence            4567899999999999999999999999999999986 78999999999988888888888877643

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

Probab=99.78  E-value=1.3e-19  Score=100.81  Aligned_cols=70  Identities=21%  Similarity=0.489  Sum_probs=56.1

Q ss_pred             cccccCCCcccccccccCCCCCeecC-CCCcchHHhHHHHhhCC--CCCCCCCccCC-CCccccCCcchhhhhc
Q psy3884          25 TKETLLGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE--QTCPLCRATLV-DDPAWRDGATSYFVQI   94 (95)
Q Consensus        25 ~~~~~~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~-~~~~~~~~~~~~~~q~   94 (95)
                      +..+...+.+.|+||++.+.+|++++ |||+||..|+..|+...  ..||.||.++. .....++..+.++++.
T Consensus         5 ~~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~~~~n~~l~~~i~~   78 (92)
T 3ztg_A            5 SEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVNN   78 (92)
T ss_dssp             SSCCCCCTTTEETTTTEECSSCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSCCTTSCEECHHHHHHHHH
T ss_pred             cccccCCcCCCCCCCChhhcCceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCCCccccCcCHHHHHHHHH
Confidence            34445567889999999999999999 99999999999998743  69999999974 4456666666666553

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

Probab=99.77  E-value=5e-19  Score=96.81  Aligned_cols=68  Identities=26%  Similarity=0.615  Sum_probs=58.2

Q ss_pred             ccccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC------CCCCCCCCccCCCCccccCCcchhhhh
Q psy3884          26 KETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR------EQTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        26 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~------~~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      ..+...+.+.|+||++.+.+|+.++|||+||..|+..|+..      ...||.||.++...+...+..+.++++
T Consensus        12 ~~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~l~~~ve   85 (85)
T 2ecw_A           12 VLEMIKEEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNLHVANIVE   85 (85)
T ss_dssp             CCCCCCTTTSCTTTCSCCSSCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEECSCCCSSCC
T ss_pred             HHHhCccCCCCcCCChhhCcceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCcCHHHHHhhC
Confidence            33445678899999999999999999999999999999986      679999999999888777777776653

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

Probab=99.77  E-value=1.3e-19  Score=98.14  Aligned_cols=66  Identities=23%  Similarity=0.565  Sum_probs=56.7

Q ss_pred             ccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC-------CCCCCCCCccCCCCccccCCcchhhhh
Q psy3884          28 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-------EQTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-------~~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      +...+.+.|+||++.+.+|+.++|||+||..|+..|+..       ...||.||.++...++..+..+.++++
T Consensus         7 ~~~~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~lve   79 (79)
T 2egp_A            7 GNVQEEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQANQHLANIVE   79 (79)
T ss_dssp             CCCCCCCEETTTTEECSSCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGTCSSSCCCCC
T ss_pred             hhcccCCCCcCCCcccCCeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCcCHHHHHhhC
Confidence            334567899999999999999999999999999999986       568999999999888777777776653

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

Probab=99.76  E-value=7.1e-19  Score=96.19  Aligned_cols=67  Identities=27%  Similarity=0.674  Sum_probs=58.0

Q ss_pred             cccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC------CCCCCCCCccCCCCccccCCcchhhhh
Q psy3884          27 ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR------EQTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~------~~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      .+...+.+.|+||++.+.+|+.++|||+||..|+..|+..      ...||.||..+...++.++..+.++++
T Consensus        13 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n~~l~~~ve   85 (85)
T 2ecv_A           13 LVNVKEEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNRHVANIVE   85 (85)
T ss_dssp             CCCCCCCCCCTTTCSCCSSCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCSCCCCCCCC
T ss_pred             HHHccCCCCCCCCCcccCCceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCccHHHHHhhC
Confidence            3445677899999999999999999999999999999876      689999999999888888877776653

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

Probab=99.76  E-value=1.4e-18  Score=92.81  Aligned_cols=60  Identities=23%  Similarity=0.604  Sum_probs=51.6

Q ss_pred             ccccCCCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884          26 KETLLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   85 (95)
Q Consensus        26 ~~~~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   85 (95)
                      ..+...+.+.|+||++.+.+|+.+ +|||+||..|+..|+.....||+||.++...+...+
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   68 (72)
T 2djb_A            8 NLSELTPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSG   68 (72)
T ss_dssp             CCCCCCGGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCC
T ss_pred             hHhhcCCCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccccc
Confidence            334456778999999999999987 999999999999999988999999999987765443

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

Probab=99.76  E-value=3.8e-19  Score=97.95  Aligned_cols=66  Identities=15%  Similarity=0.077  Sum_probs=59.5

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      ...+.+.||||++.+.+|++++|||+||..||..|+.....||.|+.++...+..++..+.+.++.
T Consensus        10 ~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn~~L~~~i~~   75 (85)
T 2kr4_A           10 DAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPVPELKEQIQA   75 (85)
T ss_dssp             TCCTTTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHHHH
T ss_pred             cCchheECcccCchhcCCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchHHHHHHHHHH
Confidence            446788999999999999999999999999999999988999999999998888888888777764

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

Probab=99.74  E-value=3.2e-18  Score=89.93  Aligned_cols=54  Identities=30%  Similarity=0.677  Sum_probs=47.7

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCcc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPA   82 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~   82 (95)
                      ...+.+.|+||++.+.+|+.++|||+||..|+..|+. ....||+||.++..+++
T Consensus        11 ~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~i   65 (66)
T 2ecy_A           11 TVEDKYKCEKCHLVLCSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDKV   65 (66)
T ss_dssp             SCCCCEECTTTCCEESSCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTTC
T ss_pred             cCCcCCCCCCCChHhcCeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhhc
Confidence            3456789999999999999999999999999999995 56799999999987654

>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=99.74  E-value=2.1e-18  Score=97.28  Aligned_cols=66  Identities=20%  Similarity=0.133  Sum_probs=59.8

Q ss_pred             cCCCcccccccccCCCCCeecCCC-CcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~Cg-H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      ...+++.||||++.+.+|++++|| |+||..||..|+.....||.|+.++...++.++..+.+.++.
T Consensus        18 ~~p~~~~CpI~~~~m~dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn~~Lk~~I~~   84 (98)
T 1wgm_A           18 DACDEFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNTELKEKIQR   84 (98)
T ss_dssp             SCCTTTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECHHHHHHHHH
T ss_pred             cCcHhcCCcCccccccCCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEcHHHHHHHHH
Confidence            346789999999999999999999 999999999999988899999999998888888888777764

>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=99.74  E-value=1.7e-18  Score=97.95  Aligned_cols=66  Identities=18%  Similarity=0.097  Sum_probs=59.9

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      ...+.+.||||++.+.+|++++|||+||..||..|+.....||.|+.++...+..++..+.+.++.
T Consensus        25 ~~p~~~~CpI~~~~m~dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn~~Lk~~I~~   90 (100)
T 2kre_A           25 DAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVPELKEQIQA   90 (100)
T ss_dssp             SCSTTTBCTTTCSBCSSEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEECHHHHHHHHH
T ss_pred             cCcHhhCCcCccCcccCCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceECHHHHHHHHH
Confidence            346788999999999999999999999999999999988999999999998888888888777764

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

Probab=99.73  E-value=3.8e-18  Score=91.60  Aligned_cols=57  Identities=25%  Similarity=0.627  Sum_probs=48.2

Q ss_pred             ccccCCCcccccccccCCCCCeecC-CCCcchHHhHHHHhhCC--CCCCCCCccCCCCcc
Q psy3884          26 KETLLGVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE--QTCPLCRATLVDDPA   82 (95)
Q Consensus        26 ~~~~~~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~~   82 (95)
                      ..+...+.+.|+||++.+.+|++++ |||+||..|+..|+...  ..||+||+++...+.
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A            8 EDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             CCCCSCGGGSCSSSCCCCTTCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             ccccCCCCCCCcCCChHHhCCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            3344567789999999999999999 99999999999999854  699999998665443

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

Probab=99.73  E-value=3e-18  Score=93.33  Aligned_cols=52  Identities=31%  Similarity=0.685  Sum_probs=47.1

Q ss_pred             cccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          27 ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .+.....+.|+||++.+.+|++++|||+||..|+..|+.....||+||.++.
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A            9 SEEEEIPFRCFICRQAFQNPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SSCCCCCSBCSSSCSBCCSEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             cccCCCCCCCcCCCchhcCeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            3444567899999999999999999999999999999998899999999986

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

Probab=99.73  E-value=4.1e-19  Score=100.09  Aligned_cols=64  Identities=22%  Similarity=0.559  Sum_probs=55.7

Q ss_pred             CCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          31 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      .+.+.|+||++.+.+|+.+ +|||+||..|+..|+.....||.||..+...+...+..+.++++.
T Consensus        20 ~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~~i~~   84 (99)
T 2y43_A           20 DDLLRCGICFEYFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNNRILDELVKS   84 (99)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECHHHHHHHHH
T ss_pred             CCCCCcccCChhhCCcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCCcCHHHHHHHHH
Confidence            4567999999999999888 899999999999999988999999999987777777767666653

>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=99.73  E-value=8.6e-19  Score=99.10  Aligned_cols=64  Identities=23%  Similarity=0.531  Sum_probs=55.1

Q ss_pred             CCCcccccccccCCCCCee-cCCCCcchHHhHHHHhhCC-CCCCCCCccCCCCccccCCcchhhhh
Q psy3884          30 LGVGCICPICHDEFKTPVQ-LTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~-~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      ..+.+.|+||++.+.+|+. ++|||+||..||..|+... ..||.||.++...++..+..+..+++
T Consensus        19 l~~~~~C~IC~~~~~~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~i~~   84 (100)
T 3lrq_A           19 IAEVFRCFICMEKLRDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRWAEEVTQ   84 (100)
T ss_dssp             HHHHTBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECTTHHHHHH
T ss_pred             CCCCCCCccCCccccCccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHhHhhHHHHHHHH
Confidence            3456799999999999999 9999999999999999977 69999999998777777666665554

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

Probab=99.72  E-value=2.7e-18  Score=91.44  Aligned_cols=52  Identities=33%  Similarity=0.587  Sum_probs=47.0

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ..+...|+||++.+.+|+.++|||.||..|+..|+.....||+||..+...+
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   63 (71)
T 2d8t_A           12 SLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPEDF   63 (71)
T ss_dssp             SSSCCBCSSSSSBCSSEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCHHH
T ss_pred             CCCCCCCccCCcccCCCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCHhh
Confidence            3566799999999999999999999999999999998899999999987543

>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=99.72  E-value=2.3e-18  Score=100.56  Aligned_cols=63  Identities=21%  Similarity=0.479  Sum_probs=53.0

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCC-CccccCCcchhhhh
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVD-DPAWRDGATSYFVQ   93 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~-~~~~~~~~~~~~~q   93 (95)
                      .+.+.|+||++.+.+|+.++|||+||..|+..|+... ..||.||.++.. .....+..+.++++
T Consensus        50 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~n~~l~~~i~  114 (124)
T 3fl2_A           50 EETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQTVLN  114 (124)
T ss_dssp             HHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTCCCCCCHHHHHHHH
T ss_pred             ccCCCCCcCChHHcCcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCCCCCCCCCHHHHHHHH
Confidence            4567999999999999999999999999999999854 499999999987 45556666666554

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

Probab=99.71  E-value=1.7e-17  Score=88.51  Aligned_cols=54  Identities=35%  Similarity=0.817  Sum_probs=47.3

Q ss_pred             ccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhh---CCCCCCCCCccCCCCc
Q psy3884          28 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLCRATLVDDP   81 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~---~~~~CP~Cr~~~~~~~   81 (95)
                      +...+.+.|+||++.+.+|+.++|||+||..|+..|+.   ....||+||.++..++
T Consensus        15 ~~~~~~~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           15 NKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCCCBCTTTCSBCSSEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             HhCccCCEeccCCcccCCeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            34456789999999999999999999999999999997   4568999999988654

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

Probab=99.70  E-value=5e-18  Score=90.13  Aligned_cols=53  Identities=30%  Similarity=0.762  Sum_probs=47.1

Q ss_pred             CCcccccccccCCCCC-------eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884          31 GVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   83 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   83 (95)
                      .+...|+||++.+.+|       +.++|||+||..|+..|+.....||+||.++...++.
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhhee
Confidence            4567999999999887       8889999999999999999999999999999876543

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

Probab=99.70  E-value=2.1e-17  Score=89.26  Aligned_cols=60  Identities=32%  Similarity=0.918  Sum_probs=49.9

Q ss_pred             ccccCCCcccccccccCCCCC---eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884          26 KETLLGVGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   85 (95)
Q Consensus        26 ~~~~~~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   85 (95)
                      ..+.......|+||++.+..+   +.++|||.||..|+..|+.....||+||..+...+...+
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   70 (78)
T 2ect_A            8 TEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN   70 (78)
T ss_dssp             CCTTSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCC
T ss_pred             CcccCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCC
Confidence            344455678999999999865   456999999999999999988999999999987765543

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

Probab=99.70  E-value=2.4e-18  Score=102.22  Aligned_cols=50  Identities=34%  Similarity=0.928  Sum_probs=45.9

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      .+++.|+||++.+.+|++++|||+||..|+..|+.....||+||.++...
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            34568999999999999999999999999999999999999999998754

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

Probab=99.70  E-value=8.2e-18  Score=88.74  Aligned_cols=52  Identities=31%  Similarity=0.761  Sum_probs=45.9

Q ss_pred             ccCCCcccccccccCCCCC-------eecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          28 TLLGVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      ....+...|+||++.+.++       +.++|||.||..|+..|+.....||+||.++..
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           10 LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cCCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            3445678999999999876       788999999999999999998999999998864

>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=99.69  E-value=6.8e-18  Score=96.45  Aligned_cols=63  Identities=22%  Similarity=0.666  Sum_probs=52.0

