Psyllid ID: psy5827

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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
Protein Sequence
MLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccHHHHccccccccccHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccEEEccccccccccccccEEccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHccHHHHccccHHHHHHcccHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccHHHHHcccccccccccHHccccccccccccccccccccHHHcccccccccccccccHccccccccccccccHHHHHHccHHHHHHHcccccHHHcccccccccccccHHHHHHccccHHHHHHHccccHHHHHccccccccHHHccccccHHHHccccccHccccccHHHHHccccccccccccccccccHHHHcccHHHHccccccccccccccccccccccccccccccccccEEEEEccccccccccccEEccccccccEcccEcccEccccccccccHHHHHHHHcccccccccccccccccccccccEEEcccccccccccHHHHHHHHHHHHHHcccHHHEccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mlqhplipqplvhppgtpppskmkdkvspkdktspkekmsskektspkekeyskvkdvelgvtpmvpnivkvtssedlgeikkdksikkdKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKmkedkekpvEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEkersshekevipkltfkfgtdmeektkresspkivikpvkspspppvaaadeydtgdskqvwicpacgvqddgslpmigcdgcdawYHWVCVGLvaepetsdwfcpkcskvdegsrkekkkrgrkkkthqDIIMSTyrferdpselvdksacagsraDLKLCLLEtdcvqvdrktprqclreglapQCEALKNTFFECKRSLLdnrtrfrghkgy
Flexible Loop (DISEMBL)
mlqhplipqplvhppgtpppskmkdkvspkdktspkekmsskektspkekeyskvkdvelgvtpmvpnivkvtssedlgeikkdksikkdkkthkkkekekikkkkdkkdkdkiknkekdkekkidkekekgkkeekekkeekekkeekefkmkedkekpvekirkeekdsekekkskdkdkklkkeklkkkkkekersshekevipkltfkfgtdmeektkresspkivikpvkspspppVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAepetsdwfcpkcskvdegsrkekkkrgrkkkthqdiimstyrferdpselVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALkntffeckrslldnrtrfrghkgy
Low Complexity Region (SEG)
MLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDktspkekmsskektspkekeyskVKDVELGVTPMVPNIVKVTSSEDLGeikkdksikkdkkthkkkekekikkkkdkkdkdkiknkekdkekkidkekekgkkeekekkeekekkeekefkmkedkekPVekirkeekdsekekkskdkdkklkkeklkkkkkekersshekeVIPKLTFKFGTDMEEKTKRESspkivikpvkspspppvaaaDEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSrkekkkrgrkkkTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
Disordered region (IsUnstruct)
*************************************************************V**MV*NI****************************************************************************************************************************************************************************************KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC***************************TY***********KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLD***********
Disordered Region (DISOPRED)
******I****************************************************************************************************************************************************************************************************************************************************DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFC***********************************************AGSRADLKLCLLETDCVQVDRK****CLREGLAPQCEALKNTFFECKRSLLDNRTRFR*****
Disordered Region (DISEMBL)
MLQHPLIPQPLVHPPGT************************************KVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKS*********************************************************************************************************************EVIPKLTFKFGTD**********PKIVIKPVK****************DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK*******************QDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
Disordered Region (DISPRO)
*****L***********************************************************************************************************************************************************************************************************************************************DEYD*GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEG*****************IIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRGHKGY
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	410	2.2.26 [Sep-21-2011]
Q3ZCK8	74	Cytochrome c oxidase asse	yes	N/A	0.153	0.851	0.636	3e-17
Q5HZG4	932	Transcription initiation	yes	N/A	0.124	0.054	0.641	4e-17
Q5VWG9	929	Transcription initiation	yes	N/A	0.124	0.054	0.641	7e-17
Q28CA1	75	Cytochrome c oxidase asse	yes	N/A	0.158	0.866	0.617	1e-16
Q5RFJ0	74	Cytochrome c oxidase asse	yes	N/A	0.153	0.851	0.621	1e-16
Q5EAW9	845	Transcription initiation	N/A	N/A	0.119	0.057	0.647	1e-15
A1L3N6	75	Cytochrome c oxidase asse	N/A	N/A	0.148	0.813	0.609	4e-15
Q5F489	930	Transcription initiation	no	N/A	0.124	0.054	0.603	5e-15
Q86WW8	74	Cytochrome c oxidase asse	no	N/A	0.151	0.837	0.630	7e-14
Q99M07	74	Cytochrome c oxidase asse	no	N/A	0.151	0.837	0.6	3e-13

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

 Score = 90.1 bits (222), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 52/66 (78%), Gaps = 3/66 (4%)

Query: 345 SACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRF 404
            ACAG + DL LCLL++DCV  + K+PRQCL+EG    C+ALK +FFECKRS+LD R+RF
Sbjct: 12  GACAGVKEDLGLCLLQSDCVLKEGKSPRQCLKEG---NCKALKYSFFECKRSMLDARSRF 68

Query: 405 RGHKGY 410
           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 = 89.4 bits (220), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 38/53 (71%), Gaps = 2/53 (3%)

Query: 254 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 305
            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 = 88.6 bits (218), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 38/53 (71%), Gaps = 2/53 (3%)

Query: 254 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCSK 305
            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: 343 DKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRT 402
           DK  CAG + DLK CLL+TDCV  + K+P++CL+EG    C+AL+ TFFECKRS+LD R 
Sbjct: 11  DKHPCAGVKEDLKSCLLQTDCVLQEGKSPKECLKEGY---CKALQVTFFECKRSILDTRA 67

Query: 403 RFRGHKGY 410
           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 = 1e-16,   Method: Compositional matrix adjust.
 Identities = 41/66 (62%), Positives = 48/66 (72%), Gaps = 3/66 (4%)

Query: 345 SACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRF 404
            AC G + DL  CLLE+DCV  + K+PRQCL+EG    C +LK  FFECKRS+LDNR RF
Sbjct: 12  GACGGLKEDLGACLLESDCVVQEGKSPRQCLKEGY---CNSLKYAFFECKRSVLDNRARF 68

Query: 405 RGHKGY 410
           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 = 84.7 bits (208), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 35/51 (68%), Gaps = 2/51 (3%)

Query: 254 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 303
            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: 347 CAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFRG 406
           C G + DLK CLL++DCV  + K+P++CL+EG    C+AL+ TFFECKRS+LDNR RFRG
Sbjct: 15  CGGVKEDLKNCLLQSDCVLQEGKSPKECLKEG---YCKALQVTFFECKRSILDNRARFRG 71

Query: 407 HKGY 410
            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 = 5e-15,   Method: Compositional matrix adjust.
 Identities = 32/53 (60%), Positives = 35/53 (66%), Gaps = 2/53 (3%)

Query: 254 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 305
            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 = 79.0 bits (193), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 41/65 (63%), Positives = 49/65 (75%), Gaps = 3/65 (4%)

Query: 346 ACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR 405
           ACAG + DL  CLL++DCV  + K+PRQCL+EG    C +LK  FFECKRS+LDNR RFR
Sbjct: 13  ACAGLKEDLGACLLQSDCVVQEGKSPRQCLKEGY---CNSLKYAFFECKRSVLDNRARFR 69

Query: 406 GHKGY 410
           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 = 76.6 bits (187), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 39/65 (60%), Positives = 49/65 (75%), Gaps = 3/65 (4%)

Query: 346 ACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR 405
           ACAG + DL  CLL++ CV  + K+PRQCL+EG    C AL+ +FFECKRS+LD R+RFR
Sbjct: 13  ACAGVKEDLGACLLQSACVLQEGKSPRQCLKEG---NCRALQYSFFECKRSMLDARSRFR 69

Query: 406 GHKGY 410
           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	410
193713718	590	PREDICTED: hypothetical protein LOC10016	0.207	0.144	0.526	2e-20
270015055	865	hypothetical protein TcasGA2_TC014217 [T	0.168	0.079	0.578	4e-20
357614210	81	hypothetical protein KGM_12107 [Danaus p	0.187	0.950	0.653	5e-20
195380361	80	GJ21319 [Drosophila virilis] gi|19414373	0.173	0.887	0.694	6e-20
328700739	906	PREDICTED: hypothetical protein LOC10016	0.165	0.075	0.586	6e-20
193671822	79	PREDICTED: uncharacterized protein C2orf	0.180	0.936	0.653	2e-19
118793122	82	AGAP011820-PA [Anopheles gambiae str. PE	0.173	0.865	0.662	3e-19
195149688	80	GL10830 [Drosophila persimilis] gi|19845	0.173	0.887	0.694	4e-19
194754419	80	GF12904 [Drosophila ananassae] gi|190620	0.170	0.875	0.647	2e-18
189233756	872	PREDICTED: similar to bip2 CG2009-PA [Tr	0.126	0.059	0.685	3e-18

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

 Score =  106 bits (264), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/93 (52%), Positives = 60/93 (64%), Gaps = 8/93 (8%)

Query: 230 VIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL 289
           VI PV   +PPP    DE       QVWICP C   DDGS PMIGCDGCD WYHWVCVG+
Sbjct: 503 VIPPVNE-TPPPAFYFDE----AGNQVWICPMCTKPDDGS-PMIGCDGCDVWYHWVCVGI 556

Query: 290 VAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKK 322
              P+ + WFCP+C  + + +++ K KRGR +K
Sbjct: 557 QCPPDCAVWFCPRC--LAKRAQQPKGKRGRPRK 587

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 (262), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 44/76 (57%), Positives = 50/76 (65%), Gaps = 7/76 (9%)

Query: 229 IVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG 288
           IV  P+  P+PP       Y   D  +VWICP CG QDDGS PMIGCDGCDAWYHWVCVG
Sbjct: 770 IVDVPIVPPAPP-----SRYIDADGNEVWICPGCGSQDDGS-PMIGCDGCDAWYHWVCVG 823

Query: 289 LVAEPETS-DWFCPKC 303
           +   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 = 5e-20,   Method: Compositional matrix adjust.
 Identities = 51/78 (65%), Positives = 60/78 (76%), Gaps = 1/78 (1%)

Query: 334 FERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAP-QCEALKNTFFE 392
           F  D   LVD S CAG RADLKLCLL +DC +  +KTPR+CL++GL P +C  L+ +FFE
Sbjct: 4   FGPDEVGLVDTSPCAGIRADLKLCLLNSDCCKEHKKTPRECLKDGLVPNECLQLRQSFFE 63

Query: 393 CKRSLLDNRTRFRGHKGY 410
           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|195380361|ref|XP_002048939.1| GJ21319 [Drosophila virilis] gi|194143736|gb|EDW60132.1| GJ21319 [Drosophila virilis]

 Score =  105 bits (261), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 50/72 (69%), Positives = 64/72 (88%), Gaps = 1/72 (1%)

Query: 340 ELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE-GLAPQCEALKNTFFECKRSLL 398
           +L D++ACAG RADLK+CLLE+DC ++DRKTPRQCL++  + P+C+ L+NTF+ECKRSLL
Sbjct: 9   KLADETACAGVRADLKMCLLESDCCRLDRKTPRQCLQDNNVPPECQVLRNTFYECKRSLL 68

Query: 399 DNRTRFRGHKGY 410
           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|328700739|ref|XP_001945181.2| PREDICTED: hypothetical protein LOC100167514 [Acyrthosiphon pisum]

 Score =  105 bits (261), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 44/75 (58%), Positives = 52/75 (69%), Gaps = 7/75 (9%)

Query: 249 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS--KV 306
           D G+  QVWICP CG QDDGS PM+GCDGCDAWYHWVCVG+   P+ + W+CP C   + 
Sbjct: 827 DAGN--QVWICPTCGKQDDGS-PMVGCDGCDAWYHWVCVGIQCPPDCAVWYCPTCLLKRA 883

Query: 307 DEGSRK--EKKKRGR 319
           + 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|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: 337 DPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE-GLAPQCEALKNTFFECKR 395
           D  EL D   CAG RADLK+CLLE+DC +++RK P+ CL+E    P+C AL+NTFFECKR
Sbjct: 5   DEGELTDHRPCAGVRADLKMCLLESDCCKIERKLPKDCLKEKNCPPECLALQNTFFECKR 64

