Psyllid ID: psy5823

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440----
Protein Sequence
MKQTEEDDQAVVRQSAPMFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
Secondary Structure (PSIPRED)
cccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccEEEccccccccccccccEEcccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccHHHHHHHHHHHccHHHHccccHHHHHHcccHHHHHHHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEccccccccEcccccccccccccccccccccccccccccccccccccccHHHcccccccccccHHHcccccccccccccccccccHHHcccccccccccccccHccccccccccccccHHHHccccHHHHcHcHccccccccccccccHHHcccHHHHHcccccHHHHHHHHHHccccccccccccccccccHHHcccccccccccccHHHHccHHHccccccccccccccHHHccccHHHHHcccccccccccccccccccccccccHcccccccEEEEEccccccccccccEEccccccccEcccEcccEccccccccccHHHHHHHccccccccccccccccccccccccEEEcccccccccccHHHHHHHHHHHHHHccccHEcccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
MKQTEEDDQAVvrqsapmfpfqfspfpsvagpgliprlppmlqhplipqplvhppgtpppskmkdkvspkdktspkekmsskektspkekeyskvkdvelgvtpmvpnivkvtssedlgeikkdksikkdKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKmkedkekpvEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEkersshekevipkltfkfgtdmeektkresspkivikpvkspspppvaaadeydtgdskqvwicpacgvqddgslpmigcdgcdawYHWVCVGLvaepetsdwfcpkcskvdegsrkekkkrgrkkkthqDIIMSTyrferdpselvdksacagsraDLKLCLLEtdcvqvdrktprqclreglapQCEALKNTFFECKRSLLdnrtrfrghkgy
Flexible Loop (DISEMBL)
MKQTEEDDQAVVRQSAPMFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGtpppskmkdkvspkdktspkekmsskektspkekeyskvkdvelgvtpmvpnivkvtssedlgeikkdksikkdkkthkkkekekikkkkdkkdkdkiknkekdkekkvdkekekgkkeekekkeekefkmkedkekpvekirkeekdsekekkskdkdkklkkeklkkkkkekersshekevipkltfkfgtdmeektkresspkivikpvkspspppVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAepetsdwfcpkcskvdegsrkekkkrgrkkkthqdiimstyrferdpselVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALkntffeckrslldnrtrfrghkgy
Low Complexity Region (SEG)
MKQTEEDDQAVVRQsapmfpfqfspfpsVAGPGLIPRLPPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDktspkekmsskektspkekeyskVKDVELGVTPMVPNIVKVTSSEDLGeikkdksikkdkkthkkkekekikkkkdkkdkdkiknkekdkekkvdkekekgkkeekekkeekefkmkedkekPVekirkeekdsekekkskdkdkklkkeklkkkkkekersshekeVIPKLTFKFGTDMEEKTKRESspkivikpvkspspppvaaaDEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSrkekkkrgrkkkTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
Disordered region (IsUnstruct)
*****************************************************************************************************V**MV*NI**********************************************************************************************************************************************************************************KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC***************************TY***********KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLD***********
Disordered Region (DISOPRED)
************RQSAPMFPFQFSPFPSVAGPGL**********************************************************************************************************************************************************************************************************************************************************GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCP*********************************************CAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR*****
Disordered Region (DISEMBL)
***********VRQSAPMFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGT************************************KVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKS***************************************************************************************************************EVIPKLTFKFGTD**********PKIVIKPVK****************DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK*******************QDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
Disordered Region (DISPRO)
*******DQAVVRQSAPMFPFQFSPFPSVAGPGLIPRLPPM*Q*PLI****************************************************************************************************************************************************************************************************************************************DEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDE******************IIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKQTEEDDQAVVRQSAPMFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
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	444	2.2.26 [Sep-21-2011]
Q3ZCK8	74	Cytochrome c oxidase asse	yes	N/A	0.141	0.851	0.636	4e-17
Q5HZG4	932	Transcription initiation	yes	N/A	0.114	0.054	0.641	6e-17
Q5VWG9	929	Transcription initiation	yes	N/A	0.114	0.054	0.641	1e-16
Q28CA1	75	Cytochrome c oxidase asse	yes	N/A	0.146	0.866	0.617	1e-16
Q5RFJ0	74	Cytochrome c oxidase asse	yes	N/A	0.141	0.851	0.621	2e-16
Q5EAW9	845	Transcription initiation	N/A	N/A	0.110	0.057	0.647	2e-15
A1L3N6	75	Cytochrome c oxidase asse	N/A	N/A	0.137	0.813	0.609	4e-15
Q5F489	930	Transcription initiation	no	N/A	0.114	0.054	0.603	6e-15
Q86WW8	74	Cytochrome c oxidase asse	no	N/A	0.139	0.837	0.630	3e-14
Q99M07	74	Cytochrome c oxidase asse	no	N/A	0.139	0.837	0.6	1e-13

>sp|Q3ZCK8|COA5_BOVIN Cytochrome c oxidase assembly factor 5 OS=Bos taurus GN=COA5 PE=3 SV=1

 Score = 89.7 bits (221), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 52/66 (78%), Gaps = 3/66 (4%)

Query: 379 SACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRF 438
            ACAG + DL LCLL++DCV  + K+PRQCL+EG    C+ALK +FFECKRS+LD R+RF
Sbjct: 12  GACAGVKEDLGLCLLQSDCVLKEGKSPRQCLKEG---NCKALKYSFFECKRSMLDARSRF 68

Query: 439 RGHKGY 444
           RG KGY
Sbjct: 69  RGRKGY 74

Involved in an early step of the mitochondrial complex IV assembly process.
Bos taurus (taxid: 9913)

>sp|Q5HZG4|TAF3_MOUSE Transcription initiation factor TFIID subunit 3 OS=Mus musculus GN=Taf3 PE=1 SV=2

 Score = 89.0 bits (219), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 38/53 (71%), Gaps = 2/53 (3%)

Query: 288 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 339
            Q+WICP C   DDGS PMIGCD CD WYHW CVG++A  PE   WFCPKC+ 
Sbjct: 865 NQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCAN 916

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.

Mus musculus (taxid: 10090)

>sp|Q5VWG9|TAF3_HUMAN Transcription initiation factor TFIID subunit 3 OS=Homo sapiens GN=TAF3 PE=1 SV=1

 Score = 88.2 bits (217), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 38/53 (71%), Gaps = 2/53 (3%)

Query: 288 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCSK 339
            Q+WICP C   DDGS PMIGCD CD WYHW CVG++ A PE   WFCPKC+ 
Sbjct: 863 NQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKCAN 914

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.

Homo sapiens (taxid: 9606)

>sp|Q28CA1|COA5_XENTR Cytochrome c oxidase assembly factor 5 OS=Xenopus tropicalis GN=coa5 PE=3 SV=1

 Score = 87.8 bits (216), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/68 (61%), Positives = 52/68 (76%), Gaps = 3/68 (4%)

Query: 377 DKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRT 436
           DK  CAG + DLK CLL+TDCV  + K+P++CL+EG    C+AL+ TFFECKRS+LD R 
Sbjct: 11  DKHPCAGVKEDLKSCLLQTDCVLQEGKSPKECLKEGY---CKALQVTFFECKRSILDTRA 67

Query: 437 RFRGHKGY 444
           RFRG KGY
Sbjct: 68  RFRGRKGY 75

Involved in an early step of the mitochondrial complex IV assembly process.

Xenopus tropicalis (taxid: 8364)

>sp|Q5RFJ0|COA5_PONAB Cytochrome c oxidase assembly factor 5 OS=Pongo abelii GN=Coa5 PE=3 SV=1

 Score = 87.8 bits (216), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 48/66 (72%), Gaps = 3/66 (4%)

Query: 379 SACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRF 438
            AC G + DL  CLLE+DCV  + K+PRQCL+EG    C +LK  FFECKRS+LDNR RF
Sbjct: 12  GACGGLKEDLGACLLESDCVVQEGKSPRQCLKEGY---CNSLKYAFFECKRSVLDNRARF 68

Query: 439 RGHKGY 444
           RG KGY
Sbjct: 69  RGRKGY 74

Involved in an early step of the mitochondrial complex IV assembly process.

Pongo abelii (taxid: 9601)

>sp|Q5EAW9|TAF3_XENLA Transcription initiation factor TFIID subunit 3 OS=Xenopus laevis GN=taf3 PE=2 SV=1

 Score = 84.3 bits (207), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 35/51 (68%), Gaps = 2/51 (3%)

Query: 288 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 337
            Q+WICP C   DDGS PMIGCD CD WYHW CVG+  A PE   WFC KC
Sbjct: 779 NQIWICPGCNKPDDGS-PMIGCDQCDDWYHWPCVGINAAPPEDEQWFCTKC 828

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.

Xenopus laevis (taxid: 8355)

>sp|A1L3N6|COA5_XENLA Cytochrome c oxidase assembly factor 5 OS=Xenopus laevis GN=coa5 PE=3 SV=1

 Score = 83.2 bits (204), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 39/64 (60%), Positives = 50/64 (78%), Gaps = 3/64 (4%)

Query: 381 CAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRG 440
           C G + DLK CLL++DCV  + K+P++CL+EG    C+AL+ TFFECKRS+LDNR RFRG
Sbjct: 15  CGGVKEDLKNCLLQSDCVLQEGKSPKECLKEG---YCKALQVTFFECKRSILDNRARFRG 71

Query: 441 HKGY 444
            KGY
Sbjct: 72  RKGY 75

Involved in an early step of the mitochondrial complex IV assembly process.

Xenopus laevis (taxid: 8355)

>sp|Q5F489|TAF3_CHICK Transcription initiation factor TFIID subunit 3 OS=Gallus gallus GN=TAF3 PE=2 SV=1

 Score = 82.4 bits (202), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 32/53 (60%), Positives = 35/53 (66%), Gaps = 2/53 (3%)

Query: 288 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 339
            Q+W CP C   DDGS PMIGCD CD WYHW CVG+ A  PE   WFC KC+ 
Sbjct: 864 NQIWFCPGCNKPDDGS-PMIGCDDCDDWYHWPCVGITAAPPEEMQWFCSKCAN 915

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.

Gallus gallus (taxid: 9031)

>sp|Q86WW8|COA5_HUMAN Cytochrome c oxidase assembly factor 5 OS=Homo sapiens GN=COA5 PE=1 SV=1

 Score = 80.5 bits (197), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 41/65 (63%), Positives = 49/65 (75%), Gaps = 3/65 (4%)

Query: 380 ACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR 439
           ACAG + DL  CLL++DCV  + K+PRQCL+EG    C +LK  FFECKRS+LDNR RFR
Sbjct: 13  ACAGLKEDLGACLLQSDCVVQEGKSPRQCLKEGY---CNSLKYAFFECKRSVLDNRARFR 69

Query: 440 GHKGY 444
           G KGY
Sbjct: 70  GRKGY 74

Involved in an early step of the mitochondrial complex IV assembly process.

Homo sapiens (taxid: 9606)

>sp|Q99M07|COA5_MOUSE Cytochrome c oxidase assembly factor 5 OS=Mus musculus GN=Coa5 PE=2 SV=1

 Score = 77.8 bits (190), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/65 (60%), Positives = 49/65 (75%), Gaps = 3/65 (4%)

Query: 380 ACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR 439
           ACAG + DL  CLL++ CV  + K+PRQCL+EG    C AL+ +FFECKRS+LD R+RFR
Sbjct: 13  ACAGVKEDLGACLLQSACVLQEGKSPRQCLKEG---NCRALQYSFFECKRSMLDARSRFR 69

Query: 440 GHKGY 444
           G KGY
Sbjct: 70  GRKGY 74

Involved in an early step of the mitochondrial complex IV assembly process.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	444
195380361	80	GJ21319 [Drosophila virilis] gi|19414373	0.159	0.887	0.694	1e-20
193713718	590	PREDICTED: hypothetical protein LOC10016	0.193	0.145	0.521	5e-20
270015055	865	hypothetical protein TcasGA2_TC014217 [T	0.155	0.079	0.578	6e-20
357614210	81	hypothetical protein KGM_12107 [Danaus p	0.173	0.950	0.653	6e-20
328700739	906	PREDICTED: hypothetical protein LOC10016	0.153	0.075	0.586	8e-20
195149688	80	GL10830 [Drosophila persimilis] gi|19845	0.159	0.887	0.694	1e-19
193671822	79	PREDICTED: uncharacterized protein C2orf	0.166	0.936	0.653	2e-19
118793122	82	AGAP011820-PA [Anopheles gambiae str. PE	0.159	0.865	0.662	3e-19
194754419	80	GF12904 [Drosophila ananassae] gi|190620	0.157	0.875	0.647	9e-19
195058006	80	GH23123 [Drosophila grimshawi] gi|193899	0.159	0.887	0.652	1e-18

>gi|195380361|ref|XP_002048939.1| GJ21319 [Drosophila virilis] gi|194143736|gb|EDW60132.1| GJ21319 [Drosophila virilis]

 Score =  107 bits (266), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 50/72 (69%), Positives = 64/72 (88%), Gaps = 1/72 (1%)

Query: 374 ELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE-GLAPQCEALKNTFFECKRSLL 432
           +L D++ACAG RADLK+CLLE+DC ++DRKTPRQCL++  + P+C+ L+NTF+ECKRSLL
Sbjct: 9   KLADETACAGVRADLKMCLLESDCCRLDRKTPRQCLQDNNVPPECQVLRNTFYECKRSLL 68

Query: 433 DNRTRFRGHKGY 444
           DNR RFRGHKGY
Sbjct: 69  DNRQRFRGHKGY 80

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193713718|ref|XP_001949510.1| PREDICTED: hypothetical protein LOC100161166 [Acyrthosiphon pisum]

 Score =  105 bits (261), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 49/94 (52%), Positives = 60/94 (63%), Gaps = 8/94 (8%)

Query: 264 VIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL 323
           VI PV   +PPP    DE       QVWICP C   DDGS PMIGCDGCD WYHWVCVG+
Sbjct: 503 VIPPVNE-TPPPAFYFDEA----GNQVWICPMCTKPDDGS-PMIGCDGCDVWYHWVCVGI 556

Query: 324 VAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKT 357
              P+ + WFCP+C  + + +++ K KRGR +K 
Sbjct: 557 QCPPDCAVWFCPRC--LAKRAQQPKGKRGRPRKN 588

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270015055|gb|EFA11503.1| hypothetical protein TcasGA2_TC014217 [Tribolium castaneum]

 Score =  105 bits (261), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 44/76 (57%), Positives = 50/76 (65%), Gaps = 7/76 (9%)

Query: 263 IVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG 322
           IV  P+  P+PP       Y   D  +VWICP CG QDDGS PMIGCDGCDAWYHWVCVG
Sbjct: 770 IVDVPIVPPAPP-----SRYIDADGNEVWICPGCGSQDDGS-PMIGCDGCDAWYHWVCVG 823

Query: 323 LVAEPETS-DWFCPKC 337
           +   P+ S DW+C  C
Sbjct: 824 IQVPPDDSEDWYCRHC 839

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357614210|gb|EHJ68964.1| hypothetical protein KGM_12107 [Danaus plexippus]

 Score =  105 bits (261), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 51/78 (65%), Positives = 60/78 (76%), Gaps = 1/78 (1%)

Query: 368 FERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAP-QCEALKNTFFE 426
           F  D   LVD S CAG RADLKLCLL +DC +  +KTPR+CL++GL P +C  L+ +FFE
Sbjct: 4   FGPDEVGLVDTSPCAGIRADLKLCLLNSDCCKEHKKTPRECLKDGLVPNECLQLRQSFFE 63

Query: 427 CKRSLLDNRTRFRGHKGY 444
           CKRSLLDNR RFRGHKGY
Sbjct: 64  CKRSLLDNRRRFRGHKGY 81

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328700739|ref|XP_001945181.2| PREDICTED: hypothetical protein LOC100167514 [Acyrthosiphon pisum]

 Score =  104 bits (260), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 44/75 (58%), Positives = 52/75 (69%), Gaps = 7/75 (9%)

Query: 283 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS--KV 340
           D G+  QVWICP CG QDDGS PM+GCDGCDAWYHWVCVG+   P+ + W+CP C   + 
Sbjct: 827 DAGN--QVWICPTCGKQDDGS-PMVGCDGCDAWYHWVCVGIQCPPDCAVWYCPTCLLKRA 883

Query: 341 DEGSRK--EKKKRGR 353
           + G     EK KRGR
Sbjct: 884 ERGVTAPVEKAKRGR 898

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195149688|ref|XP_002015788.1| GL10830 [Drosophila persimilis] gi|198456467|ref|XP_002138246.1| GA24504 [Drosophila pseudoobscura pseudoobscura] gi|194109635|gb|EDW31678.1| GL10830 [Drosophila persimilis] gi|198135625|gb|EDY68804.1| GA24504 [Drosophila pseudoobscura pseudoobscura]

 Score =  104 bits (259), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 50/72 (69%), Positives = 62/72 (86%), Gaps = 1/72 (1%)

Query: 374 ELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE-GLAPQCEALKNTFFECKRSLL 432
           +L D++ACAG RADLK+CLLE+DC +VDRKTPRQCL +  + P+C+ L+NTF+ECKRSLL
Sbjct: 9   KLADETACAGVRADLKMCLLESDCCRVDRKTPRQCLMDNNVPPECQVLRNTFYECKRSLL 68

Query: 433 DNRTRFRGHKGY 444
           DNR RFRG KGY
Sbjct: 69  DNRQRFRGRKGY 80

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193671822|ref|XP_001951331.1| PREDICTED: uncharacterized protein C2orf64 homolog [Acyrthosiphon pisum]

 Score =  103 bits (257), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/75 (65%), Positives = 58/75 (77%), Gaps = 1/75 (1%)

Query: 371 DPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE-GLAPQCEALKNTFFECKR 429
           D  EL D   CAG RADLK+CLLE+DC +++RK P+ CL+E    P+C AL+NTFFECKR
Sbjct: 5   DEGELTDHRPCAGVRADLKMCLLESDCCKIERKLPKDCLKEKNCPPECLALQNTFFECKR 64

Query: 430 SLLDNRTRFRGHKGY 444
           SLLDNR RFRG KGY
Sbjct: 65  SLLDNRQRFRGRKGY 79

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|118793122|ref|XP_320694.3| AGAP011820-PA [Anopheles gambiae str. PEST] gi|116117227|gb|EAA00792.3| AGAP011820-PA [Anopheles gambiae str. PEST]

 Score =  102 bits (255), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/74 (66%), Positives = 60/74 (81%), Gaps = 3/74 (4%)

Query: 374 ELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLR--EGLAP-QCEALKNTFFECKRS 430
           EL DKSACAG RADLK+CLL++DC + ++KTPR+CL   +G  P +C  L+NTFFECKRS
Sbjct: 9   ELADKSACAGVRADLKMCLLQSDCCKKEKKTPRECLNRTDGSVPSECFVLRNTFFECKRS 68

Query: 431 LLDNRTRFRGHKGY 444
           +LDNR RFRG KGY
Sbjct: 69  MLDNRQRFRGRKGY 82

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194754419|ref|XP_001959492.1| GF12904 [Drosophila ananassae] gi|190620790|gb|EDV36314.1| GF12904 [Drosophila ananassae]

 Score =  101 bits (251), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 46/71 (64%), Positives = 59/71 (83%), Gaps = 1/71 (1%)

Query: 375 LVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLR-EGLAPQCEALKNTFFECKRSLLD 433
           L D++ACAG RADLK+CLLE+DC ++ + TPRQCL+   + P+C+ L+NTF+ECKRSLLD
Sbjct: 10  LADETACAGVRADLKMCLLESDCCRIAKNTPRQCLQANNVPPECQVLRNTFYECKRSLLD 69

Query: 434 NRTRFRGHKGY 444
           NR RFRG KGY
Sbjct: 70  NRQRFRGRKGY 80

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195058006|ref|XP_001995367.1| GH23123 [Drosophila grimshawi] gi|193899573|gb|EDV98439.1| GH23123 [Drosophila grimshawi]

 Score =  100 bits (250), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 47/72 (65%), Positives = 63/72 (87%), Gaps = 1/72 (1%)

Query: 374 ELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE-GLAPQCEALKNTFFECKRSLL 432
           +L D ++CAG RADLK+CLLE++C ++D+KTPRQCL++  + P+C+ L+NTF+ECKRSLL
Sbjct: 9   KLADVTSCAGVRADLKMCLLESECCRLDKKTPRQCLQDNSVPPECQVLRNTFYECKRSLL 68

Query: 433 DNRTRFRGHKGY 444
           DNR RFRGHKGY
Sbjct: 69  DNRQRFRGHKGY 80

Source: Drosophila grimshawi

Species: Drosophila grimshawi

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	444
UNIPROTKB|E1BIA9	932	TAF3 "Uncharacterized protein"	0.108	0.051	0.68	1.9e-21
UNIPROTKB|F1RUM5	794	TAF3 "Uncharacterized protein"	0.108	0.060	0.7	1.5e-19
UNIPROTKB|F1NZW0	874	TAF3 "Transcription initiation	0.110	0.056	0.627	3.6e-19
UNIPROTKB|Q5F489	930	TAF3 "Transcription initiation	0.110	0.052	0.627	4.3e-19
ZFIN|ZDB-GENE-030131-6406	898	taf3 "TAF3 RNA polymerase II,	0.110	0.054	0.666	6.2e-19
UNIPROTKB|F1PI56	932	TAF3 "Uncharacterized protein"	0.110	0.052	0.666	6.7e-19
UNIPROTKB|Q3ZCK8	74	COA5 "Cytochrome c oxidase ass	0.139	0.837	0.646	1.7e-18
UNIPROTKB|Q5VWG9	929	TAF3 "Transcription initiation	0.110	0.052	0.666	1.7e-18
MGI|MGI:2388097	932	Taf3 "TAF3 RNA polymerase II,	0.110	0.052	0.666	1.7e-18
UNIPROTKB|E1C792	75	COA5 "Uncharacterized protein"	0.164	0.973	0.551	5.8e-18

UNIPROTKB|E1BIA9 TAF3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 215 (80.7 bits), Expect = 1.9e-21, Sum P(3) = 1.9e-21
 Identities = 34/50 (68%), Positives = 37/50 (74%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 337
             Q+WICP C   DDGS PMIGCD CD WYHW CVG++A P E   WFCPKC
Sbjct:   867 QIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKC 915

GO:0051457 "maintenance of protein location in nucleus" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1RUM5 TAF3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 221 (82.9 bits), Expect = 1.5e-19, Sum P(2) = 1.5e-19
 Identities = 35/50 (70%), Positives = 37/50 (74%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 337
             Q+WICP C   DDGS PMIGCDGCD WYHW CVG+ A P E   WFCPKC
Sbjct:   729 QIWICPGCNKPDDGS-PMIGCDGCDDWYHWPCVGITAAPPEEMQWFCPKC 777

GO:0051457 "maintenance of protein location in nucleus" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1NZW0 TAF3 "Transcription initiation factor TFIID subunit 3" [Gallus gallus (taxid:9031)]

 Score = 203 (76.5 bits), Expect = 3.6e-19, Sum P(2) = 3.6e-19
 Identities = 32/51 (62%), Positives = 35/51 (68%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 338
             Q+W CP C   DDGS PMIGCD CD WYHW CVG+ A P E   WFC KC+
Sbjct:   809 QIWFCPGCNKPDDGS-PMIGCDDCDDWYHWPCVGITAAPPEEMQWFCSKCA 858

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0051457 "maintenance of protein location in nucleus" evidence=IEA

UNIPROTKB|Q5F489 TAF3 "Transcription initiation factor TFIID subunit 3" [Gallus gallus (taxid:9031)]

 Score = 203 (76.5 bits), Expect = 4.3e-19, Sum P(2) = 4.3e-19
 Identities = 32/51 (62%), Positives = 35/51 (68%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 338
             Q+W CP C   DDGS PMIGCD CD WYHW CVG+ A P E   WFC KC+
Sbjct:   865 QIWFCPGCNKPDDGS-PMIGCDDCDDWYHWPCVGITAAPPEEMQWFCSKCA 914

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-030131-6406 taf3 "TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated facto" [Danio rerio (taxid:7955)]

 Score = 208 (78.3 bits), Expect = 6.2e-19, Sum P(2) = 6.2e-19
 Identities = 34/51 (66%), Positives = 37/51 (72%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 338
             Q+WICP C   DDGS PMIGCD CD WYHW CVGL+A P E   WFC KC+
Sbjct:   833 QIWICPGCNKADDGS-PMIGCDECDDWYHWPCVGLLAAPPEDQSWFCIKCA 882

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IPI

GO:0044212 "transcription regulatory region DNA binding" evidence=IPI

GO:0030097 "hemopoiesis" evidence=IMP

GO:0005669 "transcription factor TFIID complex" evidence=ISS

UNIPROTKB|F1PI56 TAF3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 216 (81.1 bits), Expect = 6.7e-19, Sum P(2) = 6.7e-19
 Identities = 34/51 (66%), Positives = 38/51 (74%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 338
             Q+WICP C   DDGS PMIGCD CD WYHW CVG++A P E   WFCPKC+
Sbjct:   867 QIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCA 916

GO:0051457 "maintenance of protein location in nucleus" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q3ZCK8 COA5 "Cytochrome c oxidase assembly factor 5" [Bos taurus (taxid:9913)]

 Score = 223 (83.6 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 42/65 (64%), Positives = 52/65 (80%)

Query:   380 ACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR 439
             ACAG + DL LCLL++DCV  + K+PRQCL+EG    C+ALK +FFECKRS+LD R+RFR
Sbjct:    13 ACAGVKEDLGLCLLQSDCVLKEGKSPRQCLKEG---NCKALKYSFFECKRSMLDARSRFR 69

Query:   440 GHKGY 444
             G KGY
Sbjct:    70 GRKGY 74

GO:0005739 "mitochondrion" evidence=IEA

UNIPROTKB|Q5VWG9 TAF3 "Transcription initiation factor TFIID subunit 3" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 1.7e-18, Sum P(2) = 1.7e-18
 Identities = 34/51 (66%), Positives = 38/51 (74%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCS 338
             Q+WICP C   DDGS PMIGCD CD WYHW CVG++ A PE   WFCPKC+
Sbjct:   864 QIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMTAPPEEMQWFCPKCA 913

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0002039 "p53 binding" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0051457 "maintenance of protein location in nucleus" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=IDA

MGI|MGI:2388097 Taf3 "TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)]

 Score = 216 (81.1 bits), Expect = 1.7e-18, Sum P(2) = 1.7e-18
 Identities = 34/51 (66%), Positives = 38/51 (74%)

Query:   289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 338
             Q+WICP C   DDGS PMIGCD CD WYHW CVG++A P E   WFCPKC+
Sbjct:   866 QIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCA 915

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO;IDA

GO:0002039 "p53 binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO;ISA

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

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

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043433 "negative regulation of sequence-specific DNA binding transcription factor activity" evidence=ISO;IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051457 "maintenance of protein location in nucleus" evidence=ISO

UNIPROTKB|E1C792 COA5 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 43/78 (55%), Positives = 53/78 (67%)

Query:   367 RFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFE 426
             ++  D  E  D  AC+G R DL+ CLLE+ CV  + K+PRQCLREG    C+ L+ TFF 
Sbjct:     3 KYYEDKEE--DGQACSGVREDLRQCLLESPCVLQENKSPRQCLREG---HCKGLQLTFFA 57

Query:   427 CKRSLLDNRTRFRGHKGY 444
             CKRS+LD R RFRG KGY
Sbjct:    58 CKRSMLDTRARFRGRKGY 75

GO:0005739 "mitochondrion" 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)
Q28CA1	COA5_XENTR	No assigned EC number	0.6176	0.1463	0.8666	yes	N/A
Q3ZCK8	COA5_BOVIN	No assigned EC number	0.6363	0.1418	0.8513	yes	N/A
Q5RFJ0	COA5_PONAB	No assigned EC number	0.6212	0.1418	0.8513	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	444
pfam10203	68	pfam10203, Pet191_N, Cytochrome c oxidase assembly	6e-22
smart00249	47	smart00249, PHD, PHD zinc finger	6e-10
pfam00628	51	pfam00628, PHD, PHD-finger	1e-09
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	8e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-07
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	8e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	9e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-05
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	2e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-05
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	4e-05
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	4e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-05
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	4e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	5e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	5e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	6e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-05
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	7e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	9e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	9e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	1e-04
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	1e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	1e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-04
pfam09592	228	pfam09592, DUF2031, Protein of unknown function (D	2e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-04
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	2e-04
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	2e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	3e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	3e-04
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	3e-04
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	3e-04
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	4e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	4e-04
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	4e-04
pfam13166	713	pfam13166, AAA_13, AAA domain	4e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	5e-04
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	5e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-04
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	9e-04
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	9e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	0.001
COG5034	271	COG5034, TNG2, Chromatin remodeling protein, conta	0.001
pfam13476	204	pfam13476, AAA_23, AAA domain	0.001
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.001
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.001
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.001
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.001
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.002
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	0.002
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.002
cd09730	579	cd09730, Cas8a1_I-A, CRISPR/Cas system-associated	0.002
COG1293	564	COG1293, COG1293, Predicted RNA-binding protein ho	0.002
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.003
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.003
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.003
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.004
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.004
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.004
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	0.004
COG5185	622	COG5185, HEC1, Protein involved in chromosome segr	0.004
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004

>gnl|CDD|192483 pfam10203, Pet191_N, Cytochrome c oxidase assembly protein PET191

 Score = 88.5 bits (220), Expect = 6e-22
 Identities = 36/67 (53%), Positives = 47/67 (70%), Gaps = 3/67 (4%)

Query: 377 DKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAP---QCEALKNTFFECKRSLLD 433
             S+C G R DL  CLLE+DCV+ +++TPR+CL+E L     +C AL+  FFECKR +LD
Sbjct: 1   MGSSCKGLREDLAECLLESDCVKKEKRTPRECLKEPLKELPEECIALRKAFFECKRGMLD 60

Query: 434 NRTRFRG 440
            R RFRG
Sbjct: 61  MRKRFRG 67

Pet191_N is the conserved N-terminal of a family of conserved proteins found from nematodes to humans. It carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex. Length = 68

>gnl|CDD|214584 smart00249, PHD, PHD zinc finger

 Score = 54.1 bits (130), Expect = 6e-10
 Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKC 337
            C  CG  DDG   ++ CDGCD WYH  C+G  L+ E     W+CPKC
Sbjct: 1   YCSVCGKPDDGGE-LLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Length = 47

>gnl|CDD|201356 pfam00628, PHD, PHD-finger

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 4/50 (8%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPET---SDWFCPKCS 338
            C  CG  DD    ++ CDGCD W+H  C+G   EPE     +W+CP+C 
Sbjct: 1   YCAVCGKVDDDGE-LLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPECK 49

PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3. Length = 51

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 60.0 bits (146), Expect = 1e-09
 Identities = 33/177 (18%), Positives = 63/177 (35%)

Query: 57  TPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSE 116
           T      +++   K K    +  S    T  + KE  + K         V   +     +
Sbjct: 6   TKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKD 65

Query: 117 DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEE 176
                + D   KK K   K    +   KKK K + D  K  EK      D +    K  +
Sbjct: 66  TDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDID 125

Query: 177 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 233
              + + +    +D +   + I  ++ D + ++   D D   + E+ K+ K+ ++ S
Sbjct: 126 VLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLS 182

Length = 509

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 57.1 bits (137), Expect = 1e-08
 Identities = 38/143 (26%), Positives = 62/143 (43%), Gaps = 4/143 (2%)

Query: 120  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
            E KK    KK  +  KKK     KK ++ K   +    E +      +  E+  +  ++K
Sbjct: 1313 EAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKK 1372

Query: 180  KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
            KEE + K    K+K  EK + +E   + E+  K  D+  K    KKK  E ++ + EK+ 
Sbjct: 1373 KEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKK 1432

Query: 240  IPKLTFKFGTDMEEKTKRESSPK 262
              +   K     EE  K + + K
Sbjct: 1433 ADEAKKK----AEEAKKADEAKK 1451

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.9 bits (134), Expect = 3e-08
 Identities = 44/172 (25%), Positives = 84/172 (48%), Gaps = 3/172 (1%)