Q ss_pred             CCCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCC----ccccCCcchhhh
Q psy3884          30 LGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDD----PAWRDGATSYFV   92 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~----~~~~~~~~~~~~   92 (95)
                      ..+.+.|+||++.+.+|+.+ +|||+||..|+..|+.....||.||..+...    ....+..+.+++
T Consensus        12 ~~~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~l~~n~~l~~~i   79 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIV   79 (108)
T ss_dssp             HGGGTBCTTTSSBCSSEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSSCGGGGEEECHHHHHHH
T ss_pred             cCCcCCCccCChHHhCcCEeCCCCChhhHHHHHHHHHhCCcCcCCCccccccCcccccCcCHHHHHHH
Confidence            35678999999999999987 9999999999999999989999999998865    333444444444

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

Probab=99.69  E-value=3.4e-17  Score=90.10  Aligned_cols=55  Identities=29%  Similarity=0.662  Sum_probs=47.7

Q ss_pred             cccCCCcccccccccCCCC----CeecCCCCcchHHhHHHHhhCC---CCCCCCCccCCCCc
Q psy3884          27 ETLLGVGCICPICHDEFKT----PVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDDP   81 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~   81 (95)
                      .+...+.+.|+||++.+.+    |+.++|||+||..|+..|+...   ..||.||..+...+
T Consensus         9 ~~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A            9 LDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CCCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             hhhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            3445667899999999998    8999999999999999999865   79999999987654

>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=99.69  E-value=2e-17  Score=94.79  Aligned_cols=62  Identities=32%  Similarity=0.720  Sum_probs=53.2

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhhCC---CCCCCCCccCCCCccccCCcchhhhh
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      +.+.|+||++.+.+|+.++|||+||..|+..|+...   ..||.||.++...+...+..+.++++
T Consensus        20 ~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~~~~l~~~~~   84 (112)
T 1jm7_A           20 KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVE   84 (112)
T ss_dssp             HHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCCSSSHHHH
T ss_pred             CCCCCcccChhhcCeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCccHHHHHHHH
Confidence            356999999999999999999999999999999865   48999999999887777766666554

>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=99.68  E-value=1.2e-17  Score=96.79  Aligned_cols=67  Identities=25%  Similarity=0.567  Sum_probs=55.8

Q ss_pred             cccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCC-CCCCCCccCCCCccccCCcchhhhh
Q psy3884          27 ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      .+...+.+.|+||++.+.+|+.++|||+||..|+..|+.... .||+||.++...+..++..+...++
T Consensus        12 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~l~~~i~   79 (118)
T 3hct_A           12 DPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREIL   79 (118)
T ss_dssp             SSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHHH
T ss_pred             ccCCCCCCCCCcCChhhcCeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhcccCHHHHHHHc
Confidence            344566789999999999999999999999999999998664 9999999998877766665555443

>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=99.68  E-value=1.3e-17  Score=100.40  Aligned_cols=64  Identities=22%  Similarity=0.591  Sum_probs=53.8

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCC-CCCCCCccCCCC-ccccCCcchhhhhc
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATLVDD-PAWRDGATSYFVQI   94 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~~~-~~~~~~~~~~~~q~   94 (95)
                      .+.+.|+||++.+.+|++++|||+||..|+..|+.... .||+||.++... ....+..+.++++.
T Consensus        76 ~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~l~~n~~l~~lv~~  141 (150)
T 1z6u_A           76 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIMIPNEILQTLLDL  141 (150)
T ss_dssp             HHHTBCTTTSSBCSSEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTTCCCCBCHHHHHHHHH
T ss_pred             ccCCEeecCChhhcCCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCCCCCCCCHHHHHHHHH
Confidence            45679999999999999999999999999999998654 899999999877 55566666666553

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

Probab=99.67  E-value=5.9e-17  Score=90.08  Aligned_cols=49  Identities=37%  Similarity=0.981  Sum_probs=43.8

Q ss_pred             CCcccccccccCCCC---CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          31 GVGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      .....|+||++.+..   ++.++|||.||..|+..|+..+..||+||.++..
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            456799999999887   6778999999999999999999999999998864

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

Probab=99.67  E-value=1.8e-17  Score=86.25  Aligned_cols=52  Identities=31%  Similarity=0.781  Sum_probs=46.0

Q ss_pred             CcccccccccCCCCC-------eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884          32 VGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   83 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   83 (95)
                      +...|+||++.+.++       +.++|||.||..|+.+|+..+..||+||.++...+..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   60 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   60 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCEE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCcccee
Confidence            456999999999876       7889999999999999999999999999999876543

>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=99.67  E-value=1.1e-16  Score=84.64  Aligned_cols=52  Identities=27%  Similarity=0.725  Sum_probs=44.3

Q ss_pred             cCCCcccccccccCCCC---CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          29 LLGVGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      .......|+||++.+..   ++.++|||.||..|+..|+..+..||+||..+...
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            34456799999998853   46789999999999999999889999999988754

>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=99.66  E-value=4.2e-17  Score=105.65  Aligned_cols=66  Identities=11%  Similarity=0.089  Sum_probs=57.6

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      .....+.||||++.+.+|++++|||+||..||..|+..+ ..||.|+.++...+..++..+...++.
T Consensus       204 ~~~~~~~c~i~~~~~~dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n~~l~~~i~~  270 (281)
T 2c2l_A          204 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDA  270 (281)
T ss_dssp             CCCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHHHHHHHHH
T ss_pred             CCCcccCCcCcCCHhcCCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCcccHHHHHHHHH
Confidence            345678999999999999999999999999999999854 459999999988888888888777764

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

Probab=99.66  E-value=1.8e-16  Score=82.39  Aligned_cols=46  Identities=41%  Similarity=0.904  Sum_probs=40.9

Q ss_pred             ccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhh---CCCCCCCC
Q psy3884          28 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLC   73 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~---~~~~CP~C   73 (95)
                      +...+.+.|+||++.+.+|++++|||+||..|+..|+.   ....||+|
T Consensus        15 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           15 NKLQEEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCCCBCTTTCSBCSSCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             HhCccCCCCCcCCchhCCeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            34567789999999999999999999999999999998   45689988

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

Probab=99.66  E-value=8.8e-17  Score=81.42  Aligned_cols=48  Identities=40%  Similarity=0.884  Sum_probs=42.5

Q ss_pred             CCcccccccccCCCC---CeecC-CCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          31 GVGCICPICHDEFKT---PVQLT-CCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~---p~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      .+...|+||++.+.+   ++.++ |||.||..|+.+|+..+..||+||+++.
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            356699999999987   67776 9999999999999999999999998874

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

Probab=99.65  E-value=1.6e-16  Score=84.96  Aligned_cols=54  Identities=28%  Similarity=0.769  Sum_probs=45.4

Q ss_pred             cCCCcccccccccCCCCCe---ecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCcc
Q psy3884          29 LLGVGCICPICHDEFKTPV---QLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   82 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~---~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   82 (95)
                      .......|+||++.+..+.   .++|||.||..|+..|+.....||+||.++.....
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2ep4_A           11 ELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQ   67 (74)
T ss_dssp             CCCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCS
T ss_pred             cCCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccccc
Confidence            3455679999999998763   44999999999999999988899999999876543

>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=99.65  E-value=8.9e-18  Score=96.90  Aligned_cols=50  Identities=30%  Similarity=0.803  Sum_probs=44.7

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC-CCCCCCCCccCCC
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVD   79 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~   79 (95)
                      ..+++.|+||++.+.+|++++|||+||..|+..|+.. ...||.||..+..
T Consensus        12 ~~~~~~C~iC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           12 SLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CHHHHBCTTTCSBCSSCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCCccCCcccCceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            3456799999999999999999999999999999976 5789999999864

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

Probab=99.64  E-value=2.6e-16  Score=80.38  Aligned_cols=47  Identities=38%  Similarity=1.070  Sum_probs=40.6

Q ss_pred             cccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhh---CCCCCCCC
Q psy3884          27 ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD---REQTCPLC   73 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~---~~~~CP~C   73 (95)
                      .+...+.+.|+||++.+.+|+.++|||+||..|+..|+.   ....||+|
T Consensus         9 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A            9 LENLQVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SSCSCCCCBCSSSCCBCSSCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             hhccccCCCCccCCcccCccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            344556789999999999999999999999999999954   55789987

>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=99.64  E-value=2.3e-17  Score=95.52  Aligned_cols=61  Identities=26%  Similarity=0.558  Sum_probs=53.0

Q ss_pred             CCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhh
Q psy3884          31 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      .+.+.|+||++.+.+|+++ +|||+||..|+..|+.  ..||+||.++...+...+..+.++++
T Consensus        20 ~~~~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~n~~l~~l~~   81 (117)
T 1jm7_B           20 EKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINRQLDSMIQ   81 (117)
T ss_dssp             HHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCCHHHHHHHH
T ss_pred             hhCCCCCCCChHhhCccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCccccccccHHHHHHHH
Confidence            4567999999999999999 9999999999999987  78999999998777777766666655

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

Probab=99.63  E-value=7.5e-17  Score=85.44  Aligned_cols=52  Identities=37%  Similarity=0.864  Sum_probs=46.3

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ...+...|+||++.+.+ +.++|||.||..|+..|+.....||+||.++...+
T Consensus        11 ~~~~~~~C~IC~~~~~~-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           11 QLTDEEECCICMDGRAD-LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCCCSSSCCSCCS-EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             cCCCCCCCeeCCcCccC-cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            34567799999999999 89999999999999999999999999999987653

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=99.63  E-value=1.7e-16  Score=80.29  Aligned_cols=47  Identities=28%  Similarity=0.704  Sum_probs=41.9

Q ss_pred             CcccccccccCCCC----CeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      +...|+||++.+.+    ++.++|||.||..|+.+|+.....||+||.++.
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            45699999999865    678899999999999999998899999999875

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

Probab=99.63  E-value=1.1e-16  Score=85.86  Aligned_cols=50  Identities=34%  Similarity=0.830  Sum_probs=44.4

Q ss_pred             CCcccccccccCCCCC---eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          31 GVGCICPICHDEFKTP---VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p---~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      .+...|+||++.+..+   +.++|||.||..|+..|+..+..||+||+++...
T Consensus        21 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A           21 SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             SSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             CCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            3567999999999877   6789999999999999999999999999988753

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

Probab=99.62  E-value=1.9e-16  Score=83.37  Aligned_cols=48  Identities=38%  Similarity=0.993  Sum_probs=43.6

Q ss_pred             CcccccccccCCCCC-eecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          32 VGCICPICHDEFKTP-VQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p-~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      ....|+||++.+.++ +.++|||.||..|+..|+..+..||.||.++..
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            456999999999987 788999999999999999988999999999864

>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=99.62  E-value=8.3e-17  Score=90.03  Aligned_cols=64  Identities=27%  Similarity=0.571  Sum_probs=54.5

Q ss_pred             CCcccccccccCCCCCeecC-CCCcchHHhHHHHhhCC------CCCCC--CCcc-CCCCccccCCcchhhhhc
Q psy3884          31 GVGCICPICHDEFKTPVQLT-CCHIFCESCVTKWFDRE------QTCPL--CRAT-LVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~-CgH~fc~~Ci~~~~~~~------~~CP~--Cr~~-~~~~~~~~~~~~~~~~q~   94 (95)
                      ...+.||||++.|.+|++++ |||+||..||..|+...      ..||+  |+.. +...++.++..+...++.
T Consensus         5 ~~~~~CPI~~~~~~dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~pn~~L~~~I~~   78 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQDEALRRAIEN   78 (94)
T ss_dssp             SSCCBCTTTCSBCSSEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEECHHHHHHHHH
T ss_pred             CcEeECcCcCchhcCCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcCCHHHHHHHHH
Confidence            45789999999999999996 99999999999999753      58999  8877 777788888777777653

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

Probab=99.61  E-value=6.1e-16  Score=95.31  Aligned_cols=66  Identities=12%  Similarity=0.098  Sum_probs=57.9

Q ss_pred             cCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      ..++.+.||||++.+.+|++++|||+||..||..|+..+ ..||.|+.++...+..++..+.+.++.
T Consensus       102 ~ip~~f~CPI~~elm~DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN~~Lk~~Ie~  168 (179)
T 2f42_A          102 EIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMKEVIDA  168 (179)
T ss_dssp             CCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECHHHHHHHHH
T ss_pred             CCcHhhcccCccccCCCCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcchHHHHHHHHH
Confidence            446788999999999999999999999999999999864 469999999988888888888777764

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

Probab=99.61  E-value=4.2e-16  Score=81.49  Aligned_cols=52  Identities=33%  Similarity=0.728  Sum_probs=43.5

Q ss_pred             Cccccccccc-CCCCC----eecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCCccc
Q psy3884          32 VGCICPICHD-EFKTP----VQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAW   83 (95)
Q Consensus        32 ~~~~C~IC~~-~~~~p----~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~   83 (95)
                      ++..|+||++ .+.+|    +.++|||+||..|+.+|+.. ...||.||.++..+++.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   59 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFR   59 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCE
T ss_pred             CCCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccce
Confidence            3568999999 88887    46799999999999999764 46899999999876543

>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=99.61  E-value=9.4e-17  Score=97.76  Aligned_cols=62  Identities=29%  Similarity=0.693  Sum_probs=49.6

Q ss_pred             CCcccccccccCCCCCeec-CCCCcchHHhHHHHhhC-CCCCCCCCccCCCC-ccccCCcchhhh
Q psy3884          31 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDR-EQTCPLCRATLVDD-PAWRDGATSYFV   92 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~-~~~~~~~~~~~~   92 (95)
                      .+.+.|+||++.+.+|+.+ +|||+||..|+..|+.. ...||+||.++... ...++..+..++
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            3456999999999999987 99999999999999997 67899999998644 333444444443

>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=9.3e-16  Score=88.16  Aligned_cols=57  Identities=21%  Similarity=0.470  Sum_probs=44.8