Query: 396 SLLDNRTRFRGHKGY 410
           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: 340 ELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLR--EGLAP-QCEALKNTFFECKRS 396
           EL DKSACAG RADLK+CLL++DC + ++KTPR+CL   +G  P +C  L+NTFFECKRS
Sbjct: 9   ELADKSACAGVRADLKMCLLQSDCCKKEKKTPRECLNRTDGSVPSECFVLRNTFFECKRS 68

Query: 397 LLDNRTRFRGHKGY 410
           +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|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 =  102 bits (254), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 50/72 (69%), Positives = 62/72 (86%), Gaps = 1/72 (1%)

Query: 340 ELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLRE-GLAPQCEALKNTFFECKRSLL 398
           +L D++ACAG RADLK+CLLE+DC +VDRKTPRQCL +  + P+C+ L+NTF+ECKRSLL
Sbjct: 9   KLADETACAGVRADLKMCLLESDCCRVDRKTPRQCLMDNNVPPECQVLRNTFYECKRSLL 68

Query: 399 DNRTRFRGHKGY 410
           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|194754419|ref|XP_001959492.1| GF12904 [Drosophila ananassae] gi|190620790|gb|EDV36314.1| GF12904 [Drosophila ananassae]

 Score = 99.8 bits (247), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 46/71 (64%), Positives = 59/71 (83%), Gaps = 1/71 (1%)

Query: 341 LVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLR-EGLAPQCEALKNTFFECKRSLLD 399
           L D++ACAG RADLK+CLLE+DC ++ + TPRQCL+   + P+C+ L+NTF+ECKRSLLD
Sbjct: 10  LADETACAGVRADLKMCLLESDCCRIAKNTPRQCLQANNVPPECQVLRNTFYECKRSLLD 69

Query: 400 NRTRFRGHKGY 410
           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|189233756|ref|XP_001814148.1| PREDICTED: similar to bip2 CG2009-PA [Tribolium castaneum]

 Score = 99.4 bits (246), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 41/54 (75%), Gaps = 2/54 (3%)

Query: 251 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETS-DWFCPKC 303
            D  +VWICP CG QDDGS PMIGCDGCDAWYHWVCVG+   P+ S DW+C  C
Sbjct: 794 ADGNEVWICPGCGSQDDGS-PMIGCDGCDAWYHWVCVGIQVPPDDSEDWYCRHC 846

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

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	410
UNIPROTKB|E1BIA9	932	TAF3 "Uncharacterized protein"	0.117	0.051	0.68	3.3e-20
UNIPROTKB|F1RUM5	794	TAF3 "Uncharacterized protein"	0.117	0.060	0.7	5.1e-19
UNIPROTKB|Q3ZCK8	74	COA5 "Cytochrome c oxidase ass	0.151	0.837	0.646	1.7e-18
MGI|MGI:2388097	932	Taf3 "TAF3 RNA polymerase II,	0.119	0.052	0.666	1.7e-18
ZFIN|ZDB-GENE-030131-6406	898	taf3 "TAF3 RNA polymerase II,	0.119	0.054	0.666	2.1e-18
UNIPROTKB|F1PI56	932	TAF3 "Uncharacterized protein"	0.119	0.052	0.666	4.5e-18
UNIPROTKB|Q5VWG9	929	TAF3 "Transcription initiation	0.119	0.052	0.666	5.7e-18
UNIPROTKB|E1C792	75	COA5 "Uncharacterized protein"	0.178	0.973	0.551	5.8e-18
UNIPROTKB|Q86WW8	74	COA5 "Cytochrome c oxidase ass	0.151	0.837	0.630	5.8e-18
WB|WBGene00006384	1007	taf-3 [Caenorhabditis elegans	0.146	0.059	0.5	1.5e-17

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

 Score = 215 (80.7 bits), Expect = 3.3e-20, Sum P(3) = 3.3e-20
 Identities = 34/50 (68%), Positives = 37/50 (74%)

Query:   255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 303
             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 = 5.1e-19, Sum P(2) = 5.1e-19
 Identities = 35/50 (70%), Positives = 37/50 (74%)

Query:   255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 303
             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|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:   346 ACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR 405
             ACAG + DL LCLL++DCV  + K+PRQCL+EG    C+ALK +FFECKRS+LD R+RFR
Sbjct:    13 ACAGVKEDLGLCLLQSDCVLKEGKSPRQCLKEG---NCKALKYSFFECKRSMLDARSRFR 69

Query:   406 GHKGY 410
             G KGY
Sbjct:    70 GRKGY 74

GO:0005739 "mitochondrion" evidence=IEA

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:   255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 304
             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

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 = 2.1e-18, Sum P(2) = 2.1e-18
 Identities = 34/51 (66%), Positives = 37/51 (72%)

Query:   255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 304
             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 = 4.5e-18, Sum P(2) = 4.5e-18
 Identities = 34/51 (66%), Positives = 38/51 (74%)

Query:   255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 304
             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|Q5VWG9 TAF3 "Transcription initiation factor TFIID subunit 3" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 5.7e-18, Sum P(2) = 5.7e-18
 Identities = 34/51 (66%), Positives = 38/51 (74%)

Query:   255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCS 304
             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

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:   333 RFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFE 392
             ++  D  E  D  AC+G R DL+ CLLE+ CV  + K+PRQCLREG    C+ L+ TFF 
Sbjct:     3 KYYEDKEE--DGQACSGVREDLRQCLLESPCVLQENKSPRQCLREG---HCKGLQLTFFA 57

Query:   393 CKRSLLDNRTRFRGHKGY 410
             CKRS+LD R RFRG KGY
Sbjct:    58 CKRSMLDTRARFRGRKGY 75

GO:0005739 "mitochondrion" evidence=IEA

UNIPROTKB|Q86WW8 COA5 "Cytochrome c oxidase assembly factor 5" [Homo sapiens (taxid:9606)]

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 41/65 (63%), Positives = 49/65 (75%)

Query:   346 ACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDNRTRFR 405
             ACAG + DL  CLL++DCV  + K+PRQCL+EG    C +LK  FFECKRS+LDNR RFR
Sbjct:    13 ACAGLKEDLGACLLQSDCVVQEGKSPRQCLKEGY---CNSLKYAFFECKRSVLDNRARFR 69

Query:   406 GHKGY 410
             G KGY
Sbjct:    70 GRKGY 74

GO:0005739 "mitochondrion" evidence=IEA

WB|WBGene00006384 taf-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 192 (72.6 bits), Expect = 1.5e-17, Sum P(3) = 1.5e-17
 Identities = 30/60 (50%), Positives = 37/60 (61%)

Query:   246 DEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK 305
             D   +  S+++WICP C V       MIGCD C  W+HW CVGL AEP  S WFC +C+K
Sbjct:   919 DSNGSESSEEIWICPVCSVAYTVGANMIGCDQCQDWFHWHCVGLTAEPTDSKWFCTRCTK 978

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q28CA1	COA5_XENTR	No assigned EC number	0.6176	0.1585	0.8666	yes	N/A
Q3ZCK8	COA5_BOVIN	No assigned EC number	0.6363	0.1536	0.8513	yes	N/A
Q5RFJ0	COA5_PONAB	No assigned EC number	0.6212	0.1536	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	410
pfam10203	68	pfam10203, Pet191_N, Cytochrome c oxidase assembly	3e-21
smart00249	47	smart00249, PHD, PHD zinc finger	1e-09
pfam00628	51	pfam00628, PHD, PHD-finger	2e-09
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-08
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-07
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	5e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-07
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	7e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	8e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-06
TIGR02794	346	TIGR02794, tolA_full, TolA protein	2e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-06
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	3e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-06
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	8e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	9e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	1e-05
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	1e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	2e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	3e-05
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	3e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	4e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-05
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	5e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	6e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	6e-05
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	6e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	1e-04
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	1e-04
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	1e-04
COG1293	564	COG1293, COG1293, Predicted RNA-binding protein ho	1e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	1e-04
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	1e-04
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	2e-04
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	2e-04
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	2e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	2e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	2e-04
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	2e-04
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	2e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	2e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	3e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	3e-04
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	3e-04
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	3e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	4e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-04
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	4e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	5e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	6e-04
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	7e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	7e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	7e-04
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	8e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	9e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.001
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.001
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	0.001
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.001
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.001
COG5034	271	COG5034, TNG2, Chromatin remodeling protein, conta	0.001
cd09730	579	cd09730, Cas8a1_I-A, CRISPR/Cas system-associated	0.001
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.002
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.002
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.002
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	0.002
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.002
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.002
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	0.002
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	0.002
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	0.003
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.003
COG2176	1444	COG2176, PolC, DNA polymerase III, alpha subunit (	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
pfam09592	228	pfam09592, DUF2031, Protein of unknown function (D	0.003
PTZ00399	651	PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Pro	0.003
COG5604	523	COG5604, COG5604, Uncharacterized conserved protei	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.004
pfam13166	713	pfam13166, AAA_13, AAA domain	0.004
pfam13166	713	pfam13166, AAA_13, AAA domain	0.004
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.004
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	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
COG1419	407	COG1419, FlhF, Flagellar GTP-binding protein [Cell	0.004

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

 Score = 86.2 bits (214), Expect = 3e-21
 Identities = 36/67 (53%), Positives = 47/67 (70%), Gaps = 3/67 (4%)

Query: 343 DKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAP---QCEALKNTFFECKRSLLD 399
             S+C G R DL  CLLE+DCV+ +++TPR+CL+E L     +C AL+  FFECKR +LD
Sbjct: 1   MGSSCKGLREDLAECLLESDCVKKEKRTPRECLKEPLKELPEECIALRKAFFECKRGMLD 60

Query: 400 NRTRFRG 406
            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 = 53.0 bits (127), Expect = 1e-09
 Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKC 303
            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 = 52.5 bits (126), Expect = 2e-09
 Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 4/50 (8%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPET---SDWFCPKCS 304
            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 = 58.5 bits (142), Expect = 3e-09
 Identities = 30/188 (15%), Positives = 67/188 (35%), Gaps = 1/188 (0%)

Query: 17  TPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSE 76
           T      +++   K K    +  S    T  + KE  + K         V   +     +
Sbjct: 6   TKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKD 65

Query: 77  DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEE 136
                + D   KK K   K    +   KKK K + D  K  EK      D +    K  +
Sbjct: 66  TDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDID 125

Query: 137 KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 196
               +  +  ++ +    +D +   +   +++ + + +    D+D++ K+ K  +K  + 
Sbjct: 126 V-LNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDD 184

Query: 197 ERSSHEKE 204
           +    +++
Sbjct: 185 DDFVWDED 192

Length = 509

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

 Score = 56.9 bits (138), Expect = 9e-09
 Identities = 21/79 (26%), Positives = 51/79 (64%)

Query: 110 DKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEK 169
            +++I+     K+     +K   K E+K ++E+KEKK++     K+++E+  EK +KEE+
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 170 DSEKEKKSKDKDKKLKKEK 188
             E+E++++++ ++ +++K
Sbjct: 455 KEEEEEEAEEEKEEEEEKK 473

Length = 482

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

 Score = 57.1 bits (137), Expect = 1e-08
 Identities = 45/129 (34%), Positives = 76/129 (58%), Gaps = 4/129 (3%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E+KK +  KK  +  KKKE E+ KK ++ K K + +NK K  E+    E++K K EE +K
Sbjct: 1624 ELKKAEEEKKKVEQLKKKEAEEKKKAEELK-KAEEENKIKAAEEAKKAEEDKKKAEEAKK 1682

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRK---EEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 196
             EE EKK  +  K + ++ K  E+++K   EEK   +E K  +++ K+K E+ KK+ +E 
Sbjct: 1683 AEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEED 1742

Query: 197  ERSSHEKEV 205
            ++ + E + 
Sbjct: 1743 KKKAEEAKK 1751

Length = 2084

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

 Score = 55.3 bits (134), Expect = 2e-08
 Identities = 28/75 (37%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 106 KDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIR 165
             KK   KIK   +  EKK ++EK++ KK++    ++KE++EE+E + KE++++  E+  
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKE-KKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEA 462