Query: 70   KDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKK 129
            + + +  E  +++EK    EK+  + K              K   ++   E  K K+ + 
Sbjct: 1351 EAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADEL 1410

Query: 130  DKKTHKKKEKEKIKKK---KDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFK 186
             K    KK+ ++ KKK   K K D+ K K +E  K  +  K+ E+ KK E+ KK+ +E K
Sbjct: 1411 KKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAK 1470

Query: 187  MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
              ++ +K  E+ +K ++  +K +++K K  + KK    KKK ++ + + E +
Sbjct: 1471 KADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAK 1522

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 5e-08
 Identities = 32/129 (24%), Positives = 63/129 (48%), Gaps = 1/129 (0%)

Query: 111  KVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKE 170
            K   ++   +  K K+ +  K     K + +    + +  ++K +  EK KE+   K   
Sbjct: 1323 KAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADA 1382

Query: 171  -KGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 229
             K K EEK+K +E + K +EDK+K  E  +      + ++  K  ++K K ++ KKK +E
Sbjct: 1383 AKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEE 1442

Query: 230  KERSSHEKE 238
             +++   K+
Sbjct: 1443 AKKADEAKK 1451

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 55.1 bits (132), Expect = 5e-08
 Identities = 47/175 (26%), Positives = 95/175 (54%), Gaps = 7/175 (4%)

Query: 88   KEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK-KKEKEKIKKKK 146
            K+ E +K+K  EL         V+    ++  E KK + +KK ++ +K K  +E  K ++
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 147  DKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSE 206
            DKK  ++ K  E+D++K     +   K+ E+ KK E+  K + +++K  E+++K E++++
Sbjct: 1673 DKKKAEEAKKAEEDEKK---AAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENK 1729

Query: 207  ---KEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRE 258
               +E K + ++ K K E+ KK ++EK++ +H K+   K   +   + E   + E
Sbjct: 1730 IKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEE 1784

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 53.2 bits (127), Expect = 2e-07
 Identities = 48/180 (26%), Positives = 82/180 (45%), Gaps = 6/180 (3%)

Query: 62   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 121
            K K + + K   + K+K    +K +   K  ++    E           +    E     
Sbjct: 1321 KKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEE---AK 1377

Query: 122  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVD---KEKEKGKKEEKE 178
            KK  + KK  +  KK ++ K K ++DKK  D++K     K+K  +   K +EK K +E +
Sbjct: 1378 KKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAK 1437

Query: 179  KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
            KK E+  K  E K+K  E  + EE   + E+  K  + K K E+ KK  + K+++   K+
Sbjct: 1438 KKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKK 1497

Length = 2084

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 53.0 bits (128), Expect = 2e-07
 Identities = 27/86 (31%), Positives = 48/86 (55%), Gaps = 9/86 (10%)

Query: 133 THKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKE 192
           T  KK  +KIKK  +K +K         K ++  KEK+K     K+K+EE+E + ++ +E
Sbjct: 403 TGSKKATKKIKKIVEKAEK---------KREEEKKEKKKKAFAGKKKEEEEEEEKEKKEE 453

Query: 193 KPVEKIRKEEKDSEKEKKSKDKDKKL 218
           +  E+  + E++ E+E++ K K   L
Sbjct: 454 EKEEEEEEAEEEKEEEEEKKKKQATL 479

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 52.6 bits (127), Expect = 2e-07
 Identities = 23/81 (28%), Positives = 50/81 (61%)

Query: 147 DKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSE 206
            +++ + +   +K  +K     ++  KK E+EKKE+K+      K++  E+  KE+K+ E
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 207 KEKKSKDKDKKLKKEKLKKKK 227
           KE++ ++ +++ ++E+ KKKK
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 52.6 bits (127), Expect = 2e-07
 Identities = 28/81 (34%), Positives = 52/81 (64%), Gaps = 1/81 (1%)

Query: 117 DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEE 176
              EI+     KK  K   KK  EK +KK++++ K+K K     K+K+ ++E+EK KKEE
Sbjct: 395 TEEEIEFLTGSKKATKK-IKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEE 453

Query: 177 KEKKEEKEFKMKEDKEKPVEK 197
           ++++EE+E + ++++E+  +K
Sbjct: 454 EKEEEEEEAEEEKEEEEEKKK 474

Length = 482

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 52.8 bits (126), Expect = 3e-07
 Identities = 38/143 (26%), Positives = 67/143 (46%), Gaps = 4/143 (2%)

Query: 120  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
            E KK    KK  +  KK ++ K K ++ KK  D  K K ++ +K  +  K + +    E 
Sbjct: 1300 EKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEA 1359

Query: 180  KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
            +  +E     +K+K   K + +    + E+K K  + K K E+ KKK  E ++++  K+ 
Sbjct: 1360 EAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKK 1419

Query: 240  IPKLTFKFGTDMEEKTKRESSPK 262
              +   K     EEK K + + K
Sbjct: 1420 ADEAKKK----AEEKKKADEAKK 1438

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 52.6 bits (126), Expect = 3e-07
 Identities = 32/126 (25%), Positives = 65/126 (51%)

Query: 109 IVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKE 168
            VK                 K+ K    KE+EK K++  ++ K K +  +++ + +  KE
Sbjct: 76  AVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKE 135

Query: 169 KEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
           + K K+  KEK++EKE K++E +++  EK R+  +   + KK   K    KK++  +++K
Sbjct: 136 EAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEK 195

Query: 229 EKERSS 234
           +++ + 
Sbjct: 196 QRQAAR 201

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 51.5 bits (124), Expect = 5e-07
 Identities = 25/83 (30%), Positives = 53/83 (63%), Gaps = 2/83 (2%)

Query: 150 DKDKIKN--KEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEK 207
            +++I+     K   KK+ K  EK +K+ +E+K+EK+ K    K+K  E+  ++EK  E+
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 208 EKKSKDKDKKLKKEKLKKKKKEK 230
           +++ +++ ++ K+E+ +KKKK+ 
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKKQA 477

Length = 482

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 51.4 bits (123), Expect = 5e-07
 Identities = 37/149 (24%), Positives = 73/149 (48%)

Query: 89  EKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDK 148
           E + S  + V+             T      + +  K  +K+K+  K+++K+K +K K++
Sbjct: 68  ESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEE 127

Query: 149 KDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKE 208
               K K + K+K    +KEKEK KK E+ +  E+E K +  + K   K   ++K   K+
Sbjct: 128 PKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKK 187

Query: 209 KKSKDKDKKLKKEKLKKKKKEKERSSHEK 237
           K+  +++K+ +  +   K K +E   +E+
Sbjct: 188 KEPPEEEKQRQAAREAVKGKPEEPDVNEE 216

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 50.9 bits (123), Expect = 8e-07
 Identities = 40/160 (25%), Positives = 88/160 (55%), Gaps = 19/160 (11%)

Query: 109 IVKVTSSEDLGEIKKD-KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKV-D 166
           + K  +   + E +++ K I ++ K    KE E IKK+   + K++I     + EK++ +
Sbjct: 24  VRKKIAEAKIKEAEEEAKRILEEAK----KEAEAIKKEALLEAKEEIHKLRNEFEKELRE 79

Query: 167 KEKEKGKKEEK-EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKK 225
           +  E  K E++  +KEE   +  E  EK  E++ K+EK+ E++++  +K ++  +E +++
Sbjct: 80  RRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEE 139

Query: 226 KKKEKER----SSHE-KEVIPKLTFKFGTDMEEKTKRESS 260
           + +E ER    ++ E KE++ +        +EE+ + E++
Sbjct: 140 QLQELERISGLTAEEAKEILLE-------KVEEEARHEAA 172

Length = 520

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 51.3 bits (122), Expect = 9e-07
 Identities = 46/176 (26%), Positives = 93/176 (52%), Gaps = 3/176 (1%)

Query: 64   KDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKK 123
            K K     K    + M+ ++    K+ E +++++V            +     +  +IK 
Sbjct: 1563 KKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKA 1622

Query: 124  DKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEK 183
            ++ +KK ++  KK E+ K K+ ++KK  +++K  E+  E K+   +E  K EE +KK E+
Sbjct: 1623 EE-LKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEE--ENKIKAAEEAKKAEEDKKKAEE 1679

Query: 184  EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
              K +ED++K  E ++KE ++++K ++ K K+ + KK+  + KK E+E     +E 
Sbjct: 1680 AKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEA 1735

Length = 2084

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 50.7 bits (122), Expect = 9e-07
 Identities = 24/72 (33%), Positives = 45/72 (62%)

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKE 181
           KK     K      +K++E+ KK+K KK     K +E+++E+K  KE+EK ++EE+ ++E
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465

Query: 182 EKEFKMKEDKEK 193
           ++E + K+ K+ 
Sbjct: 466 KEEEEEKKKKQA 477

Length = 482

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 50.0 bits (120), Expect = 2e-06
 Identities = 42/219 (19%), Positives = 75/219 (34%), Gaps = 17/219 (7%)

Query: 59   PPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKD----------VELGVTPM--V 106
              SK K K S   K   K+K   K+K+S  + + + V             +L   P    
Sbjct: 1158 LKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKK 1217

Query: 107  PNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEK--- 163
             N       +D  +  K K     +   KK    K  +  D+   D +  + K K     
Sbjct: 1218 SNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKR 1277

Query: 164  --KVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 221
               V        K    +           K+K  +++       +K+KKS+ K  + KK 
Sbjct: 1278 VSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKS 1337

Query: 222  KLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 260
            K + K+    +SS       K      ++ ++ ++ + S
Sbjct: 1338 KTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDS 1376

Length = 1388

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 48.0 bits (114), Expect = 8e-06
 Identities = 51/223 (22%), Positives = 95/223 (42%), Gaps = 16/223 (7%)

Query: 61  SKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 120
            K   K         KE  +   K   KEKE  K +  +    P           ++  +
Sbjct: 81  EKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKP-----------KEEPK 129

Query: 121 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEK-KVDKEKEKGKKEEKEK 179
            +K K   K+K+  K+KEKEK KK ++ +D+++ K +E+ + K +  K  +K    +K++
Sbjct: 130 DRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKE 189

Query: 180 KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKD-KDKKLKKEKLKKKKKEKERSSHEKE 238
             E+E + +  +E    K  + + + E+EK+  D KD++     +++ +  +      + 
Sbjct: 190 PPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRS 249

Query: 239 VIPKLTFKFGTDMEEKTKRESSPKIVIKPVKS---PSPPPVAA 278
                       M     RESS +   +P  S   PS  P +A
Sbjct: 250 SSSLKKPDPSPSMASPETRESSKRTETRPRTSLRPPSARPASA 292

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 47.7 bits (114), Expect = 9e-06
 Identities = 25/139 (17%), Positives = 51/139 (36%), Gaps = 5/139 (3%)

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKE 181
              K+    ++  KKK K+   K K K    K + KE  + KK        ++ ++    
Sbjct: 4   ASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKK-----TPEQIDQVLIF 58

Query: 182 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIP 241
                   D     +  +K+ K + K   +K   KK  K++L   KK +++++ +K+   
Sbjct: 59  LSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDL 118

Query: 242 KLTFKFGTDMEEKTKRESS 260
                     +     +  
Sbjct: 119 NYVKDIDVLNQADDDDDDD 137

Length = 509

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.4 bits (112), Expect = 1e-05
 Identities = 44/183 (24%), Positives = 89/183 (48%), Gaps = 6/183 (3%)

Query: 61   SKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 120
            ++ K + + K K   K+K  + +K + ++K+  + K            + K  +++   +
Sbjct: 1362 AEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKAD 1421

Query: 121  IKKDKSIKKDKKTHKKKEKEKIKK----KKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEE 176
              K K+ +K K    KK+ E+ KK    KK  ++  K +  +K  E+    ++ K K EE
Sbjct: 1422 EAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEE 1481

Query: 177  KEKKEEKEFKMKEDKEKPVEKIRKEE--KDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
             +K +E + K +E K+K  E  +  E  K +++ KK+++  K  + +K ++ KK  E   
Sbjct: 1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541

Query: 235  HEK 237
             E+
Sbjct: 1542 AEE 1544

Length = 2084

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 47.7 bits (113), Expect = 1e-05
 Identities = 35/132 (26%), Positives = 73/132 (55%), Gaps = 2/132 (1%)

Query: 109 IVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKE 168
           + K          +  +  K+ K   ++ +    ++++ K +  K++ ++ D E+K+ + 
Sbjct: 261 LEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKES 320

Query: 169 KEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSK--DKDKKLKKEKLKKK 226
           +++ KK EKE K+EKE   + +KE    +I++E ++ E+E+  K  +K ++L++E L KK
Sbjct: 321 EKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKK 380

Query: 227 KKEKERSSHEKE 238
           K E ER S   +
Sbjct: 381 KLESERLSSAAK 392

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 47.7 bits (113), Expect = 1e-05
 Identities = 33/145 (22%), Positives = 77/145 (53%), Gaps = 3/145 (2%)

Query: 116 EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE 175
           E+   +  D     +++    +E  + ++++ +  K +++ KE++   +V KE ++ +KE
Sbjct: 223 EEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELE-KEEEILAQVLKENKEEEKE 281

Query: 176 EKEKKEEKEFKMKEDKEKPVEKIRKE--EKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 233
           +K ++EE +   KE++E   E ++ E  + D E++ K  +K+ K  +++LKK+K+E E  
Sbjct: 282 KKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEEL 341

Query: 234 SHEKEVIPKLTFKFGTDMEEKTKRE 258
             E + +         + E+  K +
Sbjct: 342 EKELKELEIKREAEEEEEEQLEKLQ 366

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 47.2 bits (113), Expect = 1e-05
 Identities = 26/161 (16%), Positives = 64/161 (39%), Gaps = 6/161 (3%)

Query: 113 TSSEDLGEIKKDKSIKKDKKTHK----KKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKE 168
            SS++L E  K+  I  + K+H     ++E  K + K++ +++ K + +E    +  ++ 
Sbjct: 15  VSSKELLEKLKELGI--EVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEA 72

Query: 169 KEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
           K +       ++  +     E   +P E       ++   +    K  K KK    KKKK
Sbjct: 73  KAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKK 132

Query: 229 EKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVK 269
            K +++   +       +       + +++   +   + + 
Sbjct: 133 PKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIP 173

Length = 746

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 47.1 bits (111), Expect = 2e-05
 Identities = 52/223 (23%), Positives = 105/223 (47%), Gaps = 7/223 (3%)

Query: 76   KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK 135
            +E     E+    E+E  KV+ ++           ++  +E+  +IK  +  KK ++  K
Sbjct: 1616 EEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKK 1675

Query: 136  K-----KEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKED 190
            K     K +E  +KK  +  K + +  +K +E K  + +EK K EE +K EE+     E+
Sbjct: 1676 KAEEAKKAEED-EKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734

Query: 191  KEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK-EKERSSHEKEVIPKLTFKFGT 249
             +K  E+ +K+ ++++K+++ K K   LKKE+ KK ++  KE+ +  +E + +   K   
Sbjct: 1735 AKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRM 1794

Query: 250  DMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWI 292
            ++++K K        I          +  + E +    K+V  
Sbjct: 1795 EVDKKIKDIFDNFANIIEGGKEGNLVINDSKEMEDSAIKEVAD 1837

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 46.0 bits (109), Expect = 2e-05
 Identities = 49/230 (21%), Positives = 96/230 (41%), Gaps = 21/230 (9%)

Query: 52  VHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVK 111
           V   G+  P+            S KE+   KE+   ++K+                   K
Sbjct: 80  VEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKK-------------------K 120

Query: 112 VTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEK-KVDKEKE 170
               ++  + +K K   K+K+  K+KEKEK KK ++ +D+++ K +E+ + K +  K  +
Sbjct: 121 KEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPK 180

Query: 171 KGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKD-KDKKLKKEKLKKKKKE 229
           K    +K++  E+E + +  +E    K  + + + E+EK+  D KD++     +++ +  
Sbjct: 181 KKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESR 240

Query: 230 KERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAA 279
           +      +             M     RESS +   +P  S  PP    A
Sbjct: 241 QSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETRPRTSLRPPSARPA 290

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 46.3 bits (111), Expect = 2e-05
 Identities = 42/151 (27%), Positives = 84/151 (55%), Gaps = 26/151 (17%)

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKK--KDKKDK-DKIKNKEK---DKEKKVDKEKEKGKKE 175
           K+ ++IKK+     K+E  K++ +  K+ +++ ++++  EK    KE+ +D++ E  +K 
Sbjct: 49  KEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKR 108

Query: 176 EKE---KKEEKEFKMK--EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK--KK 228
           E+E   K++E E K +  E KE+ +E++ +E+   E E+ S      L  E+ K+   +K
Sbjct: 109 EEELEKKEKELEQKQQELEKKEEELEELIEEQLQ-ELERIS-----GLTAEEAKEILLEK 162

Query: 229 EKERSSHEKEVIPKLTFKFGTDMEEKTKRES 259
            +E + HE  V+ K       ++EE+ K E+
Sbjct: 163 VEEEARHEAAVLIK-------EIEEEAKEEA 186

Length = 520

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 45.7 bits (109), Expect = 3e-05
 Identities = 22/80 (27%), Positives = 51/80 (63%), Gaps = 3/80 (3%)

Query: 160 DKEKKV---DKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK 216
           ++E +     K+  K  K+  EK E+K  + K++K+K     +K+E++ E+EK+ K+++K
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 217 KLKKEKLKKKKKEKERSSHE 236
           + ++E+ +++K+E+E    +
Sbjct: 456 EEEEEEAEEEKEEEEEKKKK 475

Length = 482

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 45.9 bits (109), Expect = 3e-05
 Identities = 28/120 (23%), Positives = 49/120 (40%), Gaps = 1/120 (0%)

Query: 74  SPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKT 133
           S     + K K  P    YS V  +   +           ++    + KK+    + KK 
Sbjct: 10  SFFSGTTQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKK 69

Query: 134 HKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEK 193
            +KK+K+K +KK+ K +  + K   K  +K    +K+  K +  E  +    K+ E  EK
Sbjct: 70  SEKKKKKKKEKKEPKSEG-ETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEK 128

Length = 413

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 46.2 bits (110), Expect = 3e-05
 Identities = 26/122 (21%), Positives = 62/122 (50%)

Query: 119 GEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKE 178
           GEI   +   ++ +   ++ +E++++ K+K +  K + +E++   +  ++     +E KE
Sbjct: 302 GEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKE 361

Query: 179 KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
           + EEK   + E+ E+  E +R+E  + E E      + +  K +++  ++  ER S   E
Sbjct: 362 ELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLE 421

Query: 239 VI 240
            +
Sbjct: 422 DL 423

Length = 1163

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 45.6 bits (108), Expect = 4e-05
 Identities = 25/97 (25%), Positives = 47/97 (48%), Gaps = 12/97 (12%)

Query: 121 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKK 180
            K  + +K +      K +E +K+   K            K  +V  E +   +E + K 
Sbjct: 350 TKLYEEVKSNTDLSGDKRQELLKEYNKKLQD------YTKKLGEVKDETDA-SEEAEAKA 402

Query: 181 EEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKK 217
           +E++ K +E+++K     +KE+ D +KEK+ KD+ KK
Sbjct: 403 KEEKLKQEENEKK-----QKEQADEDKEKRQKDERKK 434

Length = 434

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 25/93 (26%), Positives = 52/93 (55%), Gaps = 2/93 (2%)

Query: 124 DKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEK 183
           +KS++K ++  K  + +  + KK     + I + ++  + K +++ EK   E KEKK  K
Sbjct: 276 EKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKK--K 333

Query: 184 EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK 216
           E K +E K+K +E++ +  +  E +   K+++K
Sbjct: 334 EKKKEEKKKKQIERLEERIEKLEVQATDKEENK 366

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 45.2 bits (107), Expect = 4e-05
 Identities = 23/109 (21%), Positives = 55/109 (50%), Gaps = 1/109 (0%)

Query: 123 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEE 182
             K  ++ KK  ++ E+ + ++  ++  + +++ +   ++     E+   + EEK+K+ E
Sbjct: 63  AKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAE 122

Query: 183 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
            E K K+  E   +   + EK +++E K + +++   K   + KKK  E
Sbjct: 123 -EAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAE 170

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 45.7 bits (108), Expect = 4e-05
 Identities = 27/99 (27%), Positives = 57/99 (57%), Gaps = 5/99 (5%)

Query: 148 KKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK-KEEKEFKMKEDKEKPVEKIRKEE--KD 204
            + +  I N ++ +EK  +K+ +K + E KEK  ++KE  + ++ + PV++   +E  K 
Sbjct: 5   NRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLKI 64

Query: 205 SEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE--KEVIP 241
           +++ KKS  ++ K   E LK K++ ++   +E  ++ IP
Sbjct: 65  ADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIP 103

Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. Length = 887

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 24/145 (16%), Positives = 74/145 (51%), Gaps = 3/145 (2%)

Query: 114 SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGK 173
              +  + + +K  +   +  K+ ++E+ +KK  +++   +  +E++ + ++ K + +  
Sbjct: 252 EEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKV 311

Query: 174 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 233
            +E++ KE ++   K +KE   +K ++E ++ EKE K  +  ++ ++E+ ++ +K +E+ 
Sbjct: 312 DDEEKLKESEKELKKLEKEL--KKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKL 369

Query: 234 SHEKEVIPKLTFKFGTDMEEKTKRE 258
              +E +     K  ++      + 
Sbjct: 370 EQLEEEL-LAKKKLESERLSSAAKL 393

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed

 Score = 45.6 bits (109), Expect = 5e-05
 Identities = 32/111 (28%), Positives = 60/111 (54%), Gaps = 12/111 (10%)

Query: 135 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK----KEEKEFKMKED 190
           K +E E + K+ +K  ++  + KEK +E++ DK  E+ +KE ++     K+E +  +KE 
Sbjct: 535 KAEEAEALLKEAEKLKEELEEKKEKLQEEE-DKLLEEAEKEAQQAIKEAKKEADEIIKEL 593

Query: 191 KEKPVEKIRKEEKDSEKEKKSKDKDKKLKK--EKLKKKKKEKERSSHEKEV 239
           ++      +K    S K  +  +  K+L K  EK +KKKK+++    E +V
Sbjct: 594 RQL-----QKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEELKV 639

Length = 782

>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 45.2 bits (107), Expect = 5e-05
 Identities = 24/103 (23%), Positives = 41/103 (39%)

Query: 129 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMK 188
            +KK H+K +K+  K  K    KD  K K K K+K   K       +     +    +  
Sbjct: 48  INKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFA 107

Query: 189 EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
                 + +  K + +  K+K + +K    KK+K+   K E  
Sbjct: 108 GPLAISLMRKPKPKTEKLKKKITVNKSTNKKKKKVLSSKDELI 150

Length = 742

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 44.9 bits (107), Expect = 6e-05
 Identities = 19/66 (28%), Positives = 40/66 (60%)

Query: 177 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 236
            +K  +K  K+ E  EK  E+ +KE+K      K K+++++ +KEK +++K+E+E  + E
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 237 KEVIPK 242
           ++   +
Sbjct: 465 EKEEEE 470

Length = 482

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 44.8 bits (106), Expect = 6e-05
 Identities = 25/104 (24%), Positives = 55/104 (52%), Gaps = 1/104 (0%)

Query: 128 KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEK-EFK 186
           +  ++  +K+ +++   +K  K  ++   + ++K+K+ ++ K K   E K K E + E K
Sbjct: 84  RAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKK 143

Query: 187 MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 230
            KE+ +K  E+  K +  +E +KK+ +  KK + E   K + + 
Sbjct: 144 AKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKA 187

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.0 bits (106), Expect = 7e-05
 Identities = 36/127 (28%), Positives = 70/127 (55%), Gaps = 3/127 (2%)

Query: 116 EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE 175
           + L +  K+K  +++K   KK+E+E+ K +   K+K+  + +EK ++ KV++EKE+  K 
Sbjct: 740 KLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKA 799

Query: 176 EKEKKEEKEFKMK---EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 232
           ++E+    E ++K   E  E+    I +EEK  E+E +    + K +++  K  ++E ER
Sbjct: 800 QEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELER 859

Query: 233 SSHEKEV 239
              E   
Sbjct: 860 LEEEITK 866

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated

 Score = 44.8 bits (106), Expect = 7e-05
 Identities = 35/128 (27%), Positives = 55/128 (42%), Gaps = 5/128 (3%)

Query: 118 LGEIKKDKSIKKDKKTHKKKEKEKIKK--KKDKKDKDKIKNKEKDKEKKVDKEK--EKGK 173
           L   K + SIK +KKT    +    KK    ++ +K+ +      K K    +K   +  
Sbjct: 368 LENKKIEISIKPEKKTINNSQIITTKKINIVEESNKNSVHFDTLYKTKIFYHKKKINQNN 427

Query: 174 KEEKEKKEEK-EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 232
           KE+  KKEE  E +  +  EK  +     +     ++K  +KD +L K  L+K  K K  
Sbjct: 428 KEQDIKKEELLEKEFVKKSEKIPKNDELLDNLELAKQKFFNKDIELSKNMLQKFNKFKNE 487

Query: 233 SSHEKEVI 240
            S E   I
Sbjct: 488 ESAENSFI 495

Length = 605

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 44.2 bits (105), Expect = 9e-05
 Identities = 24/136 (17%), Positives = 47/136 (34%), Gaps = 1/136 (0%)

Query: 103 TPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE 162
           T            E   ++KK  +  K K    K+E ++  + K K  + +I        
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPE-QIDQVLIFLS 60

Query: 163 KKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 222
             V    +  + +  +KK +   K    K    +K++ E   S+K +K    DK      
Sbjct: 61  GMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNY 120

Query: 223 LKKKKKEKERSSHEKE 238
           +K      +    + +
Sbjct: 121 VKDIDVLNQADDDDDD 136

Length = 509

>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 43.2 bits (102), Expect = 9e-05
 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 7/84 (8%)

Query: 128 KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKM 187
             D++  KK + ++  + ++ K+++K     +DKE K D EKE  + EE+ ++E      
Sbjct: 45  AADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEE------ 98

Query: 188 KEDKEKPVEKIRKEEKDSEKEKKS 211
            E+     EK   EEK     +K 
Sbjct: 99  DEESSDENEKE-TEEKTESNVEKE 121

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. Length = 214

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 44.2 bits (105), Expect = 1e-04
 Identities = 23/159 (14%), Positives = 55/159 (34%)

Query: 60  PSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLG 119
             +  D+V        K+   + E   PK+K  +  K              ++ SS+   
Sbjct: 48  TPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAE 107

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
           +                    +     D  D D + + + D +   + + E    ++ + 
Sbjct: 108 KKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDD 167

Query: 180 KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKL 218
           ++E++ + KE ++   +     ++D  +  +   KD KL
Sbjct: 168 EDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKL 206

Length = 509

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.7 bits (105), Expect = 1e-04
 Identities = 43/140 (30%), Positives = 66/140 (47%), Gaps = 4/140 (2%)

Query: 125  KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKE 184
            K+ +  K    KK +E  K  + KK ++K K  E  K +++ K +EK K EE +K EE +
Sbjct: 1517 KAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDK 1576

Query: 185  FKMKEDKE--KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPK 242
                   E  K  E+ R EE     E++ K K ++ KK +  K K E+ +    +E   K
Sbjct: 1577 NMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKK--AEEEKKK 1634

Query: 243  LTFKFGTDMEEKTKRESSPK 262
            +      + EEK K E   K
Sbjct: 1635 VEQLKKKEAEEKKKAEELKK 1654

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.4 bits (104), Expect = 1e-04
 Identities = 48/182 (26%), Positives = 79/182 (43%), Gaps = 7/182 (3%)

Query: 62   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 121
            K  ++    D+   K +   K+    K+   +K K  E           K   ++   E 
Sbjct: 1385 KKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEA--KKKAEEKKKADEAKKKAEE 1442

Query: 122  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNK--EKDKEKKVDKEKEKGKKEEKEK 179
             K     K K    KK +E  KK ++ K  D+ K K  E  K  +  K+ E+ KK+  E 
Sbjct: 1443 AKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEA 1502

Query: 180  KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKK---KKKEKERSSHE 236
            K+  E K K D+ K  E+ +K ++  + E+  K  + K  +EK K    KK E+ + + E
Sbjct: 1503 KKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEE 1562

Query: 237  KE 238
            K+
Sbjct: 1563 KK 1564

Length = 2084

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.4 bits (104), Expect = 1e-04
 Identities = 48/180 (26%), Positives = 79/180 (43%), Gaps = 10/180 (5%)

Query: 62   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 121
            K K +   K     K+  ++K+K    +K+  + K  +           K   ++   E 
Sbjct: 1397 KKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKAD-EAKKKAEEAKKADEAKKKAEE 1455

Query: 122  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVD----KEKEKGKKEEK 177
             K     K K    KK  E  KK ++ K  D+ K K ++ +KK D      + K K +E 
Sbjct: 1456 AKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEA 1515

Query: 178  EKKEEK----EFKMKEDKEKPVEKIRKEEKDSEKE-KKSKDKDKKLKKEKLKKKKKEKER 232
            +K EE     E K  E+ +K  E  + EEK    E KK+++  K  +K+K ++ KK +E 
Sbjct: 1516 KKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEED 1575

Length = 2084

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.8 bits (103), Expect = 1e-04
 Identities = 33/166 (19%), Positives = 81/166 (48%), Gaps = 3/166 (1%)

Query: 76  KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSE---DLGEIKKDKSIKKDKK 132
           +E++ S ++   KE+E       E         + +        +  E+K +    + +K
Sbjct: 251 QEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRK 310

Query: 133 THKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKE 192
              +++ ++ +K+  K +K+  K KE+ +E + + ++ + K+E +E++EE+  K++E  E
Sbjct: 311 VDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLE 370

Query: 193 KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
           +  E++  ++K   +   S  K K+ + E   +++KE +      E
Sbjct: 371 QLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSE 416

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 20/86 (23%), Positives = 48/86 (55%), Gaps = 2/86 (2%)

Query: 142 IKKKKDKKDKDKIKNKEKDKE-KKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRK 200
            K  ++ K    +   ++ +  K+ +K+ +   K+  E K+E +   +E + K  E+  K
Sbjct: 350 TKLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETD-ASEEAEAKAKEEKLK 408

Query: 201 EEKDSEKEKKSKDKDKKLKKEKLKKK 226
           +E++ +K+K+  D+DK+ +++  +KK
Sbjct: 409 QEENEKKQKEQADEDKEKRQKDERKK 434

Length = 434

>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 28/111 (25%), Positives = 47/111 (42%), Gaps = 12/111 (10%)

Query: 138  EKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEK 197
              E + KK ++K K  I + EK           K  + E   +EEKE   + + E   EK
Sbjct: 1494 GNENVNKKINQKKKGFIPSNEK-----------KSIEIENRNQEEKEPAGQGELESDKEK 1542

Query: 198  IRKEEKDSEKEKKSKDKD-KKLKKEKLKKKKKEKERSSHEKEVIPKLTFKF 247
                E     ++K+ ++D  +   +K K KK+ K  +  E +   K   +F
Sbjct: 1543 KGNLESVLSNQEKNIEEDYAESDIKKRKNKKQYKSNTEAELDFFLKRYLRF 1593

Length = 1832

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 31/151 (20%), Positives = 79/151 (52%), Gaps = 14/151 (9%)

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEK-- 177
           ++   + + K      KKE E +KK+   + K+++     + E+++ + + + ++ E+  
Sbjct: 26  KLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRLERRL 85

Query: 178 EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS--- 234
            ++EE   +  E  +K  E + K+EK+   ++K+ D+ ++  +E + ++++E ER S   
Sbjct: 86  LQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERISGLT 145

Query: 235 --HEKEVIPKLTFKFGTDMEEKTKRESSPKI 263
               KE++ +       ++EE+ + E++  I
Sbjct: 146 QEEAKEILLE-------EVEEEARHEAAKLI 169

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 44.0 bits (103), Expect = 2e-04
 Identities = 46/159 (28%), Positives = 80/159 (50%), Gaps = 9/159 (5%)

Query: 120  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEK--KVDKEKEKGKKEEK 177
            E KK    KK  +  KK ++ K K ++ KK  D+ K   + K+K  +  K +E  K +E 
Sbjct: 1468 EAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEA 1527