Q ss_pred             cccccccccCCCCCe------------------ecCCCCcchHHhHHHHh-----hCCCCCCCCCccCCCC-ccccCCcc
Q psy3884          33 GCICPICHDEFKTPV------------------QLTCCHIFCESCVTKWF-----DREQTCPLCRATLVDD-PAWRDGAT   88 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~------------------~~~CgH~fc~~Ci~~~~-----~~~~~CP~Cr~~~~~~-~~~~~~~~   88 (95)
                      +..|+||++.+..+.                  .++|||.||..||..|+     .....||+||..+... ...+.+.+
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g~qp~g~m  104 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPWGKM  104 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSSSCTTSSC
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCCCCCCCeE
Confidence            459999999987653                  67999999999999999     4567999999998755 33445544


Q ss_pred             h
Q psy3884          89 S   89 (95)
Q Consensus        89 ~   89 (95)
                      +
T Consensus       105 ~  105 (114)
T 1v87_A          105 E  105 (114)
T ss_dssp             C
T ss_pred             E
Confidence            3

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

Probab=99.59  E-value=9.7e-16  Score=83.49  Aligned_cols=49  Identities=29%  Similarity=0.710  Sum_probs=41.5

Q ss_pred             CcccccccccCCCC--------------Ceec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          32 VGCICPICHDEFKT--------------PVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        32 ~~~~C~IC~~~~~~--------------p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ++..|+||++.+.+              ++.+ +|||.||..||.+|+..+.+||+||+++...
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            45689999998865              3455 5999999999999999999999999988644

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

Probab=99.59  E-value=4.1e-16  Score=91.28  Aligned_cols=52  Identities=31%  Similarity=0.782  Sum_probs=47.1

Q ss_pred             CCcccccccccCCCCC-------eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCcc
Q psy3884          31 GVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   82 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   82 (95)
                      .+.+.|+||++.+.+|       +.++|||+||..|+.+|+.....||+||+.+...+.
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            4567999999999888       899999999999999999999999999999987654

>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=99.58  E-value=3.3e-16  Score=90.39  Aligned_cols=53  Identities=26%  Similarity=0.644  Sum_probs=47.2

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCCccc
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAW   83 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~   83 (95)
                      .+.+.|+||++.+.+|+.++|||+||..|+..|+.. ...||+||.++...+..
T Consensus        21 ~~~~~C~IC~~~~~~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~   74 (116)
T 1rmd_A           21 VKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (116)
T ss_dssp             HHHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             cCCCCCCCCCcHhcCcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhcc
Confidence            456799999999999999999999999999999986 67999999998876543

>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=99.58  E-value=5.6e-16  Score=94.69  Aligned_cols=66  Identities=26%  Similarity=0.595  Sum_probs=54.6

Q ss_pred             cccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCCCccccCCcchhhh
Q psy3884          27 ETLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFV   92 (95)
Q Consensus        27 ~~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~~~~~~~   92 (95)
                      .+...+.+.|+||++.+.+|+.++|||+||..|+..|+... ..||.||.++...+.+++..+...+
T Consensus        12 ~~~~~~~~~C~IC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~i   78 (170)
T 3hcs_A           12 DPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREI   78 (170)
T ss_dssp             SSCCCGGGBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEECHHHHHHH
T ss_pred             ccCCCCCCCCCCCChhhcCcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhhhHHHHHHH
Confidence            34456778999999999999999999999999999999754 4999999999887766665554433

>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=99.56  E-value=4.1e-16  Score=92.97  Aligned_cols=51  Identities=24%  Similarity=0.661  Sum_probs=45.2

Q ss_pred             ccCCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCC-CCCCCCccCC
Q psy3884          28 TLLGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATLV   78 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~-~CP~Cr~~~~   78 (95)
                      +...+.+.|+||++.+.+|+.++|||+||..||..|+.... .||.||.++.
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            34567889999999999999999999999999999998654 8999999764

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

Probab=99.56  E-value=1e-15  Score=77.98  Aligned_cols=48  Identities=29%  Similarity=0.625  Sum_probs=41.8

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      .+.+.|+||++.+.+|+.++|||+||..|+..   ....||+||+.+...+
T Consensus         4 ~~~~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~---~~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEA---SGMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBCCSCSTTSCCSBTTTCSS---SSSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCCeEEcCCCCcccHHHHcc---CCCCCCcCCcEeecCC
Confidence            35679999999999999999999999999876   3568999999987654

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

Probab=99.55  E-value=8.6e-15  Score=79.23  Aligned_cols=54  Identities=24%  Similarity=0.554  Sum_probs=43.1

Q ss_pred             CCCcccccccccCCC--CCeecC--CCCcchHHhHHHHhh-CCCCCCCCCccCCCCccc
Q psy3884          30 LGVGCICPICHDEFK--TPVQLT--CCHIFCESCVTKWFD-REQTCPLCRATLVDDPAW   83 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~--~p~~~~--CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~~   83 (95)
                      ..+++.|+||++.+.  ++..++  |||.||..|+..++. ....||.||+++...+..
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             cccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            456789999999885  345555  999999999999875 457899999999876543

>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=82.36  Aligned_cols=47  Identities=28%  Similarity=0.615  Sum_probs=41.3

Q ss_pred             CcccccccccCCCCC------------------eecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p------------------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ....|+||++.+..+                  +.++|||.||..||..|+..+.+||+||+++.
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                  34699999999999999999999999999865

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

Probab=99.47  E-value=7.1e-15  Score=85.97  Aligned_cols=53  Identities=30%  Similarity=0.740  Sum_probs=46.9

Q ss_pred             CCCcccccccccCCCCC-------eecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCcc
Q psy3884          30 LGVGCICPICHDEFKTP-------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPA   82 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p-------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   82 (95)
                      ..+...|+||++.+.++       +.++|||.||..|+.+|+.....||+||.++..+++
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            35677999999998876       788999999999999999999999999999987654

>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=99.47  E-value=3e-14  Score=74.38  Aligned_cols=47  Identities=28%  Similarity=0.605  Sum_probs=42.7

Q ss_pred             CcccccccccCCCCCeec--CCCCc-chHHhHHHHhhCCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKTPVQL--TCCHI-FCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~--~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ++..|+||++...+++.+  ||||. ||..|+..|...+..||+||+++.
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            455899999999999877  99999 899999999998899999999885

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

Probab=99.45  E-value=1.7e-14  Score=77.32  Aligned_cols=45  Identities=27%  Similarity=0.674  Sum_probs=40.6

Q ss_pred             CCcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      .+...|+||++.+.+++.++|||. ||..|+..|    ..||+||.++..
T Consensus        22 ~~~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           22 QEEKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHHTBCTTTSSSBCCEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             ccCCCCCCCCCCCCCEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            456799999999999999999999 999999887    789999998864

>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=99.45  E-value=3.7e-14  Score=73.81  Aligned_cols=46  Identities=17%  Similarity=0.525  Sum_probs=42.0

Q ss_pred             cccccccccCCCCCeec--CCCCc-chHHhHHHHhhCCCCCCCCCccCC
Q psy3884          33 GCICPICHDEFKTPVQL--TCCHI-FCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~--~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ...|+||++...+++.+  ||||. ||..|+..|...+..||+||+++.
T Consensus         7 ~~~C~IC~~~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSBSCEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CCCCcccCCcCCCeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            45899999999998877  99998 999999999988889999999885

>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=5.6e-14  Score=95.15  Aligned_cols=50  Identities=32%  Similarity=0.789  Sum_probs=45.3

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDP   81 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~   81 (95)
                      ....|+||++.+.+|+.++|||.||..|+..|+. ....||+||.++....
T Consensus       331 ~~~~C~ICle~~~~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          331 TFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSSBCTTTSSSBCCEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCCccCcCCCCeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            3469999999999999999999999999999998 7789999999987653

>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=99.44  E-value=1.9e-14  Score=92.81  Aligned_cols=64  Identities=20%  Similarity=0.482  Sum_probs=55.6

Q ss_pred             CCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCC--CCCCC--CCccCCCCccccCCcchhhhhc
Q psy3884          31 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDRE--QTCPL--CRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~--~~CP~--Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      ...+.||||++.|.+|++. .|||+||..||..|+..+  ..||+  |++.+...+..++..+.+++++
T Consensus       179 ~~el~CPIcl~~f~DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN~~L~~lve~  247 (267)
T 3htk_C          179 KIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPIMELRCKI  247 (267)
T ss_dssp             BCCSBCTTTSSBCSSEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEECHHHHHHHHH
T ss_pred             ceeeECcCccCcccCCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcCHHHHHHHHH
Confidence            4678999999999999985 999999999999999754  57999  9999988888888887777654

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

Probab=99.38  E-value=1.7e-13  Score=73.49  Aligned_cols=45  Identities=27%  Similarity=0.690  Sum_probs=39.6

Q ss_pred             CcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      +...|+||++.+.+++.++|||. ||..|+..    ...||+||.++...
T Consensus        24 ~~~~C~IC~~~~~~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           24 EEKLCKICMDRNIAIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHHSCSSSCSSCCCBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCCcCCCCCCCEEEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            45689999999999999999999 99999964    37899999998754

>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=99.35  E-value=8.1e-14  Score=80.58  Aligned_cols=48  Identities=27%  Similarity=0.571  Sum_probs=0.9

Q ss_pred             CcccccccccCCCCC------------------eecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          32 VGCICPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p------------------~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      ....|+||++.+..+                  +.++|+|.||..||.+|+..+.+||+||+++..
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            446999999998763                  124899999999999999999999999998653

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

Probab=99.35  E-value=8.9e-13  Score=69.51  Aligned_cols=47  Identities=30%  Similarity=0.671  Sum_probs=40.9

Q ss_pred             CCCcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ..+...|+||++...+++.+||||. ||..|+..    ...||+||.++...
T Consensus        12 ~~~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCCSSCCSSSSSSCCCCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCCCcCcCCCCEEEECCCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            3456799999999999999999999 99999974    47899999998754

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

Probab=99.34  E-value=1.1e-12  Score=71.23  Aligned_cols=51  Identities=27%  Similarity=0.764  Sum_probs=42.2

Q ss_pred             CCcccccccccCCC--CCeecCCC-----CcchHHhHHHHhhCC--CCCCCCCccCCCCc
Q psy3884          31 GVGCICPICHDEFK--TPVQLTCC-----HIFCESCVTKWFDRE--QTCPLCRATLVDDP   81 (95)
Q Consensus        31 ~~~~~C~IC~~~~~--~p~~~~Cg-----H~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~~   81 (95)
                      .+...|+||++.+.  ++.++||+     |.||..||.+|+..+  ..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            34569999998874  46788996     999999999999865  58999999987553

>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=99.31  E-value=6.4e-13  Score=68.68  Aligned_cols=55  Identities=16%  Similarity=0.201  Sum_probs=48.6

Q ss_pred             cccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCc
Q psy3884          33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGA   87 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~   87 (95)
                      .+.|+|+++.+.+|+++ ++||+|++.||.+|+..+..||+.+.++...++.++..
T Consensus         3 ~~~CpIs~~~m~dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip~~~   58 (61)
T 2bay_A            3 HMLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEIVP   58 (61)
T ss_dssp             -CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEECCC
T ss_pred             eEEecCCCCCCCCCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEECcc
Confidence            46899999999999999 99999999999999998888999999998777665543

>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=99.29  E-value=4.3e-13  Score=72.67  Aligned_cols=45  Identities=31%  Similarity=0.771  Sum_probs=39.6

Q ss_pred             CcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      +...|+||++.+.+++.+||||. ||..|+..|    ..||+||.++...
T Consensus        17 ~~~~C~IC~~~~~~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           17 EAMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHTBCTTTSSSBCCEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCCEeEEeCcccCcEEEECCCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            45589999999999999999999 999999765    4899999998754

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

Probab=99.25  E-value=2.7e-11  Score=64.70  Aligned_cols=52  Identities=27%  Similarity=0.544  Sum_probs=42.6

Q ss_pred             cCCCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCC--CCCCCCCccCCCC
Q psy3884          29 LLGVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDRE--QTCPLCRATLVDD   80 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~   80 (95)
                      .......|+||.+.+.....- .|+|.||..||.+|++.+  .+||+||.++...
T Consensus        11 y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           11 YPDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             CSSSSCBCSSSCCBCSSSEECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             ccCCCCcCcchhhHcccCCccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            344556999999999865433 899999999999999877  7999999987643

>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=99.14  E-value=7.1e-12  Score=84.01  Aligned_cols=45  Identities=27%  Similarity=0.778  Sum_probs=40.5

Q ss_pred             CCcccccccccCCCCCeecCCCCc-chHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHI-FCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~-fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      .+...|+||++.+.+|+.+||||. ||..|+..|    ..||+||.++..
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            356799999999999999999999 999999877    789999998864

>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=99.09  E-value=3.6e-11  Score=66.81  Aligned_cols=49  Identities=24%  Similarity=0.680  Sum_probs=39.1

Q ss_pred             CcccccccccCCCCCeec---CCCCcchHHhHHHHhhC--------CCCCCC--CCcc--CCCC
Q psy3884          32 VGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFDR--------EQTCPL--CRAT--LVDD   80 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~~--------~~~CP~--Cr~~--~~~~   80 (95)
                      ..+.|+||++.+..+..+   +|||.||..|+..++..        ...||.  |+..  +...
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~   67 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN   67 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHH
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHH
Confidence            456999999999887543   79999999999998862        247999  9988  5543

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

Probab=98.87  E-value=8.9e-10  Score=73.63  Aligned_cols=49  Identities=27%  Similarity=0.665  Sum_probs=38.8

Q ss_pred             CCcccccccccCCCC----Ce----ecCCCCcchHHhHHHHhhCC-----------CCCCCCCccCCC
Q psy3884          31 GVGCICPICHDEFKT----PV----QLTCCHIFCESCVTKWFDRE-----------QTCPLCRATLVD   79 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~----p~----~~~CgH~fc~~Ci~~~~~~~-----------~~CP~Cr~~~~~   79 (95)
                      .....|+||++.+.+    |.    ...|||.||..|+.+|+...           ..||.||+++..
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            456699999998876    21    23799999999999999732           479999998763