Query: 166 KEEKDSEKEKKSKDK 180
           +EEK+ E+EKK K  
Sbjct: 463 EEEKEEEEEKKKKQA 477

Length = 482

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

 Score = 56.3 bits (135), Expect = 2e-08
 Identities = 36/123 (29%), Positives = 58/123 (47%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E KK    KK  +  KKK     KK ++ K   +    E +      +  E+  +  ++K
Sbjct: 1313 EAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKK 1372

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
            KEE +KK +   K  E+K+K  E  +K E+D +K  + K      KK    KKK E+++ 
Sbjct: 1373 KEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKK 1432

Query: 200  SHE 202
            + E
Sbjct: 1433 ADE 1435

Length = 2084

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

 Score = 53.8 bits (130), Expect = 7e-08
 Identities = 31/82 (37%), Positives = 53/82 (64%), Gaps = 1/82 (1%)

Query: 77  DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEE 136
              EI+     KK  K   KK  EK +KK++++ K+K K     K+K+ ++E+EK KKEE
Sbjct: 395 TEEEIEFLTGSKKATKK-IKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEE 453

Query: 137 KEKKEEKEKKEEKEFKMKEDKE 158
           ++++EE+E +EEKE + ++ K+
Sbjct: 454 EKEEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 53.4 bits (129), Expect = 1e-07
 Identities = 26/71 (36%), Positives = 46/71 (64%)

Query: 123 KKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK 182
            K   +K K   E+ EKK E+EKKE+K+      K++  E+  KE+K+ EKE++ ++ ++
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464

Query: 183 KLKKEKLKKKK 193
           + ++E+ KKKK
Sbjct: 465 EKEEEEEKKKK 475

Length = 482

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

 Score = 54.0 bits (129), Expect = 1e-07
 Identities = 32/125 (25%), Positives = 65/125 (52%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E  K ++     +    +EK +  +KK ++ K K    +K  E+K   ++ K K EE +K
Sbjct: 1346 EAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKK 1405

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
            K ++ KK     K  ++ +K  E+ +K ++  +K +++K  D+  KK +  KK +E ++ 
Sbjct: 1406 KADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKK 1465

Query: 200  SHEKE 204
            + E +
Sbjct: 1466 AEEAK 1470

Length = 2084

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

 Score = 53.6 bits (128), Expect = 1e-07
 Identities = 47/153 (30%), Positives = 70/153 (45%), Gaps = 4/153 (2%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEK----KIDKEKEKGKKE 135
            E KK    KK  +  KKK  E  K    KK  D+ K K ++K+K    K   E+ K   E
Sbjct: 1389 EKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448

Query: 136  EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
             K+K EE +K EE + K +E K+    K + EE     E K K ++ K K ++ KK  + 
Sbjct: 1449 AKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEA 1508

Query: 196  KERSSHEKEVIPKLTFKFGTDMEEKTKRESSPK 228
            K+++   K+             EE  K + + K
Sbjct: 1509 KKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541

Length = 2084

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

 Score = 52.3 bits (126), Expect = 2e-07
 Identities = 28/171 (16%), Positives = 55/171 (32%)

Query: 32  KTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDK 91
           K   KE + SK+KT  +  +        +  T                           K
Sbjct: 35  KEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKK 94

Query: 92  KTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEF 151
           K   + +  K  +KK+  DKD   N  KD +     + +    ++ +  ++    ++ + 
Sbjct: 95  KLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDE 154

Query: 152 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 202
              ED +        EEK   KE +    D     ++   +   + R   +
Sbjct: 155 DDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAK 205

Length = 509

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

 Score = 53.2 bits (127), Expect = 2e-07
 Identities = 47/184 (25%), Positives = 87/184 (47%), Gaps = 6/184 (3%)

Query: 22   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 81
            K K + + K   + K+K    +K +   K  ++    E           +    E     
Sbjct: 1321 KKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEE---AK 1377

Query: 82   KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKID---KEKEKGKKEEKE 138
            KK  + KK  +  KK ++ K K ++DKK  D++K     K+K  +   K +EK K +E +
Sbjct: 1378 KKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAK 1437

Query: 139  KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 198
            KK E+ KK ++  K  E+ +K  E  +K E+  + ++  K  ++  K ++ KKK +E ++
Sbjct: 1438 KKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKK 1497

Query: 199  SSHE 202
             + E
Sbjct: 1498 KADE 1501

Length = 2084

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

 Score = 51.0 bits (122), Expect = 5e-07
 Identities = 35/126 (27%), Positives = 66/126 (52%)

Query: 78  LGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEK 137
             +  K+   +  K+  K+KE+ K +KKK K+   +     K KE+  +K   K K++EK
Sbjct: 91  KTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEK 150

Query: 138 EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
           EKK E+ +  E+E K +  + K   K   ++K   K+K+  +++K+ +  +   K K +E
Sbjct: 151 EKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEE 210

Query: 198 RSSHEK 203
              +E+
Sbjct: 211 PDVNEE 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 = 51.3 bits (124), Expect = 5e-07
 Identities = 33/130 (25%), Positives = 75/130 (57%), Gaps = 8/130 (6%)

Query: 85  KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE 144
           K I + K    ++E ++I ++  K+ +   K    + +++I K + + +KE +E++ E +
Sbjct: 26  KKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQ 85

Query: 145 KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK- 203
           K E++  + +E+ ++ +E + K E++ EK++K  ++    K+++L+KK++E E    E+ 
Sbjct: 86  KLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQ----KQQELEKKEEELEELIEEQL 141

Query: 204 ---EVIPKLT 210
              E I  LT
Sbjct: 142 QELERISGLT 151

Length = 520

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

 Score = 51.1 bits (123), Expect = 7e-07
 Identities = 20/81 (24%), Positives = 51/81 (62%)

Query: 107 DKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRK 166
            +++ + +   +K  +K     ++  KK E+EKKE+K+K    + K +E++E+  +K  +
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 167 EEKDSEKEKKSKDKDKKLKKE 187
           +E++ E+ ++ K+++++ KK+
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 50.6 bits (121), Expect = 7e-07
 Identities = 23/89 (25%), Positives = 45/89 (50%), Gaps = 5/89 (5%)

Query: 95  KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMK 154
           K  E+ K         + ++  +   K +   K+  + K E    +E + K +E++ K +
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 155 EDKEKPVEKIRKEEKDSEKEKKSKDKDKK 183
           E+++K     +KE+ D +KEK+ KD+ KK
Sbjct: 411 ENEKK-----QKEQADEDKEKRQKDERKK 434

Length = 434

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

 Score = 51.3 bits (122), Expect = 8e-07
 Identities = 42/184 (22%), Positives = 83/184 (45%)

Query: 21   SKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 80
            +K  + V   ++     + + K +     +E  K ++  +         +K   +    E
Sbjct: 1223 AKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADE 1282

Query: 81   IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKK 140
            +KK +  KK  +  K +EK+K  + K K ++ K  ++ K K ++  K+ +  KK+ +E K
Sbjct: 1283 LKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAK 1342

Query: 141  EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 200
            +  E  + +     ++ E   EK    EK  E+ KK  D  KK  +EK K  + +K+   
Sbjct: 1343 KAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEE 1402

Query: 201  HEKE 204
             +K+
Sbjct: 1403 DKKK 1406

Length = 2084

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

 Score = 50.5 bits (120), Expect = 1e-06
 Identities = 52/186 (27%), Positives = 94/186 (50%), Gaps = 4/186 (2%)

Query: 48   KEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK-KKEKEKIKKKK 106
            K+ E +K+K  EL         V+    ++  E KK + +KK ++ +K K  +E  K ++
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 107  DKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVE-KIR 165
            DKK  ++ K  E+D++K    E  K + EE +K EE +KKE +E K  E+ +K  E    
Sbjct: 1673 DKKKAEEAKKAEEDEKKA--AEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKI 1730

Query: 166  KEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRES 225
            K E+  ++ ++ K K ++ KK++ +KKK    +   EK+       K     EE  + + 
Sbjct: 1731 KAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDE 1790

Query: 226  SPKIVI 231
              ++ +
Sbjct: 1791 KRRMEV 1796

Length = 2084

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

 Score = 49.5 bits (118), Expect = 2e-06
 Identities = 39/132 (29%), Positives = 78/132 (59%), Gaps = 2/132 (1%)

Query: 71  KVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIK--NKEKDKEKKIDKE 128
           K++S E +  ++K  S     KT   KE +    K+++K+K+++K   K+K ++ K + +
Sbjct: 70  KLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPK 129

Query: 129 KEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 188
             K K+E KEK+  KEK++EKE K++E +++  EK R+  +   + KK   K    KK++
Sbjct: 130 DRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKE 189

Query: 189 LKKKKKEKERSS 200
             +++K+++ + 
Sbjct: 190 PPEEEKQRQAAR 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|234017 TIGR02794, tolA_full, TolA protein

 Score = 49.1 bits (117), Expect = 2e-06
 Identities = 28/117 (23%), Positives = 59/117 (50%), Gaps = 1/117 (0%)

Query: 83  KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEE 142
             K  ++ KK  ++ E+ + ++  ++  + +++ +   ++     E+   + EEK+K+ E
Sbjct: 63  AKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAE 122

Query: 143 KEK-KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 198
           + K K+  E K K + E   +   + +K +E+E K+K   +  KK    KKK E E 
Sbjct: 123 EAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEA 179

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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 48.8 bits (117), Expect = 3e-06
 Identities = 27/81 (33%), Positives = 53/81 (65%)

Query: 74  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGK 133
           + E++  +   K   K  K   +K ++K +++K +K K     K+K++E++ +KEK++ +
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 134 KEEKEKKEEKEKKEEKEFKMK 154
           KEE+E++ E+EK+EE+E K K
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 48.8 bits (117), Expect = 3e-06
 Identities = 16/81 (19%), Positives = 54/81 (66%)

Query: 118 EKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS 177
            +++ + +   K+  KK +K  ++ ++K+EE++ + K+      +K  +EE++ EK+++ 
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 178 KDKDKKLKKEKLKKKKKEKER 198
           K+++++  +E+ ++++++K++
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 49.1 bits (118), Expect = 3e-06
 Identities = 32/167 (19%), Positives = 67/167 (40%), Gaps = 8/167 (4%)

Query: 73  TSSEDLGEIKKDKSIKKDKKTH------KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKID 126
            SS++L E  K+  I  + K+H      ++  KE+ K++ +++ K + +     + ++  
Sbjct: 15  VSSKELLEKLKELGI--EVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEA 72

Query: 127 KEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK 186
           K +       +E  E     E      +++  +P E   +  K  +  KK K    K KK
Sbjct: 73  KAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKK 132

Query: 187 EKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKP 233
            K K  +  K     +     +   +     +++   E  P+ V+ P
Sbjct: 133 PKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPREVVIP 179

Length = 746

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

 Score = 49.2 bits (117), Expect = 3e-06
 Identities = 29/133 (21%), Positives = 74/133 (55%)

Query: 92  KTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEF 151
           K ++++     +  +D++++ +   +E +KE++I  +  K  KEE+++K+ +E++ +   
Sbjct: 234 KLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLA 293

Query: 152 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTF 211
           K +E+ +  + K+ + + D E++ K  +K+ K  +++LKK+K+E E    E + +     
Sbjct: 294 KEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKRE 353

Query: 212 KFGTDMEEKTKRE 224
               + E+  K +
Sbjct: 354 AEEEEEEQLEKLQ 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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 49.0 bits (116), Expect = 4e-06
 Identities = 36/126 (28%), Positives = 71/126 (56%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E  + + + K  +  KK + E+ KK ++ K K +   K ++++KK+++ K+K  +E+K+ 
Sbjct: 1590 EEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKA 1649

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
            +E K+ +EE + K  E+ +K  E  +K E+  + E+  K   + LKKE  + KK E+ + 
Sbjct: 1650 EELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709

Query: 200  SHEKEV 205
               +E 
Sbjct: 1710 KEAEEK 1715

Length = 2084

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

 Score = 48.0 bits (115), Expect = 5e-06
 Identities = 20/75 (26%), Positives = 51/75 (68%), Gaps = 1/75 (1%)

Query: 126 DKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK 185
            K+  K  K+  EK E+K ++E+KE K K+      ++  +EE+  +KE++ ++++++ +
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKE-KKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 186 KEKLKKKKKEKERSS 200
           +EK ++++K+K++++
Sbjct: 464 EEKEEEEEKKKKQAT 478