Query: 178  EKKEEK----EFKMKEDKEKPVEKIRKEE-KDSEKEKKSKDKDKKLKKEKLKKKKKEKER 232
            +K EE     E K  E+K+K  E  + EE K +E++KK+++  K  + + +  +K E+ +
Sbjct: 1528 KKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAK 1587

Query: 233  SSHEK--EVIPKLTFKFGTDMEEKTKRESSPKIVIKPVK 269
             + E   E + KL  +      E+ K+    KI  + +K
Sbjct: 1588 KAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELK 1626

Length = 2084

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 37/143 (25%), Positives = 69/143 (48%), Gaps = 3/143 (2%)

Query: 144 KKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEK 203
           +K   K         K+ + +  KE+EK K++ KE+K++K+ K KE+ +    K   +EK
Sbjct: 81  EKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEK 140

Query: 204 DSEKEK---KSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 260
              KEK   K K  ++   +E+ KK+++ + +S  +K    K   K     EE+ +R+++
Sbjct: 141 RPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAA 200

Query: 261 PKIVIKPVKSPSPPPVAAADEYD 283
            + V    + P        +E D
Sbjct: 201 REAVKGKPEEPDVNEEREKEEDD 223

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 43.8 bits (103), Expect = 2e-04
 Identities = 29/150 (19%), Positives = 67/150 (44%), Gaps = 1/150 (0%)

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
             KK++  K  ++T    E   I  ++ K  + K+K + K   +    +++   +EE   
Sbjct: 170 RKKKERLKKLIEETENLAELI-IDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLL 228

Query: 180 KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
             +     +E  +   E +R E+++ E  K+  +K++++  + LK+ K+E++    ++E 
Sbjct: 229 YLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEE 288

Query: 240 IPKLTFKFGTDMEEKTKRESSPKIVIKPVK 269
           +  L  +      E  K E       + +K
Sbjct: 289 LKLLAKEEEELKSELLKLERRKVDDEEKLK 318

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 32/124 (25%), Positives = 46/124 (37%), Gaps = 4/124 (3%)

Query: 113 TSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKG 172
           T    L  I    S              + + K       K K ++K+ E K   EK+K 
Sbjct: 16  TQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKK 75

Query: 173 KK-EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
           KK E+KE K E E K+     K     +K +K   K K ++D D    K     +K    
Sbjct: 76  KKKEKKEPKSEGETKLGFKTPKKS---KKTKKKPPKPKPNEDVDNAFNKIAELAEKSNVY 132

Query: 232 RSSH 235
             +H
Sbjct: 133 IGAH 136

Length = 413

>gnl|CDD|220303 pfam09592, DUF2031, Protein of unknown function (DUF2031)

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 36/104 (34%), Positives = 49/104 (47%), Gaps = 12/104 (11%)

Query: 130 DKKTHK-----KKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKE 184
           DKKT K     +KE E++KK+ D K     +N E   +   DK   K K E     E ++
Sbjct: 107 DKKTKKLINELRKELEEVKKELDNK-----RNGELAIQPIQDKRIIK-KDENSSVSEHED 160

Query: 185 FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
           FK  E++E  +E    E   S   KK K   +KLKK + K  K 
Sbjct: 161 FKQLENEENFLETEYNEITSSNNYKKLKIN-RKLKKAEKKLIKS 203

This protein is expressed in Plasmodium; its function is unknown. It may be the product of gene family pyst-b. Length = 228

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 43.0 bits (101), Expect = 2e-04
 Identities = 23/111 (20%), Positives = 52/111 (46%)

Query: 128 KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKM 187
           K  ++  + +E EK  + + K+ +++ +    +++KK +  K K   E  + K   E K 
Sbjct: 112 KAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAEAKK 171

Query: 188 KEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
           K ++     +  K + ++   KK  + + K   EK K + + K ++  + E
Sbjct: 172 KAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAE 222

Length = 387

>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 35/108 (32%), Positives = 57/108 (52%), Gaps = 6/108 (5%)

Query: 127 IKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDK-EKEKGKKEEKEKKEEKEF 185
            K D K   ++EKE+ +  K++K   K+K +E+ K+K+++K EK K    E  K++E ++
Sbjct: 545 WKLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEFFKRQEDKY 604

Query: 186 KMKEDKEKPVEKIRKEEKDSEKEKKS----KDKDKKLKKEKLKKKKKE 229
              ++   P      EE  S+KE+K      DK  KL +E L K  K 
Sbjct: 605 SAFDETGLPTHDADGEEI-SKKERKKLSKEYDKQAKLHEEYLAKGGKS 651

Length = 651

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 2/85 (2%)

Query: 129 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMK 188
           K KK    +E EK+KK+ ++K K   K K+K  +KK DK+K+K   ++ +K E+K+ K  
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQK--WKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEA 118

Query: 189 EDKEKPVEKIRKEEKDSEKEKKSKD 213
           EDK + + K   E   +  E K + 
Sbjct: 119 EDKLEDLTKSYSETLSTLSELKPRK 143

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 42.6 bits (101), Expect = 3e-04
 Identities = 17/70 (24%), Positives = 51/70 (72%)

Query: 114 SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGK 173
           +++ + +I +    K++++  +KK+K    KKK+++++++ + KE++KE++ ++ +E+ +
Sbjct: 408 ATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKE 467

Query: 174 KEEKEKKEEK 183
           +EE++KK++ 
Sbjct: 468 EEEEKKKKQA 477

Length = 482

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 29/111 (26%), Positives = 51/111 (45%), Gaps = 1/111 (0%)

Query: 123 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEE 182
           K K  ++ K     + K K + + +KK K++ K + +++ K     + K K  E +KK E
Sbjct: 117 KQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAE 176

Query: 183 KEFKMKED-KEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 232
            E K K + K K   +  K + ++ K K + +   K + E       E ER
Sbjct: 177 AEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAER 227

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.1 bits (99), Expect = 3e-04
 Identities = 27/109 (24%), Positives = 51/109 (46%), Gaps = 1/109 (0%)

Query: 121 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNK-EKDKEKKVDKEKEKGKKEEKEK 179
            K+ +     +K  K+ E+   + ++ +K  ++ K K   + + K + E EK  KEE +K
Sbjct: 91  QKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKK 150

Query: 180 KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
           + E+E K K   E   +    ++K   + K   +   K K E+ K K +
Sbjct: 151 QAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAE 199

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 41.2 bits (97), Expect = 3e-04
 Identities = 27/71 (38%), Positives = 44/71 (61%)

Query: 159 KDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKL 218
           K K+K++ +E EK KKE +EK++ K  K K  K+K  +K +K++K  +K +K  +K+ + 
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAED 120

Query: 219 KKEKLKKKKKE 229
           K E L K   E
Sbjct: 121 KLEDLTKSYSE 131

This is a family of fungal proteins of unknown function. Length = 182

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 28/120 (23%), Positives = 63/120 (52%), Gaps = 7/120 (5%)

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
           E  K     K++   K+ + +K ++K D    +  K +++ ++K+ + +      +    
Sbjct: 210 EDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSP 269

Query: 180 KEEKEFKMKEDKEKPVEKIRKE-EKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
           KE+K  ++ E++++ +EK + E +K+ E+  K+KD     K   LK++ K  E+ + +KE
Sbjct: 270 KEDK--QVAENQKREIEKAQIEIKKNDEEALKAKDH----KAFDLKQESKASEKEAEDKE 323

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein

 Score = 42.3 bits (99), Expect = 4e-04
 Identities = 31/127 (24%), Positives = 61/127 (48%)

Query: 112 VTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEK 171
           V    D+ ++K+ +S +  K+  + KE+   K+    K + K    + + +K+ D+ ++K
Sbjct: 194 VNFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQK 253

Query: 172 GKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
            ++ +   K       KEDK+    + R+ EK   + KK+ ++  K K  K    K+E +
Sbjct: 254 QQEAKNLPKPADTSSPKEDKQVAENQKREIEKAQIEIKKNDEEALKAKDHKAFDLKQESK 313

Query: 232 RSSHEKE 238
            S  E E
Sbjct: 314 ASEKEAE 320

This family consists of several Borrelia P83/P100 antigen proteins. Length = 489

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 42.7 bits (101), Expect = 4e-04
 Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 163 KKVDKEKEKGKKEEKEKKE-EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 221
           KK+ +  E  ++EE+   E E   + K  K++      ++     +EK+  DK + L K 
Sbjct: 224 KKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKL 283

Query: 222 KLKKKKKEKERSSHEKEVIPKLTFKF 247
           ++ K+KK++E    EK   P  T  F
Sbjct: 284 EILKEKKDEELFWFEK---PWPTLLF 306

The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. Length = 832

>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional

 Score = 41.9 bits (98), Expect = 4e-04
 Identities = 30/110 (27%), Positives = 47/110 (42%)

Query: 128 KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKM 187
           K  KK   +++K   KK    K+  K K   K    K  K+  K KK +  K   K+  +
Sbjct: 6   KTTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVTV 65

Query: 188 KEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 237
           K +K + V+K    +K  +KE  S +  +   K      K  K+  + EK
Sbjct: 66  KFEKTESVKKESVAKKTVKKEAVSAEVFEASNKLFKNTSKLPKKLFASEK 115

Length = 295

>gnl|CDD|221952 pfam13166, AAA_13, AAA domain

 Score = 42.3 bits (100), Expect = 4e-04
 Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 10/129 (7%)

Query: 118 LGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEK 177
           LGE   +    + +    KKE +K+++K ++ +  +I+ KE++ EK  +K  +K  K + 
Sbjct: 86  LGEENIEI---EAQIEELKKELKKLEEKIEQLEA-EIEKKEEELEKAKNKFLDKAWK-KL 140

Query: 178 EKKEEKEFKMKEDKEKPVEKIRKEEKD-SEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 236
            KK +      E  +    K   +EK   E +    +    L  E+L  K K K   S  
Sbjct: 141 AKKYDSNL--SEALKGLNYKKNFKEKLLKELKSVILNASSLLSLEEL--KAKIKTLFSSN 196

Query: 237 KEVIPKLTF 245
           K  +  LT 
Sbjct: 197 KPELALLTL 205

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. Length = 713

>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 42.3 bits (100), Expect = 5e-04
 Identities = 35/170 (20%), Positives = 58/170 (34%), Gaps = 10/170 (5%)

Query: 116  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE 175
             +  EI K++ +K   K    K ++   KKK+KK     K    DK KK        + +
Sbjct: 1147 VEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKK----KKSSADKSKKASVVGNSKRVD 1202

Query: 176  EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 235
              EK++  +    +           +E+   K KKS  K  K KK    K  ++ +  S 
Sbjct: 1203 SDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSS 1262

Query: 236  EKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTG 285
            +         K     +  +  + SP     P K P       +      
Sbjct: 1263 DD---LSKEGKPKNAPKRVSAVQYSPP---PPSKRPDGESNGGSKPSSPT 1306

Length = 1388

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 42.4 bits (100), Expect = 5e-04
 Identities = 24/129 (18%), Positives = 65/129 (50%), Gaps = 7/129 (5%)

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKE 181
           + + ++   K    +KE E+++++  + +++  + +E+ +E + + E+ K + EE  ++ 
Sbjct: 224 ELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREEL 283

Query: 182 EK-------EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
           E+         +  E+ E  +  +R+  ++ E E +  ++  +  KEK++  K+E E   
Sbjct: 284 EELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERE 343

Query: 235 HEKEVIPKL 243
              E + +L
Sbjct: 344 TLLEELEQL 352

Length = 1163

>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 41.7 bits (98), Expect = 5e-04
 Identities = 29/102 (28%), Positives = 52/102 (50%), Gaps = 4/102 (3%)

Query: 137 KEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVE 196
           KE   I +  D  D   +   +  +E K + +    K++E  K+  K+ +    K   V 
Sbjct: 330 KEAINIARNLDDNDLTLLALTKLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEV- 388

Query: 197 KIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
              K+E D+ +E ++K K++KLK+E+ +KK+KE+     EK 
Sbjct: 389 ---KDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKR 427

Length = 434

>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 42.0 bits (99), Expect = 5e-04
 Identities = 18/117 (15%), Positives = 51/117 (43%), Gaps = 8/117 (6%)

Query: 123 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKD-----KEKKVDKEKEKGKKEEK 177
            D+ I+ +++  K    ++ +     ++ + I  ++K+     K +  + ++ + + +  
Sbjct: 808 IDQIIESEEERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNI 867

Query: 178 EKKEEKEFKMKEDKEKPVEKI---RKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
            + + +  + K D +K  + I       K      + K  +K  KK+K   +K ++E
Sbjct: 868 NENKNEFVEFKNDPKKLNKLIIAKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTDEE 924

Length = 925

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 42.1 bits (98), Expect = 6e-04
 Identities = 35/167 (20%), Positives = 75/167 (44%), Gaps = 2/167 (1%)

Query: 115  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKK 174
            +E+    ++ +  ++ +  H  + +  IK ++ +K  +  K +EK K  +  K +EK K 
Sbjct: 1245 AEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKA 1304

Query: 175  EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
            +E +KK E+  K  E K+K  E  +K +   +K +++K   +  K E   +   ++  ++
Sbjct: 1305 DEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEA--EAAADEAEAA 1362

Query: 235  HEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADE 281
             EK    +   +      +  K+++  K      K  +      ADE
Sbjct: 1363 EEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADE 1409

Length = 2084

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.8 bits (99), Expect = 6e-04
 Identities = 21/64 (32%), Positives = 44/64 (68%)

Query: 121 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKK 180
           IKK     + K+  +KKEK+K      KK++++ + KEK +E+K ++E+E  +++E+E++
Sbjct: 412 IKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEE 471

Query: 181 EEKE 184
           ++K+
Sbjct: 472 KKKK 475

Length = 482

>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 41.8 bits (98), Expect = 6e-04
 Identities = 30/129 (23%), Positives = 60/129 (46%), Gaps = 2/129 (1%)

Query: 148 KKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEK 207
           K   D+   + +    K    K K  KE K +  ++E K KE  ++  +K +++ K+  K
Sbjct: 70  KLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPK 129

Query: 208 EKKSKD--KDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVI 265
           ++K K+  K+K+  KEK K+K+K+ E     +E   +   +  +  ++  K++   K   
Sbjct: 130 DRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKE 189

Query: 266 KPVKSPSPP 274
            P +     
Sbjct: 190 PPEEEKQRQ 198

This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. Length = 506

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 30/131 (22%), Positives = 74/131 (56%)

Query: 109 IVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKE 168
            ++  +  +L + +  +  ++ KK  ++ ++E  K K +K++    K +E   +   + +
Sbjct: 681 ELQEKAESELAKNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELK 740

Query: 169 KEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
             + K +EKE++EEK    KE++E+   ++  +EK+  +E++  +K K  ++++ K K +
Sbjct: 741 LLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQ 800

Query: 229 EKERSSHEKEV 239
           E+E  + E+E+
Sbjct: 801 EEELRALEEEL 811

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 39/128 (30%), Positives = 55/128 (42%), Gaps = 5/128 (3%)

Query: 114 SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKK-----VDKE 168
             ED  E K  K  KK  K  KK + +K  K+    D D+  + + D E +      D  
Sbjct: 232 GGEDGDEEKSKKKKKKLAKNKKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSS 291

Query: 169 KEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
                 EE+E K   E   K + E+  +    EE+ +E+E     K KKLKK K KK   
Sbjct: 292 ASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGL 351

Query: 229 EKERSSHE 236
           +K+ S   
Sbjct: 352 DKDDSDSG 359

Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. Length = 528

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.5 bits (97), Expect = 9e-04
 Identities = 28/126 (22%), Positives = 57/126 (45%)

Query: 114 SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGK 173
               L E  K        K   + E+E +      K  ++  +  ++  +   +E E  K
Sbjct: 199 QELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSK 258

Query: 174 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 233
           +E ++++E     +KE+KE+  EK  +EE+     K+ ++   +L K + +K   E++  
Sbjct: 259 QELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLK 318

Query: 234 SHEKEV 239
             EKE+
Sbjct: 319 ESEKEL 324

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 40.4 bits (95), Expect = 9e-04
 Identities = 27/115 (23%), Positives = 49/115 (42%), Gaps = 3/115 (2%)

Query: 130 DKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKE 189
           + +   ++E+   KKK+ K    K   K+K K+     +  K      +KK E+      
Sbjct: 73  EGEKELQREERLKKKKRVKTKAYKEPTKKKKKKDPTAAKSPKAAAPRPKKKSERISWAPT 132

Query: 190 DKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLT 244
             + P    RK  + S  + K    ++  ++E  +KK + K R   EK+   +LT
Sbjct: 133 LLDSP---RRKSSRSSTVQNKEATHERLKEREIRRKKIQAKARKRKEKKKEKELT 184

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 40.9 bits (95), Expect = 0.001
 Identities = 33/125 (26%), Positives = 70/125 (56%), Gaps = 2/125 (1%)

Query: 115  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKK 174
            +++  + ++ K   + KK  +KK+ +++KK ++ K  ++ K  E+ K+ + DK     K 
Sbjct: 1524 ADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKA 1583

Query: 175  EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
            EE +K EE   +      +  +K++ EE  ++K +++K K ++LKK + +KKK E+ +  
Sbjct: 1584 EEAKKAEEARIEEVMKLYEEEKKMKAEE--AKKAEEAKIKAEELKKAEEEKKKVEQLKKK 1641

Query: 235  HEKEV 239
              +E 
Sbjct: 1642 EAEEK 1646

Length = 2084

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 29/127 (22%), Positives = 68/127 (53%), Gaps = 8/127 (6%)

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
             +K+ + +++K    K E+EK +K K ++++ +   +E  +E ++ +E++   ++E++ 
Sbjct: 772 LKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKI 831

Query: 180 KEEK--------EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
           KEE+        + + K +K    E  R EE+ +++E   +   K+ + E+ K K + + 
Sbjct: 832 KEEELEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELES 891

Query: 232 RSSHEKE 238
           +   EKE
Sbjct: 892 KEEKEKE 898

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota)

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 155 KNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDK 214
           K +EK K  K   ++ K      E   + + K+K   E+  EK+  E K+ +KEKK ++K
Sbjct: 281 KLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEK 340

Query: 215 DKKL------KKEKLKKKKKEKE 231
            KK       + EKL+ +  +KE
Sbjct: 341 KKKQIERLEERIEKLEVQATDKE 363

DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras. Length = 391

>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 43/244 (17%), Positives = 79/244 (32%), Gaps = 38/244 (15%)

Query: 129 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEK----- 183
            D K     +  +      KK  D      ++ E  + KE  +   +    ++EK     
Sbjct: 31  IDAKVCDIIKNLRQMISILKKIIDLDSQTYEEVEDGLLKEIRELLLKAIYIQKEKSDLAD 90

Query: 184 --EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS-------S 234
             E  ++  ++   ++I K   +    +     D   + E+       +  S       S
Sbjct: 91  RAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSAARRSSGEHRSAAS 150

Query: 235 HEKEVIPKLTFKFG------TDMEEKTKRESSPKIVIKPV----------KSPSPPPVAA 278
            +     KL  +           E  +KRE S  +    V           +        
Sbjct: 151 SQGSRHTKLKKRKNIHNLKRRSPELSSKREVSFTLESPSVPDTATRVKEGNNGGSTKSRG 210

Query: 279 ADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDA---WYHWVCVGLVAEPETSDWFCP 335
               D  + ++++    C  Q      M+ CD  +    W+H  CVGL   P+   W+CP
Sbjct: 211 VSSEDNSEGEELY----CFCQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGK-WYCP 265

Query: 336 KCSK 339
           +C K
Sbjct: 266 ECKK 269

Length = 271

>gnl|CDD|222160 pfam13476, AAA_23, AAA domain

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 27/159 (16%), Positives = 65/159 (40%)

Query: 73  TSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKK 132
                ++   +     + +    KD     T +            L  I++ + + K K 
Sbjct: 44  YGKTSRLKKSKGRGIVKGDIEIEKDEGKKKTYVEITFENNKGKLKLRLIEESRELTKKKG 103

Query: 133 THKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKE 192
              KK   +I +  + ++      K   +   +     + + EE + K +++ +  E+ E
Sbjct: 104 KKVKKSILEIVEIDELQEFIDELLKSDKEILPLLLYLGQERLEELKFKRKEKKERLEELE 163

Query: 193 KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
           K +E++  E+   EK  + K+K K+L++ K + ++  +E
Sbjct: 164 KELEELEDEKDLLEKLLEEKEKKKELEELKEELEELLEE 202

Length = 204

>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 12/86 (13%), Positives = 39/86 (45%)

Query: 152 DKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS 211
            +++    +  K++ K  E  K  E E+++ +   +KE+ +K   +I + E+  ++ +  
Sbjct: 2   KELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAK 61

Query: 212 KDKDKKLKKEKLKKKKKEKERSSHEK 237
                +    + ++++ + E +    
Sbjct: 62  PAASGEGGGGEEEEEEAKAEAAEFRA 87

This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease [Mobile and extrachromosomal element functions, Prophage functions]. Length = 384

>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 123 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEE 182
           +     KDK   +   K   + K  +K K  IK +  +   +V K   + KKEEK+K ++
Sbjct: 19  EKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAE---RVKKLHSQEKKEEKKKPKK 75

Query: 183 KEFKM 187
           K+  +
Sbjct: 76  KKVPL 80

Length = 217

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 25/113 (22%), Positives = 41/113 (36%), Gaps = 4/113 (3%)

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDK---DKIKNKEKDKEKKVDKEKEKGKKEEKE 178
           K+    +K  +    K     K K + + K      K    + +KK + E  K    E +
Sbjct: 125 KQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAEAK 184

Query: 179 KKEEKEFKMKEDKE-KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 230
           KK E E   K   E K   +   ++K + + KK    + K    K   + K  
Sbjct: 185 KKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAA 237

Length = 387

>gnl|CDD|191249 pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylase N-terminal region

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 34/167 (20%), Positives = 73/167 (43%), Gaps = 9/167 (5%)

Query: 76  KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK 135
           KEK +S+    P+E E    ++ +L V      + +        E+K+      +K    
Sbjct: 68  KEKSTSEPTVPPEEAEPHAEEEGQLAVRKTKQKVEE--------EVKEQLQSLLEKIVVS 119

Query: 136 KKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPV 195
           K+E++   K+  + D+DK    E   +++   E  K  +E ++    +E   ++ K+   
Sbjct: 120 KQEEDGPGKEP-QLDEDKFLLAEDSDDRQETLEAGKVHEETEDSYHVEETASEQYKQDMK 178

Query: 196 EKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPK 242
           EK  ++E +  KE   K +  K + + + ++  ++E +  E     K
Sbjct: 179 EKASEQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIK 225

This family includes the N-terminal regions of the junctin, junctate and aspartyl beta-hydroxylase proteins. Junctate is an integral ER/SR membrane calcium binding protein, which comes from an alternatively spliced form of the same gene that generates aspartyl beta-hydroxylase and junctin. Aspartyl beta-hydroxylase catalyzes the post-translational hydroxylation of aspartic acid or asparagine residues contained within epidermal growth factor (EGF) domains of proteins. Length = 240

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 34/155 (21%), Positives = 68/155 (43%)

Query: 136 KKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPV 195
           ++E E+  KK   + K   +N EK+ E K  K++ K + +EK++ +E+E    E++ K  
Sbjct: 409 EEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVE 468

Query: 196 EKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKT 255
           +   K  K SEK +K +++++  ++    K      +S+ +++   K + K      + +
Sbjct: 469 KVANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANKIS 528

Query: 256 KRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQV 290
           K     K   K  KS         +E         
Sbjct: 529 KAAVKVKKKKKKEKSIDLDDDLIDEEDSIKLDVDD 563

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 22/134 (16%), Positives = 56/134 (41%), Gaps = 1/134 (0%)

Query: 120  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
            +   ++   + ++   ++    +K + + ++    +  EK+KE+   +E+E+  K     
Sbjct: 910  DNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEERNKRLLLA 969

Query: 180  KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
            KEE          +  EK  +  KD  K+++ +++ K+L +E +++  +  +    E  V
Sbjct: 970  KEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREIIEETCQRFKE-FLELFV 1028

Query: 240  IPKLTFKFGTDMEE 253
                         E
Sbjct: 1029 SINRGLNKVFFYLE 1042

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 40.2 bits (95), Expect = 0.002
 Identities = 25/140 (17%), Positives = 53/140 (37%), Gaps = 5/140 (3%)

Query: 62  KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 121
           +   K   K +   + K  ++E  + + +E +K +                  +      
Sbjct: 41  EEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAA----- 95

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKE 181
            +    +  +       + K KK   KK   K K K+  ++     ++ KG K  + ++ 
Sbjct: 96  ARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRG 155

Query: 182 EKEFKMKEDKEKPVEKIRKE 201
            +  + K+ K+KP EKI +E
Sbjct: 156 RRRRRKKKKKQKPTEKIPRE 175

Length = 746

>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 40.3 bits (94), Expect = 0.002
 Identities = 33/146 (22%), Positives = 67/146 (45%), Gaps = 21/146 (14%)

Query: 62  KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 121
           K  +K   K++   KEK+  K++    +   S VK+                SS++   +
Sbjct: 20  KDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKE---------------QSSQE--NL 62

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKD----KEKKVDKEKEKGKKEEK 177
           K    +KK  K   K+  E +K K++ + + + +  +K     + K+   +K +  K E+
Sbjct: 63  KIADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPSFEPKESILKKLEDIKPEQ 122

Query: 178 EKKEEKEFKMKEDKEKPVEKIRKEEK 203
            KK+ K F++ E K+ P+ +   E++
Sbjct: 123 AKKQTKLFRLFEPKQLPIYRANGEKE 148

Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. Length = 887

>gnl|CDD|191249 pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylase N-terminal region

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 27/124 (21%), Positives = 59/124 (47%), Gaps = 3/124 (2%)

Query: 139 KEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKI 198
           KEK   +     ++   + E++ +  V K K+K ++E KE+ +    K+   K++     
Sbjct: 68  KEKSTSEPTVPPEEAEPHAEEEGQLAVRKTKQKVEEEVKEQLQSLLEKIVVSKQEEDGPG 127

Query: 199 RKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRE 258
           ++ + D +K   ++D D + +  +  K  +E E S H +E   +   ++  DM+EK   +
Sbjct: 128 KEPQLDEDKFLLAEDSDDRQETLEAGKVHEETEDSYHVEETASE---QYKQDMKEKASEQ 184

Query: 259 SSPK 262
            +  
Sbjct: 185 ENED 188

This family includes the N-terminal regions of the junctin, junctate and aspartyl beta-hydroxylase proteins. Junctate is an integral ER/SR membrane calcium binding protein, which comes from an alternatively spliced form of the same gene that generates aspartyl beta-hydroxylase and junctin. Aspartyl beta-hydroxylase catalyzes the post-translational hydroxylation of aspartic acid or asparagine residues contained within epidermal growth factor (EGF) domains of proteins. Length = 240

>gnl|CDD|187861 cd09730, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 25/108 (23%), Positives = 45/108 (41%), Gaps = 18/108 (16%)

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKE----KDKEKKVDKEKEKGKKEEK 177
             +K     K T  +   +KIKK  +K        KE    K+ +  ++K  EK  K+ +
Sbjct: 82  PTNKITYLLKTT--EPLNKKIKKWFEKSYLLLESKKEILKLKNIKDVLEKNIEKILKDIQ 139

Query: 178 EKKE------------EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKD 213
           + K             +K  +  ED E+  +K+ K++   +K+ K K 
Sbjct: 140 DLKPGENVILTIKIDGKKLLEYDEDYEEFRDKVLKKKVFKDKKAKEKG 187

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as TM1802 family. Length = 579

>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 30/115 (26%), Positives = 51/115 (44%), Gaps = 18/115 (15%)

Query: 127 IKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKD----KEKKVDKEKEKGKKEEKEKKEE 182
           I++  K+ +  +    ++ K + DK K  ++       K KK+   K    ++  E KE 
Sbjct: 333 IEEGLKSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKVNLDRQLSELKEA 392

Query: 183 -------KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 230
                  K    K + +K +E+IR+E  + E   KSK K +K      KK+  EK
Sbjct: 393 IAYYESAKTALEKAEGKKAIEEIREELIE-EGLLKSKKKKRK------KKEWFEK 440

Length = 564

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 28/127 (22%), Positives = 70/127 (55%), Gaps = 2/127 (1%)

Query: 106 VPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKV 165
           +P+ +   +    GE K++ ++  +K +  +KE E+  +  +K  K++ K K++ +++  
Sbjct: 494 IPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEME 553

Query: 166 DKEKEKGKKEEKEKKEEKEF--KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 223
           + ++ +  K+ + +KE +E    +K++ E  + ++++++    KE KS +   KLK+ K 
Sbjct: 554 ELKERERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQ 613

Query: 224 KKKKKEK 230
           K  +K  
Sbjct: 614 KIPQKPT 620

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

 Score = 40.4 bits (94), Expect = 0.002
 Identities = 28/139 (20%), Positives = 62/139 (44%), Gaps = 16/139 (11%)

Query: 116  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE 175
            E++ +I +D S   ++K   +  +E + + + K ++    N E D   K D  K    K+
Sbjct: 3890 EEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKD 3949

Query: 176  EKEKKEEKEFK------------MKEDKEKPVEKIRK----EEKDSEKEKKSKDKDKKLK 219
             +EK++E+E              ++E+  +P  +       E+   ++++    KD  L+
Sbjct: 3950 RQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDSDLE 4009

Query: 220  KEKLKKKKKEKERSSHEKE 238
               ++   + KE +  EK+
Sbjct: 4010 DMDMEAADENKEEADAEKD 4028

Length = 4600

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 38/158 (24%), Positives = 79/158 (50%), Gaps = 13/158 (8%)

Query: 76  KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK 135
           +EK+   ++   K +EY K+ +                  ++L EI+K  S  +++    
Sbjct: 279 EEKVKELKELKEKAEEYIKLSEF------------YEEYLDELREIEKRLSRLEEEINGI 326

Query: 136 KKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPV 195
           ++  +++++K+++ ++ K K KE +K  +  +E+ +  +E K KKEE E   K       
Sbjct: 327 EERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTP 386

Query: 196 EKIRKEEKDSEKEKKS-KDKDKKLKKEKLKKKKKEKER 232
           EK+ KE ++ EK K+  +++  K+     + KK+ KE 
Sbjct: 387 EKLEKELEELEKAKEEIEEEISKITARIGELKKEIKEL 424

Length = 880

>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated

 Score = 40.2 bits (95), Expect = 0.002
 Identities = 24/124 (19%), Positives = 46/124 (37%)

Query: 108 NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDK 167
              K  S      +KK K   +  K   K   E  +    KK   K+  + +     + K
Sbjct: 101 EKAKKNSPLFKSLLKKQKVEVEGNKLIIKVNNEIERDHLKKKHLPKLIKQYEKFGFGILK 160

Query: 168 EKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 227
              +    ++E ++ +  K +ED++   E +   +K   ++KK        +      KK
Sbjct: 161 IDFEIDDSKEELEKFEAQKEEEDEKLAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKK 220

Query: 228 KEKE 231
            +KE
Sbjct: 221 IDKE 224

Length = 1437

>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 39.6 bits (92), Expect = 0.003
 Identities = 27/143 (18%), Positives = 68/143 (47%), Gaps = 4/143 (2%)

Query: 121 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEK-DKEKKVDKEKEKGKK---EE 176
            ++ + ++++    +  ++  +K+++ ++ K K + + K +KEK+  KE E+  +     
Sbjct: 854 EEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKELEEESQKDNLL 913

Query: 177 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 236
           +EK+ E E ++ E+    ++   + E+   +E   K+K++  K+E+ ++ K+        
Sbjct: 914 EEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEERNKRLLLAKEEL 973

Query: 237 KEVIPKLTFKFGTDMEEKTKRES 259
             V      +F    E   K E 
Sbjct: 974 GNVNLMAIAEFEEKEERYNKDEL 996

This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Length = 1162

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 22/123 (17%), Positives = 66/123 (53%)

Query: 116 EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE 175
             L E++++    +++    ++  E+++++ +  ++   K KE+ +E +  ++  + + E
Sbjct: 737 SRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELE 796