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

Probab=98.83  E-value=5.5e-09  Score=53.55  Aligned_cols=48  Identities=21%  Similarity=0.538  Sum_probs=39.2

Q ss_pred             CcccccccccCCCCCeecCCC--C---cchHHhHHHHhhC--CCCCCCCCccCCC
Q psy3884          32 VGCICPICHDEFKTPVQLTCC--H---IFCESCVTKWFDR--EQTCPLCRATLVD   79 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~Cg--H---~fc~~Ci~~~~~~--~~~CP~Cr~~~~~   79 (95)
                      +...|.||++...++.++||.  +   .||..|+.+|+..  +..||+|+.++..
T Consensus         5 ~~~~CrIC~~~~~~~l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            5 DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCEeEEeecCCCCceecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            455899999887777778865  4   7999999999973  5789999998753

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

Probab=98.77  E-value=5.9e-09  Score=58.07  Aligned_cols=46  Identities=24%  Similarity=0.589  Sum_probs=38.1

Q ss_pred             cccccccCCCC-CeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCC
Q psy3884          35 ICPICHDEFKT-PVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDD   80 (95)
Q Consensus        35 ~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~   80 (95)
                      .|++|.-.+.. .+++||+|+||.+|+..|.+ ..+.||.|+.++..-
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            58888877775 46779999999999999985 468999999988643

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

Probab=98.07  E-value=4.8e-06  Score=53.27  Aligned_cols=48  Identities=29%  Similarity=0.604  Sum_probs=39.5

Q ss_pred             cccccccccCCCCCeec-CCCCcchHHhHHHHhhCC--CCCCCCCccCCCC
Q psy3884          33 GCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDRE--QTCPLCRATLVDD   80 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~--~~CP~Cr~~~~~~   80 (95)
                      ...|.||.+.......- .|+|.||..|+..|++..  ..||.|+...+..
T Consensus       180 i~~C~iC~~iv~~g~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          180 VKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             CCBCTTTCSBCSSCEECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCcCcchhhHHhCCcccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            55899999998876544 499999999999999754  4999999986644

>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=98.06  E-value=1.7e-06  Score=64.33  Aligned_cols=67  Identities=15%  Similarity=0.074  Sum_probs=59.3

Q ss_pred             ccCCCcccccccccCCCCCeecCCC-CcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhc
Q psy3884          28 TLLGVGCICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQI   94 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~~Cg-H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~   94 (95)
                      ...++++.|||-.+.+.+|++++-| ++|=+..|.+|+..+.+||.-|.++...+..++..+...|+.
T Consensus       886 ~~iP~~F~cPIs~~lM~DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN~~Lk~~I~~  953 (968)
T 3m62_A          886 GDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEELRQKILC  953 (968)
T ss_dssp             CCSCGGGBCTTTCSBCSSEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECHHHHHHHHH
T ss_pred             cCCcHHhCCcchhhHHhCCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcccccccHHHHHHHHH
Confidence            3456788999999999999999998 599999999999988999999999998888888887777663

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

Probab=97.49  E-value=5.7e-05  Score=41.86  Aligned_cols=30  Identities=23%  Similarity=0.837  Sum_probs=25.7

Q ss_pred             cccccccccC-CCCCee--cCCCCcchHHhHHH
Q psy3884          33 GCICPICHDE-FKTPVQ--LTCCHIFCESCVTK   62 (95)
Q Consensus        33 ~~~C~IC~~~-~~~p~~--~~CgH~fc~~Ci~~   62 (95)
                      +..|+||.+. +.+++.  +.|+|.||..|+..
T Consensus         3 e~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~   35 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKA   35 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETTTTEEECHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCcCChHHhHHHCHH
Confidence            5689999976 566766  89999999999997

>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=96.52  E-value=0.0062  Score=32.51  Aligned_cols=35  Identities=26%  Similarity=0.665  Sum_probs=28.8

Q ss_pred             CCcccccccccCCCCCeecCC----CCcchHHhHHHHhh
Q psy3884          31 GVGCICPICHDEFKTPVQLTC----CHIFCESCVTKWFD   65 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~C----gH~fc~~Ci~~~~~   65 (95)
                      ...+.|.+|.+.+++...+.|    +|.||..|-+..++
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            457799999999998755544    59999999998886

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

Probab=94.75  E-value=0.025  Score=38.32  Aligned_cols=62  Identities=18%  Similarity=0.317  Sum_probs=43.5

Q ss_pred             CCcccccccccCCCCCeec-CCCCcchHHh--HHHHhh--CCCCCCCCCccCCCCccccCCcchhhh
Q psy3884          31 GVGCICPICHDEFKTPVQL-TCCHIFCESC--VTKWFD--REQTCPLCRATLVDDPAWRDGATSYFV   92 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~C--i~~~~~--~~~~CP~Cr~~~~~~~~~~~~~~~~~~   92 (95)
                      .-.+.||+-...+..|+.- .|.|.-|.+-  +.....  ....||+|.+.+...++..|..+..++
T Consensus       247 ~vSL~CPlS~~ri~~PvRg~~C~HlQCFDl~sfL~~~~~~~~W~CPIC~k~~~~~dL~ID~~~~~IL  313 (371)
T 3i2d_A          247 IMSLQCPISYTRMKYPSKSINCKHLQCFDALWFLHSQLQIPTWQCPVCQIDIALENLAISEFVDDIL  313 (371)
T ss_dssp             EEESBCTTTSSBCSSEEEETTCCSSCCEEHHHHHHHHHHSCCCBCTTTCCBCCGGGEEEBHHHHHHH
T ss_pred             EEeecCCCccccccccCcCCcCCCcceECHHHHHHHhhcCCceeCCCCCcccCHHHeeEcHHHHHHH
Confidence            3467999999999999754 8999855433  222222  446899999998877776665554443

>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=94.55  E-value=0.031  Score=37.75  Aligned_cols=62  Identities=21%  Similarity=0.475  Sum_probs=43.1

Q ss_pred             CCcccccccccCCCCCee-cCCCCcchHHh--HHHHhh--CCCCCCCCCccCCCCccccCCcchhhh
Q psy3884          31 GVGCICPICHDEFKTPVQ-LTCCHIFCESC--VTKWFD--REQTCPLCRATLVDDPAWRDGATSYFV   92 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~-~~CgH~fc~~C--i~~~~~--~~~~CP~Cr~~~~~~~~~~~~~~~~~~   92 (95)
                      .-.+.||+-...+..|+. ..|.|.-|.+-  +.....  ....||+|.+.+...++..|..+..++
T Consensus       213 ~vSL~CPlS~~ri~~P~Rg~~C~HlqCFDl~sfL~~~~~~~~W~CPiC~k~~~~~dL~ID~~~~~IL  279 (360)
T 4fo9_A          213 RVSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYESLILDGLFMEIL  279 (360)
T ss_dssp             EEESBCTTTCSBCSSEEEETTCCCCCCEEHHHHHHHHHHSCCCBCTTTCSBCCGGGEEEBHHHHHHH
T ss_pred             EEeeeCCCccceeccCCcCCCCCCCccCCHHHHHHHHhhCCCeECCCCCcccCHHHeEEcHHHHHHH
Confidence            346799999999999975 48999955432  222222  346899999998877776665554443

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

Probab=94.18  E-value=0.088  Score=26.90  Aligned_cols=44  Identities=25%  Similarity=0.454  Sum_probs=30.8

Q ss_pred             CcccccccccCCCCCeec--CCCCcchHHhHHHHhhC----CCCCCCCCccC
Q psy3884          32 VGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFDR----EQTCPLCRATL   77 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~~----~~~CP~Cr~~~   77 (95)
                      ....|.||.+.  ...++  .|...||..|+...+..    ...||.|....
T Consensus        11 ~~~~C~vC~~~--~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDG--TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCC--TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCC--CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            34579999864  22233  68899999999766542    35899997654

>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=93.39  E-value=0.24  Score=26.59  Aligned_cols=34  Identities=15%  Similarity=0.470  Sum_probs=24.2

Q ss_pred             cCCCcccccccccCCCCCeec---CCCCcchHHhHHHH
Q psy3884          29 LLGVGCICPICHDEFKTPVQL---TCCHIFCESCVTKW   63 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~   63 (95)
                      ....+..|.||-..- ....+   -|+.+||..|+.+.
T Consensus        11 ~~~~D~~C~VC~~~t-~~~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           11 PVVNDEMCDVCEVWT-AESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTTCCCC-SSCCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCCCcccCcccccc-ccceeccccccccccHhhcccc
Confidence            344667999998543 23344   47899999999986

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=89.57  E-value=0.2  Score=27.01  Aligned_cols=30  Identities=23%  Similarity=0.617  Sum_probs=22.3

Q ss_pred             cccccccccCCCCC----eecCCCCcchHHhHHH
Q psy3884          33 GCICPICHDEFKTP----VQLTCCHIFCESCVTK   62 (95)
Q Consensus        33 ~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~   62 (95)
                      ...|.+|...|.--    .--.||++||..|...
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            45899999887632    1237999999999754

>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=89.49  E-value=0.4  Score=23.93  Aligned_cols=40  Identities=30%  Similarity=0.693  Sum_probs=28.2

Q ss_pred             ccccccccCCCCCee---cCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884          34 CICPICHDEFKTPVQ---LTCCHIFCESCVTKWFDREQTCPLC   73 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~---~~CgH~fc~~Ci~~~~~~~~~CP~C   73 (95)
                      ..|-.|+..+.+..+   ..|++.||.+|=.-.-+.-..||.|
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            369999998865542   3689999999953222344689987

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=89.18  E-value=0.18  Score=26.74  Aligned_cols=30  Identities=33%  Similarity=0.850  Sum_probs=22.2

Q ss_pred             cccccccccCCCCCe----ecCCCCcchHHhHHH
Q psy3884          33 GCICPICHDEFKTPV----QLTCCHIFCESCVTK   62 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~~   62 (95)
                      ...|.+|...|.--.    --.||.+||..|...
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            348999999887321    227999999999753

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=88.65  E-value=0.14  Score=26.57  Aligned_cols=47  Identities=21%  Similarity=0.415  Sum_probs=32.0

Q ss_pred             CcccccccccCCCCCeec---CCCCcchHHhHHHHhh----CCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFD----REQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~----~~~~CP~Cr~~~~   78 (95)
                      +...|+||.........+   .|..-||..|+..-..    ....||.|...+.
T Consensus        17 ~~~~C~~C~~~~~~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDDGSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCSSCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCCCCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            445799998876543333   6778899999864332    2357999976654

>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=88.48  E-value=0.07  Score=23.76  Aligned_cols=14  Identities=36%  Similarity=0.966  Sum_probs=10.4

Q ss_pred             cccccccccCCCCC
Q psy3884          33 GCICPICHDEFKTP   46 (95)
Q Consensus        33 ~~~C~IC~~~~~~p   46 (95)
                      .+.||+|+..+.++
T Consensus         5 GFiCP~C~~~l~s~   18 (34)
T 3mjh_B            5 GFICPQCMKSLGSA   18 (34)
T ss_dssp             EEECTTTCCEESSH
T ss_pred             ccCCcHHHHHcCCH
Confidence            46888888877665

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=88.11  E-value=0.3  Score=23.24  Aligned_cols=41  Identities=22%  Similarity=0.561  Sum_probs=26.5

Q ss_pred             cccccccCCCCCeec---CCCCcchHHhHHHHhh----CCCCCCCCCc
Q psy3884          35 ICPICHDEFKTPVQL---TCCHIFCESCVTKWFD----REQTCPLCRA   75 (95)
Q Consensus        35 ~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~----~~~~CP~Cr~   75 (95)
                      .|.||...-....++   .|...||..|+..-+.    ....||.|..
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            478887654333233   6888899999965333    2346888854

>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=87.91  E-value=0.47  Score=26.69  Aligned_cols=49  Identities=10%  Similarity=0.137  Sum_probs=36.7

Q ss_pred             cccccccccCCCC---CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          33 GCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        33 ~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      -+.|..|...+.+   .....=|..||..|..+.+.....|..|..+|....
T Consensus        32 CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~   83 (122)
T 1m3v_A           32 CLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGD   83 (122)
T ss_dssp             HHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEE
T ss_pred             CCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchh
Confidence            3688899888852   334456778999999887765558999999887643

>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1

Probab=87.80  E-value=0.57  Score=27.21  Aligned_cols=30  Identities=20%  Similarity=0.474  Sum_probs=21.6

Q ss_pred             CcccccccccCCC---CC--eecCCCCcchHHhHH
Q psy3884          32 VGCICPICHDEFK---TP--VQLTCCHIFCESCVT   61 (95)
Q Consensus        32 ~~~~C~IC~~~~~---~p--~~~~CgH~fc~~Ci~   61 (95)
                      ....|.+|...+.   +.  .-..|.|.+|..|-.
T Consensus        54 ~~~~C~~C~~~~g~l~~~g~~C~~C~~~VC~~C~~   88 (134)
T 1zbd_B           54 GVNRCILCGEQLGMLGSASVVCEDCKKNVCTKCGV   88 (134)
T ss_dssp             SSSBCSSSCCBCSTTSCCEEECTTTCCEEETTSEE
T ss_pred             CCccccccCCCcccccCCCCCCCCCCcccccccCC
Confidence            4569999999883   22  233788999988864

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=87.78  E-value=0.52  Score=23.43  Aligned_cols=42  Identities=21%  Similarity=0.593  Sum_probs=29.0