Length = 482

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

 Score = 47.5 bits (114), Expect = 8e-06
 Identities = 26/97 (26%), Positives = 61/97 (62%), Gaps = 11/97 (11%)

Query: 82  KKDKSIKKDKKTHKKKEKEKIKKK--KDKKDK-DKIKNKEK---DKEKKIDKEKEKGKKE 135
           K+ ++IKK+     K+E  K++ +  K+ +++ ++++  EK    KE+ +D++ E  +K 
Sbjct: 49  KEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKR 108

Query: 136 EKE--KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKD 170
           E+E  KKE++ +++++E    E KE+ +E++ +E+  
Sbjct: 109 EEELEKKEKELEQKQQEL---EKKEEELEELIEEQLQ 142

Length = 520

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

 Score = 47.7 bits (113), Expect = 9e-06
 Identities = 33/125 (26%), Positives = 66/125 (52%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
           EI      +  ++  +KK +E+  K   K++++      K + +K+D E++  + E++ K
Sbjct: 266 EILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELK 325

Query: 140 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
           K EKE K+EKE   + +KE    +I++E ++ E+E+  K ++K  + E+    KK+ E  
Sbjct: 326 KLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESE 385

Query: 200 SHEKE 204
                
Sbjct: 386 RLSSA 390

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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 46.9 bits (112), Expect = 1e-05
 Identities = 27/138 (19%), Positives = 53/138 (38%), Gaps = 2/138 (1%)

Query: 89  KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEE 148
               T  +   E+  KKK KK   K K+K    +++I +  E  KK  ++  +       
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSG 61

Query: 149 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPK 208
                 +  E  + K  K+ K + K   +K   KK  K++L   KK +++++ +K+    
Sbjct: 62  MVKDTDDATESDIPK--KKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLN 119

Query: 209 LTFKFGTDMEEKTKRESS 226
                    +     +  
Sbjct: 120 YVKDIDVLNQADDDDDDD 137

Length = 509

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

 Score = 47.1 bits (111), Expect = 1e-05
 Identities = 41/124 (33%), Positives = 73/124 (58%), Gaps = 3/124 (2%)

Query: 81   IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKK 140
            +K  +  KK K    KK +E   K ++ K  ++ K K +  +KK  +EK+K ++ +K ++
Sbjct: 1598 MKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEE 1657

Query: 141  EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEK--EKKSKDKDKKLKKEKLKKKKKEKER 198
            E K K  E+  K +EDK+K  E+ +K E+D +K  E   K+ ++  K E+LKKK+ E+++
Sbjct: 1658 ENKIKAAEEAKKAEEDKKK-AEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKK 1716

Query: 199  SSHE 202
             + E
Sbjct: 1717 KAEE 1720

Length = 2084

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

 Score = 46.4 bits (110), Expect = 1e-05
 Identities = 27/119 (22%), Positives = 59/119 (49%), Gaps = 2/119 (1%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKK-KKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKE 138
             KK +   ++ +  +  E+ + K+ ++    +   K  E+  ++  +K+K+  + + K+
Sbjct: 69  RQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQ 128

Query: 139 KKEEKEKKEEK-EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 196
             E K K E + E K KE+ +K  E+  K +  +E +KK+ +  KK + E   K + + 
Sbjct: 129 AAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKA 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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 47.4 bits (113), Expect = 1e-05
 Identities = 29/132 (21%), Positives = 72/132 (54%), Gaps = 2/132 (1%)

Query: 75  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKK 134
            E++ E++ + S+ +++    + E E+++++  ++ K+KI+  +++ E++    +E  ++
Sbjct: 294 KEEIEELEGEISLLRERLEELENELEELEER-LEELKEKIEALKEELEERETLLEEL-EQ 351

Query: 135 EEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 194
              E +E KE+ EEK   + E+ E+  E +R+E  + E E      + +  K +++  ++
Sbjct: 352 LLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEE 411

Query: 195 EKERSSHEKEVI 206
             ER S   E +
Sbjct: 412 RLERLSERLEDL 423

Length = 1163

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

 Score = 46.8 bits (111), Expect = 1e-05
 Identities = 37/131 (28%), Positives = 58/131 (44%), Gaps = 5/131 (3%)

Query: 78  LGEIKKDKSIKKDKKTHKKKEKEKIKK--KKDKKDKDKIKNKEKDKEKKIDKEKEKGKKE 135
           L   K + SIK +KKT    +    KK    ++ +K+ +      K K     K+K  + 
Sbjct: 368 LENKKIEISIKPEKKTINNSQIITTKKINIVEESNKNSVHFDTLYKTKIFYH-KKKINQN 426

Query: 136 EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
            KE+  +KE+  EKEF   +  EK  +     +     ++K  +KD +L K  L+K  K 
Sbjct: 427 NKEQDIKKEELLEKEFV--KKSEKIPKNDELLDNLELAKQKFFNKDIELSKNMLQKFNKF 484

Query: 196 KERSSHEKEVI 206
           K   S E   I
Sbjct: 485 KNEESAENSFI 495

Length = 605

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

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 24/94 (25%), Positives = 51/94 (54%), Gaps = 3/94 (3%)

Query: 92  KTHKK---KEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEE 148
           KTH+K   K +EKIK  K +  + K      +    + ++ +   + + EK + + K+++
Sbjct: 273 KTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKK 332

Query: 149 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK 182
           KE K +E K+K +E++ +  +  E +   K+++K
Sbjct: 333 KEKKKEEKKKKQIERLEERIEKLEVQATDKEENK 366

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

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

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 35/219 (15%), Positives = 71/219 (32%), Gaps = 3/219 (1%)

Query: 8    PQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVP 67
                       P  K K+K   K      +K S    +   + +  +  D +        
Sbjct: 1161 KTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNS 1220

Query: 68   NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDK 127
            +       E+     K  S+K+ K       K      +   D    + K K+  K++  
Sbjct: 1221 SGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRVSA 1280

Query: 128  EKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 187
             +       K    E     +        K+K  +++       +K+KKS+ K  + KK 
Sbjct: 1281 VQYSPPPPSKRPDGESNGGSKPS---SPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKS 1337

Query: 188  KLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 226
            K + K+    +SS       K      ++ ++ ++ + S
Sbjct: 1338 KTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDS 1376

Length = 1388

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

 Score = 45.8 bits (109), Expect = 3e-05
 Identities = 22/149 (14%), Positives = 44/149 (29%), Gaps = 7/149 (4%)

Query: 82  KKDKSIKKDKKTHKKKEKEKIKKKKDKK-----DKDKIKNKEKDKEKKIDKEKEKGKKEE 136
              K+    ++  KKK K+   K K K      +  +    +K   ++ID+         
Sbjct: 4   ASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMV 63

Query: 137 KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 196
           K+  +  E    K  K  +   K        +K  + E  S  K +K             
Sbjct: 64  KDTDDATESDIPK--KKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYV 121

Query: 197 ERSSHEKEVIPKLTFKFGTDMEEKTKRES 225
           +      +           D+++    + 
Sbjct: 122 KDIDVLNQADDDDDDDDDDDLDDDDIDDD 150

Length = 509

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

 Score = 45.9 bits (108), Expect = 3e-05
 Identities = 46/159 (28%), Positives = 79/159 (49%), Gaps = 3/159 (1%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E KK    KK  +  KK ++ K K ++ KK  D+ K   + K+K  + +K +  K+  E 
Sbjct: 1468 EAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEA 1527

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
            K+ +E K+  E K  E+K+K  E  + EE    +EKK  ++ KK +++K    +K +E  
Sbjct: 1528 KKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAK 1587

Query: 200  SHEK---EVIPKLTFKFGTDMEEKTKRESSPKIVIKPVK 235
              E+   E + KL  +      E+ K+    KI  + +K
Sbjct: 1588 KAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELK 1626

Length = 2084

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

 Score = 45.2 bits (107), Expect = 3e-05
 Identities = 34/143 (23%), Positives = 71/143 (49%), Gaps = 6/143 (4%)

Query: 85  KSIKKDKKTHKKKEKEKIKK---KKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKE 141
             I++ KK   KKE+E+ KK   + ++ +K +   + + KE +     EK  K+ ++  +
Sbjct: 53  NRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAK 112

Query: 142 EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 201
           + E+K+++  + K  +    E   K E ++EK+ K + K K+ ++E   K   E ++ + 
Sbjct: 113 QAEEKQKQAEEAKAKQAA--EAKAKAEAEAEKKAKEEAK-KQAEEEAKAKAAAEAKKKAA 169

Query: 202 EKEVIPKLTFKFGTDMEEKTKRE 224
           E +   +   K   + + K K E
Sbjct: 170 EAKKKAEAEAKAKAEAKAKAKAE 192

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|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682)

 Score = 45.3 bits (108), Expect = 3e-05
 Identities = 23/70 (32%), Positives = 45/70 (64%), Gaps = 2/70 (2%)

Query: 108 KKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKE 167
            +   K+    +++E+KI K  E+ ++EE ++K+E++KKEE+E K+   K  P E+ + E
Sbjct: 255 PEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKKEEREAKL--AKLSPEEQRKLE 312

Query: 168 EKDSEKEKKS 177
           EK+ +K+ + 
Sbjct: 313 EKERKKQARK 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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.7 bits (108), Expect = 4e-05
 Identities = 32/118 (27%), Positives = 63/118 (53%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
           E K+ K  +++ K   K+E+E   +    + +     ++  + +K  K+ EK  K+EKE+
Sbjct: 278 EEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEE 337

Query: 140 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
            EE EK+ ++    +E +E+  E++ K ++  E+ ++     KKL+ E+L    K KE
Sbjct: 338 IEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKE 395

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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 44.0 bits (104), Expect = 4e-05
 Identities = 25/80 (31%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 88  KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKE 147
             D++  KK + ++  + ++ K+++K     +DKE K D EKE  + EE+ ++E++E  +
Sbjct: 45  AADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSD 104

Query: 148 EKEFKMKEDKEKPVEKIRKE 167
           E E   KE +EK    + KE
Sbjct: 105 ENE---KETEEKTESNVEKE 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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 32/139 (23%), Positives = 75/139 (53%), Gaps = 4/139 (2%)

Query: 93  THKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFK 152
           + +  ++ +    K    K K   + K++  K ++++++  KEEK+KK+EK K+E K+ K
Sbjct: 73  SDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRK 132

Query: 153 MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK----KKKKEKERSSHEKEVIPK 208
            KE+ ++      KE++  +K ++ +D++++ K+E+++     KK  K++  ++K+  P+
Sbjct: 133 PKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPE 192

Query: 209 LTFKFGTDMEEKTKRESSP 227
              +     E    +   P
Sbjct: 193 EEKQRQAAREAVKGKPEEP 211

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|234017 TIGR02794, tolA_full, TolA protein

 Score = 44.8 bits (106), Expect = 5e-05
 Identities = 30/129 (23%), Positives = 63/129 (48%), Gaps = 8/129 (6%)

Query: 88  KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKE 147
           +  ++  +K+ +++   +K  K  ++   + ++K+K+ ++ K K   E K K E + +K+
Sbjct: 84  RAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKK 143

Query: 148 EKEFKMK----EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK----KKKKEKERS 199
            KE   K    E K K   + +K+  +++K+ +++ K K   K K K    K K E  ++
Sbjct: 144 AKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKA 203

Query: 200 SHEKEVIPK 208
               E   K
Sbjct: 204 KAAAEAAAK 212

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|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 45.0 bits (107), Expect = 5e-05
 Identities = 23/150 (15%), Positives = 61/150 (40%), Gaps = 17/150 (11%)

Query: 69  IVKVTSSEDLGEIKKDKSIKKDKKTHK--------------KKEKEKIKKKKDKKDKDKI 114
           IV + ++ +  +I     I  D   +               + E+E++K  + +++    
Sbjct: 772 IVSLFNNPNAEKILIITEILSDGINNSDINDRPQELIDQIIESEEERLKALRIQRE---E 828