Query: 176 EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 235
           E E++ E+  +  +  E+ +E + +  +  E+E +  +++ +  +EKL + ++E E    
Sbjct: 797 ELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEK 856

Query: 236 EKE 238
           E E
Sbjct: 857 ELE 859

Length = 1163

>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein

 Score = 40.0 bits (94), Expect = 0.003
 Identities = 26/118 (22%), Positives = 57/118 (48%)

Query: 122 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKE 181
           K+ +S K  K+   + +++K   ++++ + ++    EK   K + + ++  K+EE+E+ +
Sbjct: 432 KEAESKKLKKENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELD 491

Query: 182 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
           E+   +K          +++ K     K  K  +K  K     KKKK+KE+S    + 
Sbjct: 492 EENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANKISKAAVKVKKKKKKEKSIDLDDD 549

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. Length = 728

>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase

 Score = 39.9 bits (93), Expect = 0.003
 Identities = 28/99 (28%), Positives = 51/99 (51%)

Query: 168 EKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 227
           EK+   +EE E+K++KE K KE + K ++  +KE K   + +++ D     KK + K +K
Sbjct: 9   EKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEKKSRK 68

Query: 228 KEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIK 266
           ++ E  + E  + P   F     +  +  ++ SP  V K
Sbjct: 69  RDVEDENPEDFIDPDTPFGQKKRLSSQMAKQYSPSAVEK 107

Length = 1066

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 16/52 (30%), Positives = 24/52 (46%)

Query: 181 EEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 232
           +E   K K   EK   K  K+      EKK K+K+K   K++ +  K   +R
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKR 425

Length = 434

>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 25/91 (27%), Positives = 48/91 (52%), Gaps = 16/91 (17%)

Query: 140 EKIKKKKDKKD-KDKIKNKEKDKEKKVDKEKEKGKKEE-KEKKEEKEFKMKEDKEKPVEK 197
           +K+   K   +   K+    +++E+K+ K  E+ ++EE +EKKEEK+ + +E        
Sbjct: 246 DKLANLKLSPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEERE-------- 297

Query: 198 IRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
             K  K S +E++     K  +KE+ K+ +K
Sbjct: 298 -AKLAKLSPEEQR-----KLEEKERKKQARK 322

The members of this family are all hypothetical eukaryotic proteins of unknown function. One member is described as being an adipocyte-specific protein, but no evidence of this was found. Length = 322

>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 20/131 (15%), Positives = 67/131 (51%), Gaps = 9/131 (6%)

Query: 116 EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNK-------EKDKEKKVDKE 168
           E+L  ++++  +++ ++  ++ EKE  + K + ++  +   +        K++ ++++ E
Sbjct: 246 EELSRLEEE--LEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGE 303

Query: 169 KEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 228
               ++  +E + E E   +  +E   +    +E+  E+E   ++ ++ L + +  K++ 
Sbjct: 304 ISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEEL 363

Query: 229 EKERSSHEKEV 239
           E++ S+  +E+
Sbjct: 364 EEKLSALLEEL 374

Length = 1163

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 38.8 bits (90), Expect = 0.004
 Identities = 30/133 (22%), Positives = 59/133 (44%), Gaps = 5/133 (3%)

Query: 135 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEK-----EKGKKEEKEKKEEKEFKMKE 189
           K+ EKE++K ++ +K  ++ + + + ++K+ +++      E+ KK E  K +      K 
Sbjct: 104 KQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKL 163

Query: 190 DKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGT 249
                 +K  +E   + +E K+K +    KK+   + K   E++  E E   K   K   
Sbjct: 164 KAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEA 223

Query: 250 DMEEKTKRESSPK 262
             EEK   E    
Sbjct: 224 AAEEKAAAEKKKA 236

Length = 387

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 35/117 (29%), Positives = 59/117 (50%), Gaps = 15/117 (12%)

Query: 138 EKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKE---KKEEKEFKMKEDKEKP 194
           E+ K    + K++ + +  K    EK+++++ E  +K  KE    K+E E +M+E KE  
Sbjct: 500 EQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKE-- 557

Query: 195 VEKIRKEEKDSEKEKKSKDKDKKLKKE------KLKKKKKEKERSSHEKEVIPKLTF 245
               R+  K  E EK++++  K LKKE      +LK+KK  K +     E + KL  
Sbjct: 558 ----RERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKE 610

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 27/129 (20%), Positives = 68/129 (52%), Gaps = 6/129 (4%)

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKD-----KKDKDKIKNKEKDKEKKVDKEKEKGKK 174
           E+K  +   + ++   KK +E++ K  +     +K  ++++ + ++ EKK  +E+ +  +
Sbjct: 606 ELKDAEKELEREEKELKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELR 665

Query: 175 EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
           EE  +   +   ++ + E+  ++  + +K  EK K+  ++ +K  K++L+K +K  ER  
Sbjct: 666 EEYLELSRELAGLRAELEELEKRREEIKKTLEKLKEELEEREK-AKKELEKLEKALERVE 724

Query: 235 HEKEVIPKL 243
             +E + K 
Sbjct: 725 ELREKVKKY 733

Length = 880

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 18/54 (33%), Positives = 29/54 (53%)

Query: 123 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEE 176
           K  S KK  K  KK   ++ +KK+ +K+K K+K + +D +    + K  G  EE
Sbjct: 381 KAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR)

 Score = 39.3 bits (91), Expect = 0.004
 Identities = 39/139 (28%), Positives = 62/139 (44%), Gaps = 5/139 (3%)

Query: 130 DKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKK----EEKEKKEEKEF 185
           +KK+ K K+KEK +K+K+ +DKDK K  E  K   +  +          E  E       
Sbjct: 196 EKKSKKPKKKEKKEKEKE-RDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLANTV 254

Query: 186 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTF 245
                  +P E    E ++++K  K K K ++ +KE+ KKKKK      H  +   +   
Sbjct: 255 SGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHRCHHSDGGAEQPV 314

Query: 246 KFGTDMEEKTKRESSPKIV 264
           + G   EE     SS K++
Sbjct: 315 QNGAVEEEPLPPMSSYKLL 333

This family consists of several bovine specific leukaemia virus receptors which are thought to function as transmembrane proteins, although their exact function is unknown. Length = 561

>gnl|CDD|227512 COG5185, HEC1, Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]

 Score = 39.2 bits (91), Expect = 0.004
 Identities = 38/194 (19%), Positives = 86/194 (44%), Gaps = 18/194 (9%)

Query: 79  MSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKE 138
           +  ++   P E+E       +LG    V  I    ++         + I++  K  +K +
Sbjct: 245 LKLEDNYEPSEQEL------KLGFEKFVHIINTDIANLKTQNDNLYEKIQEAMKISQKIK 298

Query: 139 KEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKK--EEKEKKEEKEFKMKEDKEKPVE 196
             + K +  K D +K +N     ++K  +   K +K   E E KEE+   ++ + ++  +
Sbjct: 299 TLREKWRALKSDSNKYENYVNAMKQKSQEWPGKLEKLKSEIELKEEEIKALQSNIDELHK 358

Query: 197 KIRK--------EEKDSEKEKKSKDKDK-KLKKEKLKKKKKEKERSSHEK-EVIPKLTFK 246
           ++RK        E  + E+EK +++ DK  ++ +KL K  K ++  +    + + K   +
Sbjct: 359 QLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLTKSVKSRKLEAQGIFKSLEKTLRQ 418

Query: 247 FGTDMEEKTKRESS 260
           + + ++  T+  S 
Sbjct: 419 YDSLIQNITRSRSQ 432

Length = 622

>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 26/164 (15%), Positives = 66/164 (40%), Gaps = 5/164 (3%)

Query: 122 KKDKSIKKDKKTHKKKEK--EKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
           +    + K ++   + E    +I++K ++   +K   +++ +E +  +   K + +  EK
Sbjct: 795 EIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEK 854

Query: 180 KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
           + E     KE+ E+ +E++    +D E       K++   + +L++ +++ E    + E 
Sbjct: 855 EIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEK 914

Query: 240 IPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYD 283
             K   +    +E   +  S    +  P       P       D
Sbjct: 915 KRKRLSELKAKLEALEEELSE---IEDPKGEDEEIPEEELSLED 955

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1164

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	444
PF10203	68	Pet191_N: Cytochrome c oxidase assembly protein PE	99.91
KOG4114|consensus	73		99.9
KOG1973|consensus	274		99.05
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	98.91
COG5034	271	TNG2 Chromatin remodeling protein, contains PhD zi	98.85
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	98.77
KOG0825|consensus	1134		98.33
KOG1244|consensus	336		98.0
KOG4323|consensus	464		97.81
KOG1844|consensus	508		97.67
KOG4299|consensus	613		97.66
KOG1512|consensus	381		97.6
KOG1245|consensus	1404		96.98
KOG0383|consensus	696		96.79
KOG4364|consensus	811		96.67
PF13831	36	PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.	96.67
KOG1632|consensus	345		96.66
KOG0955|consensus	1051		96.66
KOG0954|consensus	893		96.34
KOG0957|consensus	707		96.28
KOG4364|consensus	811		96.08
KOG0957|consensus	707		96.03
PF07227	446	DUF1423: Protein of unknown function (DUF1423); In	95.65
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	95.49
KOG1632|consensus	345		95.03
KOG4443|consensus	694		94.76
COG5141	669	PHD zinc finger-containing protein [General functi	94.35
KOG0956|consensus	900		92.52
KOG1144|consensus	1064		91.81
PF15446	175	zf-PHD-like: PHD/FYVE-zinc-finger like domain	89.61
PF07649	30	C1_3: C1-like domain; InterPro: IPR011424 This sho	87.83
KOG1029|consensus	1118		86.98
PF07496	50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	86.9
KOG4443|consensus	694		86.52
KOG0163|consensus	1259		85.55
KOG1473|consensus	1414		82.4
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	82.19
KOG2752|consensus	345		81.69

>PF10203 Pet191_N: Cytochrome c oxidase assembly protein PET191; InterPro: IPR018793 This entry represents a family of conserved proteins found from nematodes to humans

Probab=99.91  E-value=6.3e-25  Score=176.00  Aligned_cols=64  Identities=47%  Similarity=1.062  Sum_probs=61.9

Q ss_pred             cccchhhHHHHHHhhhcCcccccCCCChhhHhhcC---ChhhHHHHHhhHhhhhccccccccccccC
Q psy5823         378 KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREG---LAPQCEALKNTFFECKRSLLDNRTRFRGH  441 (444)
Q Consensus       378 ~saCk~~r~dL~~CL~~SdCv~~~~~t~~eCL~~~---~~~~C~~L~~~f~eCKR~llD~r~rfrG~  441 (444)
                      ++||++++.+|+.||++||||+++++||++||+++   +|.+|++|+++||+|||||||||+|||||
T Consensus         2 ~~sC~~~~~~L~~Cl~~SdCv~~~~~t~~~Cl~~~~~~~p~eC~~lr~~f~eCKrg~lDmr~RfRGn   68 (68)
T PF10203_consen    2 SKSCKGIREALAECLQESDCVKKEKRTPKDCLKDPSDELPEECQQLRKAFFECKRGMLDMRKRFRGN   68 (68)
T ss_pred             CchHHHHHHHHHHHHhhChhhccCCCCHHHHHcCCCCcCCHHHHHHHHHHHHHhcccccccccccCc
Confidence            47999999999999999999999999999999975   89999999999999999999999999998

Cytochrome c oxidase assembly protein Pet191 carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex [].

>KOG4114|consensus

Probab=99.90  E-value=5.8e-25  Score=174.56  Aligned_cols=67  Identities=51%  Similarity=1.037  Sum_probs=64.3

Q ss_pred             cccchhhHHHHHHhhhcCcccccCCCChhhHhhc----CChhhHHHHHhhHhhhhccccccccccccCCCC
Q psy5823         378 KSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE----GLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY  444 (444)
Q Consensus       378 ~saCk~~r~dL~~CL~~SdCv~~~~~t~~eCL~~----~~~~~C~~L~~~f~eCKR~llD~r~rfrG~~~~  444 (444)
                      +.||.+++.+|++||++||||++++++|++||..    ++|.+|++|+.+|++|||||||||+||||++||
T Consensus         2 g~sC~~~r~alk~Cl~~S~Cv~v~~ks~reCldn~~~~~vPeeC~al~~af~dCKRslvDmrkRfrgrkg~   72 (73)
T KOG4114|consen    2 GASCKDQRKALKICLLRSDCVMVERKSPRECLDNPELKDVPEECIALMKAFLDCKRSLVDMRKRFRGRKGT   72 (73)
T ss_pred             cccHHHHHHHHHHHHhcCcceeeecCCHHHHhcCCccccCcHHHHHHHHHHHHHHHHHHHHHHHHccccCC
Confidence            5699999999999999999999999999999995    389999999999999999999999999999997

>KOG1973|consensus

Probab=99.05  E-value=7.5e-11  Score=117.23  Aligned_cols=54  Identities=37%  Similarity=1.064  Sum_probs=44.2

Q ss_pred             CCCCCCceeccccCCCCCCCCCeeecCC--CC-CcccccccccCCCCCCCceecCCCCCcc
Q psy5823         284 TGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKVD  341 (444)
Q Consensus       284 ded~~~~~~C~VC~~~ddg~~~mI~CD~--C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~~~  341 (444)
                      ..+.+...|| +|+...+|.  ||.||+  |+ .|||+.||||... +.+.|||+.|....
T Consensus       213 ~~d~~e~~yC-~Cnqvsyg~--Mi~CDn~~C~~eWFH~~CVGL~~~-PkgkWyC~~C~~~~  269 (274)
T KOG1973|consen  213 AVDPDEPTYC-ICNQVSYGK--MIGCDNPGCPIEWFHFTCVGLKTK-PKGKWYCPRCKAEN  269 (274)
T ss_pred             ccCCCCCEEE-Eeccccccc--ccccCCCCCCcceEEEeccccccC-CCCcccchhhhhhh
Confidence            3445567899 999877877  999998  99 9999999999865 44679999998543

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.91  E-value=1.8e-10  Score=85.97  Aligned_cols=46  Identities=48%  Similarity=1.284  Sum_probs=39.2

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCC---CCCCceecCCCC
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE---PETSDWFCPKCS  338 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~---~~~~~w~Cp~C~  338 (444)
                      +|.+|+..++++ .||+||.|+.|||..|++++..   .....|+|+.|.
T Consensus         1 ~C~vC~~~~~~~-~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    1 YCPVCGQSDDDG-DMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             EBTTTTSSCTTS-SEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             eCcCCCCcCCCC-CeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            588999976666 8999999999999999999977   223489999986

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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

Probab=98.85  E-value=2.2e-09  Score=105.07  Aligned_cols=48  Identities=35%  Similarity=1.061  Sum_probs=41.9

Q ss_pred             CCCceeccccCCCCCCCCCeeecCC--CC-CcccccccccCCCCCCCceecCCCC
Q psy5823         287 SKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCS  338 (444)
Q Consensus       287 ~~~~~~C~VC~~~ddg~~~mI~CD~--C~-~WfH~~CvG~~~~~~~~~w~Cp~C~  338 (444)
                      +....|| .|++...|.  ||.||+  |. .|||+.|||+... +.|.|||+.|.
T Consensus       218 e~e~lYC-fCqqvSyGq--MVaCDn~nCkrEWFH~~CVGLk~p-PKG~WYC~eCk  268 (271)
T COG5034         218 EGEELYC-FCQQVSYGQ--MVACDNANCKREWFHLECVGLKEP-PKGKWYCPECK  268 (271)
T ss_pred             cCceeEE-Eeccccccc--ceecCCCCCchhheeccccccCCC-CCCcEeCHHhH
Confidence            3457899 999999998  999997  98 9999999999654 56899999997

>smart00249 PHD PHD zinc finger

Probab=98.77  E-value=7.1e-09  Score=74.03  Aligned_cols=45  Identities=47%  Similarity=1.305  Sum_probs=38.4

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCceecCCC
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKC  337 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~w~Cp~C  337 (444)
                      +|.+|+..++++ .||+||.|+.|||..|+++...  .....|+|+.|
T Consensus         1 ~C~~C~~~~~~~-~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~~C~~C   47 (47)
T smart00249        1 YCSVCGKPDDGG-ELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC   47 (47)
T ss_pred             CcccCCCcCCCC-CEEECCCCCchhhhhhCCCcccCCCCCCCEECcCC
Confidence            377899887555 7999999999999999998776  45678999987

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

>KOG0825|consensus

Probab=98.33  E-value=1.9e-07  Score=102.67  Aligned_cols=53  Identities=26%  Similarity=0.758  Sum_probs=46.5

Q ss_pred             CCceeccccCCCCCCCCCeeecCCCCCc-ccccccccCCC-CCCCceecCCCCCcc
Q psy5823         288 KQVWICPACGVQDDGSLPMIGCDGCDAW-YHWVCVGLVAE-PETSDWFCPKCSKVD  341 (444)
Q Consensus       288 ~~~~~C~VC~~~ddg~~~mI~CD~C~~W-fH~~CvG~~~~-~~~~~w~Cp~C~~~~  341 (444)
                      ...+.|.||+.++..+ +||+||.|+.. ||.+||++++. .+.+.|||..|.-..
T Consensus       213 ~E~~~C~IC~~~DpEd-VLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~  267 (1134)
T KOG0825|consen  213 QEEVKCDICTVHDPED-VLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLE  267 (1134)
T ss_pred             cccccceeeccCChHH-hheeecccccceeeccccCcccccccccceecCcchhhh
Confidence            3568899999998888 99999999977 99999999987 777899999997544

>KOG1244|consensus

Probab=98.00  E-value=2.3e-06  Score=85.07  Aligned_cols=48  Identities=29%  Similarity=0.803  Sum_probs=43.6

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  339 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~  339 (444)
                      -+|.|||..++++ .++.||.|++.||.+|+.++.. ++.+.|.|-.|..
T Consensus       282 k~csicgtsendd-qllfcddcdrgyhmyclsppm~eppegswsc~KOG~  330 (336)
T KOG1244|consen  282 KYCSICGTSENDD-QLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLE  330 (336)
T ss_pred             ceeccccCcCCCc-eeEeecccCCceeeEecCCCcCCCCCCchhHHHHHH
Confidence            3699999988887 8999999999999999999988 7889999999973

>KOG4323|consensus

Probab=97.81  E-value=8e-06  Score=86.59  Aligned_cols=49  Identities=33%  Similarity=0.922  Sum_probs=39.4

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-----CCCCceecCCCCCc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  340 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~~~  340 (444)
                      .+|| -|+.+..++ .||+|++|+.|||..|+.+...     .....|||..|...
T Consensus       171 c~vC-~~g~~~~~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~  224 (464)
T KOG4323|consen  171 CSVC-YCGGPGAGN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG  224 (464)
T ss_pred             eeee-ecCCcCccc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence            3556 566777777 8999999999999999987766     45568999999844

>KOG1844|consensus

Probab=97.67  E-value=7.3e-05  Score=79.48  Aligned_cols=59  Identities=27%  Similarity=0.759  Sum_probs=49.4

Q ss_pred             CCceeccccCCCCC-CCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCccccchhhh
Q psy5823         288 KQVWICPACGVQDD-GSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEK  348 (444)
Q Consensus       288 ~~~~~C~VC~~~dd-g~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~~~~~k~k  348 (444)
                      .....| +|+..++ ++ +||+|+.|..|+|..|+|+.....+..|.|..|.+.........
T Consensus        84 ~~~~~c-~c~~~~~~~g-~~i~c~~c~~Wqh~~C~g~~~~~~p~~y~c~~c~~~~~~~~~~~  143 (508)
T KOG1844|consen   84 REISRC-DCGLEDDMEG-LMIQCDWCGRWQHKICCGSFKSTKPDKYVCEICTPRNKEVERAL  143 (508)
T ss_pred             Cccccc-ccccccCCCc-eeeCCcccCcccCceeeeecCCCCchhceeeeeccccccchhhh
Confidence            456789 9999888 76 99999999999999999988774567899999998776655433

>KOG4299|consensus

Probab=97.66  E-value=1.7e-05  Score=86.15  Aligned_cols=48  Identities=33%  Similarity=0.780  Sum_probs=40.4

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC---CCCCceecCCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE---PETSDWFCPKCSK  339 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~---~~~~~w~Cp~C~~  339 (444)
                      .+|..|+..+.-. ..|+||+|+..||+.|+.++..   .+.+.|+|+.|.-
T Consensus       254 ~fCsaCn~~~~F~-~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~  304 (613)
T KOG4299|consen  254 DFCSACNGSGLFN-DIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKI  304 (613)
T ss_pred             HHHHHhCCccccc-cceeecCCchHHHHhhcCCCCCcccCCCCccccCCCee
Confidence            3899999865432 4799999999999999999966   7788999999964

>KOG1512|consensus

Probab=97.60  E-value=2.7e-05  Score=78.06  Aligned_cols=47  Identities=32%  Similarity=0.688  Sum_probs=39.3

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecC-CCCCc
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCP-KCSKV  340 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp-~C~~~  340 (444)
                      .|.||+.|...+ .|+.||.|++.||++|||+... +.|.|+|. .|...
T Consensus       316 lC~IC~~P~~E~-E~~FCD~CDRG~HT~CVGL~~l-P~G~WICD~~C~~~  363 (381)
T KOG1512|consen  316 LCRICLGPVIES-EHLFCDVCDRGPHTLCVGLQDL-PRGEWICDMRCREA  363 (381)
T ss_pred             hhhccCCcccch-heeccccccCCCCccccccccc-cCccchhhhHHHHh
Confidence            488999998777 7999999999999999999654 55799998 46543

>KOG1245|consensus

Probab=96.98  E-value=0.00014  Score=86.34  Aligned_cols=51  Identities=27%  Similarity=0.751  Sum_probs=45.2

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCccc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  342 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~~  342 (444)
                      ..|.+|....+.. .|+.||.|+.|||+.|+.+... .+.++|+|+.|.....
T Consensus      1109 ~~c~~cr~k~~~~-~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1109 ALCKVCRRKKQDE-KMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred             hhhhhhhhcccch-hhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence            4799999877765 7999999999999999999888 7788999999997664

>KOG0383|consensus

Probab=96.79  E-value=0.00055  Score=76.23  Aligned_cols=50  Identities=26%  Similarity=0.689  Sum_probs=39.9

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCccc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  342 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~~  342 (444)
                      ..-.|.+|..  +|.  .|+||.|..|||.+|++++.. .+.+.|.|+.|.....
T Consensus        46 ~~e~c~ic~~--~g~--~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~   96 (696)
T KOG0383|consen   46 EQEACRICAD--GGE--LLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPKN   96 (696)
T ss_pred             hhhhhhhhcC--CCc--EEEeccccHHHHHHccCCCCCcCCccceeeeeeccCCC
Confidence            3456889987  565  889999999999999999888 5555699999954443

>KOG4364|consensus

Probab=96.67  E-value=0.036  Score=61.37  Aligned_cols=18  Identities=11%  Similarity=-0.121  Sum_probs=9.3

Q ss_pred             hHHHHHHhhhcCcccccC
Q psy5823         384 SRADLKLCLLETDCVQVD  401 (444)
Q Consensus       384 ~r~dL~~CL~~SdCv~~~  401 (444)
                      +...++.|+-.+.|+++.
T Consensus       610 ~~A~~ah~a~d~ak~~~~  627 (811)
T KOG4364|consen  610 LQALTAHAAKDTAKLIIC  627 (811)
T ss_pred             HHHHHHHHhhhhHHHhhh
Confidence            344455555555555543

>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A

Probab=96.67  E-value=0.00031  Score=50.11  Aligned_cols=34  Identities=35%  Similarity=1.055  Sum_probs=19.7

Q ss_pred             CeeecCCCCCcccccccccCCCCCCCceecCCCC
Q psy5823         305 PMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS  338 (444)
Q Consensus       305 ~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~  338 (444)
                      .||.|++|+.+.|..|.|+........|+|..|.
T Consensus         3 ~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~   36 (36)
T PF13831_consen    3 PLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE   36 (36)
T ss_dssp             EEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred             ceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence            5899999999999999999888666579998773

>KOG1632|consensus

Probab=96.66  E-value=0.00065  Score=70.23  Aligned_cols=50  Identities=32%  Similarity=0.729  Sum_probs=42.3

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccc--cccCCC--CCCCceecCCCCCcc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVC--VGLVAE--PETSDWFCPKCSKVD  341 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~C--vG~~~~--~~~~~w~Cp~C~~~~  341 (444)
                      .+| .|..+.+.+.+|+.||.|..|||..|  +|++..  .....|+|..|....
T Consensus        61 ~~~-~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~  114 (345)
T KOG1632|consen   61 RYC-KCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ  114 (345)
T ss_pred             chh-hcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchhh
Confidence            477 88888776558999999999999999  998877  567789999998554

>KOG0955|consensus

Probab=96.66  E-value=0.0014  Score=75.80  Aligned_cols=52  Identities=23%  Similarity=0.607  Sum_probs=41.2

Q ss_pred             CceeccccCCCCC--CCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCccc
Q psy5823         289 QVWICPACGVQDD--GSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDE  342 (444)
Q Consensus       289 ~~~~C~VC~~~dd--g~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~~  342 (444)
                      ++..|.||...+-  .+ +.|.||.|+..+|..|+|++. .+.+.|+|..|.....
T Consensus       218 ~D~~C~iC~~~~~~n~n-~ivfCD~Cnl~VHq~Cygi~~-ipeg~WlCr~Cl~s~~  271 (1051)
T KOG0955|consen  218 EDAVCCICLDGECQNSN-VIVFCDGCNLAVHQECYGIPF-IPEGQWLCRRCLQSPQ  271 (1051)
T ss_pred             CCccceeecccccCCCc-eEEEcCCCcchhhhhccCCCC-CCCCcEeehhhccCcC
Confidence            3446889987663  35 899999999999999999654 4568999999986543

>KOG0954|consensus

Probab=96.34  E-value=0.0016  Score=72.34  Aligned_cols=49  Identities=29%  Similarity=0.758  Sum_probs=40.1

Q ss_pred             ceeccccCCCC--CCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCc
Q psy5823         290 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       290 ~~~C~VC~~~d--dg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      .+.|.||..+|  .++ .||.||.|+.-.|..|.||... +.+.|.|..|.-.
T Consensus       271 dviCDvCrspD~e~~n-eMVfCd~Cn~cVHqaCyGIle~-p~gpWlCr~Calg  321 (893)
T KOG0954|consen  271 DVICDVCRSPDSEEAN-EMVFCDKCNICVHQACYGILEV-PEGPWLCRTCALG  321 (893)
T ss_pred             cceeceecCCCccccc-eeEEeccchhHHHHhhhceeec-CCCCeeehhcccc
Confidence            46799999886  233 7999999999999999999765 4478999888643

>KOG0957|consensus

Probab=96.28  E-value=0.0017  Score=69.53  Aligned_cols=48  Identities=25%  Similarity=0.684  Sum_probs=41.0

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-----CCCCceecCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCS  338 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~  338 (444)
                      .+.|.||.+..|-. ++++||.|+.-||+.|+.+++.     ....-|.|..|-
T Consensus       544 ~ysCgiCkks~dQH-ll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd  596 (707)
T KOG0957|consen  544 NYSCGICKKSTDQH-LLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD  596 (707)
T ss_pred             ceeeeeeccchhhH-HHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence            45699999876665 8999999999999999999988     335679999994

>KOG4364|consensus

Probab=96.08  E-value=0.068  Score=59.28  Aligned_cols=7  Identities=29%  Similarity=0.805  Sum_probs=3.5

Q ss_pred             ceecCCC
Q psy5823         331 DWFCPKC  337 (444)
Q Consensus       331 ~w~Cp~C  337 (444)
                      .||=|+|
T Consensus       557 gffVPhg  563 (811)
T KOG4364|consen  557 GFFVPHG  563 (811)
T ss_pred             CeecCCc
Confidence            4555554

>KOG0957|consensus

Probab=96.03  E-value=0.0049  Score=66.15  Aligned_cols=49  Identities=31%  Similarity=0.678  Sum_probs=35.6

Q ss_pred             eeccccCC--CCCCCCCeeecCCCCCcccccccccCCC------C---CCCceecCCCCCc
Q psy5823         291 WICPACGV--QDDGSLPMIGCDGCDAWYHWVCVGLVAE------P---ETSDWFCPKCSKV  340 (444)
Q Consensus       291 ~~C~VC~~--~ddg~~~mI~CD~C~~WfH~~CvG~~~~------~---~~~~w~Cp~C~~~  340 (444)
                      ++|.||..  .+|.+ .+|+||.|+.-.|-.|.|+...      .   ....|||.-|.-.
T Consensus       120 ~iCcVClg~rs~da~-ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G  179 (707)
T KOG0957|consen  120 VICCVCLGQRSVDAG-EILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG  179 (707)
T ss_pred             eEEEEeecCcccccc-ceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence            35669953  33444 6999999999999999998733      1   2367999887643

>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []

Probab=95.65  E-value=0.0079  Score=63.92  Aligned_cols=52  Identities=31%  Similarity=0.747  Sum_probs=37.7

Q ss_pred             ceeccccCCCCC--CCCCeeecCCCCCccccccc--------ccCCC----CCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDD--GSLPMIGCDGCDAWYHWVCV--------GLVAE----PETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~dd--g~~~mI~CD~C~~WfH~~Cv--------G~~~~----~~~~~w~Cp~C~~~~  341 (444)
                      .+.|.||++.|+  +.-.||-||.|+.|-|+.|.        |++..    ..+..|+|..|....
T Consensus       128 ~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s  193 (446)
T PF07227_consen  128 RCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS  193 (446)
T ss_pred             cCCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence            466888987652  22389999999999999994        33332    235689999998554

Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.