Q ss_pred             CcccccccccCCCCCeec--CCCCcchHHhHHHHhh----CCCCCCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRA   75 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~----~~~~CP~Cr~   75 (95)
                      ....|.+|...  ...+.  .|...||..|+..-+.    ....||.|..
T Consensus        10 ~~~~C~vC~~~--g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A           10 HQDYCEVCQQG--GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCSSCTTTSCC--SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCccCCCC--CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            45689999874  23333  6888999999976433    2357999954

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=87.13  E-value=0.34  Score=25.00  Aligned_cols=28  Identities=25%  Similarity=0.609  Sum_probs=21.1

Q ss_pred             ccccccccCCCCCe----ecCCCCcchHHhHH
Q psy3884          34 CICPICHDEFKTPV----QLTCCHIFCESCVT   61 (95)
Q Consensus        34 ~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~   61 (95)
                      ..|.+|...|.--.    --.||.+||..|..
T Consensus        12 ~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~   43 (73)
T 1vfy_A           12 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSS   43 (73)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSC
T ss_pred             CcccCCCCccCCccccccCCCCCEEEcccccC
Confidence            48999999876421    22699999999964

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=86.93  E-value=0.44  Score=25.28  Aligned_cols=31  Identities=26%  Similarity=0.520  Sum_probs=23.0

Q ss_pred             CcccccccccCCCCCe----ecCCCCcchHHhHHH
Q psy3884          32 VGCICPICHDEFKTPV----QLTCCHIFCESCVTK   62 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~~   62 (95)
                      +...|.+|...|.--.    --.||.+||..|...
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            4458999999886421    227999999999754

>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=86.89  E-value=0.23  Score=27.73  Aligned_cols=33  Identities=18%  Similarity=0.578  Sum_probs=21.6

Q ss_pred             CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884          46 PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   83 (95)
Q Consensus        46 p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   83 (95)
                      +.-..||+.|.     .-+.....||.|+..-...+.|
T Consensus        68 ~~C~~CG~~F~-----~~~~kPsrCP~CkSe~Ie~P~F  100 (105)
T 2gmg_A           68 AQCRKCGFVFK-----AEINIPSRCPKCKSEWIEEPRF  100 (105)
T ss_dssp             CBBTTTCCBCC-----CCSSCCSSCSSSCCCCBCCCCE
T ss_pred             cChhhCcCeec-----ccCCCCCCCcCCCCCccCCcce
Confidence            34457999981     2223557899999876665544

>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural genomics consortium, DH domain, SGC, L binding protein; 2.80A {Homo sapiens}

Probab=86.87  E-value=0.23  Score=33.69  Aligned_cols=45  Identities=22%  Similarity=0.536  Sum_probs=0.0

Q ss_pred             cccccccccCCCCC----eecCCCCcchHHhHHHHhh-------CCCCCCCCCccC
Q psy3884          33 GCICPICHDEFKTP----VQLTCCHIFCESCVTKWFD-------REQTCPLCRATL   77 (95)
Q Consensus        33 ~~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~-------~~~~CP~Cr~~~   77 (95)
                      ...|.+|...|.--    .--.||++||..|......       ....|-.|-..+
T Consensus       375 ~~~c~~c~~~f~~~~r~h~Cr~Cg~~~C~~Cs~~~~~~~~~~~~~~rvC~~C~~~l  430 (434)
T 3mpx_A          375 VMMCMNCGCDFSLTLRRHHCHACGKIVCRNCSRNKYPLKYLKDRMAKVCDGCFGEL  430 (434)
T ss_dssp             --------------------------------------------------------
T ss_pred             CCcCCCcCCCCCCcchhhhcccCcCEeehhhCCCeeeCCCCCCCcCEecHHHHHHH
Confidence            45899999987632    1227999999999865432       124566665443

>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=1.5  Score=22.98  Aligned_cols=43  Identities=16%  Similarity=0.236  Sum_probs=32.7

Q ss_pred             CCcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          31 GVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      .....|..|.+.+...++..-+..||..|        +.|-.|...+....
T Consensus        23 ~~~~~C~~C~~~I~~~~~~a~~~~~H~~C--------F~C~~C~~~L~~~~   65 (89)
T 1x64_A           23 QRMPLCDKCGSGIVGAVVKARDKYRHPEC--------FVCADCNLNLKQKG   65 (89)
T ss_dssp             CSCCBCTTTCCBCCSCCEESSSCEECTTT--------CCCSSSCCCTTTSC
T ss_pred             CcCCCcccCCCEecccEEEECCceECccC--------CEecCCCCCCCCCC
Confidence            34568999999888766667778888877        46899988887643

>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=86.60  E-value=0.85  Score=23.45  Aligned_cols=40  Identities=15%  Similarity=0.201  Sum_probs=30.6

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      ....|+-|.+.+...++..-+..||..|+        .|-.|+..+..
T Consensus        14 ~~~~C~~C~~~I~~~~~~a~~~~~H~~CF--------~C~~C~~~L~~   53 (79)
T 1x62_A           14 KLPMCDKCGTGIVGVFVKLRDRHRHPECY--------VCTDCGTNLKQ   53 (79)
T ss_dssp             CCCCCSSSCCCCCSSCEECSSCEECTTTT--------SCSSSCCCHHH
T ss_pred             CCCccccCCCCccCcEEEECcceeCcCcC--------eeCCCCCCCCC
Confidence            45699999998887666677888888774        58888887753

>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=86.10  E-value=0.95  Score=23.35  Aligned_cols=41  Identities=20%  Similarity=0.372  Sum_probs=30.3

Q ss_pred             cccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ...|+-|.+.+....+..-|..||..|        +.|..|+.++....
T Consensus        15 ~~~C~~C~~~I~~~~v~a~~~~~H~~C--------F~C~~C~~~L~~~~   55 (79)
T 2cor_A           15 KYICQKCHAIIDEQPLIFKNDPYHPDH--------FNCANCGKELTADA   55 (79)
T ss_dssp             CCBCTTTCCBCCSCCCCCSSSCCCTTT--------SBCSSSCCBCCTTC
T ss_pred             CCCCccCCCEecceEEEECcceeCCCC--------CEeCCCCCccCCCC
Confidence            458999998888665666677777766        46888988887553

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=85.71  E-value=0.16  Score=33.64  Aligned_cols=46  Identities=17%  Similarity=0.491  Sum_probs=34.9

Q ss_pred             CCcccccccccCCCCCeec----CCC--CcchHHhHHHHhhCCCCCCCCCcc
Q psy3884          31 GVGCICPICHDEFKTPVQL----TCC--HIFCESCVTKWFDREQTCPLCRAT   76 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~----~Cg--H~fc~~Ci~~~~~~~~~CP~Cr~~   76 (95)
                      .....||+|.....-.++.    .=|  +.+|..|-..|--....||.|...
T Consensus       180 ~~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~~R~~C~~Cg~~  231 (309)
T 2fiy_A          180 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEES  231 (309)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCC
T ss_pred             ccCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEeecCcCCcCCCCC
Confidence            4567999999976655433    234  457899999998888999999775

>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=85.03  E-value=0.32  Score=27.89  Aligned_cols=29  Identities=31%  Similarity=0.703  Sum_probs=21.7

Q ss_pred             ccccccccCCCCC----eecCCCCcchHHhHHH
Q psy3884          34 CICPICHDEFKTP----VQLTCCHIFCESCVTK   62 (95)
Q Consensus        34 ~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~   62 (95)
                      ..|.+|...|.--    .--.||++||..|...
T Consensus        70 ~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~  102 (125)
T 1joc_A           70 QNCMACGKGFSVTVRRHHCRQCGNIFCAECSAK  102 (125)
T ss_dssp             CBCTTTCCBCCSSSCCEECTTTCCEECGGGSCE
T ss_pred             CCCcCcCCccccccccccCCCCCeEEChHHhCC
Confidence            4899999988632    1227999999999643

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=84.61  E-value=1.7  Score=25.54  Aligned_cols=44  Identities=18%  Similarity=0.510  Sum_probs=29.8

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhh-----------CCCCCCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-----------REQTCPLCRA   75 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-----------~~~~CP~Cr~   75 (95)
                      .+..|.+|.+--.--.--.|-..||..|+.+-+.           ....||.|+.
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 MDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             CBCSCSSSCCCSSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCeecccCCCCcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            4568999987432111116888999999986542           3358999964

>2zet_C Melanophilin; complex, GTP-binding protein, GTPase, G-protein, RAB, RAB27B, effector, SLP homology domain, acetylation, lipoprotein, membrane; HET: GTP; 3.00A {Mus musculus}

Probab=84.49  E-value=1.7  Score=25.81  Aligned_cols=29  Identities=24%  Similarity=0.674  Sum_probs=21.4

Q ss_pred             CcccccccccCCC---CC--eecCCCCcchHHhH
Q psy3884          32 VGCICPICHDEFK---TP--VQLTCCHIFCESCV   60 (95)
Q Consensus        32 ~~~~C~IC~~~~~---~p--~~~~CgH~fc~~Ci   60 (95)
                      ....|.+|...|.   +.  .-..|.|.+|..|-
T Consensus        67 ~~~~C~~C~~~fg~l~~~g~~C~~C~~~VC~~C~  100 (153)
T 2zet_C           67 NETHCARCLQPYRLLLNSRRQCLECSLFVCKSCS  100 (153)
T ss_dssp             GGTBCTTTCCBGGGCSSCCEECTTTCCEECGGGE
T ss_pred             CCccchhhcCccccccCCCCcCCCCCchhhcccc
Confidence            3559999999764   22  23379999999997

>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=84.48  E-value=3.4  Score=22.37  Aligned_cols=47  Identities=26%  Similarity=0.605  Sum_probs=33.7

Q ss_pred             CcccccccccCCCC----Ceec---CCCCcchHHhHHHHh-hCCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKT----PVQL---TCCHIFCESCVTKWF-DREQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~----p~~~---~CgH~fc~~Ci~~~~-~~~~~CP~Cr~~~~   78 (95)
                      ..-.|.||-+.+-.    .+.+   .|+-..|+.|..--. ..+..||.|+..+.
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            34599999998542    1333   577778999996433 35679999999886

>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=84.44  E-value=0.41  Score=25.70  Aligned_cols=30  Identities=23%  Similarity=0.520  Sum_probs=21.9

Q ss_pred             cccccccccCCCCCe----ecCCCCcchHHhHHH
Q psy3884          33 GCICPICHDEFKTPV----QLTCCHIFCESCVTK   62 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~~   62 (95)
                      ...|.+|...|.--.    --.||.+||..|...
T Consensus         9 ~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   42 (88)
T 1wfk_A            9 ESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSF   42 (88)
T ss_dssp             CSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCE
T ss_pred             CCCCcCcCCcccCccccccCCCCCCEEChhHcCC
Confidence            348999999876421    227999999999753

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=84.26  E-value=1.1  Score=22.28  Aligned_cols=39  Identities=21%  Similarity=0.392  Sum_probs=24.9

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ..|+.|.+.+....+..-+..||..|        +.|-.|+.++...
T Consensus         6 ~~C~~C~~~I~~~~~~a~~~~~H~~C--------F~C~~C~~~L~~~   44 (70)
T 2d8z_A            6 SGCVQCKKPITTGGVTYREQPWHKEC--------FVCTACRKQLSGQ   44 (70)
T ss_dssp             CBCSSSCCBCCSSEEESSSSEEETTT--------SBCSSSCCBCTTS
T ss_pred             CCCcccCCeeccceEEECccccCCCC--------CccCCCCCcCCcC
Confidence            36777777776555555666666665        3477777776543

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B

Probab=83.99  E-value=0.71  Score=22.77  Aligned_cols=39  Identities=15%  Similarity=0.336  Sum_probs=28.2

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ..|+.|.+.+....+..-|..||..|        +.|..|+.++...
T Consensus         6 ~~C~~C~~~I~~~~~~a~~~~~H~~C--------F~C~~C~~~L~~~   44 (66)
T 1nyp_A            6 PICGACRRPIEGRVVNAMGKQWHVEH--------FVCAKCEKPFLGH   44 (66)
T ss_dssp             CEETTTTEECCSCEECCTTSBEETTT--------CBCTTTCCBCSSS
T ss_pred             CCCcccCCEecceEEEECccccccCc--------CEECCCCCCCCCC
Confidence            47888888877666666677777766        4588888877654

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=83.82  E-value=1.2  Score=22.62  Aligned_cols=37  Identities=19%  Similarity=0.372  Sum_probs=24.9

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ..|+-|...+...++..-+..||..|        +.|-.|..++.
T Consensus         6 ~~C~~C~~~I~~~~v~a~~~~wH~~C--------F~C~~C~~~L~   42 (73)
T 1wig_A            6 SGCDSCEKYITGRVLEAGEKHYHPSC--------ALCVRCGQMFA   42 (73)
T ss_dssp             CSCSSSCCCCSSCCBCCSSCCBCTTT--------SCCSSSCCCCC
T ss_pred             CCcccCCCEecCeeEEeCCCCCCCCc--------CEeCCCCCCCC
Confidence            36777877776655556666677666        45777777766

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=83.68  E-value=0.74  Score=24.32  Aligned_cols=42  Identities=14%  Similarity=0.334  Sum_probs=31.9

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ....|+.|.+.+....+..-+..||..|        +.|..|+.++....
T Consensus        24 ~~~~C~~C~~~I~~~~v~a~~~~~H~~C--------F~C~~C~~~L~~~~   65 (90)
T 2dar_A           24 RTPMCAHCNQVIRGPFLVALGKSWHPEE--------FNCAHCKNTMAYIG   65 (90)
T ss_dssp             CCCBBSSSCCBCCSCEEEETTEEECTTT--------CBCSSSCCBCSSSC
T ss_pred             CCCCCccCCCEecceEEEECCccccccC--------CccCCCCCCCCCCE
Confidence            3458999999887766667777788777        45889988887543

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=83.25  E-value=1.3  Score=23.88  Aligned_cols=46  Identities=24%  Similarity=0.531  Sum_probs=31.3