Query: 115 KNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKE 174
                ++ + I++E++  K+E K +  E ++ EE+   + E+K + VE     +K ++  
Sbjct: 829 MLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNINENKNEFVEFKNDPKKLNKLI 888

Query: 175 KKSKDKDKKLKKEKLKKKKKEKERSSHEKE 204
                  K +      K+ ++  +   +  
Sbjct: 889 IAKDVLIKLVISSDEIKQDEKTTKKKKKDL 918

Length = 925

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

 Score = 44.9 bits (107), Expect = 6e-05
 Identities = 22/75 (29%), Positives = 44/75 (58%)

Query: 134 KEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 193
           +EE E     +K  +K  K+ E  EK  E+ +KE+K      K K+++++ +KEK +++K
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 194 KEKERSSHEKEVIPK 208
           +E+E  + E++   +
Sbjct: 456 EEEEEEAEEEKEEEE 470

Length = 482

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

 Score = 44.8 bits (106), Expect = 6e-05
 Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 9/93 (9%)

Query: 102 IKKKKDKKDKDKIKNKEKDKE-KKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKP 160
            K  ++ K    +   ++ +  K+ +K+ +   K+  E K+E +  EE E K KE+K K 
Sbjct: 350 TKLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLK- 408

Query: 161 VEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 193
               ++E +  +KE+  +DK+K+   +K ++KK
Sbjct: 409 ----QEENEKKQKEQADEDKEKR---QKDERKK 434

Length = 434

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

 Score = 45.0 bits (106), Expect = 6e-05
 Identities = 31/129 (24%), Positives = 69/129 (53%), Gaps = 8/129 (6%)

Query: 77  DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEE 136
           DL E +  +  K+ ++  ++ +K++I   K ++  D       DK++   ++K++  K  
Sbjct: 202 DLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADF-AQDNADKQRDEVRQKQQEAKNL 260

Query: 137 KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKE-EKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
            +  +    KE+K  ++ E++++ +EK + E +K+ E+  K+KD     K   LK++ K 
Sbjct: 261 PKPADTSSPKEDK--QVAENQKREIEKAQIEIKKNDEEALKAKDH----KAFDLKQESKA 314

Query: 196 KERSSHEKE 204
            E+ + +KE
Sbjct: 315 SEKEAEDKE 323

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

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

 Score = 45.1 bits (106), Expect = 7e-05
 Identities = 38/131 (29%), Positives = 77/131 (58%), Gaps = 8/131 (6%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDK-----EKEKGKK 134
            + KK +  KK ++  KK  +   K+ ++ K  +++K KE +++KK ++     E+ K K 
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKA 1732

Query: 135  EEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 194
            EE +K+ E++KK+ +E K  E+++K +  ++KEE   EK+ +   K+K+   E+   ++ 
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEE---EKKAEEIRKEKEAVIEEELDEED 1789

Query: 195  EKERSSHEKEV 205
            EK R   +K++
Sbjct: 1790 EKRRMEVDKKI 1800

Length = 2084

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

 Score = 45.1 bits (106), Expect = 7e-05
 Identities = 46/186 (24%), Positives = 89/186 (47%), Gaps = 3/186 (1%)

Query: 22   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 81
            + K     K K    +K    +K    +K     K  E           ++  +E+L + 
Sbjct: 1501 EAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKA 1560

Query: 82   KKDKSIKKDKKTHKKKEKEKIKK---KKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKE 138
            ++ K  ++ KK  + K     K    KK ++ + +   K  ++EKK+  E+ K  +E K 
Sbjct: 1561 EEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKI 1620

Query: 139  KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 198
            K EE +K EE++ K+++ K+K  E+ +K E+  + E+++K K  +  K+  + KKK +E 
Sbjct: 1621 KAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEA 1680

Query: 199  SSHEKE 204
               E++
Sbjct: 1681 KKAEED 1686

Length = 2084

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

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 32/201 (15%), Positives = 67/201 (33%), Gaps = 11/201 (5%)

Query: 63  TPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKD------KIKN 116
           T            E   ++KK  +  K K    K+E ++  + K K  +        +  
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSG 61

Query: 117 KEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKK 176
             KD +   + +  K K +   K    +   +K+ K + D  K  E   K+    + +  
Sbjct: 62  MVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAE---KKNALDKDDDL 118

Query: 177 SKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFG--TDMEEKTKRESSPKIVIKPV 234
           +  KD  +  +       + +    + ++      +     D ++    E   K   K +
Sbjct: 119 NYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKEL 178

Query: 235 KSPSPPPVAAADEYDTGDSKQ 255
           +  S       DE D+   +Q
Sbjct: 179 EKLSDDDDFVWDEDDSEALRQ 199

Length = 509

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

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 50/225 (22%), Positives = 92/225 (40%), Gaps = 15/225 (6%)

Query: 21  SKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 80
            K   K         KE  +   K   KEKE  K +  +    P           ++  +
Sbjct: 81  EKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKP-----------KEEPK 129

Query: 81  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKK 140
            +K K   K+K+    KEKEK K+KK ++ +D+ + K++++ +   + K+  KK+   KK
Sbjct: 130 DRKPKEEAKEKR--PPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKK 187

Query: 141 EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 200
           +E  ++E++    +E  +   E+    E+  ++E   KD++      +  + ++  E S 
Sbjct: 188 KEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISR 247

Query: 201 HEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAA 245
                           M     RESS +   +P  S  PP    A
Sbjct: 248 RSSS--SLKKPDPSPSMASPETRESSKRTETRPRTSLRPPSARPA 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|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 44.1 bits (105), Expect = 1e-04
 Identities = 26/143 (18%), Positives = 56/143 (39%), Gaps = 3/143 (2%)

Query: 25  DKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKD 84
             V  ++    + K  ++E+   + +E +  +  E              + E        
Sbjct: 36  STVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEE---EAKAEAAAAAPAEEAAEAAAAA 92

Query: 85  KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE 144
           ++  +  +    +  E   ++   K   K K   K K+KK  ++  +G K  K  K  + 
Sbjct: 93  EAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRR 152

Query: 145 KKEEKEFKMKEDKEKPVEKIRKE 167
           ++  +  + K+ K+KP EKI +E
Sbjct: 153 RRGRRRRRKKKKKQKPTEKIPRE 175

Length = 746

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

 Score = 44.2 bits (104), Expect = 1e-04
 Identities = 32/162 (19%), Positives = 75/162 (46%)

Query: 68  NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDK 127
              +    + L E +     K++++   +  K + +K  D++   + + + K  EK++ K
Sbjct: 274 ENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKK 333

Query: 128 EKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 187
           EKE+ ++ EKE KE + K+E +E + ++ ++   +  + EE+   K+K   ++     K 
Sbjct: 334 EKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

Query: 188 KLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKI 229
           K ++ + + E     K ++     +     EEK +     + 
Sbjct: 394 KEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEE 435

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 = 44.3 bits (105), Expect = 1e-04
 Identities = 27/129 (20%), Positives = 69/129 (53%), Gaps = 1/129 (0%)

Query: 82  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKE 141
           + + ++   K    +KE E+++++  + +++  + +E+ +E + + E+ K + EE  ++ 
Sbjct: 224 ELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREEL 283

Query: 142 EKEKKEEKEFK-MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 200
           E+ ++E  E K   E+ E  +  +R+  ++ E E +  ++  +  KEK++  K+E E   
Sbjct: 284 EELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERE 343

Query: 201 HEKEVIPKL 209
              E + +L
Sbjct: 344 TLLEELEQL 352

Length = 1163

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 44.2 bits (105), Expect = 1e-04
 Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 129 KEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 188
           K K   E +E++EE + + E   + K  K++      ++     +EK+  DK + L K +
Sbjct: 225 KLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLE 284

Query: 189 LKKKKKEKERSSHEKEVIPKLTFKF 213
           + K+KK++E    EK   P  T  F
Sbjct: 285 ILKEKKDEELFWFEK---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|217756 pfam03839, Sec62, Translocation protein Sec62

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 91  KKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKE 150
           K+  +  E EK K  KDK    +I NK   ++K I+K K   K +  E + +K   +EK+
Sbjct: 10  KRVVRALESEKYKANKDKG-NPEIYNKINSQDKAIEKFKLLIKAQMAE-RVKKLHSQEKK 67

Query: 151 FKMKEDKEKPVEKIRKEEKD 170
            + K+ K+K V       + 
Sbjct: 68  EEKKKPKKKKVPLQVNPAQL 87

Length = 217

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

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 25/101 (24%), Positives = 48/101 (47%), Gaps = 3/101 (2%)

Query: 116  NKEKDKEKKIDKEKEKGKKEEKEK--KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEK 173
            N  ++  KKI+++K+      ++K  + E   +EEKE   + + E   EK    E     
Sbjct: 1493 NGNENVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSN 1552

Query: 174  EKKSKDKD-KKLKKEKLKKKKKEKERSSHEKEVIPKLTFKF 213
            ++K+ ++D  +   +K K KK+ K  +  E +   K   +F
Sbjct: 1553 QEKNIEEDYAESDIKKRKNKKQYKSNTEAELDFFLKRYLRF 1593

Length = 1832

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

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 6/107 (5%)

Query: 87  IKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKK 146
           I++  K+ +  +    ++ K + DK K  ++   +  K  K+ +  K     +  E ++ 
Sbjct: 333 IEEGLKSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKVNLDRQLSELKEA 392

Query: 147 EE-----KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 188
                  K    K + +K +E+IR+E  + E   KSK K +K K+  
Sbjct: 393 IAYYESAKTALEKAEGKKAIEEIREELIE-EGLLKSKKKKRKKKEWF 438

Length = 564

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

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 31/151 (20%), Positives = 76/151 (50%), Gaps = 7/151 (4%)

Query: 85  KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE 144
           K I + K    ++  ++I ++  K+ +   K    + ++++ K + + ++E KE++ E  
Sbjct: 20  KRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNE-L 78

Query: 145 KKEEKEFKMKEDK-EKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 203
           ++ E+    +E+  ++ +E + K+E++ EK++K     +K   EK ++ ++       E 
Sbjct: 79  QRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREEL 138

Query: 204 EVIPKLTF-----KFGTDMEEKTKRESSPKI 229
           E I  LT          ++EE+ + E++  I
Sbjct: 139 ERISGLTQEEAKEILLEEVEEEARHEAAKLI 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|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 42.0 bits (99), Expect = 1e-04
 Identities = 30/110 (27%), Positives = 60/110 (54%)

Query: 89  KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEE 148
           K KK    +E EK+KK+ ++K K K K K+  K+K  DK+K+  KK++K +K+++++ E+
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAED 120

Query: 149 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 198
           K   + +   + +  + + +       K   + +  +K + +  KKE E 
Sbjct: 121 KLEDLTKSYSETLSTLSELKPRKYALHKDIYQSRLDRKRRAEVAKKEAEE 170

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

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

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 30/92 (32%), Positives = 53/92 (57%), Gaps = 1/92 (1%)

Query: 84  DKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEK 143
           +KS++K ++  K  + +  + KK     + I + ++  + K +++ EK   E KEKK+EK
Sbjct: 276 EKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEK 335

Query: 144 EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEK 175
            KKEEK+ K  E  E+ +EK+  +  D E+ K
Sbjct: 336 -KKEEKKKKQIERLEERIEKLEVQATDKEENK 366

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

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

 Score = 43.1 bits (101), Expect = 2e-04
 Identities = 24/129 (18%), Positives = 64/129 (49%), Gaps = 1/129 (0%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
           +  K++  KK     K ++K    +    K +D+++ K+++ +           KE+K+ 
Sbjct: 216 QQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQKQQEAKNLPKPADTSSPKEDKQV 275

Query: 140 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
            E ++++ EK     +  ++   K  K+ K  + +++SK  +K+ + ++L+ +KK +  +
Sbjct: 276 AENQKREIEKAQIEIKKNDEEALK-AKDHKAFDLKQESKASEKEAEDKELEAQKKREPVA 334

Query: 200 SHEKEVIPK 208
              ++  P+
Sbjct: 335 EDLQKTKPQ 343

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

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

 Score = 43.2 bits (102), Expect = 2e-04
 Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 115  KNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKM-KEDKEKPVEKIRKEEKDSEK 173
            K   + K+  I   ++K  + E   +EEKE   + E +  KE K      +  +EK+ E+
Sbjct: 1500 KKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQEKNIEE 1559