>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=95.49  E-value=0.0085  Score=55.36  Aligned_cols=29  Identities=28%  Similarity=0.732  Sum_probs=24.6

Q ss_pred             cccccccccCCC-CCCCceecCCCCCcccc
Q psy5823         315 WYHWVCVGLVAE-PETSDWFCPKCSKVDEG  343 (444)
Q Consensus       315 WfH~~CvG~~~~-~~~~~w~Cp~C~~~~~~  343 (444)
                      .||+.|+.+++. .+.++|+|+.|......
T Consensus         1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~   30 (148)
T cd04718           1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSG   30 (148)
T ss_pred             CcccccCCCCCCCCCCCCcCCCCCcCCCCC
Confidence            489999999999 77899999999865443

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG1632|consensus

Probab=95.03  E-value=0.0025  Score=65.95  Aligned_cols=54  Identities=30%  Similarity=0.738  Sum_probs=42.6

Q ss_pred             CCceeccccCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCc----eecCCCCCcc
Q psy5823         288 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSD----WFCPKCSKVD  341 (444)
Q Consensus       288 ~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~----w~Cp~C~~~~  341 (444)
                      .....|..||..+....+||+|+.|..|||+.|+.+...  ..+..    |+|++|....
T Consensus       237 ~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~~  296 (345)
T KOG1632|consen  237 YSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVLK  296 (345)
T ss_pred             cccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeecc
Confidence            344679889987755459999999999999999999877  22334    9999998633

>KOG4443|consensus

Probab=94.76  E-value=0.015  Score=64.26  Aligned_cols=48  Identities=31%  Similarity=0.857  Sum_probs=39.6

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  339 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~  339 (444)
                      ..|..|+...|.. ..+.|+.|+..||.+|..+... .+.+.|+|.-|..
T Consensus        69 rvCe~c~~~gD~~-kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~  117 (694)
T KOG4443|consen   69 RVCEACGTTGDPK-KFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTR  117 (694)
T ss_pred             eeeeeccccCCcc-cccccccccccccccccCCccccccCcccccHHHHh
Confidence            4577788766665 6778999999999999999888 7778999997764

>COG5141 PHD zinc finger-containing protein [General function prediction only]

Probab=94.35  E-value=0.017  Score=62.05  Aligned_cols=48  Identities=29%  Similarity=0.717  Sum_probs=38.8

Q ss_pred             eeccccCCCCC--CCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCc
Q psy5823         291 WICPACGVQDD--GSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       291 ~~C~VC~~~dd--g~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      ..|.+|...+.  .+ .+|.||+|+-..|-.|.|+.-. +.|.|+|..|.-.
T Consensus       194 ~~C~~c~~t~~eN~n-aiVfCdgC~i~VHq~CYGI~f~-peG~WlCrkCi~~  243 (669)
T COG5141         194 DICTKCTSTHNENSN-AIVFCDGCEICVHQSCYGIQFL-PEGFWLCRKCIYG  243 (669)
T ss_pred             hhhHhccccccCCcc-eEEEecCcchhhhhhcccceec-Ccchhhhhhhccc
Confidence            47999998764  34 6899999999999999999655 4578999988643

>KOG0956|consensus

Probab=92.52  E-value=0.054  Score=60.29  Aligned_cols=47  Identities=36%  Similarity=0.869  Sum_probs=35.6

Q ss_pred             ccccCCCC-CCCCCeeecCC--CCCcccccccccCCCCCCCceecCCCCCc
Q psy5823         293 CPACGVQD-DGSLPMIGCDG--CDAWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       293 C~VC~~~d-dg~~~mI~CD~--C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      |-||.... +.+-.+|.||+  |..+.|..|.||... +.+.|||..|...
T Consensus         8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqV-PtGpWfCrKCesq   57 (900)
T KOG0956|consen    8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQV-PTGPWFCRKCESQ   57 (900)
T ss_pred             eeeecCcCCCccCceeeecCCCceeeeehhcceeEec-CCCchhhhhhhhh
Confidence            43897543 22237999996  999999999999654 5678999999743

>KOG1144|consensus

Probab=91.81  E-value=0.39  Score=54.51  Aligned_cols=7  Identities=14%  Similarity=0.017  Sum_probs=3.9

Q ss_pred             hhhHhhc
Q psy5823         405 PRQCLRE  411 (444)
Q Consensus       405 ~~eCL~~  411 (444)
                      .-+||+.
T Consensus       491 lld~ir~  497 (1064)
T KOG1144|consen  491 LLDKIRG  497 (1064)
T ss_pred             HHHHhhc
Confidence            4566663

>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain

Probab=89.61  E-value=0.23  Score=47.03  Aligned_cols=48  Identities=27%  Similarity=0.804  Sum_probs=35.5

Q ss_pred             eccccCCC---CCCCCCeeecCCCCCcccccccccCCC---------CCCCceecCCCCCc
Q psy5823         292 ICPACGVQ---DDGSLPMIGCDGCDAWYHWVCVGLVAE---------PETSDWFCPKCSKV  340 (444)
Q Consensus       292 ~C~VC~~~---ddg~~~mI~CD~C~~WfH~~CvG~~~~---------~~~~~w~Cp~C~~~  340 (444)
                      .|.+|+..   ..-+ .||.|-+|...||-.|+|+...         ...+...|..|...
T Consensus         1 ~C~~C~~~g~~~~kG-~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~   60 (175)
T PF15446_consen    1 TCDTCGYEGDDRNKG-PLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGI   60 (175)
T ss_pred             CcccccCCCCCccCC-CeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcCh
Confidence            37788542   2334 7999999999999999999876         23445678888743

>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines

Probab=87.83  E-value=0.21  Score=33.75  Aligned_cols=29  Identities=38%  Similarity=0.703  Sum_probs=13.1

Q ss_pred             eccccCCCCCCCCCeeecCCCCCccccccc
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCV  321 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~Cv  321 (444)
                      .|.+|+.+.+++ .+-.|..|+.+.|..|+
T Consensus         2 ~C~~C~~~~~~~-~~Y~C~~Cdf~lH~~Ca   30 (30)
T PF07649_consen    2 RCDACGKPIDGG-WFYRCSECDFDLHEECA   30 (30)
T ss_dssp             --TTTS----S---EEE-TTT-----HHHH
T ss_pred             cCCcCCCcCCCC-ceEECccCCCccChhcC
Confidence            588999988774 67889999999999985

The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.

>KOG1029|consensus

Probab=86.98  E-value=17  Score=41.89  Aligned_cols=39  Identities=18%  Similarity=0.287  Sum_probs=21.8

Q ss_pred             hhhhhhcchHHHHhhhhhhHHHHhhhhhHHHHHHHHHHH
Q psy5823         186 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK  224 (444)
Q Consensus       186 ~~~~~kekk~ekerke~~~ke~~kk~k~~~kk~kkek~k  224 (444)
                      +...|.|++++.+++|...+|-++-|+.+=++++..++.
T Consensus       384 E~qrEEerkkeie~rEaar~ElEkqRqlewErar~qem~  422 (1118)
T KOG1029|consen  384 ERQREEERKKEIERREAAREELEKQRQLEWERARRQEML  422 (1118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333445556666666666666666665555555554443

>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.90  E-value=0.28  Score=37.16  Aligned_cols=32  Identities=22%  Similarity=0.593  Sum_probs=17.7

Q ss_pred             CeeecCCCCCcccccccccCC--CCCCCceecCCC
Q psy5823         305 PMIGCDGCDAWYHWVCVGLVA--EPETSDWFCPKC  337 (444)
Q Consensus       305 ~mI~CD~C~~WfH~~CvG~~~--~~~~~~w~Cp~C  337 (444)
                      .|||||.|..|=.+. .++..  ...++.|+|..-
T Consensus         2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~n   35 (50)
T PF07496_consen    2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSMN   35 (50)
T ss_dssp             EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGGS
T ss_pred             eEEECCCCCceeeCC-hhhCcccccCCCeEEcCCC
Confidence            599999999998877 44444  223348999863

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 a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.

>KOG4443|consensus

Probab=86.52  E-value=0.14  Score=56.90  Aligned_cols=49  Identities=31%  Similarity=0.773  Sum_probs=38.5

Q ss_pred             ceeccccCCCCCCC--CCeeecCCCCCcccccccccCCC-----CCCCceecCCCC
Q psy5823         290 VWICPACGVQDDGS--LPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCS  338 (444)
Q Consensus       290 ~~~C~VC~~~ddg~--~~mI~CD~C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~  338 (444)
                      ..+|++|...+...  ..|++|+.|.+|.|..|-|+...     ..+-.|-|..|+
T Consensus       145 ~~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR  200 (694)
T KOG4443|consen  145 LSYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR  200 (694)
T ss_pred             cccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence            36899998766332  25799999999999999998766     233479999998

>KOG0163|consensus

Probab=85.55  E-value=9.6  Score=43.85  Aligned_cols=21  Identities=19%  Similarity=0.173  Sum_probs=9.9

Q ss_pred             hhhhcchhceeccccCccccc
Q psy5823          89 EKEYSKVKDVELGVTPMVPNI  109 (444)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~i  109 (444)
                      ++--+.+.+.+.-|..+|.-|
T Consensus       864 ~e~~~~~~~~~~~id~lv~~I  884 (1259)
T KOG0163|consen  864 EEIISGANSTYRQIDDLVKKI  884 (1259)
T ss_pred             HHHHhhhhhHHHHHHHHHHHh
Confidence            334445555555554444443

>KOG1473|consensus

Probab=82.40  E-value=0.77  Score=53.99  Aligned_cols=44  Identities=25%  Similarity=0.509  Sum_probs=36.7

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCS  338 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~  338 (444)
                      .+|.+|+.  .++  .+||+.|++.||+.|+.++.. .+...|-|..|.
T Consensus       345 dhcrf~~d--~~~--~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~  389 (1414)
T KOG1473|consen  345 DHCRFCHD--LGD--LLCCETCPRVVHLECVFHPRFAVPSAFWECEVCN  389 (1414)
T ss_pred             ccccccCc--ccc--eeecccCCceEEeeecCCccccCCCccchhhhhh
Confidence            46877876  444  899999999999999998887 666789999886

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=82.19  E-value=0.9  Score=35.52  Aligned_cols=33  Identities=33%  Similarity=0.704  Sum_probs=26.6

Q ss_pred             ceeccccCCCCC-CCCCeeecCCCCCccccccccc
Q psy5823         290 VWICPACGVQDD-GSLPMIGCDGCDAWYHWVCVGL  323 (444)
Q Consensus       290 ~~~C~VC~~~dd-g~~~mI~CD~C~~WfH~~CvG~  323 (444)
                      ...|.+|+...- ++ ..|.|..|..-||-.|...
T Consensus         5 ~~~C~~Cg~~~~~~d-DiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGD-DIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCC-CEEECCCCCCcccHHHHhh
Confidence            357999998872 22 4999999999999999843

>KOG2752|consensus

Probab=81.69  E-value=0.68  Score=47.70  Aligned_cols=32  Identities=28%  Similarity=0.719  Sum_probs=25.4

Q ss_pred             CceeccccCCCCCC-----CCCeeecCCCCCccc-cccc
Q psy5823         289 QVWICPACGVQDDG-----SLPMIGCDGCDAWYH-WVCV  321 (444)
Q Consensus       289 ~~~~C~VC~~~ddg-----~~~mI~CD~C~~WfH-~~Cv  321 (444)
                      ...+| .|..++++     +..|+||..|..||| -.|+
T Consensus       127 qG~~C-~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~  164 (345)
T KOG2752|consen  127 QGLFC-KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCM  164 (345)
T ss_pred             cceeE-EecCCCCCccccccceeeeEEeccchhcccccC
Confidence            34689 99987754     347999999999999 6665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	444
2k16_A	75	Solution Structure Of The Free Taf3 Phd Domain Leng		2e-13
1weu_A	91	Solution Structure Of Phd Domain In Ing1-Like Prote		8e-04

>pdb|2K16|A Chain A, Solution Structure Of The Free Taf3 Phd Domain Length = 75

Iteration: 1
 Score = 73.9 bits (180), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/54 (62%), Positives = 38/54 (70%), Gaps = 2/54 (3%)
Query: 287 SKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 339
             Q+WICP C   DDGS PMIGCD CD WYHW CVG++A  PE   WFCPKC+ 
Sbjct: 15  GNQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCAN 67

>pdb|1WEU|A Chain A, Solution Structure Of Phd Domain In Ing1-Like Protein Bac25009 Length = 91

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 4/37 (10%)
Query: 306 MIGCDGCDA---WYHWVCVGLVAEPETSDWFCPKCSK 339
           MIGCD  D    W+H+ CVGL  +P    WFCP+CS+
Sbjct: 49  MIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQ 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	444
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	3e-18
1we9_A	64	PHD finger family protein; structural genomics, PH	7e-17
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	4e-14
1wee_A	72	PHD finger family protein; structural genomics, PH	2e-13
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	3e-13
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	5e-13
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	9e-13
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	5e-12
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	2e-11
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	3e-11
1wem_A	76	Death associated transcription factor 1; structura	4e-11
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	5e-11
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	3e-07
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	2e-04
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	8e-11
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	1e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-04
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	2e-09
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	4e-09
3kv5_D	488	JMJC domain-containing histone demethylation prote	4e-09
1weu_A	91	Inhibitor of growth family, member 4; structural g	1e-08
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	1e-08
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	2e-08
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	5e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	8e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-04
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	8e-08
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	9e-08
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	1e-07
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	2e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	4e-05
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	3e-07
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	3e-07
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	3e-07
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	4e-07
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	4e-07
1wew_A	78	DNA-binding family protein; structural genomics, P	6e-07
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	7e-07
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	9e-07
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	9e-07
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	1e-06
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	2e-06
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	3e-06
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	3e-06
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	3e-06
2yt5_A	66	Metal-response element-binding transcription facto	3e-06
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	6e-06
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	6e-06
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	8e-06
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	1e-05
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	2e-05
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	2e-05
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	2e-05
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	3e-05
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	5e-05
3lu0_C	1342	DNA-directed RNA polymerase subunit beta; E. coli	8e-05
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	1e-04
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	1e-04
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-04
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	6e-04
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	2e-04

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A* Length = 75

 Score = 78.0 bits (192), Expect = 3e-18
 Identities = 35/62 (56%), Positives = 40/62 (64%), Gaps = 2/62 (3%)

Query: 286 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCSKVDEGS 344
              Q+WICP C   DDGS PMIGCD CD WYHW CVG+  A PE   WFCPKC+   +  
Sbjct: 14  WGNQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD 72

Query: 345 RK 346
           +K
Sbjct: 73  KK 74

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Length = 64

 Score = 73.7 bits (181), Expect = 7e-17
 Identities = 19/62 (30%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 285 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDE 342
           G S     C ACG         I CD C+ W+H  CV +          + CP CS    
Sbjct: 1   GSSGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG 60

Query: 343 GS 344
            S
Sbjct: 61  PS 62

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A* Length = 52

 Score = 65.3 bits (159), Expect = 4e-14
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 292 ICPA--CGVQDDGSLPMIGCDG-CDAWYHWVCVGLVAEP-ETSDWFCPKCS 338
           +C A  C       +  + CDG CD W+H VCVG+  E  E  D+ C  C+
Sbjct: 2   VCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA 52

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Length = 72

 Score = 64.1 bits (156), Expect = 2e-13
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 4/65 (6%)

Query: 278 AADEYDTGDSKQVWI--CPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFC 334
           ++           W   C  CG +DD    M+ CDGC  W+H  C+G+  A+   S + C
Sbjct: 2   SSGSSGMERGVDNWKVDCK-CGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLC 60

Query: 335 PKCSK 339
            +C +
Sbjct: 61  FRCIE 65

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens} Length = 68

 Score = 63.7 bits (155), Expect = 3e-13
 Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 2/62 (3%)

Query: 278 AADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC 337
            +   +    + +  C  C     G  PMI C+ C  W H  C  +        + C KC
Sbjct: 7   HSSGRENLYFQGLVTCF-CMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 64

Query: 338 SK 339
             
Sbjct: 65  RD 66

>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} Length = 75

 Score = 63.0 bits (153), Expect = 5e-13
 Identities = 24/62 (38%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 296 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKKKRGR 353
           C +  D +  MI CD C  W+H  CVG+  E  P+   + CP C K   G    KKKR  
Sbjct: 15  CRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEK-THGKSTLKKKRTW 73

Query: 354 KK 355
            K
Sbjct: 74  HK 75

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens} Length = 52

 Score = 61.6 bits (150), Expect = 9e-13
 Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 1/42 (2%)

Query: 296 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC 337
           C     G  PMI C+ C  W H  C  +        + C KC
Sbjct: 9   CMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 49

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens} Length = 105

 Score = 61.5 bits (148), Expect = 5e-12
 Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 8/70 (11%)

Query: 290 VWICPACGVQDDGSLPMIGCDG-CDAWYHWVCVGL-------VAEPETSDWFCPKCSKVD 341
           V+ C AC  + +     I C+  C  W+H  C G+       +    ++ W C  C K  
Sbjct: 3   VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK 62

Query: 342 EGSRKEKKKR 351
           EGS      +
Sbjct: 63  EGSGSGSGSQ 72

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2 Length = 79

 Score = 58.4 bits (141), Expect = 2e-11
 Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 296 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKKKRGR 353
           C    + +  MI C  C  W+H  CVG+  E   +   + CP C  V  G    K     
Sbjct: 17  CRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV-FGPSIMKNWHSG 75

Query: 354 KKK 356
              
Sbjct: 76  PSS 78

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 58.0 bits (140), Expect = 3e-11
 Identities = 24/74 (32%), Positives = 32/74 (43%), Gaps = 8/74 (10%)

Query: 285 GDSKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPKCSKVD 341
           G S     C  C     G   M+GCD  D    W+H+ CVGL   P+   W+CP+C+   
Sbjct: 1   GSSGSSGYCI-CNQVSYG--EMVGCDNQDCPIEWFHYGCVGLTEAPK-GKWYCPQCTA-A 55

Query: 342 EGSRKEKKKRGRKK 355
              R  + K G   
Sbjct: 56  MKRRGSRHKSGPSS 69

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2 Length = 76

 Score = 57.6 bits (139), Expect = 4e-11
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 7/69 (10%)

Query: 277 AAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL------VAEPETS 330
           ++    +        +   C    +    MI CD C+ W+H  CVG+      + E    
Sbjct: 2   SSGSSGECEVYDPNALYCICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGE 60

Query: 331 DWFCPKCSK 339
           D+ CP C+ 
Sbjct: 61  DYICPNCTI 69

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 63.9 bits (156), Expect = 5e-11
 Identities = 11/120 (9%), Positives = 37/120 (30%), Gaps = 3/120 (2%)

Query: 116  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE 175
              L +++   + K       +        +   K+ +    + +  E + + +      +
Sbjct: 893  RILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQ 952

Query: 176  EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 235
              E       ++ E K+       ++    +   ++       + E+L+K +       H
Sbjct: 953  LTELNYNGVPELTERKD---TFFAQQWTGVKSSAETYKNTLLAELERLQKIEDLHHHHHH 1009

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 52.0 bits (125), Expect = 3e-07
 Identities = 16/155 (10%), Positives = 46/155 (29%), Gaps = 1/155 (0%)

Query: 84  KTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIK 143
           +  PK +E S+++ +   +   +  I +       G    +           ++E  +  
Sbjct: 815 EKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQEHAEAL 874

Query: 144 KKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEK 203
           + + K+ K      +K        E     K       E         +  ++ +   + 
Sbjct: 875 RIELKRQKKIAVLLQKYNRILKKLENWATTKSVYLGSNETG-DSITAVQAKLKNLEAFDG 933

Query: 204 DSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
           + +  +   + D      +L +          E++
Sbjct: 934 ECQSLEGQSNSDLLSILAQLTELNYNGVPELTERK 968

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 11/120 (9%), Positives = 35/120 (29%), Gaps = 21/120 (17%)

Query: 76   KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK 135
               + S E         +K+K++E                       + +S++    +  
Sbjct: 906  SVYLGSNETGDSITAVQAKLKNLEA-------------------FDGECQSLEGQSNSDL 946

Query: 136  KKEKEKIKKKKDKKDKDKIKNKE--KDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEK 193
                 ++ +       +  + K+    ++    K   +  K     + E+  K+++    
Sbjct: 947  LSILAQLTELNYNGVPELTERKDTFFAQQWTGVKSSAETYKNTLLAELERLQKIEDLHHH 1006

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A* Length = 65

 Score = 56.6 bits (136), Expect = 8e-11
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 8/60 (13%)

Query: 286 DSKQVWICPACGVQDDGSLPMIGCDG-CDAWYHWVCVGL-------VAEPETSDWFCPKC 337
            S  V+ C  C  + +     I C+  C  W+H +C G+       +    ++ W C  C
Sbjct: 4   SSDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 63

>3pur_A Lysine-specific demethylase 7 homolog; oxidoreductase-oxidoreductase inhibitor complex; HET: 2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A* 3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A* Length = 528

 Score = 62.0 bits (149), Expect = 1e-10
 Identities = 27/121 (22%), Positives = 38/121 (31%), Gaps = 3/121 (2%)

Query: 250 DMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGC 309
            ME+KT +ES                 A  +E      K +                IGC
Sbjct: 3   HMEQKTPKESDRCGGCGKFTHEDDLI-ALEEEKKKEKEKPLMSKKKSHHHKKNDFQWIGC 61

Query: 310 DGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYR 367
           D C  WYH++C GL          +FCPKC      S + K     + + +         
Sbjct: 62  DSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGI 121

Query: 368 F 368
            
Sbjct: 122 E 122

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 59.0 bits (143), Expect = 2e-09
 Identities = 27/131 (20%), Positives = 56/131 (42%), Gaps = 5/131 (3%)

Query: 135  KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEF--KMKEDKE 192
               ++E  K K + +  ++ K      E K+ + + K  ++ KE K   E    ++    
Sbjct: 900  MMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYS 959

Query: 193  KPVEKIRKEEKD---SEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGT 249
               EK+R + +    SE+E K+        +E++ K +KE  ++  EK+ I +   K+  
Sbjct: 960  TETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKH 1019

Query: 250  DMEEKTKRESS 260
            + E+       
Sbjct: 1020 ETEQLVSELKE 1030

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 58.2 bits (141), Expect = 4e-09
 Identities = 23/136 (16%), Positives = 61/136 (44%), Gaps = 13/136 (9%)

Query: 116  EDLGEIKKDKSIKKDK-KTHKKKEKEKIKKKKDK-----KDKDKIKNKEKDKEKKVDKEK 169
            ++  +  K    K +  +     E EK++   ++     ++     N+    ++++ K +
Sbjct: 938  DEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLR 997

Query: 170  EKGKKEEKEKK--EEKEFKMKEDKEKPVEKIRKEEKDSEKEK-----KSKDKDKKLKKEK 222
            ++  + + EKK  EE   K K + E+ V +++++    + EK     +  D+ K++ +  
Sbjct: 998  KELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITETM 1057

Query: 223  LKKKKKEKERSSHEKE 238
             KK  +E ++   +  
Sbjct: 1058 EKKLVEETKQLELDLN 1073

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 52.0 bits (125), Expect = 3e-07
 Identities = 23/129 (17%), Positives = 48/129 (37%), Gaps = 4/129 (3%)

Query: 114  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGK 173
                L         K D++  + K   +     +     + +    D E+    E+E   
Sbjct: 922  LHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKN 981

Query: 174  KEEKEKKEEKEFKM--KEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE--KLKKKKKE 229
               +    ++E     KE  +   EK   EE   + + +++    +LK++   LK +K+E
Sbjct: 982  ATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEE 1041

Query: 230  KERSSHEKE 238
              R  H++ 
Sbjct: 1042 LNRRIHDQA 1050

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 50.9 bits (122), Expect = 7e-07
 Identities = 20/121 (16%), Positives = 45/121 (37%), Gaps = 3/121 (2%)

Query: 121  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKK 180
            I +     K         +     + +K   D  + +  ++E K    +    +EE  K 
Sbjct: 937  IDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKL 996

Query: 181  E---EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 237
                 +    K+  E+  +K + E +    E K ++   K +KE+L ++  ++ +   E 
Sbjct: 997  RKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEITET 1056

Query: 238  E 238
             
Sbjct: 1057 M 1057

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 49.7 bits (119), Expect = 2e-06
 Identities = 18/123 (14%), Positives = 55/123 (44%), Gaps = 5/123 (4%)

Query: 125  KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKE 184
            +S+++ KK H   E + ++ ++   +++K      +K   ++      + E+     E+ 
Sbjct: 914  RSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYST-ETEKLRSDVERL 972

Query: 185  FKMKEDKEKPVEKIRKEEKDSEKEK----KSKDKDKKLKKEKLKKKKKEKERSSHEKEVI 240
               +E+ +    ++   +++  K +    +++ + K +++   K K + ++  S  KE  
Sbjct: 973  RMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQN 1032

Query: 241  PKL 243
              L
Sbjct: 1033 TLL 1035

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 48.2 bits (115), Expect = 4e-06
 Identities = 16/137 (11%), Positives = 43/137 (31%), Gaps = 17/137 (12%)

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
           + +      K     K       +    +  K  +  +   +     +E +K K E +  
Sbjct: 857 KYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSV 916

Query: 180 KEEKEFK----------------MKEDKEKPVEKIRKEEKDSEKEKKS-KDKDKKLKKEK 222
           +  K+                    ++ +  +EK+   E     E +  +   ++L+  +
Sbjct: 917 ERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSE 976

Query: 223 LKKKKKEKERSSHEKEV 239
            + K       S ++E+
Sbjct: 977 EEAKNATNRVLSLQEEI 993

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 43.9 bits (104), Expect = 8e-05
 Identities = 17/125 (13%), Positives = 45/125 (36%), Gaps = 5/125 (4%)

Query: 120 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
                +++ +      K +    + K     K       +    +  K     +   +  
Sbjct: 841 ATIALQALLRGYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRM 900

Query: 180 KEEKEFKMKEDKEKPVEKIRK-----EEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
             ++E K  + + + VE+ +K     E K  + ++K  +++K+ K    K    E   S+
Sbjct: 901 MAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYST 960

Query: 235 HEKEV 239
             +++
Sbjct: 961 ETEKL 965

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 18/111 (16%), Positives = 49/111 (44%), Gaps = 4/111 (3%)

Query: 116  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDK--KDKDKIKNKEKDKEKKVDKEKEKGK 173
            E L   +++     ++    ++E  K++K+  +   +K  I+      + + ++   + K
Sbjct: 970  ERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELK 1029

Query: 174  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK 224
            ++    K EKE   +   ++   K   E  + +  +++K  +  L  E+L+
Sbjct: 1030 EQNTLLKTEKEELNRRIHDQ--AKEITETMEKKLVEETKQLELDLNDERLR 1078

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A* Length = 59

 Score = 52.5 bits (126), Expect = 2e-09
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 291 WICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWFCPKCSK 339
             C  C     G   MIGCD       W+H+ CV L  +P+   WFCP+C +
Sbjct: 10  TYCL-CHQVSYGE--MIGCDNPDCPIEWFHFACVDLTTKPK-GKWFCPRCVQ 57

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens} Length = 71

 Score = 51.8 bits (124), Expect = 4e-09
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%)

Query: 292 ICPACG-VQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC 337
           +C  C   +   S  ++ CD C+   H  C G+   PE   W C  C
Sbjct: 18  VCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEG-QWLCRHC 63

>3kv5_D JMJC domain-containing histone demethylation protein 1D; epigenetics, histone CODE, jumonji lysine demethylase, metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo sapiens} PDB: 3kv6_A* Length = 488

 Score = 57.3 bits (137), Expect = 4e-09
 Identities = 24/166 (14%), Positives = 50/166 (30%), Gaps = 4/166 (2%)

Query: 255 TKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDA 314
               +          + +    A            V+ C  C    D +  MI CD C  
Sbjct: 3   GAAAAVAAGAAAGAAAAAVSVAAPGRASAPPPPPPVY-C-VCRQPYDVNRFMIECDICKD 60

Query: 315 WYHWVCVGL--VAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDP 372
           W+H  CVG+      +   + CP C+ +   S  +K++   +    +    S        
Sbjct: 61  WFHGSCVGVEEHHAVDIDLYHCPNCAVLHGSSLMKKRRNWHRHDYTEIDDGSKPVQAGTR 120

Query: 373 SELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCE 418
           + + +  +     AD  +  +    +              + P+ +
Sbjct: 121 TFIKELRSRVFPSADEIIIKMHGSQLTQRYLEKHGFDVPIMVPKLD 166

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2 Length = 91

 Score = 51.3 bits (122), Expect = 1e-08
 Identities = 28/88 (31%), Positives = 37/88 (42%), Gaps = 9/88 (10%)

Query: 255 TKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG--- 311
           +    SP+  +  V   S  P    D     D  +   C  C     G   MIGCD    
Sbjct: 3   SGSSGSPEYGMPSVTFGSVHPSDVLDM--PVDPNEPTYCL-CHQVSYGE--MIGCDNPDC 57

Query: 312 CDAWYHWVCVGLVAEPETSDWFCPKCSK 339
              W+H+ CVGL  +P    WFCP+CS+
Sbjct: 58  SIEWFHFACVGLTTKPR-GKWFCPRCSQ 84

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A* Length = 60

 Score = 50.2 bits (120), Expect = 1e-08
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 9/57 (15%)

Query: 286 DSKQVWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWFCPKCSK 339
           +     +C      +     MIGCD       W+H+ CVGL  +P    WFCP+CS+
Sbjct: 8   NEPTYCLCHQVSYGE-----MIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQ 58

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A Length = 71

 Score = 50.3 bits (120), Expect = 2e-08
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 7/66 (10%)

Query: 277 AAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWF 333
           + +      D  +   C  C     G   MIGCD       W+H+ CVGL  +P    WF
Sbjct: 3   SGSSGDMPVDPNEPTYCL-CHQVSYGE--MIGCDNPDCSIEWFHFACVGLTTKPR-GKWF 58

Query: 334 CPKCSK 339
           CP+CS+
Sbjct: 59  CPRCSQ 64

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens} Length = 88

 Score = 49.3 bits (117), Expect = 5e-08
 Identities = 16/73 (21%), Positives = 24/73 (32%), Gaps = 4/73 (5%)

Query: 266 KPVKSPSPPPVAAADEYDTGDSKQVWICPACG-VQDDGSLPMIGCDGCDAWYHWVCVGLV 324
               +      ++       D   V  C  C   +   S  ++ CD C+   H  C G+ 
Sbjct: 3   TKQTARKSTGGSSGSSQSLIDEDAV--CSICMDGESQNSNVILFCDMCNLAVHQECYGVP 60

Query: 325 AEPETSDWFCPKC 337
             PE   W C  C
Sbjct: 61  YIPEG-QWLCRHC 72

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 54.1 bits (130), Expect = 6e-08
 Identities = 29/141 (20%), Positives = 67/141 (47%)

Query: 120  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
            +++++++ ++  +  K     KIKK +D     + +N +  KE+K+ +E+         +
Sbjct: 963  QLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAE 1022

Query: 180  KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 239
            +EEK   + + K K    I + E   +KE+KS+ + +K+K++   +     E+ +  +  
Sbjct: 1023 EEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQ 1082

Query: 240  IPKLTFKFGTDMEEKTKRESS 260
            I +L  +     EE     + 
Sbjct: 1083 IAELKAQLAKKEEELQAALAR 1103

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 53.3 bits (128), Expect = 1e-07
 Identities = 29/128 (22%), Positives = 59/128 (46%)

Query: 111  KVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKE 170
            KVT+   + +++ D  I +D+     KE++ ++++      +  + +EK K     K K 
Sbjct: 978  KVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKH 1037

Query: 171  KGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 230
            +    E E + +KE K +++ EK   K+  E  D  ++           K +L KK++E 
Sbjct: 1038 ESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEEL 1097

Query: 231  ERSSHEKE 238
            + +    E
Sbjct: 1098 QAALARLE 1105

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 50.6 bits (121), Expect = 8e-07
 Identities = 26/126 (20%), Positives = 55/126 (43%), Gaps = 3/126 (2%)

Query: 113  TSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKG 172
               ++L EI  +   + +++  + ++ +  KKK  ++  D  +  E+++  +   + EK 
Sbjct: 920  AKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKV 979

Query: 173  KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 232
              + K KK E +  + ED+     K+ KE K  E+       +   ++EK K   K K +
Sbjct: 980  TADGKIKKMEDDILIMEDQ---NNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNK 1036

Query: 233  SSHEKE 238
                  
Sbjct: 1037 HESMIS 1042

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.4 bits (118), Expect = 2e-06
 Identities = 20/146 (13%), Positives = 69/146 (47%), Gaps = 5/146 (3%)

Query: 120  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEK 179
            E K  +  ++     +K + E     + ++ + ++  K+++ E+ + + + + ++EE+  
Sbjct: 884  EQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERS 943

Query: 180  KEEKEFKMK-----EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
            ++ +  K K      D E+ +E+     +  + EK + D   K  ++ +   + +  + +
Sbjct: 944  QQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLT 1003

Query: 235  HEKEVIPKLTFKFGTDMEEKTKRESS 260
             E++++ +      T++ E+ ++  +
Sbjct: 1004 KERKLLEERVSDLTTNLAEEEEKAKN 1029

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.1 bits (117), Expect = 2e-06
 Identities = 25/118 (21%), Positives = 52/118 (44%), Gaps = 2/118 (1%)

Query: 122  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKE 181
            K  + +   ++  +++E  + K + +K   D    K +D    ++ +  K  KE K  +E
Sbjct: 952  KMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEE 1011

Query: 182  EKEFKMKEDKEKPVEKIRKEEKDSEK-EKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
                 +  +  +  EK +   K   K E    + + +LKKE+  +++ EK +   E E
Sbjct: 1012 RVS-DLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGE 1068

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 46.0 bits (109), Expect = 2e-05
 Identities = 21/119 (17%), Positives = 61/119 (51%), Gaps = 3/119 (2%)

Query: 121  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKK 180
            I++++   +  +  KKK ++++   +++ ++++   ++   EK     K K  +++    
Sbjct: 936  IEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIM 995

Query: 181  EEKEFKMKEDKEKPVEKIRKEEKD-SEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
            E++  K+ ++++   E++     + +E+E+K+K+  K   K K +    E E    ++E
Sbjct: 996  EDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTK--LKNKHESMISELEVRLKKEE 1052

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 45.6 bits (108), Expect = 3e-05
 Identities = 25/133 (18%), Positives = 62/133 (46%), Gaps = 4/133 (3%)

Query: 116  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKK-KDKKDKDKIKNKEKDKEKKVDKEKEKGKK 174
            E   + + +    + K T   +EK  +++K + + +      + + +     +E E+   
Sbjct: 871  ERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILH 930