Q ss_pred             cCCCcccccccccCCCCCeec--CCCCcchHHhHHHHhhC----CCCCCCCCcc
Q psy3884          29 LLGVGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFDR----EQTCPLCRAT   76 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~~----~~~CP~Cr~~   76 (95)
                      .......|.+|...-  ....  .|...||..|+.+-+..    ...||.|...
T Consensus        21 ~d~n~~~C~vC~~~g--~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           21 LDDSATICRVCQKPG--DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSSSCCSSSCSSS--CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             cCCCCCcCcCcCCCC--CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            344566999999752  2222  68888999999765442    3579999754

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=82.80  E-value=0.49  Score=25.07  Aligned_cols=29  Identities=24%  Similarity=0.547  Sum_probs=21.4

Q ss_pred             cccccccccCCCCCe----ecCCCCcchHHhHH
Q psy3884          33 GCICPICHDEFKTPV----QLTCCHIFCESCVT   61 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~   61 (95)
                      ...|.+|...|.--.    --.||.+||..|..
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            348999999886321    22699999999964

>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=82.78  E-value=0.51  Score=23.47  Aligned_cols=43  Identities=23%  Similarity=0.512  Sum_probs=28.5

Q ss_pred             CcccccccccCCCCCeec--CCCCcchHHhHHHHhh----CCCCCCCCCcc
Q psy3884          32 VGCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRAT   76 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~----~~~~CP~Cr~~   76 (95)
                      ....|.+|.+.  ...+.  .|...||..|+..-+.    ....||.|...
T Consensus         8 ~~~~C~vC~~~--g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   56 (61)
T 1mm2_A            8 HMEFCRVCKDG--GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SCSSCTTTCCC--SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCCcCCCCCCC--CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCc
Confidence            45689999863  22222  5788899999875333    23479999654

>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=82.51  E-value=1.9  Score=24.85  Aligned_cols=44  Identities=18%  Similarity=0.526  Sum_probs=28.5

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHh-----------hCCCCCCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWF-----------DREQTCPLCRA   75 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~-----------~~~~~CP~Cr~   75 (95)
                      .+..|.+|.+--.-..--.|-..||..|+.+.+           .....|+.|+.
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            345799998642211111678899999998652           13368999954

>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=82.49  E-value=2  Score=22.21  Aligned_cols=44  Identities=30%  Similarity=0.600  Sum_probs=30.2

Q ss_pred             CCCcccccccccCCCC-CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          30 LGVGCICPICHDEFKT-PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~-p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ......|+.|.+.+.. ..+..-+..||..|        +.|-.|+..+....
T Consensus        12 ~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~C--------F~C~~C~~~L~~~~   56 (82)
T 2co8_A           12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSC--------FRCHTCEATLWPGG   56 (82)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTT--------CBCSSSCCBCCTTS
T ss_pred             CCCCCCCcccCCCcccceEEEECCCeeCCCc--------CEEcCCCCCcCCCc
Confidence            3445689999998753 34445566777777        45888888776554

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.39  E-value=1.1  Score=22.32  Aligned_cols=40  Identities=18%  Similarity=0.345  Sum_probs=26.8

Q ss_pred             ccccccccCCC--CCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          34 CICPICHDEFK--TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        34 ~~C~IC~~~~~--~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      ..|+.|.+.+.  +.++..-+..||..|        +.|-.|..++....
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~C--------F~C~~C~~~L~~~~   47 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLEYGGQTWHEHC--------FLCSGCEQPLGSRS   47 (72)
T ss_dssp             CBCSSSCCBCCSSSCEECSTTCCEETTT--------CBCTTTCCBTTTSC
T ss_pred             CCCccCCCccccCccEEEECccccCccc--------CeECCCCCcCCCCc
Confidence            47888888777  345556677777766        45777877776543

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=81.47  E-value=1.2  Score=25.02  Aligned_cols=48  Identities=13%  Similarity=0.333  Sum_probs=34.1

Q ss_pred             CcccccccccCCCC---CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          32 VGCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        32 ~~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      +-+.|..|...+..   +....=|..||..|..+.+.....|..|..++..
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            45788888888752   3445567788999987765544478888887764

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=81.18  E-value=0.2  Score=25.02  Aligned_cols=33  Identities=27%  Similarity=0.669  Sum_probs=22.4

Q ss_pred             ccccccccCCCCC-----eecC---CCCcchHHhHHHHhhC
Q psy3884          34 CICPICHDEFKTP-----VQLT---CCHIFCESCVTKWFDR   66 (95)
Q Consensus        34 ~~C~IC~~~~~~p-----~~~~---CgH~fc~~Ci~~~~~~   66 (95)
                      -.||-|...++..     ++-.   |++.||..|..+|...
T Consensus         7 k~CP~C~~~Iek~~GCnhmtC~~~~C~~~FCw~C~~~~~~~   47 (60)
T 1wd2_A            7 KECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPH   47 (60)
T ss_dssp             CCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGGG
T ss_pred             eECcCCCCeeEeCCCCCcEEECCCCcCCEEeeCcCCCcccC
Confidence            4788888877643     2223   7888888888777543

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.11  E-value=2.3  Score=21.22  Aligned_cols=39  Identities=18%  Similarity=0.354  Sum_probs=26.5

Q ss_pred             ccccccccCCCC----CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          34 CICPICHDEFKT----PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        34 ~~C~IC~~~~~~----p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ..|+-|.+.+..    .++..-+..||..|        +.|-.|+.++...
T Consensus         6 ~~C~~C~~~I~~~~~~~~~~a~~~~wH~~C--------F~C~~C~~~L~~~   48 (72)
T 1x4l_A            6 SGCAGCTNPISGLGGTKYISFEERQWHNDC--------FNCKKCSLSLVGR   48 (72)
T ss_dssp             CSBTTTTBCCCCSSSCSCEECSSCEECTTT--------CBCSSSCCBCTTS
T ss_pred             CCCcCCCccccCCCCcceEEECCcccCccc--------CEeccCCCcCCCC
Confidence            478888887774    44445667777766        4577887777644

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=80.92  E-value=1.3  Score=22.40  Aligned_cols=40  Identities=20%  Similarity=0.432  Sum_probs=28.9

Q ss_pred             cccccccccCCC-CCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCC
Q psy3884          33 GCICPICHDEFK-TPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDD   80 (95)
Q Consensus        33 ~~~C~IC~~~~~-~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   80 (95)
                      ...|+.|.+.+. ...+..-+..||..|        +.|..|+.++...
T Consensus         9 ~~~C~~C~~~I~~~~~v~a~~~~~H~~C--------F~C~~C~~~L~~~   49 (76)
T 2cu8_A            9 ASKCPKCDKTVYFAEKVSSLGKDWHKFC--------LKCERCSKTLTPG   49 (76)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTT--------CBCSSSCCBCCTT
T ss_pred             CCCCcCCCCEeECCeEEEECCeEeeCCC--------CCCCCCCCccCCC
Confidence            348999999887 445555667777766        4588888888754

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=80.55  E-value=0.57  Score=25.60  Aligned_cols=43  Identities=16%  Similarity=0.267  Sum_probs=28.7

Q ss_pred             CcccccccccCCCCCeec---CCCCcchHHhHHHHhh---CCCCCCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQL---TCCHIFCESCVTKWFD---REQTCPLCRA   75 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~---~~~~CP~Cr~   75 (95)
                      +...| ||........++   .|..-||..|+..-..   ....||.|+.
T Consensus        27 d~vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           27 DVTRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CBCCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CCEEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            34577 898776555455   5777899999854222   2358999964

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=80.35  E-value=4.1  Score=22.53  Aligned_cols=29  Identities=21%  Similarity=0.363  Sum_probs=19.5

Q ss_pred             cccccccccCCC-------CCeec--CCCCcchHHhHH
Q psy3884          33 GCICPICHDEFK-------TPVQL--TCCHIFCESCVT   61 (95)
Q Consensus        33 ~~~C~IC~~~~~-------~p~~~--~CgH~fc~~Ci~   61 (95)
                      ...|.+|+..-.       +..+.  .|+..||..|+.
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            447889986521       12222  699999999994

---

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	95
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	2e-11
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-11
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-10
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-10
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-10
d1t1ha_	78	g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cre	5e-07
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	7e-07
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-05
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-05
d1wgma_	98	g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Hu	7e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	1e-04
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-04
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-04
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	9e-04

>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 = 53.1 bits (127), Expect = 2e-11
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATL 77
          +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 = 51.9 bits (124), Expect = 3e-11
 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 36 CPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 77
          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 = 50.7 bits (121), Expect = 1e-10
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ-TCPLCRATL 77
           C IC      PV+ +C H+FC  C+ +        CP CR   
Sbjct: 25 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 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 = 49.9 bits (119), Expect = 2e-10
 Identities = 14/49 (28%), Positives = 17/49 (34%), Gaps = 3/49 (6%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW 83
           C  C  E K P  L C H  C  C+         CP+C+A        
Sbjct: 8  RCQQCQAEAKCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGADT 53

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 3e-10
 Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 3/45 (6%)

Query: 36 CPICHDEFKTPVQLTCCHIFCESCVTKWFDREQ---TCPLCRATL 77
          CPIC +  K PV   C HIFC+ C+ K  ++++    CPLC+  +
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>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 = 49.1 bits (117), Expect = 3e-10
 Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 36 CPICHDEFK---TPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLV 78
          C +C  E +       L  C H F   CV  W     TCPLCR T+V
Sbjct: 8  CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>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 = 41.6 bits (97), Expect = 5e-07
 Identities = 10/40 (25%), Positives = 15/40 (37%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCR 74
           CPI  +  K PV ++    +  S + KW D         
Sbjct: 10 RCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKS 49

>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 = 7e-07
 Identities = 11/42 (26%), Positives = 14/42 (33%)

Query: 34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRA 75
                  E  T     C H F   C+++W    Q CPL   
Sbjct: 40 ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 81

>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 = 37.5 bits (86), Expect = 2e-05
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 3/62 (4%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQ 93
           C  C +  + PV L  C HIFC +CV+        CP+C           +      +Q
Sbjct: 24 RCSRCTNILREPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDLKINRQLDSMIQ 81

Query: 94 IF 95
          + 
Sbjct: 82 LC 83

>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 = 35.9 bits (82), Expect = 4e-05
 Identities = 15/48 (31%), Positives = 16/48 (33%), Gaps = 6/48 (12%)

Query: 36 CPICHDEFKTP-----VQLTCCHIFCESCVTKWFD-REQTCPLCRATL 77
          CP C            +   C H  CESCV   F      CP C   L
Sbjct: 6  CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 36.3 bits (83), Expect = 7e-05
 Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 35 ICPICHDEFKTPVQLTCCHIFCE-SCVTKWFDREQTCPLCR 74
          + PI       PV L    +  + S + +    +QT P  R
Sbjct: 24 LDPIMSTLMCDPVVLPSSRVTVDRSTIARHLLSDQTDPFNR 64

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.7 bits (79), Expect = 1e-04
 Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)

Query: 35 ICPICHDEFKTPVQLTCC-HIFCESCVTKWFDREQTCPLCRATL 77
          +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 = 34.7 bits (79), Expect = 1e-04
 Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 5/50 (10%)

Query: 36 CPICHDEF----KTPVQLTCCHIFCESCVTKWFDREQT-CPLCRATLVDD 80
          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 = 33.7 bits (76), Expect = 4e-04
 Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 7/49 (14%)

Query: 35 ICPICHDEFKTP-----VQLTCCHIFCESCVTKWFDREQ--TCPLCRAT 76
          +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 = 33.5 bits (75), Expect = 9e-04
 Identities = 7/32 (21%), Positives = 10/32 (31%), Gaps = 5/32 (15%)

Query: 49 LTCCHIFCESCVTKWFDREQ-----TCPLCRA 75
            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	95
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.76
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.76
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.76
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.72
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.71
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.71
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.69
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.68
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.67
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.66
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.65
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	99.52
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.48
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.34
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.79
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	96.32
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.52
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	94.2
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	93.41
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	90.15
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	89.34
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	88.54
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	88.36
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	87.39
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	87.2
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	86.42
d2epqa1	32	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	86.27
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	85.97
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	85.84
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	84.94
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	84.83
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	84.37
d2gmga1	105	Hypothetical protein PF0610 {Pyrococcus furiosus [	84.13
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	83.92
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	83.27
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	83.04
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	82.1
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	81.83
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	80.81
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	80.69

>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=99.76  E-value=8e-20  Score=98.32  Aligned_cols=66  Identities=12%  Similarity=0.150  Sum_probs=58.1

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      ..+++.||||++.+.+|++++|||+||..||..|+.. +..||.|+.++...+..++..+.+.++.|
T Consensus         4 iP~~l~CpIc~~l~~dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN~~L~~~I~~~   70 (80)
T d2c2la2           4 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAF   70 (80)
T ss_dssp             CCSTTBCTTTCSBCSSEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHHHHHHHHHH
T ss_pred             CCccccCcCcCchhhhhcccCCcCeecHHHHHHHHhcCCccCCCccccccccccccHHHHHHHHHHH
Confidence            4578899999999999999999999999999999974 56899999999888888888888777643

>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=99.76  E-value=2.7e-19  Score=95.79  Aligned_cols=66  Identities=23%  Similarity=0.449  Sum_probs=59.0

Q ss_pred             CCCcccccccccCCCCCeecCCCCcchHHhHHHHhhCC-CCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          30 LGVGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        30 ~~~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      ..+++.|+||++.+.+|++++|||+||..|+..|+..+ ..||.|+.++...+..++..+.+.|+.|
T Consensus         5 iP~~l~CpIc~~~m~dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN~~L~~~I~~~   71 (78)
T d1t1ha_           5 FPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLKSLIALW   71 (78)
T ss_dssp             CSSSSSCTTTSCCCSSEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECTTTHHHHHHH
T ss_pred             CCccCCCcCcCchhhCceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccccchHHHHHHHHHH
Confidence            45788999999999999999999999999999999764 6799999999988888898888887743