Query: 174  EKKSKDKDKKLKKEKLKKKKKEKE 197
            +    D  KK K +K  K   E E
Sbjct: 1560 DYAESDI-KKRKNKKQYKSNTEAE 1582

Length = 1832

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

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 25/120 (20%), Positives = 68/120 (56%), Gaps = 5/120 (4%)

Query: 95  KKKEKEKIKKKKDKKDK-DKIKNKEKDKEKKIDKEKEKGKKEEKEKKEE--KEKKEEKEF 151
           +++ ++K ++ +    + +K+K + ++K++K+ +E++K  +E +++ ++  KE K+E + 
Sbjct: 529 ERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADE 588

Query: 152 KMKEDKEKPVEKIR--KEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKL 209
            +KE ++         K  +  E  K+    ++K +K+K K+K+K++E    ++     L
Sbjct: 589 IIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVGDEVKYLSL 648

Length = 782

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

 Score = 43.3 bits (103), Expect = 2e-04
 Identities = 32/132 (24%), Positives = 68/132 (51%), Gaps = 18/132 (13%)

Query: 92  KTHKKKEKEKI---------KKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEE 142
           K    ++KEK+          +++ ++  ++ +   K+ EK  ++ +EK +K ++E+ + 
Sbjct: 508 KKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKL 567

Query: 143 KEKKEEK-EFKMKEDKEKPVEKIR------KEEKDSEKEKKSKDKDKKLKK--EKLKKKK 193
            E+ E++ +  +KE K++  E I+      K    S K  +  +  K+L K  EK +KKK
Sbjct: 568 LEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKK 627

Query: 194 KEKERSSHEKEV 205
           K+++    E +V
Sbjct: 628 KKQKEKQEELKV 639

Length = 782

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

 Score = 43.1 bits (101), Expect = 2e-04
 Identities = 38/141 (26%), Positives = 62/141 (43%), Gaps = 3/141 (2%)

Query: 90  DKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEK 149
           +KK+ K K+KEK   K+ +K++DK K KE +  K +    +          E  E     
Sbjct: 196 EKKSKKPKKKEK---KEKEKERDKDKKKEVEGFKSLLLALDDSPASAASVAEADEASLAN 252

Query: 150 EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKL 209
                    +P E    E ++++K  K K K ++ +KE+ KKKKK      H  +   + 
Sbjct: 253 TVSGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKKKKKKHHHHRCHHSDGGAEQ 312

Query: 210 TFKFGTDMEEKTKRESSPKIV 230
             + G   EE     SS K++
Sbjct: 313 PVQNGAVEEEPLPPMSSYKLL 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|177089 CHL00189, infB, translation initiation factor 2; Provisional

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 29/109 (26%), Positives = 43/109 (39%), Gaps = 6/109 (5%)

Query: 89  KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEE 148
            +KK H+K +K+  K  K    KD  K K K K KKI K+       +     +   K+ 
Sbjct: 48  INKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQK-KKIKKKLHIDDDYDNFFDSKNNSKQF 106

Query: 149 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
                     KP  K      +  K+K + +K    KK+K+   K E  
Sbjct: 107 AGPLAISLMRKPKPK-----TEKLKKKITVNKSTNKKKKKVLSSKDELI 150

Length = 742

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

 Score = 42.8 bits (101), Expect = 2e-04
 Identities = 25/117 (21%), Positives = 45/117 (38%)

Query: 34  SPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKT 93
           S     + K K  P    YS V  +   +           ++    + KK+    + KK 
Sbjct: 10  SFFSGTTQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKK 69

Query: 94  HKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKE 150
            +KK+K+K +KK+ K + +     +  K+ K  K+K    K  ++      K  E  
Sbjct: 70  SEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELA 126

Length = 413

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

 Score = 42.6 bits (101), Expect = 3e-04
 Identities = 22/70 (31%), Positives = 48/70 (68%)

Query: 133 KKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK 192
           KK  K+ K+  EK E+K  + K++K+K     +K+E++ E+EK+ K+++K+ ++E+ +++
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465

Query: 193 KKEKERSSHE 202
           K+E+E    +
Sbjct: 466 KEEEEEKKKK 475

Length = 482

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

 Score = 43.2 bits (101), Expect = 3e-04
 Identities = 41/124 (33%), Positives = 63/124 (50%), Gaps = 7/124 (5%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E  K     K K    KK  E  KK ++ K  D+ K K ++ +KK D+ K+    E K+K
Sbjct: 1454 EEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKA--AEAKKK 1511

Query: 140  KEEKEKKEEK----EFKMKEDKEKPVEKIRKEEKDSEKE-KKSKDKDKKLKKEKLKKKKK 194
             +E +K EE     E K  E+ +K  E  + EEK    E KK+++  K  +K+K ++ KK
Sbjct: 1512 ADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKK 1571

Query: 195  EKER 198
             +E 
Sbjct: 1572 AEED 1575

Length = 2084

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

 Score = 42.8 bits (100), Expect = 3e-04
 Identities = 37/127 (29%), Positives = 66/127 (51%), Gaps = 2/127 (1%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKE--KDKEKKIDKEKEKGKKEEK 137
            E KK     K  +  KKK +E  K  + KK  ++ K  +  K K ++  K+ ++ KK  +
Sbjct: 1448 EAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAE 1507

Query: 138  EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
             KK+  E K+ +E K  ++ +K  E  + +E    +EKK  D+ KK ++ K  ++KK+ E
Sbjct: 1508 AKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAE 1567

Query: 198  RSSHEKE 204
             +   +E
Sbjct: 1568 EAKKAEE 1574

Length = 2084

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

 Score = 43.0 bits (101), Expect = 3e-04
 Identities = 27/126 (21%), Positives = 70/126 (55%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
             +K+ + +++K    K E+EK +K K ++++ +   +E  +E ++ +E++   ++E++ 
Sbjct: 772 LKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKI 831

Query: 140 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
           KEE+ ++   E K ++  EK  E+  +  ++   +++   +    ++E  ++K K++  S
Sbjct: 832 KEEELEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELES 891

Query: 200 SHEKEV 205
             EKE 
Sbjct: 892 KEEKEK 897

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 = 42.6 bits (100), Expect = 3e-04
 Identities = 27/147 (18%), Positives = 68/147 (46%), Gaps = 8/147 (5%)

Query: 74  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIK--------KKKDKKDKDKIKNKEKDKEKKI 125
               L E  K        K   + E+E +         +++    ++ +++++++ E   
Sbjct: 199 QELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSK 258

Query: 126 DKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK 185
            + +++ +   +  KE KE+++EK+ + +E K    E+   + +  + E++  D ++KLK
Sbjct: 259 QELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLK 318

Query: 186 KEKLKKKKKEKERSSHEKEVIPKLTFK 212
           + + + KK EKE    ++E+       
Sbjct: 319 ESEKELKKLEKELKKEKEEIEELEKEL 345

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|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 42.7 bits (101), Expect = 3e-04
 Identities = 24/118 (20%), Positives = 55/118 (46%), Gaps = 4/118 (3%)

Query: 83  KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEE 142
            D+ I+ +++  K    ++ +     ++ + I  ++K+ +++I  E  + ++ E+E +  
Sbjct: 808 IDQIIESEEERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNI 867

Query: 143 KEKKEEKEFKMKEDKEKPVEKI---RKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
            E K E   + K D +K  + I       K      + K  +K  KK+K   +K ++E
Sbjct: 868 NENKNEF-VEFKNDPKKLNKLIIAKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTDEE 924

Length = 925

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

 Score = 42.4 bits (100), Expect = 3e-04
 Identities = 33/129 (25%), Positives = 49/129 (37%), Gaps = 8/129 (6%)

Query: 73  TSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKG 132
           T    L  I    S              + + K       K K ++K+ E K        
Sbjct: 16  TQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESK-------- 67

Query: 133 KKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK 192
           KK EK+KK++KEKKE K     +   K  +K +K +K   K K ++D D    K     +
Sbjct: 68  KKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAE 127

Query: 193 KKEKERSSH 201
           K      +H
Sbjct: 128 KSNVYIGAH 136

Length = 413

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

 Score = 43.0 bits (101), Expect = 3e-04
 Identities = 26/99 (26%), Positives = 50/99 (50%), Gaps = 17/99 (17%)

Query: 115 KNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKE 174
           +N+ +      D+ +EK    + EK+++K + E KE K+ + KE+ V     +  DS  +
Sbjct: 4   RNRREANINNNDRMQEK----DDEKQDQKNRMELKE-KVLDKKEEVVT----DNVDSPVK 54

Query: 175 KKSKDKDKKLKKEKLKKKKKE--------KERSSHEKEV 205
           ++S  ++ K+  E  K  K+E        K +  H+KE+
Sbjct: 55  EQSSQENLKIADEVKKSTKEESKQLLEVLKTKEEHQKEI 93

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|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 42.6 bits (100), Expect = 3e-04
 Identities = 27/104 (25%), Positives = 57/104 (54%), Gaps = 9/104 (8%)

Query: 108 KKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKE 167
            + +  I N ++ +EK  +K+ +K + E KEK       ++KE  + ++ + PV++   +
Sbjct: 5   NRREANINNNDRMQEKDDEKQDQKNRMELKEK-----VLDKKEEVVTDNVDSPVKEQSSQ 59

Query: 168 E--KDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE--KEVIP 207
           E  K +++ KKS  ++ K   E LK K++ ++   +E  ++ IP
Sbjct: 60  ENLKIADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIP 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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 42.3 bits (100), Expect = 4e-04
 Identities = 19/166 (11%), Positives = 51/166 (30%), Gaps = 4/166 (2%)

Query: 30  KDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI-KKDKSIK 88
           +   S K+     ++         K  D                 +       KK    +
Sbjct: 40  EALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDE 99

Query: 89  KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEE 148
            D     +K+    K       KD     + D +   D + +    +  +  ++++  E+
Sbjct: 100 LDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDED 159

Query: 149 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 194
            +    +D +   E+ ++ ++  +          +   E L++ +K
Sbjct: 160 DD---DDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARK 202

Length = 509

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

 Score = 41.7 bits (98), Expect = 4e-04
 Identities = 30/126 (23%), Positives = 59/126 (46%), Gaps = 2/126 (1%)

Query: 81  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNK-EKDKEKKIDKEKEKGKKEEKEK 139
            K+ +     +K  K+ E+   + ++ +K  ++ K K   + + K + E EK  KEE +K
Sbjct: 91  QKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKK 150

Query: 140 K-EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 198
           + EE+ K +      K+  E   +   + +  +E + K+K ++ K K E  K K   +  
Sbjct: 151 QAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAA 210

Query: 199 SSHEKE 204
           +  E E
Sbjct: 211 AKAEAE 216

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 = 42.3 bits (99), Expect = 4e-04
 Identities = 24/144 (16%), Positives = 60/144 (41%), Gaps = 1/144 (0%)

Query: 76   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKE 135
            +   E +  K    ++K ++ +E+   +     K + + +    ++  + +KE++  ++E
Sbjct: 900  KKELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEE 959

Query: 136  EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
            E+  K     KEE          +  EK  +  KD  K+++ +++ K+L +E +++  + 
Sbjct: 960  EERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREIIEETCQR 1019

Query: 196  KERSSHEKEVIPKLTFKFGTDMEE 219
             +    E  V             E
Sbjct: 1020 FKE-FLELFVSINRGLNKVFFYLE 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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 42.3 bits (99), Expect = 4e-04
 Identities = 37/179 (20%), Positives = 90/179 (50%)

Query: 48  KEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKD 107
           K +   + ++++     +   + K+   ++     K +  +       K  ++KIK+K++
Sbjct: 692 KNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEE 751

Query: 108 KKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKE 167
           +++K ++K +E+++EK     KEK   EE+EK E+ + +EEKE K+K  +E+      + 
Sbjct: 752 EEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEEL 811

Query: 168 EKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 226
           ++++E  ++ +   ++ +K K ++ ++       E+++      +     EE TK E  
Sbjct: 812 KEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLEEEITKEELL 870