Query: 175  EEKEKKEEKE---FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 231
            E + + EE+E    +++ +K+K  +++   E+  E+E+ ++ K +  K     K KK ++
Sbjct: 931  EMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMED 990

Query: 232  RSSHEKEVIPKLT 244
                 ++   KLT
Sbjct: 991  DILIMEDQNNKLT 1003

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 43.7 bits (103), Expect = 1e-04
 Identities = 24/138 (17%), Positives = 65/138 (47%), Gaps = 6/138 (4%)

Query: 107 PNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVD 166
           P +        L ++ + +   + K    ++ KE+ +K + +  + + K+ +  +EK + 
Sbjct: 838 PWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLL 897

Query: 167 KEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK------ 220
           +EK + + E   + EE   ++   K++  E + + E   E+E++   + +  KK      
Sbjct: 898 QEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQM 957

Query: 221 EKLKKKKKEKERSSHEKE 238
             L+++ +E+E +  + +
Sbjct: 958 LDLEEQLEEEEAARQKLQ 975

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 17/123 (13%), Positives = 58/123 (47%)

Query: 116 EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE 175
           E+L   K+ +   + +    +++  ++ ++K+   +      E   E +  + +   KK+
Sbjct: 864 EELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQ 923

Query: 176 EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 235
           E E+   +     E++E+  ++++ E+K  +++    ++  + ++   +K + EK  +  
Sbjct: 924 ELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADG 983

Query: 236 EKE 238
           + +
Sbjct: 984 KIK 986

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.1 bits (99), Expect = 3e-04
 Identities = 21/128 (16%), Positives = 54/128 (42%), Gaps = 8/128 (6%)

Query: 120  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKD---KDKIKNKEKDKEKKVDKEKEKGKKEE 176
            +  K    +K  +         + ++++K     K K K++    E +V  +KE+  ++E
Sbjct: 998  QNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQE 1057

Query: 177  KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKD-----KKLKKEKLKKKKKEKE 231
             EK + K      D  + + +++ +  + + +   K+++      +L+ E  +K    K+
Sbjct: 1058 LEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKK 1117

Query: 232  RSSHEKEV 239
                E  +
Sbjct: 1118 IRELESHI 1125

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.4 bits (97), Expect = 7e-04
 Identities = 34/218 (15%), Positives = 90/218 (41%), Gaps = 19/218 (8%)

Query: 62   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTS-SEDLGE 120
            KM+ ++   ++   +E+ + ++    K     K+K +E  +  M     K+T   + L E
Sbjct: 952  KMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEE 1011

Query: 121  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGK------- 173
               D +    ++  K K   K+K K +    +     +K+++ + + EK K K       
Sbjct: 1012 RVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSD 1071

Query: 174  --------KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEK-EKKSKDKDKKLK--KEK 222
                    + +  + + +  K +E+ +  + ++  E        KK ++ +  +   +E 
Sbjct: 1072 LHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQED 1131

Query: 223  LKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 260
            L+ +K  + ++  +K  + +      T++E+     ++
Sbjct: 1132 LESEKAARNKAEKQKRDLSEELEALKTELEDTLDTTAT 1169

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A* Length = 90

 Score = 49.0 bits (116), Expect = 8e-08
 Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 267 PVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGL 323
           P+ S          +   G++ Q  +   C     G   M+ CD       W+H+ CVGL
Sbjct: 2   PLGSHMASEFINQGDVTEGNNNQEEVYCFCRNVSYGP--MVACDNPACPFEWFHYGCVGL 59

Query: 324 VAEPETSDWFCPKCSKVDEGSRKEKKKRGRKK 355
              P+   W+C K  K     R + K++ R+K
Sbjct: 60  KQAPK-GKWYCSKDCKEIANQRSKSKRQKRRK 90

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus} Length = 62

 Score = 48.0 bits (114), Expect = 9e-08
 Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 8/67 (11%)

Query: 279 ADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCP 335
             E+    ++  + C  C     G   MIGCD       W+H+ CV L  +P+   W+CP
Sbjct: 1   GSEFAIDPNEPTY-CL-CNQVSYGE--MIGCDNEQCPIEWFHFSCVSLTYKPK-GKWYCP 55

Query: 336 KCSKVDE 342
           KC   +E
Sbjct: 56  KCRGDNE 62

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens} Length = 226

 Score = 51.3 bits (122), Expect = 1e-07
 Identities = 25/129 (19%), Positives = 46/129 (35%), Gaps = 5/129 (3%)

Query: 213 DKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPS 272
           D +   K+E    ++        +  +            + +   E SP +     +   
Sbjct: 99  DAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSG 158

Query: 273 PPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETS 330
           P      D+ +     +V  C  CG + D     + CD CD  +H  C+   L + P   
Sbjct: 159 PSCKHCKDDVN--RLCRVCACHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSED 215

Query: 331 DWFCPKCSK 339
           +W+CP+C  
Sbjct: 216 EWYCPECRN 224

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B Length = 70

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 293 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 339
           C  CG + D     + CD CD  +H  C+   L + P   +W+CP+C  
Sbjct: 21  CHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN 68

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 50.2 bits (119), Expect = 2e-07
 Identities = 19/82 (23%), Positives = 43/82 (52%), Gaps = 10/82 (12%)

Query: 135 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKP 194
             +E E I+K ++++ K   + +E D   KV +++ +    EK KK+ +E+  ++ ++  
Sbjct: 80  LTQEPESIRKWREEQRK---RLQELDAASKVMEQEWR----EKAKKDLEEWNQRQSEQV- 131

Query: 195 VEKIRKEEKDSEKE-KKSKDKD 215
            EK +   + ++K   +  D D
Sbjct: 132 -EKNKINNRIADKAFYQQPDAD 152

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 44.4 bits (104), Expect = 2e-05
 Identities = 15/84 (17%), Positives = 43/84 (51%), Gaps = 9/84 (10%)

Query: 161 KEKKVDKEKEKGKK--EEKEKK-EEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKK 217
           +  ++ +E E  +K  EE+ K+ +E +   K  +++  EK +K+ ++  +      + ++
Sbjct: 76  QADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQR-----QSEQ 130

Query: 218 LKKEKLKKKKKEKE-RSSHEKEVI 240
           ++K K+  +  +K      + ++I
Sbjct: 131 VEKNKINNRIADKAFYQQPDADII 154

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 43.2 bits (101), Expect = 4e-05
 Identities = 9/58 (15%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 122 KKDKSI-KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKE 178
           ++ K + + D  +   +++ + K KKD ++ ++ ++++ +K K  ++  +K   ++ +
Sbjct: 93  EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPD 150

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens} Length = 77

 Score = 46.8 bits (111), Expect = 3e-07
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 293 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 339
           C  CG + D     + CD CD  +H  C+   L + P   +W+CP+C  
Sbjct: 29  CHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN 76

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group} Length = 68

 Score = 46.5 bits (110), Expect = 3e-07
 Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 11/68 (16%)

Query: 283 DTGDSKQVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVGLVAEPETSD-----WFCP 335
           D+   +    C  C         MI C+   C  W H  CV +  +P  S      ++C 
Sbjct: 3   DSFQPEAKVRCI-CSSTMVND-SMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCE 60

Query: 336 KC--SKVD 341
            C  S+ D
Sbjct: 61  LCRLSRAD 68

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 56

 Score = 45.8 bits (109), Expect = 3e-07
 Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 7/59 (11%)

Query: 283 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 339
            +G S     C  C         ++ CD C   YH  C+   L   P+   W CP+C  
Sbjct: 2   SSGSSGHEDFCSVCRKSGQ----LLMCDTCSRVYHLDCLDPPLKTIPK-GMWICPRCQD 55

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 77

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 293 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 339
           C  CG + + ++  + CD C+  YH  C+   L   PE   W+CP C  
Sbjct: 29  CRVCGGKHEPNM-QLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT 76

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A Length = 183

 Score = 49.2 bits (116), Expect = 4e-07
 Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 8/56 (14%)

Query: 291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCS 338
            +C  C   DD    M+ C  CD W H  C  L  E        PE+  + C  C+
Sbjct: 6   PLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCT 61

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2 Length = 78

 Score = 45.9 bits (108), Expect = 6e-07
 Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 11/69 (15%)

Query: 277 AAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVGLVAEPETSD--- 331
            ++ E       +V  C  CG   +    MI C+   C  W H  CV L  +P   +   
Sbjct: 4   GSSGEDPFQPEIKVR-CV-CGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPL 60

Query: 332 ---WFCPKC 337
              ++C  C
Sbjct: 61  PESFYCEIC 69

>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 Length = 61

 Score = 45.1 bits (107), Expect = 7e-07
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 7/50 (14%)

Query: 291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCS 338
             C  C   D G L  + CD C + YH  C+   L   P   +W CP+C+
Sbjct: 10  EFCRVCK--DGGEL--LCCDTCPSSYHIHCLNPPLPEIPN-GEWLCPRCT 54

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2 Length = 51

 Score = 44.6 bits (106), Expect = 9e-07
 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 4/48 (8%)

Query: 293 CPACGVQDDGSLPMIGCDGCDAWYHWVCV--GLVAEPETSDWFCPKCS 338
           C  C  + +    +I CD C+  +H  C+   L   P+  +W CP C 
Sbjct: 3   CKVCRKKGEDDK-LILCDECNKAFHLFCLRPALYEVPD-GEWQCPACQ 48

>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone modifications, jumonji demethylase, mental retardation, metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo sapiens} Length = 447

 Score = 50.0 bits (118), Expect = 9e-07
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKK 349
           +   C +  D +  MI CD C  W+H  CVG+  E   +   + CP C  +   S  +K+
Sbjct: 6   VYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPSIMKKR 65

Query: 350 KRGRKKKTHQDIIMS 364
           +   K          
Sbjct: 66  RGSSKGHDTHKGKPV 80

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens} Length = 61

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 7/49 (14%)

Query: 293 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 339
           C  C     G +  I CD C   YH VC+   +   PE   W CP C K
Sbjct: 14  CEVCQ--QGGEI--ILCDTCPRAYHMVCLDPDMEKAPE-GKWSCPHCEK 57

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 49.0 bits (116), Expect = 2e-06
 Identities = 39/210 (18%), Positives = 75/210 (35%), Gaps = 37/210 (17%)

Query: 67  VSPKDKTSPKEKMSSKEKTS----PKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIK 122
           +   D+  PK +M+   K      P+  E +  K+VE      V   V  T+        
Sbjct: 772 IRGSDQAIPKFQMNCYAKEDAFSYPRMYEEASGKEVE-----KVATAVLSTT-------- 818

Query: 123 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEE 182
                 + K   KK +KEK   +++KK + + K KE++  KK  KE ++  +E  + K  
Sbjct: 819 -----ARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKNKYS 873

Query: 183 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSK----DKDKKL--------KKEKLKKKKKEK 230
            +       +     + ++ +     K  +     K K          ++ K      E 
Sbjct: 874 SKP---YKVDNMTRILPQQSRYISFIKDDRFVPVRKFKGNNGVVVLRDREPKEPVALIET 930

Query: 231 ERSSHEKEVIPKLTFKFGTDMEEKTKRESS 260
            R   +        FK   +++  +  + S
Sbjct: 931 VRQMKDVNAPLPTPFKVDDNVDFPSALQPS 960

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A Length = 66

 Score = 43.6 bits (103), Expect = 3e-06
 Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 8/64 (12%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCSKVDEGSRKEKKK 350
            C  C   D G L  I CDGC   +H  C+     E  +  W C  C    + + +E + 
Sbjct: 10  ECAVCR--DGGEL--ICCDGCPRAFHLACLSPPLREIPSGTWRCSSCL---QATVQEVQP 62

Query: 351 RGRK 354
           R  +
Sbjct: 63  RAEE 66

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSKVDEGSRKEK 348
           IC  C   D+    ++ CDGCD  YH  C+   L   P    W CPKC   +     E 
Sbjct: 18  ICQVCSRGDEDD-KLLFCDGCDDNYHIFCLLPPLPEIPRG-IWRCPKCILAECKQPPEA 74

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens} Length = 60

 Score = 43.6 bits (103), Expect = 3e-06
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 9/59 (15%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSKVDEGSRKEK 348
            C  C         ++ CD C   YH  C+   L   P+   W CP+C   D+  +KE+
Sbjct: 7   FCSVCRKSGQ----LLMCDTCSRVYHLDCLDPPLKTIPK-GMWICPRC--QDQMLKKEE 58

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus} Length = 66

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 5/66 (7%)

Query: 285 GDSKQVWICPACGVQDDGSL-PMIGCDGCDAWYHWVC----VGLVAEPETSDWFCPKCSK 339
           G S    +C  C  +   +   M+ CD C   YH +C    +          W C +C  
Sbjct: 1   GSSGSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVF 60

Query: 340 VDEGSR 345
                R
Sbjct: 61  ATTTKR 66

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A Length = 112

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 3/49 (6%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCS 338
            C +C  Q   +  M+ CD CD  +H  C    L   P+   W C  C 
Sbjct: 63  TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPK-GMWICQICR 110

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A* Length = 114

 Score = 44.3 bits (104), Expect = 6e-06
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 286 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG-LVAEPETSDWFCPKCSKVDEG 343
              +   C  CG  ++    ++ CD CD  YH  C+   VAEP    W C  C ++ + 
Sbjct: 54  QCIECKSCILCGTSENDD-QLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKE 111

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A* Length = 174

 Score = 45.3 bits (107), Expect = 8e-06
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL--VAEPETSDWFCPKCSKVDEGSRKEKK 349
           +   C   +D S   IGCD C  WYH  CVG+         ++ CP+C   ++       
Sbjct: 9   LYCICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTP 68

Query: 350 KRGRKKKTHQDIIMS 364
              +  +  + ++ S
Sbjct: 69  LTEKDYEGLKRVLRS 83

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 45.0 bits (106), Expect = 1e-05
 Identities = 12/79 (15%), Positives = 16/79 (20%), Gaps = 26/79 (32%)

Query: 272 SPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSD 331
           +   +         +   V  CP C V                        +V      D
Sbjct: 3   TRESIDKRAGRRGPNLNIVLTCPECKVYPP--------------------KIVERFSEGD 42

Query: 332 WFCPKCSKV------DEGS 344
             C  C  V      D  S
Sbjct: 43  VVCALCGLVLSDKLVDTRS 61

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Length = 111

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG-LVAEPETSDWFCPKCSK 339
           +C  C    + S  M+ CD CD  YH  C+  ++    T+ W C  C  
Sbjct: 56  VCQNCKQSGEDS-KMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRI 103

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Length = 111

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCP---KCSKVDEGSRKE 347
            C  C    D       C  C   YH +C+ +   P + + W CP    C    +     
Sbjct: 9   NCAVCDSPGDLL-DQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDS 67

Query: 348 K 348
           K
Sbjct: 68  K 68

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 45.7 bits (108), Expect = 2e-05
 Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 6/102 (5%)

Query: 135 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKK------EEKEKKEEKEFKMK 188
                  +    D  D+++      ++  K  + K+K  K      E++  KE      +
Sbjct: 7   VAASGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDE 66

Query: 189 EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 230
             ++     +  +E+D + E    D D    K+K KKKKK  
Sbjct: 67  VARQLERSALEDKERDEDDEDGDGDGDGATGKKKKKKKKKRG 108

>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A {Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A* 1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A* 1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A* 2ga2_A* 2oaz_A* Length = 478

 Score = 45.3 bits (107), Expect = 3e-05
 Identities = 17/109 (15%), Positives = 42/109 (38%), Gaps = 1/109 (0%)

Query: 126 SIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKEF 185
            +               +++      ++   K++ K+KK       G++E  ++      
Sbjct: 6   EVAASGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVD 65

Query: 186 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
           ++    E+   + ++ ++D E      D     KK+K KKKK+  +  +
Sbjct: 66  EVARQLERSALEDKERDEDDEDGDGDGDGATG-KKKKKKKKKRGPKVQT 113

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2 Length = 88

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 8/69 (11%)

Query: 293 CPACGVQDDGSL-PMIGCDGCDAWYHWVC------VGLVAEPETSDWFCPKCSKVDEGSR 345
           C  C      S   ++ C  C   YH  C         V +P    W+C +C++  +   
Sbjct: 19  CVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRL-VWYCARCTRQMKRMA 77

Query: 346 KEKKKRGRK 354
           ++ +K G  
Sbjct: 78  QKNQKSGPS 86

>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_C* Length = 1342

 Score = 43.9 bits (104), Expect = 8e-05
 Identities = 38/169 (22%), Positives = 75/169 (44%), Gaps = 28/169 (16%)

Query: 66   KVSPKDKT--SPKEKMSSK---EKTSPKEKEYSKVKDVELGVTPMVPNIV---KVTSSED 117
            KV+PK +T  +P+EK+      EK S        VKD  L V   V   V   +V + + 
Sbjct: 886  KVTPKGETQLTPEEKLLRAIFGEKAS-------DVKDSSLRVPNGVSGTVIDVQVFTRDG 938

Query: 118  LGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKI---KNKEKDKEKKVDKEKEKGKK 174
                     ++KDK+  + +E +  + KKD  ++ +I       + +   V    E  K 
Sbjct: 939  ---------VEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKL 989

Query: 175  EEKEKKEEKEFKMK-EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 222
            ++  +    E  +  E+K+  +E++ ++  + + E + K + K+ K  +
Sbjct: 990  DKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQ 1038

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B* Length = 371

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 16/128 (12%), Positives = 42/128 (32%), Gaps = 9/128 (7%)

Query: 116 EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKD---------KKDKDKIKNKEKDKEKKVD 166
             L  I + +   +      K+ ++++++ +          K    ++ N EK+KEK   
Sbjct: 153 AKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKEESLKARLKEMSNLEKEKEKLTK 212

Query: 167 KEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK 226
             +   K      +   +  ++E     ++K   E         S  +  K  + ++   
Sbjct: 213 FVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAP 272

Query: 227 KKEKERSS 234
                  +
Sbjct: 273 NGVLTIDN 280

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2 Length = 88

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 7/48 (14%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCV--GLVAEPETSDWFCPKC 337
           IC  C    D    ++ C+ C+  +H  C    L   P   +W C  C
Sbjct: 27  ICRVCQKPGD----LVMCNQCEFCFHLDCHLPALQDVPG-EEWSCSLC 69

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 43.0 bits (100), Expect = 2e-04
 Identities = 15/118 (12%), Positives = 51/118 (43%), Gaps = 4/118 (3%)

Query: 121 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKK 180
           I+ ++ ++   K+ +      ++  +   +K+K    E+ K +      +   K   E +
Sbjct: 455 IQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAE----SAQASAKMLHEMQ 510

Query: 181 EEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 238
            + E  M++ +    E +++  +  E ++    K+++       +++++  +   +KE
Sbjct: 511 RKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKE 568

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 41.1 bits (95), Expect = 6e-04
 Identities = 14/112 (12%), Positives = 56/112 (50%), Gaps = 5/112 (4%)

Query: 128 KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKE-----EKEKKEE 182
            +     +K+ + +  K +  +   K+ ++ + K +++ ++KE+  +E      ++ + +
Sbjct: 479 DQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMEND 538

Query: 183 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 234
           +   +KE +     K++++E+  ++  + + +  K + + L+ K + ++  +
Sbjct: 539 RVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRKACT 590

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens} Length = 189

 Score = 41.0 bits (95), Expect = 2e-04
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 337
           IC  C  Q  G L  + C+ C+  +H  C    + +    +W C  C
Sbjct: 4   ICRVC--QKPGDL--VMCNQCEFCFHLDCHLPALQDVPGEEWSCSLC 46

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	444
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	99.44
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	99.39
1weu_A	91	Inhibitor of growth family, member 4; structural g	99.37
1wee_A	72	PHD finger family protein; structural genomics, PH	99.34
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	99.32
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	99.29
1wew_A	78	DNA-binding family protein; structural genomics, P	99.28
1we9_A	64	PHD finger family protein; structural genomics, PH	99.28
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	99.28
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	99.27
1wem_A	76	Death associated transcription factor 1; structura	99.27
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	99.26
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	99.26
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	99.22
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	99.15
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	99.13
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	99.13
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	99.12
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	99.1
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	99.1
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	99.1
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	98.97
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	98.97
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	98.96
3kv5_D	488	JMJC domain-containing histone demethylation prote	98.96
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	98.95
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	98.94
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	98.91
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	98.91
2yt5_A	66	Metal-response element-binding transcription facto	98.91
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	98.87
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	98.87
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	98.86
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	98.85
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	98.83
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	98.82
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	98.81
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	98.78
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	98.77
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	98.74
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	98.69
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	98.68
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	98.64
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	98.64
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	98.58
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	98.52
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	98.46
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.45
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	98.43
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	98.32
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.07
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	97.96
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	97.79
3rsn_A	177	SET1/ASH2 histone methyltransferase complex subun;	97.78
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	97.55
4bbq_A	117	Lysine-specific demethylase 2A; oxidoreductase, ub	97.53
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	97.51
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	97.34
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	96.22
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	92.74
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	91.92
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	88.67
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	86.71
2ect_A	78	Ring finger protein 126; metal binding protein, st	86.48
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	85.64
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	82.75
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	82.35
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	82.2
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	82.03
2lq6_A	87	Bromodomain-containing protein 1; PHD finger, meta	81.92
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	81.51

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=99.44  E-value=6.5e-14  Score=118.15  Aligned_cols=62  Identities=26%  Similarity=0.646  Sum_probs=50.7

Q ss_pred             CCCCceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCccccchhhhh
Q psy5823         286 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKK  349 (444)
Q Consensus       286 d~~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~~~~~k~kr  349 (444)
                      ++.+++.| ||+..++++ .||+||.|+.|||+.|+|++....++.|+|+.|.+......+...
T Consensus        24 ~~~d~vrC-iC~~~~~~~-~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~~~~~~~~~~   85 (98)
T 2lv9_A           24 YGTDVTRC-ICGFTHDDG-YMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPRNLDKERAVL   85 (98)
T ss_dssp             CCCCBCCC-TTSCCSCSS-CEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSSCCCHHHHHH
T ss_pred             CCCCCEEe-ECCCccCCC-cEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCCCCCHHHHHH
Confidence            33456789 999988777 899999999999999999987755568999999987766554443

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=99.39  E-value=8.3e-14  Score=111.38  Aligned_cols=55  Identities=62%  Similarity=1.550  Sum_probs=46.9

Q ss_pred             CCCCCceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         285 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       285 ed~~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      +++....+|.+|+.+++++ +||+||.|+.|||+.|+|++.. .+.+.|||+.|...
T Consensus        13 ~~~~~~~~C~~C~~~~~~~-~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~   68 (75)
T 2k16_A           13 EWGNQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANK   68 (75)
T ss_dssp             SSSCEEECBTTTTBCCSSC-CEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHH
T ss_pred             ccCCCCcCCCCCCCCCCCC-CEEEcCCCCcccccccCCCCccCCCCCCEEChhccCc
Confidence            3445678899999998876 8999999999999999999888 44579999999843

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.37  E-value=1.4e-12  Score=109.22  Aligned_cols=53  Identities=43%  Similarity=1.156  Sum_probs=43.0

Q ss_pred             CCCCCCceeccccCCCCCCCCCeeecCC--CC-CcccccccccCCCCCCCceecCCCCCc
Q psy5823         284 TGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       284 ded~~~~~~C~VC~~~ddg~~~mI~CD~--C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      ..+.+...|| +|+.++++  +||+||+  |. .|||+.|||++..+ .+.|||+.|...
T Consensus        30 ~~d~~e~~yC-iC~~~~~g--~MI~CD~~dC~~~WfH~~CVgl~~~p-~g~W~Cp~C~~~   85 (91)
T 1weu_A           30 PVDPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTKP-RGKWFCPRCSQE   85 (91)
T ss_dssp             CCCSCCCBCS-TTCCBCCS--CCCCCSCSSCSCCCCCSTTTTCSSCC-CSSCCCTTTCCC
T ss_pred             CcCCCCCcEE-ECCCCCCC--CEeEecCCCCCCCCEecccCCcCcCC-CCCEECcCccCc
Confidence            3444567899 99998775  5999999  76 79999999987654 478999999854

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=99.34  E-value=3.8e-13  Score=107.17  Aligned_cols=56  Identities=32%  Similarity=0.809  Sum_probs=46.2

Q ss_pred             CCCCCCceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         284 TGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       284 ded~~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      ++++.+..+| +|+.+++++.+||+||.|..|||+.|+|++.. ..++.|+|+.|...
T Consensus        10 ~~~~~~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~   66 (72)
T 1wee_A           10 RGVDNWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             CSSCSSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             CCCCCcceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCC
Confidence            3455678999 99998754448999999999999999999865 45689999999843

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=99.32  E-value=4.3e-13  Score=106.35  Aligned_cols=52  Identities=27%  Similarity=0.669  Sum_probs=44.8

Q ss_pred             CCCCceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCC
Q psy5823         286 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       286 d~~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      ++....+| +|+.+++++ +||+||.|..|||+.|+|++.....+.|+|+.|..
T Consensus        15 ~~~~~~~C-iC~~~~~~~-~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           15 YFQGLVTC-FCMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TTTTCCCS-TTCCCCTTC-CEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CCCCceEe-ECCCcCCCC-CEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            33456899 999998877 99999999999999999999875557999999973

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A*

Probab=99.29  E-value=3.1e-13  Score=112.92  Aligned_cols=49  Identities=35%  Similarity=0.994  Sum_probs=40.6

Q ss_pred             CCCceeccccCCCCCCCCCeeecCCCC---CcccccccccCCCCCCCceecCC-CCC
Q psy5823         287 SKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPK-CSK  339 (444)
Q Consensus       287 ~~~~~~C~VC~~~ddg~~~mI~CD~C~---~WfH~~CvG~~~~~~~~~w~Cp~-C~~  339 (444)
                      +++..|| +|+.++++.  ||+||+|+   .|||+.|||++..+ .+.|||+. |..
T Consensus        23 ~~~~~yC-iC~~~~~g~--MI~CD~c~C~~eWfH~~CVgl~~~p-~~~W~Cp~cC~~   75 (90)
T 2jmi_A           23 NQEEVYC-FCRNVSYGP--MVACDNPACPFEWFHYGCVGLKQAP-KGKWYCSKDCKE   75 (90)
T ss_dssp             -CCSCCS-TTTCCCSSS--EECCCSSSCSCSCEETTTSSCSSCT-TSCCCSSHHHHH
T ss_pred             CCCCcEE-EeCCCCCCC--EEEecCCCCccccCcCccCCCCcCC-CCCccCChhhcc
Confidence            3456799 999987765  99999977   99999999998764 47999999 973

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=99.28  E-value=9.6e-13  Score=106.53  Aligned_cols=54  Identities=28%  Similarity=0.654  Sum_probs=44.8

Q ss_pred             CCCCCceeccccCCCCCCCCCeeecC--CCCCcccccccccCCCC------CCCceecCCCCCc
Q psy5823         285 GDSKQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAEP------ETSDWFCPKCSKV  340 (444)
Q Consensus       285 ed~~~~~~C~VC~~~ddg~~~mI~CD--~C~~WfH~~CvG~~~~~------~~~~w~Cp~C~~~  340 (444)
                      .++++.++| +|+.+++++ +||+||  .|..|||+.|||++...      .+..|||+.|...
T Consensus        11 ~~~~~~~~C-iC~~~~~~g-~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T 1wew_A           11 FQPEIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             SSCCCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             cCCCCCEEe-ECCCcCCCC-CEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcc
Confidence            344567899 999996666 899999  99999999999998762      3578999999843

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=99.28  E-value=9e-13  Score=102.32  Aligned_cols=52  Identities=31%  Similarity=0.698  Sum_probs=43.5

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCCC--CCCceecCCCCCc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP--ETSDWFCPKCSKV  340 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~--~~~~w~Cp~C~~~  340 (444)
                      ...+|.+|+.+++++.+||+||.|..|||+.|+|++...  ....|+|+.|...
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            356899999998644489999999999999999998772  3478999999854

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=99.28  E-value=4.2e-12  Score=101.49  Aligned_cols=53  Identities=43%  Similarity=1.156  Sum_probs=42.7

Q ss_pred             CCCCCCceeccccCCCCCCCCCeeecCC--CC-CcccccccccCCCCCCCceecCCCCCc
Q psy5823         284 TGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       284 ded~~~~~~C~VC~~~ddg~~~mI~CD~--C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      ..+++...+| +|+.++++  +||+||+  |. .|||+.|||++..+ .+.|||+.|...
T Consensus        10 ~~d~~~~~~C-~C~~~~~g--~MI~CD~~~C~~~wfH~~Cvgl~~~p-~g~w~Cp~C~~~   65 (71)
T 1wen_A           10 PVDPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTKP-RGKWFCPRCSQE   65 (71)
T ss_dssp             CCCTTSCCCS-TTCCCSCS--SEECCSCSSCSCCCEETTTTTCSSCC-SSCCCCTTTSSC
T ss_pred             ccCCCCCCEE-ECCCCCCC--CEeEeeCCCCCCccEecccCCcCcCC-CCCEECCCCCcc
Confidence            3344567899 99998775  5999999  77 79999999987654 478999999854

>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} SCOP: g.50.1.2

Probab=99.27  E-value=2.6e-13  Score=108.99  Aligned_cols=55  Identities=33%  Similarity=0.776  Sum_probs=45.5

Q ss_pred             CCCCceeccccCCCCCCCCCeeecCCCCCcccccccccCCCC--CCCceecCCCCCcc
Q psy5823         286 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP--ETSDWFCPKCSKVD  341 (444)
Q Consensus       286 d~~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~--~~~~w~Cp~C~~~~  341 (444)
                      .+++..+| +|+.+++++.+||+||.|..|||+.|+|++...  ..+.|+|+.|....
T Consensus         6 ~~~~~~yC-iC~~~~~~~~~MI~Cd~C~~WfH~~Cvg~~~~~~~~~~~~~C~~C~~~~   62 (75)
T 3kqi_A            6 MATVPVYC-VCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTH   62 (75)
T ss_dssp             TCCCCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCTTTGGGBSSCCCHHHHHHH
T ss_pred             CCCCeeEE-ECCCcCCCCCCEEEcCCCCCCEecccccccccccCCCCEEECCCCcccC
Confidence            34567899 999997754589999999999999999999873  24689999998654

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.27  E-value=3.3e-13  Score=108.33  Aligned_cols=51  Identities=31%  Similarity=0.897  Sum_probs=43.1

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCCC------CCCceecCCCCCcc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP------ETSDWFCPKCSKVD  341 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~------~~~~w~Cp~C~~~~  341 (444)
                      +..+| +|+.+++++ +||+||.|..|||+.|+|++...      ....|+|+.|....
T Consensus        15 ~~~~C-~C~~~~~~~-~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~   71 (76)
T 1wem_A           15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CCCEE-ECCCccCCC-CEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCcc
Confidence            35889 999998876 89999999999999999998652      35789999998443

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.26  E-value=1.7e-12  Score=105.11  Aligned_cols=53  Identities=30%  Similarity=0.664  Sum_probs=44.1

Q ss_pred             CCceeccccCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCceecCCCCCcc
Q psy5823         288 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVD  341 (444)
Q Consensus       288 ~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~w~Cp~C~~~~  341 (444)
                      .+..+| +|+.+++++.+||+||.|..|||+.|+|++..  ...+.|+|+.|....
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            346789 99999864448999999999999999999876  335799999999654

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=99.26  E-value=1e-12  Score=98.69  Aligned_cols=47  Identities=30%  Similarity=0.773  Sum_probs=41.9

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS  338 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~  338 (444)
                      ..+| +|+.+++++ +||+||.|+.|||+.|+|++....++.|+|+.|.
T Consensus         4 ~~~C-~C~~~~~~~-~MI~Cd~C~~W~H~~Cvgi~~~~~~~~~~C~~C~   50 (52)
T 3o7a_A            4 LVTC-FCMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCR   50 (52)
T ss_dssp             CBCS-TTCCBCTTC-CEEECTTTCCEEETTTTTCCGGGCCSSCCCHHHH
T ss_pred             CeEE-EeCCcCCCC-CEEEcCCCCccccccccCCCcccCCCcEECcCCC
Confidence            4689 999998876 8999999999999999999887545799999996