>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=99.76  E-value=2.2e-19  Score=100.71  Aligned_cols=62  Identities=32%  Similarity=0.720  Sum_probs=53.4

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhhCC---CCCCCCCccCCCCccccCCcchhhhh
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDRE---QTCPLCRATLVDDPAWRDGATSYFVQ   93 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~---~~CP~Cr~~~~~~~~~~~~~~~~~~q   93 (95)
                      +.+.|+||++.+.+|++++|||+||..|+..|+...   ..||.||.++...+..++..+.++++
T Consensus        20 ~~l~CpIC~~~~~~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n~~l~~~ve   84 (103)
T d1jm7a_          20 KILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVE   84 (103)
T ss_dssp             HHTSCSSSCCCCSSCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCCCSSSHHHH
T ss_pred             cCcCCCccCchhCCeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcCHHHHHHHH
Confidence            356899999999999999999999999999999754   48999999998887777777766654

>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=90.93  Aligned_cols=48  Identities=33%  Similarity=0.857  Sum_probs=43.4

Q ss_pred             ccccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCc
Q psy3884          34 CICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDP   81 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~   81 (95)
                      ..|+||++.+.++++++|||.||..|+..|+. +...||+||..+....
T Consensus        24 ~~C~IC~~~~~~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          24 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TBCTTTSSSBCCEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCccCCCcCCCeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            47999999999999999999999999999997 4578999999998654

>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=99.71  E-value=2e-18  Score=93.70  Aligned_cols=52  Identities=27%  Similarity=0.679  Sum_probs=45.7

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhh-CCCCCCCCCccCCCCccc
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFD-REQTCPLCRATLVDDPAW   83 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~-~~~~CP~Cr~~~~~~~~~   83 (95)
                      +.+.|+||++.+.+|++++|||+||..|+.+|++ +...||.||.++...+..
T Consensus        22 ~~l~C~IC~~~~~~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~   74 (86)
T d1rmda2          22 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE   74 (86)
T ss_dssp             HHTBCTTTCSBCSSEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCB
T ss_pred             cCcCCccCCcchhcceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhhcc
Confidence            4579999999999999999999999999999997 456899999998766543

>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=99.71  E-value=1.3e-18  Score=87.63  Aligned_cols=52  Identities=17%  Similarity=0.241  Sum_probs=46.7

Q ss_pred             ccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccC
Q psy3884          34 CICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRD   85 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~   85 (95)
                      +.|+||++.+.+|+.+ .|||+||..||.+|+.++..||+||+++..+++.+.
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLipi   53 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVEI   53 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEEC
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhceeC
Confidence            4799999999999987 599999999999999999999999999987766543

>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=99.69  E-value=1.3e-18  Score=96.54  Aligned_cols=63  Identities=25%  Similarity=0.551  Sum_probs=53.6

Q ss_pred             CCcccccccccCCCCCeec-CCCCcchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          31 GVGCICPICHDEFKTPVQL-TCCHIFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      .+.+.|+||++.+.+|+.+ +|||+||..|+.+|+.  ..||.||.++...+...+..+..+++.|
T Consensus        20 ~~~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~n~~l~~lv~~~   83 (97)
T d1jm7b_          20 EKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKINRQLDSMIQLC   83 (97)
T ss_dssp             HHTTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCCHHHHHHHHHH
T ss_pred             hhcCCCccCCchhhcCceeCCCCCchhHHHHHHHHh--ccccccCCcCchhhCcccHHHHHHHHHH
Confidence            3456999999999999875 8999999999999985  4599999999888888888777777643

>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=99.68  E-value=7.5e-18  Score=87.91  Aligned_cols=47  Identities=36%  Similarity=0.971  Sum_probs=42.0

Q ss_pred             cccccccccCCCCCe-ecCCCCcchHHhHHHHhhCCCCCCCCCccCCC
Q psy3884          33 GCICPICHDEFKTPV-QLTCCHIFCESCVTKWFDREQTCPLCRATLVD   79 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~-~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   79 (95)
                      ...|+||++.+.+++ .++|||+||..|+.+|++.+..||+||.++..
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            348999999998775 57999999999999999999999999998864

>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=99.67  E-value=2.3e-17  Score=82.64  Aligned_cols=48  Identities=40%  Similarity=0.868  Sum_probs=41.0

Q ss_pred             CCcccccccccCCCCC---eec-CCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          31 GVGCICPICHDEFKTP---VQL-TCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p---~~~-~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      +++..|+||++.+...   ..+ +|||.||..|+.+|++.+..||+||+++.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            3556899999999753   344 69999999999999999999999999864

>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=99.66  E-value=3.3e-17  Score=90.95  Aligned_cols=67  Identities=19%  Similarity=0.162  Sum_probs=59.4

Q ss_pred             cCCCcccccccccCCCCCeecCCCC-cchHHhHHHHhhCCCCCCCCCccCCCCccccCCcchhhhhcC
Q psy3884          29 LLGVGCICPICHDEFKTPVQLTCCH-IFCESCVTKWFDREQTCPLCRATLVDDPAWRDGATSYFVQIF   95 (95)
Q Consensus        29 ~~~~~~~C~IC~~~~~~p~~~~CgH-~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~~~~~~~q~~   95 (95)
                      ...+++.||||.+.|.+|++++||| +||..||..|+..+..||.|+.++...++.++..+...|+.|
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            4567899999999999999998775 899999999999999999999999988888888887777643

>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=99.65  E-value=1.5e-17  Score=83.58  Aligned_cols=47  Identities=30%  Similarity=0.653  Sum_probs=41.2

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCc
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDP   81 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   81 (95)
                      +.+.|+||++.+.+|++++|||+||..|+.+|   ...||+||+++....
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            45699999999999999999999999998643   568999999998654

>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=6e-17  Score=83.72  Aligned_cols=50  Identities=32%  Similarity=0.616  Sum_probs=40.0

Q ss_pred             CcccccccccCCCC-----CeecCCCCcchHHhHHHHhhC-CCCCCCCCccCCCCc
Q psy3884          32 VGCICPICHDEFKT-----PVQLTCCHIFCESCVTKWFDR-EQTCPLCRATLVDDP   81 (95)
Q Consensus        32 ~~~~C~IC~~~~~~-----p~~~~CgH~fc~~Ci~~~~~~-~~~CP~Cr~~~~~~~   81 (95)
                      ++..||||++.+..     .++++|||.||..|+..|+.. +..||+||+++...+
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            45699999986532     245699999999999999964 568999999987654

>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=1.6e-16  Score=78.69  Aligned_cols=46  Identities=26%  Similarity=0.666  Sum_probs=38.6

Q ss_pred             ccccccccCCCCC----eecCCCCcchHHhHHHHhhCC-CCCCCCCccCCC
Q psy3884          34 CICPICHDEFKTP----VQLTCCHIFCESCVTKWFDRE-QTCPLCRATLVD   79 (95)
Q Consensus        34 ~~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~-~~CP~Cr~~~~~   79 (95)
                      ++|+||++.+...    ..++|||.||..|+.+|+... ..||+||+++.+
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            4799999988643    345899999999999999854 579999999875

>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=99.52  E-value=4.7e-15  Score=80.65  Aligned_cols=47  Identities=28%  Similarity=0.619  Sum_probs=39.3

Q ss_pred             CcccccccccCCCC------------------CeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKT------------------PVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~------------------p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ....|+||++.+..                  .+.++|||.||..||.+|++.+.+||+||+++.
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            34479999887654                  245689999999999999999999999999875

>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=2.1e-14  Score=81.31  Aligned_cols=48  Identities=21%  Similarity=0.533  Sum_probs=38.6

Q ss_pred             cccccccccCCCCC------------------eecCCCCcchHHhHHHHhhC-----CCCCCCCCccCCCC
Q psy3884          33 GCICPICHDEFKTP------------------VQLTCCHIFCESCVTKWFDR-----EQTCPLCRATLVDD   80 (95)
Q Consensus        33 ~~~C~IC~~~~~~p------------------~~~~CgH~fc~~Ci~~~~~~-----~~~CP~Cr~~~~~~   80 (95)
                      +..|+||++.+..+                  ..++|||.||..||..|+..     +.+||+||..+...
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            44899999987532                  35689999999999999974     24799999988654

>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=99.34  E-value=4.9e-13  Score=67.61  Aligned_cols=48  Identities=23%  Similarity=0.603  Sum_probs=39.9

Q ss_pred             CcccccccccCCCCCeecCC-----CCcchHHhHHHHhh--CCCCCCCCCccCCC
Q psy3884          32 VGCICPICHDEFKTPVQLTC-----CHIFCESCVTKWFD--REQTCPLCRATLVD   79 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~C-----gH~fc~~Ci~~~~~--~~~~CP~Cr~~~~~   79 (95)
                      +...|+||++.+.++...+|     +|.||..|+..|+.  ++.+||+||+++..
T Consensus         5 d~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           5 DVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            45689999999888766655     59999999999995  45689999998764

>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=98.79  E-value=1.2e-09  Score=59.31  Aligned_cols=43  Identities=23%  Similarity=0.655  Sum_probs=32.9

Q ss_pred             cccccccccCCCC---CeecCCCCcchHHhHHHHhhC-----C---CCCCCCCc
Q psy3884          33 GCICPICHDEFKT---PVQLTCCHIFCESCVTKWFDR-----E---QTCPLCRA   75 (95)
Q Consensus        33 ~~~C~IC~~~~~~---p~~~~CgH~fc~~Ci~~~~~~-----~---~~CP~Cr~   75 (95)
                      ...|+||++.+..   +..++|||.||..|+..|+..     .   ..||.|+-
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            4599999998864   345589999999999999861     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=96.32  E-value=0.0028  Score=31.73  Aligned_cols=34  Identities=26%  Similarity=0.680  Sum_probs=27.9

Q ss_pred             CcccccccccCCCCCeecCC----CCcchHHhHHHHhh
Q psy3884          32 VGCICPICHDEFKTPVQLTC----CHIFCESCVTKWFD   65 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~C----gH~fc~~Ci~~~~~   65 (95)
                      ..+.|.+|.+.+++...+.|    +|.||..|-+..++
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik   44 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIK   44 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHH
Confidence            35799999999998755544    69999999998876

>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=95.52  E-value=0.011  Score=30.35  Aligned_cols=35  Identities=14%  Similarity=0.584  Sum_probs=26.6

Q ss_pred             ccCCCcccccccccCCCCCeecC---CCCcchHHhHHHH
Q psy3884          28 TLLGVGCICPICHDEFKTPVQLT---CCHIFCESCVTKW   63 (95)
Q Consensus        28 ~~~~~~~~C~IC~~~~~~p~~~~---CgH~fc~~Ci~~~   63 (95)
                      +....+..|.|| +.+.....+|   |+.+||..|+.+.
T Consensus        10 e~v~~D~mC~vC-~v~t~~~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          10 EPVVNDEMCDVC-EVWTAESLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCSCCCTTT-CCCCSSCCSSCSSSSSCCCHHHHHHH
T ss_pred             cCCCcCcccccc-CcccccceecceeecchhhHHHHHHh
Confidence            344567799999 6666655666   6789999999986

>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=94.20  E-value=0.012  Score=27.17  Aligned_cols=41  Identities=22%  Similarity=0.572  Sum_probs=28.2

Q ss_pred             cccccccCCCCCeec---CCCCcchHHhHHHHhhC----CCCCCCCCc
Q psy3884          35 ICPICHDEFKTPVQL---TCCHIFCESCVTKWFDR----EQTCPLCRA   75 (95)
Q Consensus        35 ~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~~----~~~CP~Cr~   75 (95)
                      .|.||...-....++   .|...||..|+..-+..    ...||.|+.
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   68899999999765442    347998865

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.41  E-value=0.051  Score=25.98  Aligned_cols=41  Identities=29%  Similarity=0.679  Sum_probs=29.3

Q ss_pred             cccccccccCCCCCeec---CCCCcchHHhHHHHhhCCCCCCCC
Q psy3884          33 GCICPICHDEFKTPVQL---TCCHIFCESCVTKWFDREQTCPLC   73 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~~~~~~~~~CP~C   73 (95)
                      ...|--|+..+.+....   .|++.||.+|=.-.-+.-..||-|
T Consensus        15 ~~~C~gC~~~l~~~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          15 ERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CCEETTTTEECTTSEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCccCCCCcCCCCceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            45799999888776444   688999999954322344689987

>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Effector domain of rabphilin-3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=90.15  E-value=0.17  Score=27.45  Aligned_cols=28  Identities=18%  Similarity=0.470  Sum_probs=20.5

Q ss_pred             cccccccccCCCC---Ce--ecCCCCcchHHhH
Q psy3884          33 GCICPICHDEFKT---PV--QLTCCHIFCESCV   60 (95)
Q Consensus        33 ~~~C~IC~~~~~~---p~--~~~CgH~fc~~Ci   60 (95)
                      ...|.+|...|..   ..  -..||+.||..|.
T Consensus        48 ~~~C~~C~~~f~~~~~~~~~C~~C~~~~C~~C~   80 (124)
T d1zbdb_          48 VNRCILCGEQLGMLGSASVVCEDCKKNVCTKCG   80 (124)
T ss_dssp             SSBCSSSCCBCSTTSCCEEECTTTCCEEETTSE
T ss_pred             CCcCcccCCcccCCCCCCCcCccCCcccccCCC
Confidence            3479999987652   22  2379999999995

>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=89.34  E-value=0.72  Score=23.49  Aligned_cols=49  Identities=24%  Similarity=0.570  Sum_probs=34.6

Q ss_pred             CcccccccccCCCC----Ceec---CCCCcchHHhHHH-HhhCCCCCCCCCccCCCC
Q psy3884          32 VGCICPICHDEFKT----PVQL---TCCHIFCESCVTK-WFDREQTCPLCRATLVDD   80 (95)
Q Consensus        32 ~~~~C~IC~~~~~~----p~~~---~CgH~fc~~Ci~~-~~~~~~~CP~Cr~~~~~~   80 (95)
                      ..-.|.||.+.+-.    ...+   .|+--.|+.|..- ....+..||.|+.++...
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~   71 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRL   71 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhh
Confidence            45599999987642    1333   4777789999863 334668999999887643