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|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 25/123 (20%), Positives = 65/123 (52%), Gaps = 1/123 (0%)

Query: 91  KKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKE 150
           K+    KE E+I ++  K+ ++K++    + ++ + +E+ + ++E + ++EE +++EE+ 
Sbjct: 27  KRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERL 86

Query: 151 FKMKEDKEKPVEKIR-KEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKL 209
            + +E  +   EK+   E +  E+EK    ++ +L++ + +   +    +    E   KL
Sbjct: 87  VQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQARKL 146

Query: 210 TFK 212
             K
Sbjct: 147 LLK 149

Length = 508

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

 Score = 41.7 bits (98), Expect = 5e-04
 Identities = 25/105 (23%), Positives = 46/105 (43%), Gaps = 3/105 (2%)

Query: 96  KKEKEKIKKKK---DKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFK 152
           K+  E   K +   +KK K++ K + +++ K     + K K  E +KK E E K + E K
Sbjct: 127 KQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAK 186

Query: 153 MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
            K   E+   K    +  +  E  +K + +       + ++K  E
Sbjct: 187 AKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAERKADE 231

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 = 42.3 bits (99), Expect = 5e-04
 Identities = 26/140 (18%), Positives = 68/140 (48%), Gaps = 2/140 (1%)

Query: 68  NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDK 127
           N+ ++    +  ++++ K  ++ KK  +  + ++  + +++        K  ++   + +
Sbjct: 185 NLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQ 244

Query: 128 EKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRK--EEKDSEKEKKSKDKDKKLK 185
           E  + ++EE E  +++ +KEE+       + K  EK +K  EE+     K+ ++   +L 
Sbjct: 245 ELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELL 304

Query: 186 KEKLKKKKKEKERSSHEKEV 205
           K + +K   E++    EKE+
Sbjct: 305 KLERRKVDDEEKLKESEKEL 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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.9 bits (98), Expect = 5e-04
 Identities = 16/111 (14%), Positives = 51/111 (45%)

Query: 94  HKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKM 153
            K+K+KE++KK  ++ +       + ++ K  + + ++  K+  E  + KEK E +E  +
Sbjct: 168 EKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENL 227

Query: 154 KEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 204
                  + + R +        + ++ +   ++ + +++   +    +++E
Sbjct: 228 LYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEE 278

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

 Score = 42.3 bits (99), Expect = 5e-04
 Identities = 29/139 (20%), Positives = 65/139 (46%), Gaps = 10/139 (7%)

Query: 76   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKE 135
            E++ +I +D S   ++K   +  +E + + + K ++    N E D   K D  K    K+
Sbjct: 3890 EEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKD 3949

Query: 136  EKEKKEEKEKK------EEKEFKMKEDKEKPVEKIRK----EEKDSEKEKKSKDKDKKLK 185
             +EK++E+E        +E +  ++E+  +P  +       E+   ++++    KD  L+
Sbjct: 3950 RQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDSDLE 4009

Query: 186  KEKLKKKKKEKERSSHEKE 204
               ++   + KE +  EK+
Sbjct: 4010 DMDMEAADENKEEADAEKD 4028

Length = 4600

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

 Score = 41.7 bits (97), Expect = 6e-04
 Identities = 42/182 (23%), Positives = 80/182 (43%), Gaps = 14/182 (7%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDK----------IKNKEKDKEKKIDKEK 129
             +KK +  KKD +  KK E+E+  ++  K ++ +          IK +E  K  ++ K +
Sbjct: 1228 AVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAE 1287

Query: 130  EKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 189
            EK K +E +K EEK+K +E + K +E K+    K + EE   + +   K  ++  K  + 
Sbjct: 1288 EKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEA 1347

Query: 190  KK----KKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAA 245
             K       ++  ++ EK    +   +      +  K+++  K      K  +      A
Sbjct: 1348 AKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKA 1407

Query: 246  DE 247
            DE
Sbjct: 1408 DE 1409

Length = 2084

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

 Score = 41.3 bits (97), Expect = 6e-04
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
           E+K +  +  DK+    KE  K  +   KK  +     +  +E +   ++EK K+EE E 
Sbjct: 355 EVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENE- 413

Query: 140 KEEKEKKEEKEFKMKEDKEK 159
           K++KE+ +E + K ++D+ K
Sbjct: 414 KKQKEQADEDKEKRQKDERK 433

Length = 434

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

 Score = 41.6 bits (98), Expect = 7e-04
 Identities = 30/166 (18%), Positives = 56/166 (33%), Gaps = 2/166 (1%)

Query: 76   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKE 135
             +  EI K++ +K   K    K ++   KKK+KK K    +K K      + ++    ++
Sbjct: 1147 VEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEK 1206

Query: 136  EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
             K   +   KK       +ED E+   K +K      K KK+         ++       
Sbjct: 1207 RKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLS 1266

Query: 196  KERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPP 241
            KE     K    +++    +      + +       KP        
Sbjct: 1267 KEGKP--KNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKV 1310

Length = 1388

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

 Score = 41.1 bits (96), Expect = 7e-04
 Identities = 33/134 (24%), Positives = 60/134 (44%), Gaps = 1/134 (0%)

Query: 95  KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMK 154
           K+ EKE++K ++ +K  ++ + K+   E+K  +E+ +    E++KK E  K +      K
Sbjct: 104 KQLEKERLKAQEQQKQAEEAE-KQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAK 162

Query: 155 EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFG 214
                  +K  +E   + +E K+K +    KK+   + K   E++  E E   K   K  
Sbjct: 163 LKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAE 222

Query: 215 TDMEEKTKRESSPK 228
              EEK   E    
Sbjct: 223 AAAEEKAAAEKKKA 236

Length = 387

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

 Score = 41.6 bits (98), Expect = 7e-04
 Identities = 40/143 (27%), Positives = 68/143 (47%), Gaps = 11/143 (7%)

Query: 74  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDK--KDKDKIKNKEKDKEKKIDKEKEK 131
           S E+  E    K++ + K   +  EKE   KK  K  K++ K K +  ++E+  D+E+ K
Sbjct: 407 SDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAK 466

Query: 132 GKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDK---------DK 182
            +K   +  +  EK +++E + + D+E P  K       S K++ SK K         +K
Sbjct: 467 VEKVANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANK 526

Query: 183 KLKKEKLKKKKKEKERSSHEKEV 205
             K     KKKK+KE+S    + 
Sbjct: 527 ISKAAVKVKKKKKKEKSIDLDDD 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|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 41.0 bits (96), Expect = 8e-04
 Identities = 13/96 (13%), Positives = 35/96 (36%), Gaps = 1/96 (1%)

Query: 94  HKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK-KEEKEKKEEKEFK 152
            + K+    +K + K  K +I  K +  E++I++E  + +     + +  +   + K+  
Sbjct: 330 AEIKKTRTAEKNEAKARKKEIAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKG 389

Query: 153 MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 188
           + +           EE      +       +  +E 
Sbjct: 390 LIDASPNEDTPSENEESKGSPPQVEATTTAEPNREP 425

Length = 429

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

 Score = 41.1 bits (97), Expect = 9e-04
 Identities = 17/70 (24%), Positives = 51/70 (72%)

Query: 74  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGK 133
           +++ + +I +    K++++  +KK+K    KKK+++++++ + KE++KE++ ++ +E+ +
Sbjct: 408 ATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKE 467

Query: 134 KEEKEKKEEK 143
           +EE++KK++ 
Sbjct: 468 EEEEKKKKQA 477

Length = 482

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

 Score = 40.9 bits (96), Expect = 9e-04
 Identities = 30/124 (24%), Positives = 49/124 (39%), Gaps = 8/124 (6%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE---KKIDKEKEKGKKEE 136
           E KK       +   K+K+ E+   K     K K + + K      KK   E +K  + E
Sbjct: 115 EQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAE 174

Query: 137 KEKKEEKEKKEEKE----FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK 192
             KK   E K++ E     K   + +K  E   K++  +E +KK+   + K    K   +
Sbjct: 175 AAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKA-AAEAKAAAAKAAAE 233

Query: 193 KKEK 196
            K  
Sbjct: 234 AKAA 237

Length = 387

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

 Score = 40.9 bits (95), Expect = 0.001
 Identities = 38/177 (21%), Positives = 80/177 (45%), Gaps = 28/177 (15%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEK----------------------------IKKKKDKKDK 111
            + KK +++KK ++  K  E+ K                            IK ++ +K  
Sbjct: 1222 DAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKAD 1281

Query: 112  DKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDS 171
            +  K +EK K  +  K +EK K +E +KK E+ KK ++  K  E+ +K  +  +K+ +++
Sbjct: 1282 ELKKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEA 1341

Query: 172  EKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPK 228
            +K  ++   + +   ++ +  +++ E +  +KE   K         EEK K + + K
Sbjct: 1342 KKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKK 1398

Length = 2084

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

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 27/154 (17%), Positives = 78/154 (50%), Gaps = 7/154 (4%)

Query: 75  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKK 134
            ++L   ++++     ++  K++E      K++K+++ + K +E++ +    +E+E   +
Sbjct: 243 LQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSE 302

Query: 135 EEKEK----KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK 190
             K +     +E++ KE ++   K +KE   +K ++E ++ EKE K  +  ++ ++E+ +
Sbjct: 303 LLKLERRKVDDEEKLKESEKELKKLEKEL--KKEKEEIEELEKELKELEIKREAEEEEEE 360

Query: 191 KKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRE 224
           + +K +E+    +E +     K  ++      + 
Sbjct: 361 QLEKLQEKLEQLEEEL-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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 38/152 (25%), Positives = 81/152 (53%), Gaps = 1/152 (0%)

Query: 75  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKI-KNKEKDKEKKIDKEKEKGK 133
             +  ++  ++ +K+ +K  KK EKE  K+K++ ++ +K  K  E  +E + ++E++  K
Sbjct: 305 KLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEK 364

Query: 134 KEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 193
            +EK ++ E+E   +K+ + +        K  + E  +E+EK++K   +  ++E+   K+
Sbjct: 365 LQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKE 424

Query: 194 KEKERSSHEKEVIPKLTFKFGTDMEEKTKRES 225
           ++KE     +E+   L  K G   EEK + E 
Sbjct: 425 EKKEELKIVEELEESLETKQGKLTEEKEELEK 456

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 = 40.7 bits (95), Expect = 0.001
 Identities = 25/148 (16%), Positives = 71/148 (47%), Gaps = 3/148 (2%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
           + ++      +++  + +E+   ++   +    + + +E+  + +++ ++EK K+E+KE 
Sbjct: 844 KEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKKEL 903

Query: 140 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK---EKLKKKKKEK 196
           +EE +K    E K  E +E+  E+     K   + ++   ++   K+   +  +++++  
Sbjct: 904 EEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEERN 963

Query: 197 ERSSHEKEVIPKLTFKFGTDMEEKTKRE 224
           +R    KE +  +      + EEK +R 
Sbjct: 964 KRLLLAKEELGNVNLMAIAEFEEKEERY 991

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 = 41.2 bits (97), Expect = 0.001
 Identities = 26/138 (18%), Positives = 64/138 (46%), Gaps = 8/138 (5%)

Query: 75  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDK-------EKKIDK 127
            E+L E +K+    K +   + +E+ +  +++  + K++I+  E +        E+  ++
Sbjct: 259 QEELEEAEKEIEELKSEL-EELREELEELQEELLELKEEIEELEGEISLLRERLEELENE 317

Query: 128 EKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 187
            +E  ++ E+ K++ +  KEE E +    +E        EE   E E+K     ++L++ 
Sbjct: 318 LEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEEL 377

Query: 188 KLKKKKKEKERSSHEKEV 205
               +++  E  +   E+
Sbjct: 378 FEALREELAELEAELAEI 395

Length = 1163

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

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 83  KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDK-EKEKGKKEEKEKKE 141
           +     KDK   +   K   + K  +K K  IK +  ++ KK+   EK++ KK+ K+KK 
Sbjct: 19  EKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKKKKV 78

Query: 142 EKEKKEEKEFKMKE 155
             +    + F   E
Sbjct: 79  PLQVNPAQLFVDDE 92

Length = 217

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 24/118 (20%), Positives = 42/118 (35%), Gaps = 1/118 (0%)