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=99.22  E-value=2.3e-12  Score=101.73  Aligned_cols=51  Identities=24%  Similarity=0.627  Sum_probs=41.8

Q ss_pred             CCCceeccccCCCCCCCCCeeecCC--CCCcccccccccCCC-----CCCCceecCCCCC
Q psy5823         287 SKQVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVGLVAE-----PETSDWFCPKCSK  339 (444)
Q Consensus       287 ~~~~~~C~VC~~~ddg~~~mI~CD~--C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~~  339 (444)
                      +...++| +|+.+++++ +||+||+  |..|||+.|||++..     ..++.|||+.|+.
T Consensus         7 ~e~~v~C-~C~~~~~~g-~mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr~   64 (68)
T 2rsd_A            7 PEAKVRC-ICSSTMVND-SMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRL   64 (68)
T ss_dssp             SSCEECC-TTCCCSCCS-CEEECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHHH
T ss_pred             CCCCEEe-ECCCCcCCC-CEEEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCccC
Confidence            3456899 999987777 8999995  999999999999765     2235799999973

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.15  E-value=1.1e-11  Score=98.87  Aligned_cols=49  Identities=37%  Similarity=1.049  Sum_probs=40.9

Q ss_pred             CCceeccccCCCCCCCCCeeecCCCC---CcccccccccCCCCCCCceecCCCCCc
Q psy5823         288 KQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       288 ~~~~~C~VC~~~ddg~~~mI~CD~C~---~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      +...|| +|+.++++  +||+||.|+   .|||+.|||++.. +.+.|||+.|...
T Consensus         4 ~~~~yC-~C~~~~~g--~MI~CD~cdC~~~WfH~~Cvgl~~~-p~~~w~Cp~C~~~   55 (70)
T 1x4i_A            4 GSSGYC-ICNQVSYG--EMVGCDNQDCPIEWFHYGCVGLTEA-PKGKWYCPQCTAA   55 (70)
T ss_dssp             SCCCCS-TTSCCCCS--SEECCSCTTCSCCCEEHHHHTCSSC-CSSCCCCHHHHHH
T ss_pred             CCCeEE-EcCCCCCC--CEeEeCCCCCCccCCcccccccCcC-CCCCEECCCCCcc
Confidence            456799 89998766  599999985   8999999999775 4579999999843

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=99.13  E-value=7.5e-12  Score=96.63  Aligned_cols=49  Identities=43%  Similarity=1.193  Sum_probs=39.7

Q ss_pred             CCCceeccccCCCCCCCCCeeecCC--CC-CcccccccccCCCCCCCceecCCCCC
Q psy5823         287 SKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       287 ~~~~~~C~VC~~~ddg~~~mI~CD~--C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      +++..+| +|+.+++|  .||+||+  |. .|||+.|+|++..+ .+.|||+.|..
T Consensus         6 ~~e~~yC-~C~~~~~g--~mi~CD~~~C~~~wfH~~Cvgl~~~p-~~~w~Cp~C~~   57 (59)
T 3c6w_A            6 SNEPTYC-LCHQVSYG--EMIGCDNPDCPIEWFHFACVDLTTKP-KGKWFCPRCVQ   57 (59)
T ss_dssp             --CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSCC-SSCCCCHHHHC
T ss_pred             CCCCcEE-ECCCCCCC--CeeEeeCCCCCCCCEecccCCcccCC-CCCEECcCccC
Confidence            4456799 99998765  4999999  77 79999999987664 37899999973

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=99.13  E-value=7e-12  Score=94.14  Aligned_cols=48  Identities=35%  Similarity=0.931  Sum_probs=39.7

Q ss_pred             eeccccCCCCCCCCCeeecC-CCCCcccccccccCCC-CCCCceecCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-PETSDWFCPKCS  338 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD-~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~  338 (444)
                      +.|.+|+++++++.+||+|| .|+.|||+.|+|++.. ...+.|+|+.|.
T Consensus         3 c~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            3 CAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             CSCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             ccCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            45669999987555999999 8999999999999876 223789999994

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=99.12  E-value=9.2e-12  Score=97.09  Aligned_cols=50  Identities=40%  Similarity=1.102  Sum_probs=39.8

Q ss_pred             CCCCceeccccCCCCCCCCCeeecCC--CC-CcccccccccCCCCCCCceecCCCCC
Q psy5823         286 DSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       286 d~~~~~~C~VC~~~ddg~~~mI~CD~--C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      ++++..+| +|+.++++  +||+||+  |. .|||+.|||++.. +.+.|||+.|..
T Consensus         7 d~~e~~yC-~C~~~~~g--~MI~CD~c~C~~~WfH~~Cvgl~~~-p~~~w~Cp~C~~   59 (62)
T 2g6q_A            7 DPNEPTYC-LCNQVSYG--EMIGCDNEQCPIEWFHFSCVSLTYK-PKGKWYCPKCRG   59 (62)
T ss_dssp             ---CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSC-CSSCCCCHHHHT
T ss_pred             CCCCCcEE-ECCCCCCC--CeeeeeCCCCCcccEecccCCcCcC-CCCCEECcCccc
Confidence            34456899 99998775  4999999  55 9999999999765 357999999973

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=99.10  E-value=3.3e-11  Score=89.57  Aligned_cols=47  Identities=26%  Similarity=0.767  Sum_probs=41.2

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCC
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  339 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~  339 (444)
                      +|.+|+..++++ .||.||+|+.|||+.|++++.. .+.+.|+|+.|..
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588999987766 8999999999999999987766 6678999999974

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=99.10  E-value=1.2e-11  Score=95.61  Aligned_cols=50  Identities=46%  Similarity=1.259  Sum_probs=39.3

Q ss_pred             CCCCceeccccCCCCCCCCCeeecCC--CC-CcccccccccCCCCCCCceecCCCCC
Q psy5823         286 DSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       286 d~~~~~~C~VC~~~ddg~~~mI~CD~--C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      ++++..+| +|+.++++  .||+||+  |. .|||+.|+|++..+ .+.|||+.|..
T Consensus         6 d~~e~~~C-~C~~~~~g--~mi~CD~cdC~~~wfH~~Cvgl~~~p-~g~w~C~~C~~   58 (60)
T 2vnf_A            6 DPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTKP-RGKWFCPRCSQ   58 (60)
T ss_dssp             ---CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSCC-SSCCCCHHHHC
T ss_pred             CCCCCCEE-ECCCcCCC--CEEEeCCCCCCCceEehhcCCCCcCC-CCCEECcCccC
Confidence            34456899 99998765  4999999  55 89999999987654 47899999973

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=99.10  E-value=8e-12  Score=98.33  Aligned_cols=50  Identities=26%  Similarity=0.824  Sum_probs=41.8

Q ss_pred             CceeccccCCCCCCCCCeeecC-CCCCcccccccccCCC-------CCCCceecCCCC
Q psy5823         289 QVWICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-------PETSDWFCPKCS  338 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD-~C~~WfH~~CvG~~~~-------~~~~~w~Cp~C~  338 (444)
                      .+..|.+|+++++++.+||+|| .|..|||+.|+|++..       .+...|+|+.|.
T Consensus         7 ~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvglt~~~~~~l~~e~~~~w~C~~C~   64 (65)
T 2vpb_A            7 PVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCM   64 (65)
T ss_dssp             --CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTCCHHHHHHHHHCTTEEECCHHHH
T ss_pred             CcCcCccCCCccCCCCCeEecccCccccCchhccCCCHHHHHHhhccCCCcEECcCcc
Confidence            3457999999987666999999 9999999999999975       245689999985

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=98.97  E-value=2.5e-10  Score=88.42  Aligned_cols=48  Identities=35%  Similarity=0.805  Sum_probs=40.5

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      ...+|.+|+.  ++  .||+||.|+.|||+.|++++.. .+.+.|+|+.|...
T Consensus        10 ~~~~C~vC~~--~g--~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A           10 HQDYCEVCQQ--GG--EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCSSCTTTSC--CS--SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCccCCC--CC--cEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            3457999997  34  4999999999999999999866 67789999999854

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=98.97  E-value=5.9e-11  Score=107.96  Aligned_cols=51  Identities=35%  Similarity=0.930  Sum_probs=42.8

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCceecCCCCCc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  340 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~w~Cp~C~~~  340 (444)
                      +..+| +|+.+++++.+||+||.|+.|||+.|+|++..  ...+.|+|+.|...
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            46799 99998764448999999999999999998765  34679999999854

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.96  E-value=1.9e-10  Score=96.05  Aligned_cols=49  Identities=35%  Similarity=0.814  Sum_probs=42.5

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  339 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~  339 (444)
                      ...|.||+..++.+ .||+||.|+.|||+.|+++++. .+.+.|||+.|..
T Consensus        16 ~~~C~vC~~~~~~~-~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~   65 (92)
T 2e6r_A           16 SYICQVCSRGDEDD-KLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCIL   65 (92)
T ss_dssp             CCCCSSSCCSGGGG-GCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCccCCCcCCCC-CEEEcCCCCchhccccCCCCcccCCCCCcCCccCcC
Confidence            34799999987665 7999999999999999998776 6678999999974

>3kv5_D JMJC domain-containing histone demethylation protein 1D; epigenetics, histone CODE, jumonji lysine demethylase, metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo sapiens} PDB: 3kv6_A*

Probab=98.96  E-value=4.4e-11  Score=125.91  Aligned_cols=56  Identities=29%  Similarity=0.681  Sum_probs=45.5

Q ss_pred             CCCCceeccccCCCCCCCCCeeecCCCCCcccccccccCCCC--CCCceecCCCCCccc
Q psy5823         286 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP--ETSDWFCPKCSKVDE  342 (444)
Q Consensus       286 d~~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~--~~~~w~Cp~C~~~~~  342 (444)
                      .+....+| +|+.+++.+.+||+||.|+.|||+.|+|++...  ..+.|+|+.|.....
T Consensus        33 ~~~~~~yC-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~   90 (488)
T 3kv5_D           33 PPPPPVYC-VCRQPYDVNRFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCAVLHG   90 (488)
T ss_dssp             CCCCCEET-TTTEECCTTSCEEEBTTTCCEEEHHHHTCCGGGGGGEEEBCCHHHHHHHC
T ss_pred             CCCCCeEE-eCCCcCCCCCCeEEccCCCCceeeeecCcCcccccCCCEEECCCCcCCcC
Confidence            34567899 999997644489999999999999999998772  246899999986543

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=98.95  E-value=1e-10  Score=99.90  Aligned_cols=52  Identities=29%  Similarity=0.816  Sum_probs=42.4

Q ss_pred             ceeccccCCCCCCCCCeeecC-CCCCcccccccccCCC-------CCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD-~C~~WfH~~CvG~~~~-------~~~~~w~Cp~C~~~~  341 (444)
                      ++.|.+|+++++++..||+|| .|..|||+.|+|++..       .+...|+|+.|....
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            467999999965444799998 9999999999999863       244789999998543

>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=98.94  E-value=5.8e-10  Score=86.32  Aligned_cols=48  Identities=27%  Similarity=0.805  Sum_probs=40.1

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      ...+|.+|+.  .+  .||+||.|+.+||+.|++++.. .+.+.|+|+.|...
T Consensus         8 ~~~~C~vC~~--~g--~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   56 (61)
T 1mm2_A            8 HMEFCRVCKD--GG--ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SCSSCTTTCC--CS--SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCCcCCCCCC--CC--CEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCc
Confidence            3457999986  34  4999999999999999998766 66789999999854

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=98.91  E-value=2.4e-10  Score=89.62  Aligned_cols=47  Identities=28%  Similarity=0.725  Sum_probs=39.6

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      ..+|.+|+.  ++  .||+||.|+.|||+.|+++++. .+.+.|+|+.|...
T Consensus         8 ~~~C~vC~~--~g--~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            8 EDECAVCRD--GG--ELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCSBSSSSC--CS--SCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCccCCC--CC--CEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            357999997  34  4999999999999999998776 66789999999844

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.91  E-value=4.6e-10  Score=85.27  Aligned_cols=46  Identities=28%  Similarity=0.805  Sum_probs=39.0

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCC
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCS  338 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~  338 (444)
                      ...+|.+|+..  +  .||.||.|+.|||+.|++++.. .+.+.|+|+.|.
T Consensus         8 ~~~~C~vC~~~--g--~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~   54 (56)
T 2yql_A            8 HEDFCSVCRKS--G--QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQ   54 (56)
T ss_dssp             SCCSCSSSCCS--S--CCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHH
T ss_pred             CCCCCccCCCC--C--eEEEcCCCCcceECccCCCCcCCCCCCceEChhhh
Confidence            34579999983  4  4999999999999999998776 667899999996

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=98.91  E-value=2.8e-10  Score=88.56  Aligned_cols=52  Identities=23%  Similarity=0.618  Sum_probs=42.1

Q ss_pred             CceeccccCCCC--CCCCCeeecCCCCCcccccccccCCCC----CCCceecCCCCCcc
Q psy5823         289 QVWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEP----ETSDWFCPKCSKVD  341 (444)
Q Consensus       289 ~~~~C~VC~~~d--dg~~~mI~CD~C~~WfH~~CvG~~~~~----~~~~w~Cp~C~~~~  341 (444)
                      ....|.+|+..+  +++ .||+||.|+.|||+.|++++...    +.+.|||+.|....
T Consensus         5 ~~~~C~vC~~~~~~~~~-~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPN-EMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCBSSSCCCCCBTTB-CEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCC-CEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            345799999863  234 79999999999999999997752    67899999998544

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

Probab=98.87  E-value=1.5e-09  Score=85.51  Aligned_cols=46  Identities=26%  Similarity=0.606  Sum_probs=39.2

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      ..|.+|+.  +++  ||+||.|+.|||++|+++++. .+.+.|||+.|...
T Consensus        13 ~~C~vC~~--~~~--ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           13 ARCGVCGD--GTD--VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             CCCTTTSC--CTT--CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCcCCCCC--CCe--EEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            46999985  444  999999999999999998877 66789999999843

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=98.87  E-value=5.4e-10  Score=92.59  Aligned_cols=49  Identities=22%  Similarity=0.602  Sum_probs=40.6

Q ss_pred             ceeccccCCCC--CCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCc
Q psy5823         290 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       290 ~~~C~VC~~~d--dg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      ...|.||+..+  +++ .||+||.|+.|||+.|++++. .+.+.|||+.|...
T Consensus        25 ~~~C~vC~~~~s~~~~-~ll~CD~C~~~fH~~Cl~p~~-vP~g~W~C~~C~~~   75 (88)
T 2l43_A           25 DAVCSICMDGESQNSN-VILFCDMCNLAVHQECYGVPY-IPEGQWLCRHCLQS   75 (88)
T ss_dssp             CCCCSSCCSSSSCSEE-EEEECSSSCCCCCHHHHTCSS-CCSSCCCCHHHHHH
T ss_pred             CCcCCcCCCCCCCCCC-CEEECCCCCchhhcccCCCCc-cCCCceECccccCc
Confidence            35799999864  444 799999999999999999985 55689999999843

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=98.86  E-value=1.1e-09  Score=87.17  Aligned_cols=48  Identities=29%  Similarity=0.857  Sum_probs=40.8

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCC-ceecCCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  339 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~-~w~Cp~C~~  339 (444)
                      ..|.+|+..++++ .||+||+|+.|||++|+++++. .+.+ .|+|+.|..
T Consensus        19 C~C~~C~~~~~~~-~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   68 (70)
T 3asl_A           19 CACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   68 (70)
T ss_dssp             TSBTTTCCCSCGG-GEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSC
T ss_pred             CCCcCCCCcCCCC-CEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccC
Confidence            3577889877766 7999999999999999998777 5566 999999984

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=98.85  E-value=6.3e-10  Score=88.91  Aligned_cols=48  Identities=23%  Similarity=0.621  Sum_probs=40.3

Q ss_pred             ceeccccCCCC--CCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCC
Q psy5823         290 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       290 ~~~C~VC~~~d--dg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      ...|.+|+..+  +++ .||+||.|+.|||+.|++++. .+.+.|||+.|..
T Consensus        16 ~~~C~vC~~~~s~~~~-~ll~CD~C~~~~H~~Cl~~~~-vP~g~W~C~~C~~   65 (71)
T 2ku3_A           16 DAVCSICMDGESQNSN-VILFCDMCNLAVHQECYGVPY-IPEGQWLCRHCLQ   65 (71)
T ss_dssp             SCSCSSSCCCCCCSSS-CEEECSSSCCEEEHHHHTCSS-CCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCC-CEEECCCCCCccccccCCCCc-CCCCCcCCccCcC
Confidence            35799999864  444 799999999999999999985 5568999999974

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=98.83  E-value=9.5e-10  Score=84.53  Aligned_cols=46  Identities=28%  Similarity=0.800  Sum_probs=39.1

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  339 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~  339 (444)
                      ..+|.+|+..  +  .||+||.|+.|||+.|++++.. .+.+.|+|+.|..
T Consensus         5 ~~~C~vC~~~--g--~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~   51 (60)
T 2puy_A            5 EDFCSVCRKS--G--QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   51 (60)
T ss_dssp             CSSCTTTCCC--S--SCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHH
T ss_pred             CCCCcCCCCC--C--cEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccC
Confidence            3479999983  4  4999999999999999998776 6678999999974

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.82  E-value=2.2e-09  Score=87.04  Aligned_cols=48  Identities=27%  Similarity=0.794  Sum_probs=41.5

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCC-ceecCCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  339 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~-~w~Cp~C~~  339 (444)
                      ..|.+|+..++++ .||+||.|+.+||++|+++++. .+.+ .|||+.|..
T Consensus        27 c~C~vC~~~~~~~-~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           27 CSCRVCGGKHEPN-MQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSCSSSCCCCCST-TEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCcCcCCcCCCC-CEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            4788999887776 7999999999999999998777 5566 899999973

>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone modifications, jumonji demethylase, mental retardation, metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo sapiens}

Probab=98.81  E-value=2.1e-10  Score=119.55  Aligned_cols=54  Identities=31%  Similarity=0.741  Sum_probs=44.4

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCceecCCCCCcccc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEG  343 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~w~Cp~C~~~~~~  343 (444)
                      ...+| +|+.+++++.+||+||.|+.|||+.|+|++..  ...+.|+|+.|......
T Consensus         4 ~~~yC-iC~~~~d~~~~MIqCD~C~~WfH~~CVgi~~~~~~~~~~y~C~~C~~~~~~   59 (447)
T 3kv4_A            4 VPVYC-LCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGP   59 (447)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTEEECCCHHHHHHHCC
T ss_pred             CCeEE-eCCCcCCCCCCeEEcCCCCcccccccCCcCcccccCCCEEECCCCccccCC
Confidence            46799 99999764448999999999999999999877  33478999999865443

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=98.78  E-value=2.4e-09  Score=100.46  Aligned_cols=48  Identities=23%  Similarity=0.654  Sum_probs=40.9

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~  341 (444)
                      ..+|.+|+.  +|+  ||+||+|+.|||+.|++++.. .+.+.|+|+.|....
T Consensus         7 ~~~C~~C~~--~g~--ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            7 EDWCAVCQN--GGD--LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             CSSBTTTCC--CEE--EEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCC--CCc--eEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            456999996  444  999999999999999998877 677899999998654

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=98.77  E-value=1.6e-09  Score=89.71  Aligned_cols=51  Identities=22%  Similarity=0.644  Sum_probs=42.7

Q ss_pred             CceeccccCCCCC--CCCCeeecCCCCCcccccccccCCC-----CCCCceecCCCCCc
Q psy5823         289 QVWICPACGVQDD--GSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  340 (444)
Q Consensus       289 ~~~~C~VC~~~dd--g~~~mI~CD~C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~~~  340 (444)
                      ...+|.+|+..++  ++ .||+||.|+.+||+.|+++++.     .+.+.|||+.|...
T Consensus        15 ~~~~C~vC~~~~~~~~~-~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~   72 (88)
T 1wev_A           15 MGLACVVCRQMTVASGN-QLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             HCCSCSSSCCCCCCTTC-CEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             CCCcCCCCCCCCCCCCC-ceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccch
Confidence            3467999998754  24 6999999999999999999876     57789999999843

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=98.74  E-value=1.4e-09  Score=101.24  Aligned_cols=52  Identities=31%  Similarity=0.725  Sum_probs=41.7

Q ss_pred             eccccCCCCCCCC---CeeecCCCCCcccccccccCCC----C----CCCceecCCCCCcccc
Q psy5823         292 ICPACGVQDDGSL---PMIGCDGCDAWYHWVCVGLVAE----P----ETSDWFCPKCSKVDEG  343 (444)
Q Consensus       292 ~C~VC~~~ddg~~---~mI~CD~C~~WfH~~CvG~~~~----~----~~~~w~Cp~C~~~~~~  343 (444)
                      +|++|+++++++.   .||+||.|+.|||+.|+|++..    .    ....|+|+.|......
T Consensus         4 ~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~~   66 (183)
T 3lqh_A            4 FCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPA   66 (183)
T ss_dssp             BCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSSC
T ss_pred             cCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCCH
Confidence            6999999886553   4999999999999999999753    0    1237999999976543

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=98.69  E-value=1.5e-08  Score=84.31  Aligned_cols=47  Identities=23%  Similarity=0.678  Sum_probs=40.1

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      ..+|.+|+.  +++  +|+||.|+.+||+.|+.++.. .+.+.|+|+.|...
T Consensus        25 ~~~C~vC~~--~g~--LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           25 ATICRVCQK--PGD--LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSCCSSSCS--SSC--CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCcCcCcCC--CCC--EEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            347999997  344  999999999999999988877 67789999999844

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=98.68  E-value=7.4e-09  Score=84.01  Aligned_cols=49  Identities=33%  Similarity=0.876  Sum_probs=41.3

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCc-eecCCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSD-WFCPKCSK  339 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~-w~Cp~C~~  339 (444)
                      .+.|.+|+..++.+ .||+||.|+.+||++|+++++. .+.+. |+|+.|..
T Consensus        26 ~C~C~vC~~~~d~~-~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           26 VCACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             TTSBTTTCCCSCGG-GEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             CCcCCccCCCCCCc-ceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            35688899887766 8999999999999999998877 55667 99999974

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=98.64  E-value=1.4e-08  Score=93.49  Aligned_cols=47  Identities=21%  Similarity=0.671  Sum_probs=40.1

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCcc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  341 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~  341 (444)
                      .+|.+|+.  +|+  +|+||+|+.|||..|++++.. .+.+.|+|+.|....
T Consensus         5 ~~C~~C~~--~g~--ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            5 DWCAVCQN--GGE--LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SSCTTTCC--CSS--CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CccccCCC--CCe--eeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            46999996  444  999999999999999998877 667899999998654

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=98.64  E-value=1.2e-08  Score=97.97  Aligned_cols=49  Identities=31%  Similarity=0.863  Sum_probs=38.8

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCC-ceecCCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  339 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~-~w~Cp~C~~  339 (444)
                      .+.|.+|+..++++ .||+||+|+.|||+.|+++++. .+.+ .|+|+.|..
T Consensus       174 ~c~C~vC~~~~~~~-~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~  224 (226)
T 3ask_A          174 VCACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN  224 (226)
T ss_dssp             TTSCSSSCCCCC---CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC-
T ss_pred             CCCCcCCCCCCCCC-CeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcC
Confidence            45799999987776 8999999999999999998877 5666 899999974

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=98.58  E-value=1.4e-08  Score=87.41  Aligned_cols=47  Identities=30%  Similarity=0.824  Sum_probs=41.1

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCC
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  339 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~  339 (444)
                      +|.+|+..++++ .||.||.|+.|||++|+++++. .+.+.|||+.|..
T Consensus        60 ~C~~C~~~~~~~-~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~  107 (114)
T 2kwj_A           60 SCILCGTSENDD-QLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWE  107 (114)
T ss_dssp             CCTTTTCCTTTT-TEEECSSSCCEEETTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             ccCcccccCCCC-ceEEcCCCCccccccccCCCccCCCCCCeECccccc
Confidence            588899887666 7999999999999999998777 6778999999973

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=98.52  E-value=6.1e-08  Score=83.05  Aligned_cols=47  Identities=28%  Similarity=0.704  Sum_probs=39.4

Q ss_pred             eccccCCCC-CCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCC
Q psy5823         292 ICPACGVQD-DGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  339 (444)
Q Consensus       292 ~C~VC~~~d-dg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~  339 (444)
                      +|.+|+..+ +++ .||+||.|+.+||++|+++++. .+.+.|+|+.|.+
T Consensus        63 ~C~vC~~~~~~~~-~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNAD-NMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTC-CCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCcc-ceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            588888754 334 7999999999999999998777 6778999999985

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=98.46  E-value=6.6e-08  Score=82.99  Aligned_cols=44  Identities=34%  Similarity=0.838  Sum_probs=35.8

Q ss_pred             ceeccccCCCCCCCCCeeecC--CCCCcccccccccCCCCCCCceecCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAEPETSDWFCPKCS  338 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD--~C~~WfH~~CvG~~~~~~~~~w~Cp~C~  338 (444)
                      ..+|.+|+.  +|+  ||+||  .|+.|||+.|+++.. .+.+.|||+.|.
T Consensus        15 ~~~C~~C~~--~G~--ll~CD~~~Cp~~fH~~Cl~L~~-~P~g~W~Cp~c~   60 (107)
T 4gne_A           15 EDYCFQCGD--GGE--LVMCDKKDCPKAYHLLCLNLTQ-PPYGKWECPWHQ   60 (107)
T ss_dssp             CSSCTTTCC--CSE--EEECCSTTCCCEECTGGGTCSS-CCSSCCCCGGGB
T ss_pred             CCCCCcCCC--CCc--EeEECCCCCCcccccccCcCCc-CCCCCEECCCCC
Confidence            457989984  444  99999  899999999999654 456899999775

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=98.45  E-value=5.7e-08  Score=82.62  Aligned_cols=49  Identities=33%  Similarity=0.761  Sum_probs=41.9

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCcc
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  341 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~  341 (444)
                      +|.+|+..++++ .||.||.|+.|||+.|+++++. .+.+.|+|+.|....
T Consensus        56 ~C~~C~~~~~~~-~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~c~  105 (111)
T 2ysm_A           56 VCQNCKQSGEDS-KMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRICI  105 (111)
T ss_dssp             CCTTTCCCSCCT-TEEECSSSCCEEEGGGSSSCCSSCCSSCCCCHHHHCCS
T ss_pred             cccccCccCCCC-CeeECCCCCcHHhHHhcCCccccCCCCCcCCcCCcCcC
Confidence            588899887766 8999999999999999998777 667899999997544

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=98.43  E-value=1e-07  Score=88.63  Aligned_cols=47  Identities=23%  Similarity=0.672  Sum_probs=39.8

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCcc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  341 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~  341 (444)
                      .+|.+|+.  +|+  +|+||+|+.+||+.|+.++.. .+.+.|+|+.|....
T Consensus         3 ~~C~~C~~--~g~--ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            3 TICRVCQK--PGD--LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCBTTTCC--CSS--CCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CcCccCCC--CCc--eeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            36999996  444  999999999999999988776 677899999998653

>3pur_A Lysine-specific demethylase 7 homolog; oxidoreductase-oxidoreductase inhibitor complex; HET: 2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A* 3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A*

Probab=98.32  E-value=1.5e-07  Score=99.64  Aligned_cols=46  Identities=35%  Similarity=0.891  Sum_probs=36.4

Q ss_pred             cCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCceecCCCCCcc
Q psy5823         296 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVD  341 (444)
Q Consensus       296 C~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~w~Cp~C~~~~  341 (444)
                      +....+.+.+||+||.|+.|||+.|||++..  ...+.|+|+.|....
T Consensus        48 ~~~~~n~~~~mI~CD~C~~WfH~~CVgi~~~~a~~~~~y~Cp~C~~~~   95 (528)
T 3pur_A           48 SHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHT   95 (528)
T ss_dssp             TTTTTTSTTSEEECTTTCCEEEGGGTTCCGGGTTTEEECCCTTTHHHH
T ss_pred             cccCCCcCCCEEECCCCCcCCCCcCCCCChhHhcCCCeEECcCCcCCC
Confidence            3333344559999999999999999999987  334789999998643

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=98.07  E-value=2.4e-06  Score=72.51  Aligned_cols=47  Identities=26%  Similarity=0.712  Sum_probs=39.8

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCC
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCS  338 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~  338 (444)
                      .+|.+|+..++.+ .||.|+.|+..||..|+++... ...+.|+|+.|.
T Consensus         8 ~~C~~C~~~g~~~-~ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            8 ANCAVCDSPGDLL-DQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             SCBTTTCCCCCTT-TSEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCcCCCCCCCCc-CCeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            4799999976544 6899999999999999999877 445789999986

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=97.96  E-value=2.9e-06  Score=76.20  Aligned_cols=49  Identities=24%  Similarity=0.543  Sum_probs=41.0

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC--------CCCCceecCCCCCcc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVD  341 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--------~~~~~w~Cp~C~~~~  341 (444)
                      ...+|.+|+.  +|+  +|+||.|.+.||..|+.++..        .+.+.|+|+.|....
T Consensus        62 ~~d~C~vC~~--GG~--LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~p  118 (142)
T 2lbm_A           62 MDEQCRWCAE--GGN--LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEP  118 (142)
T ss_dssp             CBCSCSSSCC--CSS--EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCCT
T ss_pred             CCCeecccCC--CCc--EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCcc
Confidence            3568999997  666  999999999999999997764        367899999998654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=97.79  E-value=4.3e-06  Score=71.17  Aligned_cols=37  Identities=35%  Similarity=0.872  Sum_probs=30.3

Q ss_pred             eeecCCCCCcccccccccCCC--------CCCCceecCCCCCccc
Q psy5823         306 MIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVDE  342 (444)
Q Consensus       306 mI~CD~C~~WfH~~CvG~~~~--------~~~~~w~Cp~C~~~~~  342 (444)
                      ||+||.|..|||..|++++..        +....|.|+.|.....
T Consensus         2 mi~c~~c~~w~H~~c~~~~~~~~~~l~~lp~~~~~~c~~C~~~~~   46 (140)
T 2ku7_A            2 MMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHV   46 (140)
T ss_dssp             CCCCSCCSSCHHHHHCCCCHHHHHHHHSSCTTTTCCSSCCTTTSC
T ss_pred             ccccccCCCccCCcccccCHHHHHHHhhccccceeeCcccccccc
Confidence            999999999999999999752        3344799999986543

>3rsn_A SET1/ASH2 histone methyltransferase complex subun; PHD domain, winged helix domain, binding, transcription; 2.10A {Homo sapiens} PDB: 3s32_A

Probab=97.78  E-value=1.5e-05  Score=74.00  Aligned_cols=51  Identities=12%  Similarity=0.240  Sum_probs=36.5

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-----CCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~~~~  341 (444)
                      ..+| -||.+.+-+..|++|+.|..|||..|++....     ...-.|.|..|...+
T Consensus         5 ~~yC-YCG~~~~~~~~mLqC~~C~qWFH~~Cl~~~~~~~lp~~~fY~F~C~~C~~~g   60 (177)
T 3rsn_A            5 AGSV-DEENGRQLGEVELQCGICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHHSG   60 (177)
T ss_dssp             -------CTTCCTTSCEEECTTTCCEEEGGGGTCCCTTCCTTCCSEEEECTTTSTTS
T ss_pred             eeEE-EcCCCCCCCceeEeeccccceecHHHhcccccCccccceeEEEEccccCCCC
Confidence            4578 89998876779999999999999999986543     223468899998765

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=97.55  E-value=1.5e-05  Score=68.18  Aligned_cols=47  Identities=26%  Similarity=0.582  Sum_probs=36.6

Q ss_pred             eeccccCCCC------CCCCCeeecCCCCCcccccccccCCC----CCCCceecCCCC
Q psy5823         291 WICPACGVQD------DGSLPMIGCDGCDAWYHWVCVGLVAE----PETSDWFCPKCS  338 (444)
Q Consensus       291 ~~C~VC~~~d------dg~~~mI~CD~C~~WfH~~CvG~~~~----~~~~~w~Cp~C~  338 (444)
                      .+|.+|...+      +++ .||.|++|+.+||.+|+++...    ...+.|+|+.|.
T Consensus         6 ~~C~~C~~~~~~~~~g~~~-~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            6 PICSFCLGTKEQNREKKPE-ELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             SSBTTTCCCTTCCTTSCCC-CCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             ccccccCCchhhCcCCCch-hceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            4688997642      333 6999999999999999987432    345689999996