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.54  E-value=0.051  Score=34.11  Aligned_cols=45  Identities=18%  Similarity=0.508  Sum_probs=32.9

Q ss_pred             CcccccccccCCCCCeecC----CC--CcchHHhHHHHhhCCCCCCCCCcc
Q psy3884          32 VGCICPICHDEFKTPVQLT----CC--HIFCESCVTKWFDREQTCPLCRAT   76 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~----Cg--H~fc~~Ci~~~~~~~~~CP~Cr~~   76 (95)
                      ....||||.....-.++..    =|  +..|.-|-..|--....||.|...
T Consensus       163 ~~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~~~R~~C~~Cg~~  213 (290)
T d2fiya1         163 SRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEES  213 (290)
T ss_dssp             TCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCC
T ss_pred             cCCcCCCCCCcchhheeeccCCCCCceEEECCCCCCccccccccCCCCCCC
Confidence            4458999999765444432    23  457888999998888899999654

>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=88.36  E-value=0.31  Score=23.84  Aligned_cols=45  Identities=22%  Similarity=0.556  Sum_probs=29.3

Q ss_pred             CCcccccccccCCCCCeec---CCCCcchHHhHH------H---HhhCCCCCCCCCcc
Q psy3884          31 GVGCICPICHDEFKTPVQL---TCCHIFCESCVT------K---WFDREQTCPLCRAT   76 (95)
Q Consensus        31 ~~~~~C~IC~~~~~~p~~~---~CgH~fc~~Ci~------~---~~~~~~~CP~Cr~~   76 (95)
                      .....| ||.........+   .|.--||..|+.      .   .......||.|+..
T Consensus        14 ~~~~~C-iC~~~~~~~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          14 PNALYC-ICRQPHNNRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TTCCCS-TTCCCCCSSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCcCEE-ECCCccCCCeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            345568 898766554455   577789999982      1   11235789999644

>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=87.39  E-value=0.008  Score=28.14  Aligned_cols=39  Identities=28%  Similarity=0.702  Sum_probs=22.8

Q ss_pred             cccccccCCCCC----eecCCCCcchHHhHHHHhhCCCCCCCC
Q psy3884          35 ICPICHDEFKTP----VQLTCCHIFCESCVTKWFDREQTCPLC   73 (95)
Q Consensus        35 ~C~IC~~~~~~p----~~~~CgH~fc~~Ci~~~~~~~~~CP~C   73 (95)
                      .|.+|...|..-    .--.||.+||..|..........|..|
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C   44 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLC   44 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhH
Confidence            477788777632    122699999999965433333445554

>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=87.20  E-value=0.089  Score=22.38  Aligned_cols=27  Identities=11%  Similarity=0.290  Sum_probs=22.3

Q ss_pred             cccccccccCCCCCeecCCCCcchHHh
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESC   59 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~C   59 (95)
                      ...|.+|...+.+.+.-..|..||-.|
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            458999999999887778888887766

>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=86.42  E-value=0.16  Score=25.10  Aligned_cols=29  Identities=31%  Similarity=0.813  Sum_probs=21.3

Q ss_pred             cccccccccCCCCCe----ecCCCCcchHHhHH
Q psy3884          33 GCICPICHDEFKTPV----QLTCCHIFCESCVT   61 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~   61 (95)
                      ...|.+|...|.--.    --.||++||..|..
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~   45 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTA   45 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSC
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhC
Confidence            347999999876421    22699999999964

>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=86.27  E-value=0.11  Score=21.05  Aligned_cols=13  Identities=38%  Similarity=0.892  Sum_probs=7.8

Q ss_pred             cccccccccCCCC
Q psy3884          33 GCICPICHDEFKT   45 (95)
Q Consensus        33 ~~~C~IC~~~~~~   45 (95)
                      .+.||||...|+.
T Consensus         3 p~~cpic~qrfkr   15 (32)
T d2epqa1           3 PYSCPVCGLRFKR   15 (32)
T ss_dssp             SSEETTTTEECSC
T ss_pred             CcccchHHHHhhc
Confidence            3466777666653

>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=85.97  E-value=0.17  Score=24.54  Aligned_cols=28  Identities=25%  Similarity=0.655  Sum_probs=20.5

Q ss_pred             ccccccccCCCCCee----cCCCCcchHHhHH
Q psy3884          34 CICPICHDEFKTPVQ----LTCCHIFCESCVT   61 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~----~~CgH~fc~~Ci~   61 (95)
                      ..|.+|...|.--..    -.||.+||..|..
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            379999988763211    1699999999964

>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=85.84  E-value=0.075  Score=23.47  Aligned_cols=28  Identities=18%  Similarity=0.361  Sum_probs=23.9

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHh
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESC   59 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~C   59 (95)
                      ....|..|.+.++.+++..=+|.||..|
T Consensus        14 fG~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          14 YGTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CCCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             hCcccccccCEeeeeeeEecCcccCCCC
Confidence            4569999999999998888888898766

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.94  E-value=0.052  Score=27.76  Aligned_cols=47  Identities=15%  Similarity=0.475  Sum_probs=30.3

Q ss_pred             CcccccccccCCCCC--eec---CCCCcchHHhHHHHh-----h---CCCCCCCCCccCC
Q psy3884          32 VGCICPICHDEFKTP--VQL---TCCHIFCESCVTKWF-----D---REQTCPLCRATLV   78 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p--~~~---~CgH~fc~~Ci~~~~-----~---~~~~CP~Cr~~~~   78 (95)
                      ....|.||.......  .++   .|...||..|+...+     .   ....||.|.....
T Consensus        15 ~~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             CcCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            356899998754321  233   688899999975321     1   2467999965433

>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=84.83  E-value=0.16  Score=24.38  Aligned_cols=28  Identities=32%  Similarity=0.755  Sum_probs=20.7

Q ss_pred             ccccccccCCCCCe----ecCCCCcchHHhHH
Q psy3884          34 CICPICHDEFKTPV----QLTCCHIFCESCVT   61 (95)
Q Consensus        34 ~~C~IC~~~~~~p~----~~~CgH~fc~~Ci~   61 (95)
                      ..|.+|...|..-.    --.||.+||..|..
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            37999998876421    12699999999964

>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=84.37  E-value=0.32  Score=23.59  Aligned_cols=44  Identities=23%  Similarity=0.554  Sum_probs=29.1

Q ss_pred             cccccccccCCCCCeec--CCCCcchHHhHHHHhhC----CCCCCCCCccCC
Q psy3884          33 GCICPICHDEFKTPVQL--TCCHIFCESCVTKWFDR----EQTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~~----~~~CP~Cr~~~~   78 (95)
                      ...|.+|.+.  ...+.  .|...||..|+...+..    ...||.|+..-.
T Consensus         7 c~~C~~C~~~--~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           7 ATICRVCQKP--GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSCCSSSCSS--SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCc--CEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            3477788653  22233  68899999999865542    357999966543

>d2gmga1 a.4.5.82 (A:1-105) Hypothetical protein PF0610 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF0610-like
domain: Hypothetical protein PF0610
species: Pyrococcus furiosus [TaxId: 2261]

Probab=84.13  E-value=0.16  Score=27.02  Aligned_cols=33  Identities=18%  Similarity=0.578  Sum_probs=22.2

Q ss_pred             CeecCCCCcchHHhHHHHhhCCCCCCCCCccCCCCccc
Q psy3884          46 PVQLTCCHIFCESCVTKWFDREQTCPLCRATLVDDPAW   83 (95)
Q Consensus        46 p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   83 (95)
                      |.-..||-+|=     .-++..+.||.|+...-+.+.|
T Consensus        68 p~CrkCGfvFr-----~~~kkPSRCP~CKSE~Ie~P~F  100 (105)
T d2gmga1          68 AQCRKCGFVFK-----AEINIPSRCPKCKSEWIEEPRF  100 (105)
T ss_dssp             CBBTTTCCBCC-----CCSSCCSSCSSSCCCCBCCCCE
T ss_pred             hhhhhcCCeec-----ccCCCCCCCCCCCCccccCCce
Confidence            34446888872     2245668999999987766554

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {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: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.92  E-value=0.11  Score=22.18  Aligned_cols=27  Identities=11%  Similarity=0.218  Sum_probs=22.7

Q ss_pred             cccccccccCCCCCeecCCCCcchHHh
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESC   59 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~C   59 (95)
                      ...|..|...+...++..-|..||..|
T Consensus         8 apkC~~C~~~I~g~~v~Al~~~wHpeC   34 (35)
T d1x3ha1           8 SPKCGGCNRPVLENYLSAMDTVWHPEC   34 (35)
T ss_dssp             SCBCTTTCCBCCSSCEEETTEEECTTT
T ss_pred             ChhhhhcCCcccchheeecCCccCccc
Confidence            348999999999988888888888776

>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=83.27  E-value=0.16  Score=24.10  Aligned_cols=42  Identities=24%  Similarity=0.508  Sum_probs=27.6

Q ss_pred             cccccccccCCCCCeec--CCCCcchHHhHHHHhh----CCCCCCCCCcc
Q psy3884          33 GCICPICHDEFKTPVQL--TCCHIFCESCVTKWFD----REQTCPLCRAT   76 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~--~CgH~fc~~Ci~~~~~----~~~~CP~Cr~~   76 (95)
                      ...|.+|.+.-  .++.  .|.-.||..|+...+.    ....||.|+..
T Consensus         9 ~~~C~~C~~~g--~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_           9 MEFCRVCKDGG--ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             CSSCTTTCCCS--SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             cCCCcCCCCCC--eEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            34799998632  2222  6888999999864443    23579999654

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.04  E-value=0.51  Score=23.06  Aligned_cols=41  Identities=27%  Similarity=0.505  Sum_probs=24.9

Q ss_pred             ccccccccCCCCCeec-C---CCC-cchHHhHHHHhh---CCCCCCCCCcc
Q psy3884          34 CICPICHDEFKTPVQL-T---CCH-IFCESCVTKWFD---REQTCPLCRAT   76 (95)
Q Consensus        34 ~~C~IC~~~~~~p~~~-~---CgH-~fc~~Ci~~~~~---~~~~CP~Cr~~   76 (95)
                      ..| ||.+......++ .   |-. -||..|+. ...   ....||.|+..
T Consensus        17 ~~C-iC~~~~~~~~i~c~~~~C~~~wfH~~Cvg-l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          17 TYC-LCNQVSYGEMIGCDNEQCPIEWFHFSCVS-LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCS-TTCCCCCSSEECCSCTTCSCCCEETTTTT-CSSCCSSCCCCTTTSSC
T ss_pred             CEE-EeCCCCCCCEEEEECCCCCCcCccCccCC-CCcCCCCcEECcCCccc
Confidence            456 999765444333 2   433 58999983 221   23589999754

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=82.10  E-value=0.27  Score=24.60  Aligned_cols=11  Identities=36%  Similarity=1.645  Sum_probs=10.2

Q ss_pred             chHHhHHHHhh
Q psy3884          55 FCESCVTKWFD   65 (95)
Q Consensus        55 fc~~Ci~~~~~   65 (95)
                      ||..|+.+|..
T Consensus        40 FCRNCLskWy~   50 (79)
T d2o35a1          40 FCRNCLSNWYR   50 (79)
T ss_dssp             CCHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999985

>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=81.83  E-value=0.0091  Score=29.71  Aligned_cols=41  Identities=27%  Similarity=0.603  Sum_probs=26.1

Q ss_pred             cccccccccCCCCCeecCCCCcchHHhHHHHhhCCCCCCCCCccCC
Q psy3884          33 GCICPICHDEFKTPVQLTCCHIFCESCVTKWFDREQTCPLCRATLV   78 (95)
Q Consensus        33 ~~~C~IC~~~~~~p~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   78 (95)
                      ++.||.|...+...    =||.+|..|-.. +.....||.|.+++.
T Consensus         2 ~~~CP~C~~eL~~~----~~~~~C~~C~~~-~~~~a~CPdC~~~Le   42 (71)
T d2jnea1           2 ELHCPQCQHVLDQD----NGHARCRSCGEF-IEMKALCPDCHQPLQ   42 (71)
T ss_dssp             CCBCSSSCSBEEEE----TTEEEETTTCCE-EEEEEECTTTCSBCE
T ss_pred             CCcCCCccCccccc----CCCEehhhhhhh-heeEEeCCccccHHH
Confidence            35899998875531    256667666432 123457999988875

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {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: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.81  E-value=0.41  Score=19.91  Aligned_cols=28  Identities=18%  Similarity=0.389  Sum_probs=23.1

Q ss_pred             CcccccccccCCCCCeecCCCCcchHHh
Q psy3884          32 VGCICPICHDEFKTPVQLTCCHIFCESC   59 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p~~~~CgH~fc~~C   59 (95)
                      ....|..|.+.+..|+++.=.|.||..|
T Consensus         7 fge~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           7 FGEFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             HHHHhhhhHhhcccceeeecccccCCCC
Confidence            3458999999999998888888888765

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=80.69  E-value=0.092  Score=25.13  Aligned_cols=45  Identities=20%  Similarity=0.502  Sum_probs=29.8

Q ss_pred             CcccccccccCCCCC-eec---CCCCcchHHhHHHHhh-----CCCCCCCCCcc
Q psy3884          32 VGCICPICHDEFKTP-VQL---TCCHIFCESCVTKWFD-----REQTCPLCRAT   76 (95)
Q Consensus        32 ~~~~C~IC~~~~~~p-~~~---~CgH~fc~~Ci~~~~~-----~~~~CP~Cr~~   76 (95)
                      ....|.+|.+..... ..+   .|+.-||..|+..-..     ....||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            345899999866543 233   6888899999852111     34689999653