>4bbq_A Lysine-specific demethylase 2A; oxidoreductase, ubiquitin, ligase, ubiquitination, demethyla ZF-CXXC DNA binding domain, CPG island, chromatin; 2.24A {Homo sapiens}

Probab=97.53  E-value=2.7e-05  Score=66.34  Aligned_cols=49  Identities=24%  Similarity=0.454  Sum_probs=33.7

Q ss_pred             ccccCCCCCCCCCeeecCCCCCcccccccccCCC-----CCCCceecCCCCCcc
Q psy5823         293 CPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKVD  341 (444)
Q Consensus       293 C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~~~~  341 (444)
                      |..|....+.+..||+|+.|+.|||..|+++...     ...+.|+|+.|.+.+
T Consensus        62 c~~c~~~~~~~~~m~~C~~C~~~~H~~C~~~~~~~~~~~~~~~~~~C~~C~~~~  115 (117)
T 4bbq_A           62 VDQNEETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQED  115 (117)
T ss_dssp             BCCHHHHCCGGGSCEEETTTCCEECGGGCCSCCCCEECSSSSSEEECTTTC---
T ss_pred             ccccccccccCcceEEeeecCCeEECCCCCCCccccccccCCCCeECCCCcCCC
Confidence            3334333333337999999999999999998765     234569999998654

>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=97.51  E-value=2.4e-05  Score=69.21  Aligned_cols=49  Identities=24%  Similarity=0.543  Sum_probs=39.4

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC--------CCCCceecCCCCCcc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVD  341 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--------~~~~~w~Cp~C~~~~  341 (444)
                      ...+|.+|+.  +|+  +|+||.|.+.||..|+.+...        .+.+.|+|..|....
T Consensus        56 ~~~~C~vC~d--GG~--LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~p  112 (129)
T 3ql9_A           56 MDEQCRWCAE--GGN--LICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEP  112 (129)
T ss_dssp             CBSSCTTTCC--CSE--EEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCGG
T ss_pred             CCCcCeecCC--CCe--eEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCHH
Confidence            3457999996  555  999999999999999986532        256889999998654

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=97.34  E-value=3.2e-05  Score=66.35  Aligned_cols=46  Identities=22%  Similarity=0.573  Sum_probs=35.9

Q ss_pred             eccccCCCC-------CCCCCeeecCCCCCcccccccccCCC----CCCCceecCCCC
Q psy5823         292 ICPACGVQD-------DGSLPMIGCDGCDAWYHWVCVGLVAE----PETSDWFCPKCS  338 (444)
Q Consensus       292 ~C~VC~~~d-------dg~~~mI~CD~C~~WfH~~CvG~~~~----~~~~~w~Cp~C~  338 (444)
                      +|.+|...+       +++ .||.|+.|+..||.+|+++...    ...+.|+|+.|.
T Consensus         3 ~C~~C~~~~~~n~k~g~~~-~Li~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   59 (114)
T 2kwj_A            3 YCDFCLGGSNMNKKSGRPE-ELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECK   59 (114)
T ss_dssp             CCSSSCCBTTBCTTTCCCC-CCEECSSSCCEECTTTTTCCHHHHHHHHHTTCCCGGGC
T ss_pred             cCccCCCCccccccCCCCC-CCeEeCCCCCccchhhCCChhhhhhccCCCccCccccC
Confidence            688897543       233 6999999999999999998743    345689999885

>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=96.22  E-value=0.003  Score=52.22  Aligned_cols=48  Identities=23%  Similarity=0.613  Sum_probs=37.4

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccC------------CC-CCCCceecCCCCCc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV------------AE-PETSDWFCPKCSKV  340 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~------------~~-~~~~~w~Cp~C~~~  340 (444)
                      ..|.||.....++  ++.|..|.+.||..|+...            .. ....-|.|+.|...
T Consensus        16 ~~C~VC~~~t~~~--l~pCRvC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T~~GWSC~~CenL   76 (89)
T 1wil_A           16 EMCDVCEVWTAES--LFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNI   76 (89)
T ss_dssp             CCCTTTCCCCSSC--CSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCC
T ss_pred             cccCccccccccc--eeccccccccccHhhcccccccccHHHHHHHHccCCCCCccccccchh
Confidence            4699999866665  9999999999999997542            11 34567999999754

>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger, histone binding, chromosomal protein, DNA damag repair, DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens} PDB: 3a1a_A*

Probab=92.74  E-value=0.036  Score=50.53  Aligned_cols=49  Identities=20%  Similarity=0.525  Sum_probs=38.9

Q ss_pred             ceeccccCCCCCCCCCeeecC--CCCCcccccccccCCC-------CCCCceecCCCCCccc
Q psy5823         290 VWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVDE  342 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD--~C~~WfH~~CvG~~~~-------~~~~~w~Cp~C~~~~~  342 (444)
                      ..||.+|+.  +++  +|+||  .|.+.|-..|+.....       ...+.|.|..|.+...
T Consensus        79 ~~yC~wC~~--Gg~--l~~Cdn~~C~r~FC~~CI~~nvG~~~~~~i~~~d~W~Cy~C~P~~l  136 (159)
T 3a1b_A           79 QSYCTICCG--GRE--VLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGT  136 (159)
T ss_dssp             BSSCTTTSC--CSE--EEECSSTTTCCEEEHHHHHHHTCTTHHHHHHTSSSCCCTTTCSSCE
T ss_pred             cceeeEecC--CCe--EEeeCCCCCCCchhHHHHHHhcCHhHHHHHhccCCCEEEecCCccH
Confidence            568999997  555  99999  7999999999764443       3457899999997653

>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*

Probab=91.92  E-value=0.046  Score=56.15  Aligned_cols=50  Identities=22%  Similarity=0.591  Sum_probs=39.9

Q ss_pred             CCceeccccCCCCCCCCCeeecC--CCCCcccccccccCCC-------CCCCceecCCCCCcc
Q psy5823         288 KQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVD  341 (444)
Q Consensus       288 ~~~~~C~VC~~~ddg~~~mI~CD--~C~~WfH~~CvG~~~~-------~~~~~w~Cp~C~~~~  341 (444)
                      ....||.+|+.  +++  +|+||  .|.+.|-..|+.....       ...+.|.|..|.+..
T Consensus        91 G~~~yCr~C~~--Gg~--l~~Cdn~~C~r~FC~~Ci~~n~g~~~~~~i~~~d~W~Cf~C~p~p  149 (386)
T 2pv0_B           91 GYQSYCSICCS--GET--LLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSS  149 (386)
T ss_dssp             SSBCSCTTTCC--CSS--CEECCSTTCCCEECHHHHHHHTCTTHHHHHHHCSSCCCTTTSSCC
T ss_pred             CCcccceEcCC--CCe--EEEeCCCCCCcchHHHHHHHhcChhHHHHhhccCCceEEEcCCcc
Confidence            34678999997  455  99999  8999999999876554       234689999999876

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

Probab=88.67  E-value=0.42  Score=36.03  Aligned_cols=48  Identities=21%  Similarity=0.427  Sum_probs=33.2

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~  341 (444)
                      ...|.||......-  ++.  .|+-.||..|+............||.|....
T Consensus        20 ~~~C~IC~~~~~~~--~~~--~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   67 (73)
T 2ysl_A           20 EVICPICLDILQKP--VTI--DCGHNFCLKCITQIGETSCGFFKCPLCKTSV   67 (73)
T ss_dssp             CCBCTTTCSBCSSE--EEC--TTCCEEEHHHHHHHCSSSCSCCCCSSSCCCC
T ss_pred             CCEeccCCcccCCe--EEc--CCCChhhHHHHHHHHHcCCCCCCCCCCCCcC
Confidence            45799999865533  333  7999999999875544223467899998543

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

Probab=86.71  E-value=0.47  Score=33.86  Aligned_cols=47  Identities=19%  Similarity=0.335  Sum_probs=32.5

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  340 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~  340 (444)
                      ..|.||......+...+....|+-.||..|+......   ...||.|+..
T Consensus         6 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~---~~~CP~Cr~~   52 (55)
T 1iym_A            6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS---HSTCPLCRLT   52 (55)
T ss_dssp             CCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT---CCSCSSSCCC
T ss_pred             CcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc---CCcCcCCCCE
Confidence            3599998765443244555579999999998755442   3579999843

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

Probab=86.48  E-value=0.57  Score=35.94  Aligned_cols=48  Identities=23%  Similarity=0.365  Sum_probs=31.4

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~  341 (444)
                      ...|.||....... ..+.--.|+-.||..|+.-...   ....||.|+...
T Consensus        15 ~~~C~IC~~~~~~~-~~~~~~~C~H~fc~~Ci~~~~~---~~~~CP~Cr~~~   62 (78)
T 2ect_A           15 GLECPVCKEDYALG-ESVRQLPCNHLFHDSCIVPWLE---QHDSCPVCRKSL   62 (78)
T ss_dssp             SCCCTTTTSCCCTT-SCEEECTTSCEEETTTTHHHHT---TTCSCTTTCCCC
T ss_pred             CCCCeeCCccccCC-CCEEEeCCCCeecHHHHHHHHH---cCCcCcCcCCcc
Confidence            35699998765443 2222235888999999865433   235899998544

>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=85.64  E-value=0.25  Score=37.10  Aligned_cols=48  Identities=21%  Similarity=0.258  Sum_probs=31.1

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~  341 (444)
                      ...|.||......+ ..+..-.|+-.||..|+......   ...||.|+...
T Consensus        14 ~~~C~IC~~~~~~~-~~~~~~~C~H~fc~~Ci~~~~~~---~~~CP~Cr~~~   61 (69)
T 2kiz_A           14 EEKCTICLSILEEG-EDVRRLPCMHLFHQVCVDQWLIT---NKKCPICRVDI   61 (69)
T ss_dssp             CCSBTTTTBCCCSS-SCEEECTTSCEEEHHHHHHHHHH---CSBCTTTCSBS
T ss_pred             CCCCeeCCccccCC-CcEEEeCCCCHHHHHHHHHHHHc---CCCCcCcCccc
Confidence            34699998765433 23344469999999998643321   23599998543

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

Probab=82.75  E-value=1.1  Score=32.11  Aligned_cols=44  Identities=23%  Similarity=0.411  Sum_probs=29.4

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC  337 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C  337 (444)
                      ...|.||.....+. .++   .|+-.||..|+............||.|
T Consensus        15 ~~~C~IC~~~~~~p-~~~---~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           15 EASCSVCLEYLKEP-VII---ECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCBCSSSCCBCSSC-CCC---SSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             CCCCccCCcccCcc-EeC---CCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            35799999876554 232   588889999986543322245778877

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

Probab=82.35  E-value=1.1  Score=35.59  Aligned_cols=48  Identities=25%  Similarity=0.545  Sum_probs=34.2

Q ss_pred             CCceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCC
Q psy5823         288 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       288 ~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      ..+..|.||......+   +.|..|+..||..|+.--.... ..=.||.|..
T Consensus        13 ~~i~~C~IC~~~i~~g---~~C~~C~h~fH~~Ci~kWl~~~-~~~~CP~Cr~   60 (74)
T 2ct0_A           13 DAVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSN-AEPRCPHCND   60 (74)
T ss_dssp             SSSCBCSSSCCBCSSS---EECSSSCCEECHHHHHHHSTTC-SSCCCTTTCS
T ss_pred             CCCCcCcchhhHcccC---CccCCCCchhhHHHHHHHHHhc-CCCCCCCCcC
Confidence            3456799999865533   5788999999999997544421 1246999984

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

Probab=82.20  E-value=0.59  Score=34.43  Aligned_cols=44  Identities=23%  Similarity=0.494  Sum_probs=28.6

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC  337 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C  337 (444)
                      ...|.||......-  .+.  .|+-.||..|+.-..........||.|
T Consensus        20 ~~~C~IC~~~~~~p--~~~--~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           20 EVICPICLDILQKP--VTI--DCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCBCTTTCSBCSSC--EEC--TTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CCCCCcCCchhCCe--EEe--CCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            45799998765543  333  799889999986433211234678877

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

Probab=82.03  E-value=0.6  Score=36.29  Aligned_cols=51  Identities=22%  Similarity=0.315  Sum_probs=33.6

Q ss_pred             ceeccccCCCCCCCCC-eeecCCCCCcccccccccCCCCCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLP-MIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~-mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~  341 (444)
                      ...|.||......+.. .+.- .|+-.||..|+.-..........||.|....
T Consensus        15 ~~~C~IC~~~~~~~~~~~~~~-~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   66 (88)
T 2ct2_A           15 VLECPICMESFTEEQLRPKLL-HCGHTICRQCLEKLLASSINGVRCPFCSKIT   66 (88)
T ss_dssp             CCBCTTTCCBCCTTSSCEEEC-SSSCEEEHHHHHHHHHHCSSCBCCTTTCCCB
T ss_pred             CCCCccCCccccccCCCeEEC-CCCChhhHHHHHHHHHcCCCCcCCCCCCCcc
Confidence            4569999976654312 3332 6999999999865433222358899998544

>2lq6_A Bromodomain-containing protein 1; PHD finger, metal binding protein; NMR {Homo sapiens}

Probab=81.92  E-value=0.87  Score=37.17  Aligned_cols=31  Identities=26%  Similarity=0.592  Sum_probs=25.0

Q ss_pred             CceeccccCCCCCCCCCeeecCC--CCCccccccc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCV  321 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~--C~~WfH~~Cv  321 (444)
                      |...|.+|+....|.  .|+|..  |..+||..|.
T Consensus        16 ~~l~C~iC~~~~~GA--ciqC~~~~C~~~fHv~CA   48 (87)
T 2lq6_A           16 WKLTCYLCKQKGVGA--SIQCHKANCYTAFHVTCA   48 (87)
T ss_dssp             CCCCBTTTTBCCSSC--EEECSCTTTCCEEEHHHH
T ss_pred             hcCCCcCCCCCCCcE--eEecCCCCCCCcCcHHHH
Confidence            456799998754454  899986  9999999995

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

Probab=81.51  E-value=0.93  Score=36.15  Aligned_cols=50  Identities=24%  Similarity=0.519  Sum_probs=31.5

Q ss_pred             eccccCCCCCCCCCeee---cCCCCCcccccccccCCCCCCCceecCCCCCccc
Q psy5823         292 ICPACGVQDDGSLPMIG---CDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDE  342 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~---CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~~  342 (444)
                      .|.||...++.+..+|.   |.++..+||..|+..-.... +...|+.|.....
T Consensus        17 ~C~IC~~~~~~~~~l~~pC~C~Gs~h~fH~~Cl~~Wl~~~-~~~~CplCr~~~~   69 (80)
T 2d8s_A           17 ICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSS-DTRCCELCKYEFI   69 (80)
T ss_dssp             CCSSSCCCCCSSSCEECSSSCCSSSCCEETTHHHHHHHHH-CCSBCSSSCCBCC
T ss_pred             CCeEcCccccCCCeeEeccccCCcCCeeCHHHHHHHHhhC-CCCCCCCCCCeee
Confidence            69999865543224553   23335999999996543311 2368999986553

---

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	444
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	5e-14
d1wepa_	79	g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus mus	8e-12
d1weea_	72	g.50.1.2 (A:) PHD finger protein At1g33420 {Thale	3e-11
d1wema_	76	g.50.1.2 (A:) Death associated transcription facto	9e-11
d1f62a_	51	g.50.1.2 (A:) Williams-Beuren syndrome transcripti	6e-09
d1mm2a_	61	g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens	3e-08
d1wewa_	78	g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale c	7e-08
d1fp0a1	70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	9e-08
d2pnxa1	51	g.50.1.2 (A:195-245) Inhibitor of growth protein 4	1e-07
d1weva_	88	g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu	2e-07
d1wesa_	71	g.50.1.2 (A:) PHD Inhibitor of growth protein 2, I	1e-06
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	4e-04
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.002

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64

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]

 Score = 64.3 bits (156), Expect = 5e-14
 Identities = 18/57 (31%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 285 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSK 339
           G S     C ACG         I CD C+ W+H  CV +          + CP CS 
Sbjct: 1   GSSGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN 57

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.5 bits (141), Expect = 8e-12
 Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 3/69 (4%)

Query: 290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKE 347
           V +   C    + +  MI C  C  W+H  CVG+  E   +   + CP C +   G    
Sbjct: 11  VPVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDC-EAVFGPSIM 69

Query: 348 KKKRGRKKK 356
           K        
Sbjct: 70  KNWHSGPSS 78

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 72

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 56.6 bits (136), Expect = 3e-11
 Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 296 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCSK 339
           CG +DD    M+ CDGC  W+H  C+G+       S + C +C +
Sbjct: 21  CGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIE 65

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 76

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]

 Score = 55.5 bits (133), Expect = 9e-11
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)

Query: 296 CGVQDDGSLPMIGCDGCDAWYHWVCVGL------VAEPETSDWFCPKCS 338
           C    +    MI CD C+ W+H  CVG+      + E    D+ CP C+
Sbjct: 21  CRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCT 68

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]} Length = 51

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]

 Score = 49.6 bits (118), Expect = 6e-09
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 293 CPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 337
           C  C  + +    +I CD C+  +H  C+   + E    +W CP C
Sbjct: 3   CKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPAC 47

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]} Length = 61

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]

 Score = 48.0 bits (114), Expect = 3e-08
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 5/55 (9%)

Query: 285 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCS 338
           G    +  C  C    +    ++ CD C + YH  C+   + E    +W CP+C+
Sbjct: 4   GSDHHMEFCRVCKDGGE----LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCT 54

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 47.4 bits (112), Expect = 7e-08
 Identities = 12/62 (19%), Positives = 18/62 (29%), Gaps = 6/62 (9%)

Query: 283 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP------ETSDWFCPK 336
           D    +    C      +  S+       C  W H  CV L  +P          ++C  
Sbjct: 9   DPFQPEIKVRCVCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEI 68

Query: 337 CS 338
           C 
Sbjct: 69  CR 70

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 70

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]

 Score = 46.9 bits (111), Expect = 9e-08
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCSKVDEGSRKEKKK 350
           IC  C    D    ++ C+ C+  +H  C    + +    +W C  C  + +   ++   
Sbjct: 9   ICRVCQKPGD----LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDVDL 64

Query: 351 RGRK 354
           +  K
Sbjct: 65  QACK 68

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]} Length = 51

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

 Score = 45.7 bits (108), Expect = 1e-07
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 296 CGVQDDGSLPMI-GCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK 339
           C     G +      D    W+H+ CVGL  +P    WFCP+CS+
Sbjct: 7   CHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQ 50

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]} Length = 88

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]

 Score = 46.4 bits (109), Expect = 2e-07
 Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 293 CPACG-VQDDGSLPMIGCDGCDAWYHWVCVG-----LVAEPETSDWFCPKCSKVDEGSRK 346
           C  C  +       ++ C  C   YH  C                W+C +C++  +   +
Sbjct: 19  CVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRMAQ 78

Query: 347 EKKKRG 352
           + +K G
Sbjct: 79  KNQKSG 84

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 71

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]

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 296 CGVQDDGSLPMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKC 337
           C     G +     + C   W+H+ CV L  +P+   W+CPKC
Sbjct: 21  CNQVSYGEMIGCDNEQCPIEWFHFSCVSLTYKPK-GKWYCPKC 62

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.6 bits (94), Expect = 4e-04
 Identities = 30/192 (15%), Positives = 67/192 (34%), Gaps = 1/192 (0%)

Query: 39   PPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDV 98
             P L   L P                +  + K  T   E     +  S    E  ++  +
Sbjct: 1112 TPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQL 1171

Query: 99   ELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKE 158
               +            S  L  ++ D++   DK     +  E+I K+  K D   I +++
Sbjct: 1172 HFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERI-KQTFKNDLFVIWSED 1230

Query: 159  KDKEKKVDKEKEKGKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKL 218
             D++  +     + K  + E + E++  +K+ +   +E I     ++ +       D+K+
Sbjct: 1231 NDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKV 1290

Query: 219  KKEKLKKKKKEK 230
                 +  K+ +
Sbjct: 1291 PSPTGEYVKEPE 1302

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 17/105 (16%), Positives = 49/105 (46%)

Query: 125 KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKVDKEKEKGKKEEKEKKEEKE 184
            S+ + +    ++ ++K++  ++++   + +  +   EK+  + +   K  E+     K 
Sbjct: 34  ASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKM 93

Query: 185 FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 229
            K K  ++    K  +E   +   ++ ++KDK  ++ +  K+ KE
Sbjct: 94  AKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKE 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	444
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	99.22
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	99.21
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	99.09
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	99.08
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	99.07
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	99.06
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	99.02
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	99.0
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	98.97
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	98.96
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	98.83
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	90.41
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	90.27
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	86.7
d1weqa_	85	PHD finger protein 7 (NYD-SP6) {Mouse (Mus musculu	85.31

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {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 At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.22  E-value=1.7e-12  Score=101.19  Aligned_cols=53  Identities=32%  Similarity=0.833  Sum_probs=44.6

Q ss_pred             CCCceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         287 SKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       287 ~~~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      +.+.++| +|+..++++..||+||.|+.|||+.|+|++.. .+.+.|+|+.|...
T Consensus        13 ~~~~~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~   66 (72)
T d1weea_          13 DNWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             CSSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             CCCeEEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCc
Confidence            4567789 99988766558999999999999999999877 55678999999844

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.21  E-value=2.8e-12  Score=101.96  Aligned_cols=51  Identities=31%  Similarity=0.714  Sum_probs=42.9

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~w~Cp~C~~~~  341 (444)
                      .++| +|+.+++.+.+||+||.|+.|||+.|+|++..  ...+.|+|+.|....
T Consensus        12 pv~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          12 PVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CeEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            5789 99998765558999999999999999999866  445689999998543

>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=99.09  E-value=1.9e-11  Score=89.24  Aligned_cols=48  Identities=25%  Similarity=0.751  Sum_probs=42.2

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCc
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  340 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~  340 (444)
                      .|.+|+..++++ .||+||.|+.|||+.|++++.. .+.+.|+|+.|.+.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~~   50 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQPA   50 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSCC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcCc
Confidence            588999988777 8999999999999999999877 66679999999853

>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=99.08  E-value=1.5e-11  Score=93.67  Aligned_cols=50  Identities=32%  Similarity=0.733  Sum_probs=42.6

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC--CCCCceecCCCCCc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  340 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~--~~~~~w~Cp~C~~~  340 (444)
                      ..|.+|+..++++.+||+||.|+.|||..|++++..  .....|+|+.|...
T Consensus         7 ~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           7 GQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            479999998766558999999999999999999877  34568999999854

>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=99.07  E-value=4.8e-11  Score=93.49  Aligned_cols=52  Identities=27%  Similarity=0.786  Sum_probs=38.4

Q ss_pred             CCceeccccCCCCCCCCCeeecCCCC-CcccccccccCCCCCCCceecCCCCCcc
Q psy5823         288 KQVWICPACGVQDDGSLPMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKCSKVD  341 (444)
Q Consensus       288 ~~~~~C~VC~~~ddg~~~mI~CD~C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~~~  341 (444)
                      ++..+| ||+.+++++.+|+.|+.|. .|||+.||+++.. +.+.|||+.|....
T Consensus        14 ~e~~~C-iC~~~~~~~~i~c~~~~C~~~wfH~~Cvgl~~~-p~~~w~C~~C~~~~   66 (71)
T d1wesa_          14 NEPTYC-LCNQVSYGEMIGCDNEQCPIEWFHFSCVSLTYK-PKGKWYCPKCRGDS   66 (71)
T ss_dssp             SSCCCS-TTCCCCCSSEECCSCTTCSCCCEETTTTTCSSC-CSSCCCCTTTSSCC
T ss_pred             CCCCEE-EeCCCCCCCEEEEECCCCCCcCccCccCCCCcC-CCCcEECcCCcccc
Confidence            345689 9999877772333345675 7999999998755 45689999998544

>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=99.06  E-value=9e-12  Score=97.49  Aligned_cols=50  Identities=32%  Similarity=0.911  Sum_probs=41.3

Q ss_pred             CceeccccCCCCCCCCCeeecCCCCCcccccccccCCC------CCCCceecCCCCCc
Q psy5823         289 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE------PETSDWFCPKCSKV  340 (444)
Q Consensus       289 ~~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~------~~~~~w~Cp~C~~~  340 (444)
                      ...+| +|+.+++++ .||+||.|+.|||+.|+|++..      .....|+|+.|...
T Consensus        15 ~~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CcCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            45679 999988776 8999999999999999998653      23467999999744

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.02  E-value=4.4e-11  Score=94.65  Aligned_cols=52  Identities=29%  Similarity=0.707  Sum_probs=41.1

Q ss_pred             CCCceeccccCCCCCCCCCeeecC--CCCCcccccccccCCC------CCCCceecCCCCCc
Q psy5823         287 SKQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE------PETSDWFCPKCSKV  340 (444)
Q Consensus       287 ~~~~~~C~VC~~~ddg~~~mI~CD--~C~~WfH~~CvG~~~~------~~~~~w~Cp~C~~~  340 (444)
                      +++.++| +|+..++++ .||+|+  .|..|||+.|||++..      .....|+|+.|...
T Consensus        13 ~~~~~~C-~C~~~~~~~-~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T d1wewa_          13 PEIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCCccEe-ECCCccCCC-cEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCc
Confidence            3445789 999987766 799987  6999999999999754      23347999999743

>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=99.00  E-value=1.2e-10  Score=88.04  Aligned_cols=47  Identities=28%  Similarity=0.801  Sum_probs=39.0

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCcc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  341 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~  341 (444)
                      .+|.+|+.  ++  .||+||+|+.|||+.|+++... .+.+.|+|+.|....
T Consensus        10 ~~C~~C~~--~g--~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_          10 EFCRVCKD--GG--ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCTTTCC--CS--SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCC--CC--eEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            47999985  44  4999999999999999998777 556789999998543

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=98.97  E-value=4.4e-11  Score=87.93  Aligned_cols=46  Identities=46%  Similarity=1.205  Sum_probs=38.5

Q ss_pred             ceeccccCCCCCCCCCeeecCC---CCCcccccccccCCCCCCCceecCCCCC
Q psy5823         290 VWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~---C~~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      ..|| +|+.+++++  ||+||.   |..|||+.|||++..+ .+.|||+.|..
T Consensus         2 ~~yC-~C~~~~~~~--mi~Cd~~~C~~~WfH~~Cvgl~~~p-~~~w~C~~C~~   50 (51)
T d2pnxa1           2 PTYC-LCHQVSYGE--MIGCDNPDCSIEWFHFACVGLTTKP-RGKWFCPRCSQ   50 (51)
T ss_dssp             CEET-TTTEECCSE--EEECSCTTCSSCEEEGGGGTCSSCC-SSCCCCHHHHC
T ss_pred             CcEE-EcCCCCCCC--EEEEecCCCCCCCEeCCccCCCcCC-CCcEECcCCCC
Confidence            4689 999988776  999997   5789999999987654 56899999974

>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=98.96  E-value=3.9e-11  Score=96.45  Aligned_cols=51  Identities=20%  Similarity=0.588  Sum_probs=40.3

Q ss_pred             ceeccccCCCCCC-CCCeeecCCCCCcccccccccCCC-----CCCCceecCCCCCc
Q psy5823         290 VWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  340 (444)
Q Consensus       290 ~~~C~VC~~~ddg-~~~mI~CD~C~~WfH~~CvG~~~~-----~~~~~w~Cp~C~~~  340 (444)
                      ..+|.+|+..... ...||+||.|..|||..|++++..     .+.+.|||+.|...
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~   72 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCch
Confidence            4568899876432 227999999999999999998765     45668999999843

>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=98.83  E-value=9.8e-10  Score=85.18  Aligned_cols=48  Identities=23%  Similarity=0.659  Sum_probs=39.1

Q ss_pred             ceeccccCCCCCCCCCeeecCCCCCcccccccccCCC-CCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~-~~~~~w~Cp~C~~~~  341 (444)
                      -.+|.+|+.  .++  ||+||+|+.|||..|++++.. .+.+.|+|+.|....
T Consensus         7 c~~C~~C~~--~~~--ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQK--PGD--LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCS--SSC--CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCC--cCE--EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            346878876  344  999999999999999998876 666789999998554

>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=90.41  E-value=0.014  Score=42.22  Aligned_cols=51  Identities=22%  Similarity=0.333  Sum_probs=34.0

Q ss_pred             ceeccccCCCCCCCC-CeeecCCCCCcccccccccCCCCCCCceecCCCCCcc
Q psy5823         290 VWICPACGVQDDGSL-PMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVD  341 (444)
Q Consensus       290 ~~~C~VC~~~ddg~~-~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~~~  341 (444)
                      ...|.||....++.. ....|.+|..+||..|+..-... .+.+.||.|....
T Consensus         6 ~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~-~~~~~CP~Cr~~~   57 (60)
T d1vyxa_           6 VPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTI-SRNTACQICGVVY   57 (60)
T ss_dssp             CCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHH-HTCSBCTTTCCBC
T ss_pred             CCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhh-CCCCCCcccCCee
Confidence            346999987655441 22246788899999999754321 1246899998654

>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=90.27  E-value=0.089  Score=37.50  Aligned_cols=45  Identities=20%  Similarity=0.369  Sum_probs=34.0

Q ss_pred             eccccCCCCCCCCCeeecCCCCCcccccccccCCCCCCCceecCCCCC
Q psy5823         292 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  339 (444)
Q Consensus       292 ~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~~~~~~~~w~Cp~C~~  339 (444)
                      .|.||......+...+.+..|+-.||..|+..-...   .-.||.|+.
T Consensus         7 ~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~---~~~CP~CR~   51 (55)
T d1iyma_           7 ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS---HSTCPLCRL   51 (55)
T ss_dssp             CCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT---CCSCSSSCC
T ss_pred             CCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHh---CCcCCCCCC
Confidence            499998776543256667789999999999876653   246999984

>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=86.70  E-value=0.24  Score=38.82  Aligned_cols=49  Identities=22%  Similarity=0.651  Sum_probs=35.2

Q ss_pred             eeccccCCCCCCCCCeeecCCCCCcccccccccC----CC---------CCCCceecCCCCCcc
Q psy5823         291 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV----AE---------PETSDWFCPKCSKVD  341 (444)
Q Consensus       291 ~~C~VC~~~ddg~~~mI~CD~C~~WfH~~CvG~~----~~---------~~~~~w~Cp~C~~~~  341 (444)
                      ..|.||.....+.  .+.|-.|.+.||..|+.--    ..         ....-|.|..|...+
T Consensus        16 ~mC~vC~v~t~~~--l~pCRvCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~nl~   77 (89)
T d1wila_          16 EMCDVCEVWTAES--LFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNIN   77 (89)
T ss_dssp             CCCTTTCCCCSSC--CSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCCC
T ss_pred             ccccccCcccccc--eecceeecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcchh
Confidence            4699997765555  7799999999999996311    11         234469999998544

>d1weqa_ g.50.1.2 (A:) PHD finger protein 7 (NYD-SP6) {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 7 (NYD-SP6)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.31  E-value=0.42  Score=37.34  Aligned_cols=36  Identities=25%  Similarity=0.601  Sum_probs=28.6

Q ss_pred             CeeecCCCC-CcccccccccCCCCCCCceecCCCCCccc
Q psy5823         305 PMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKCSKVDE  342 (444)
Q Consensus       305 ~mI~CD~C~-~WfH~~CvG~~~~~~~~~w~Cp~C~~~~~  342 (444)
                      .||.|..|+ ..-|..|..+...  ...|.|..|.....
T Consensus        45 ~ii~C~~CGS~gtH~~C~~l~~~--~~~y~C~~C~~v~~   81 (85)
T d1weqa_          45 RLILCATCGSHGTHRDCSSLRPN--SKKWECNECLPASG   81 (85)
T ss_dssp             BCEECSSSCCCEECSGGGTCCTT--CSCCCCTTTSCCSS
T ss_pred             EEEeecccCCccchhhhcCCcCC--CCCEECCcCcchhC
Confidence            489999999 8899999766533  34799999986543