Query: 114 IKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEK 173
            +  +      I        KE      E+E K       K+ KE    + +K+ +  +K
Sbjct: 16  TQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKK 75

Query: 174 EKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEE-KTKRESSPKIV 230
           +KK K + K   + KL  K  +K + + +K   PK          +     E S   +
Sbjct: 76  KKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEKSNVYI 133

Length = 413

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

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 35/148 (23%), Positives = 68/148 (45%), Gaps = 19/148 (12%)

Query: 22  KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 81
           K  +K   K++   KEK+  K++    +   S VK+                SS++   +
Sbjct: 20  KDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKE---------------QSSQE--NL 62

Query: 82  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKE 141
           K    +KK  K   K+  E +K K++   + +I+ +   K     + KE   K+ ++ K 
Sbjct: 63  KIADEVKKSTKEESKQLLEVLKTKEE--HQKEIQYEILQKTIPSFEPKESILKKLEDIKP 120

Query: 142 EKEKKEEKEFKMKEDKEKPVEKIRKEEK 169
           E+ KK+ K F++ E K+ P+ +   E++
Sbjct: 121 EQAKKQTKLFRLFEPKQLPIYRANGEKE 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|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 4/115 (3%)

Query: 95  KKKEKEKIKKKKD-KKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKM 153
           KK E  K K   +  K K   + K+K +E     E+ K K E    K++ E + +   + 
Sbjct: 147 KKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEK 206

Query: 154 KEDKEKPVEKIRKEEKDSEKEKKSKDKDK---KLKKEKLKKKKKEKERSSHEKEV 205
            + + +   K  K+ + + +EK + +K K   K K +K     K  ER +    +
Sbjct: 207 AKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAKADKAAAAAKAAERKAAAAAL 261

Length = 387

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

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 24/103 (23%), Positives = 45/103 (43%)

Query: 95  KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMK 154
           K+ EKE++  ++ KK  ++   +   K+K+ ++   K     K K E + K+     K  
Sbjct: 104 KQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKA 163

Query: 155 EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
             + K   +    +K + + KK  + +   K     KKK E E
Sbjct: 164 AAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAE 206

Length = 387

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

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 45/244 (18%), Positives = 82/244 (33%), Gaps = 32/244 (13%)

Query: 89  KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKE-KEKGKKEEKEKKEEKEKKE 147
            D K     +  +      KK  D      ++ E  + KE +E   K    +KE+ +  +
Sbjct: 31  IDAKVCDIIKNLRQMISILKKIIDLDSQTYEEVEDGLLKEIRELLLKAIYIQKEKSDLAD 90

Query: 148 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS-------S 200
             E  ++  ++   ++I K   +    +     D   + E+       +  S       S
Sbjct: 91  RAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSAARRSSGEHRSAAS 150

Query: 201 HEKEVIPKLTFKFG------TDMEEKTKRESSPKIVIKPV----------KSPSPPPVAA 244
            +     KL  +           E  +KRE S  +    V           +        
Sbjct: 151 SQGSRHTKLKKRKNIHNLKRRSPELSSKREVSFTLESPSVPDTATRVKEGNNGGSTKSRG 210

Query: 245 ADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDA---WYHWVCVGLVAEPETSDWFCP 301
               D  + ++++    C  Q      M+ CD  +    W+H  CVGL   P+   W+CP
Sbjct: 211 VSSEDNSEGEELY----CFCQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGK-WYCP 265

Query: 302 KCSK 305
           +C K
Sbjct: 266 ECKK 269

Length = 271

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

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 25/108 (23%), Positives = 47/108 (43%), Gaps = 12/108 (11%)

Query: 82  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKE----KDKEKKIDKEKEKGKKEEK 137
             +K     K T  +   +KIKK  +K        KE    K+ +  ++K  EK  K+ +
Sbjct: 82  PTNKITYLLKTT--EPLNKKIKKWFEKSYLLLESKKEILKLKNIKDVLEKNIEKILKDIQ 139

Query: 138 EKKEEK------EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKD 179
           + 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|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 30/153 (19%), Positives = 52/153 (33%), Gaps = 2/153 (1%)

Query: 81   IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKK 140
              K K+ K  K   K K+KEK KKK       K       K    D++++   K + +K 
Sbjct: 1161 KTKGKASKLRKP--KLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKS 1218

Query: 141  EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 200
                  +E + + K   +K   K  K +K++  +    + +        + K K   +  
Sbjct: 1219 NSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKRV 1278

Query: 201  HEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKP 233
               +  P    K          + SSP      
Sbjct: 1279 SAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVK 1311

Length = 1388

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

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 17/72 (23%), Positives = 34/72 (47%)

Query: 134 KEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 193
            E ++ K  K+K   + +     ++K +EK +   K    E+  K   ++ K+EK K KK
Sbjct: 16  LESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKK 75

Query: 194 KEKERSSHEKEV 205
           K+     +  ++
Sbjct: 76  KKVPLQVNPAQL 87

Length = 217

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 25/94 (26%), Positives = 50/94 (53%)

Query: 98  EKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDK 157
            +    KKK K+  ++I+  +K+ E+K   + +K K ++K+ K++ +K ++K+ K ++  
Sbjct: 55  AEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKD 114

Query: 158 EKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKK 191
           EK  E   ++   S  E  S   + K +K  L K
Sbjct: 115 EKEAEDKLEDLTKSYSETLSTLSELKPRKYALHK 148

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

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

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 34/142 (23%), Positives = 56/142 (39%), Gaps = 10/142 (7%)

Query: 74  SSEDLGEIKKDKSIK-KDKKTHKKKEKEKIKKK-----KDKKDKDKIKNKEKDKEKKIDK 127
           SSE+  ++K    IK     ++K + +  IK        +KK  +K+  K K K  K D 
Sbjct: 10  SSENTIDLKNPLFIKNLKHSSYKIRLESDIKDSLLNLDINKKLHEKLDKKNK-KFNKTDD 68

Query: 128 EKEKGKKEEKEKKEEK---EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKL 184
            K+  K + K+KK+ K      ++ +                      K K   +K KK 
Sbjct: 69  LKDSKKTKLKQKKKIKKKLHIDDDYDNFFDSKNNSKQFAGPLAISLMRKPKPKTEKLKKK 128

Query: 185 KKEKLKKKKKEKERSSHEKEVI 206
                   KK+K+  S + E+I
Sbjct: 129 ITVNKSTNKKKKKVLSSKDELI 150

Length = 742

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

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 29/115 (25%), Positives = 57/115 (49%), Gaps = 2/115 (1%)

Query: 83  KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEE 142
           + KS K+ ++  KKKE+++ ++ + K+  ++ + K+ +KE+   +E++K + EE  K+  
Sbjct: 70  QQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKK-QAEEAAKQAA 128

Query: 143 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
            ++K+ +E   K        K   E K +    K    + K K E    KK   E
Sbjct: 129 LKQKQAEEAAAKA-AAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAE 182

Length = 387

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

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 27/103 (26%), Positives = 52/103 (50%)

Query: 130 EKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 189
           E   +++   +EE E+K++KE K KE + K ++  +KE K   + +++ D     KK + 
Sbjct: 5   ESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEK 64

Query: 190 KKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIK 232
           K +K++ E  + E  + P   F     +  +  ++ SP  V K
Sbjct: 65  KSRKRDVEDENPEDFIDPDTPFGQKKRLSSQMAKQYSPSAVEK 107

Length = 1066

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

 Score = 40.2 bits (95), Expect = 0.002
 Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 1/100 (1%)

Query: 69  IVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKE 128
           I+KV +  +   +KK K + K  K ++K     +K   +  D  +   K + ++++ D++
Sbjct: 127 IIKVNNEIERDHLKK-KHLPKLIKQYEKFGFGILKIDFEIDDSKEELEKFEAQKEEEDEK 185

Query: 129 KEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEE 168
             K   E  +K E ++KK+ K F  KE   +  +KI KEE
Sbjct: 186 LAKEALEAMKKLEAEKKKQSKNFDPKEGPVQIGKKIDKEE 225

Length = 1437

>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter subunit G; Reviewed

 Score = 38.5 bits (89), Expect = 0.002
 Identities = 21/87 (24%), Positives = 53/87 (60%), Gaps = 4/87 (4%)

Query: 98  EKEKIKKKKD----KKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKM 153
           +K+ IKKKK     ++  +K + + ++ E++++ E+ + K +E+E +EE+E++ E++   
Sbjct: 111 KKDDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQTIE 170

Query: 154 KEDKEKPVEKIRKEEKDSEKEKKSKDK 180
           ++  +   E I ++E ++E +    +K
Sbjct: 171 EQSDDSEHEIIEQDESETESDDDKTEK 197

Length = 197

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

 Score = 39.2 bits (92), Expect = 0.003
 Identities = 23/146 (15%), Positives = 49/146 (33%), Gaps = 1/146 (0%)

Query: 24  KDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKK 83
           KD     +   PK+K  +  K +  +    K    EL  +            +D     K
Sbjct: 64  KDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSK-KAEKKNALDKDDDLNYVK 122

Query: 84  DKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEK 143
           D  +          + +      D  D D  ++ ++D +     ++++ KKE KE ++  
Sbjct: 123 DIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLS 182

Query: 144 EKKEEKEFKMKEDKEKPVEKIRKEEK 169
           +  +    +   +  +   K  K   
Sbjct: 183 DDDDFVWDEDDSEALRQARKDAKLTA 208

Length = 509

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

 Score = 39.6 bits (92), Expect = 0.003
 Identities = 26/123 (21%), Positives = 57/123 (46%), Gaps = 2/123 (1%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
             KK++  K  ++T    E   I  ++ K  + K+K + K   +    +++   +EE   
Sbjct: 170 RKKKERLKKLIEETENLAELI-IDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLL 228

Query: 140 KEEKEKKEEKEFKMKEDKEKP-VEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 198
             +  K  E+   + ++  +   E+I   +++ EKE++   +  K  KE+ K+KK ++E 
Sbjct: 229 YLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEE 288

Query: 199 SSH 201
              
Sbjct: 289 LKL 291

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|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 22/109 (20%), Positives = 51/109 (46%), Gaps = 4/109 (3%)

Query: 42  KEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEK 101
           + K    ++E   ++  EL +       +K     +L EI+     +++ +   + + E 
Sbjct: 818 RLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQ---EAEEEIQNINENKNEF 874

Query: 102 IKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKE 150
           ++ K D K  +K+    KD   K+    ++ K++EK  K++K+  E+ +
Sbjct: 875 VEFKNDPKKLNKLII-AKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTD 922

Length = 925

>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase component YidC; Validated

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 24/146 (16%), Positives = 50/146 (34%), Gaps = 21/146 (14%)

Query: 90  DKKTHKKKEKEKIKKKKD--------KKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKE 141
            +K  +KK      ++          +  +   +N E  K +  +K + K +K     KE
Sbjct: 295 REKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARK-----KE 349

Query: 142 EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 201
             +K+   E ++  ++E   E+     +   +    K K K L  +    +    E    
Sbjct: 350 IAQKRRAAEREI--NREARQERAAAMARARARRAAVKAKKKGL-IDASPNEDTPSENEES 406

Query: 202 EKEVIPKLTFKFGTDMEEKTKRESSP 227
           +    P++          +  RE S 
Sbjct: 407 KGSP-PQVE----ATTTAEPNREPSQ 427

Length = 429

>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]

 Score = 40.0 bits (94), Expect = 0.003
 Identities = 20/120 (16%), Positives = 43/120 (35%), Gaps = 10/120 (8%)

Query: 81  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKK---IDKEKEKGKKEEK 137
           + K K   K      ++     +    K    +++ K +        I+ E     +E++
Sbjct: 116 LNKLKLKVKGNNILIEQVLNNPEFDHFKNKSPELQKKLQSFGFPQLLIEFEVNDISEEQE 175

Query: 138 EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
            +K E+   E       E ++   E +  E+K   +  K +        +K +K K  +E
Sbjct: 176 FEKFEEAINE-------EVEKAAQEALEAEKKLKAESPKVEKPKPLFDGQKGRKIKSTEE 228

Length = 1444

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 28/163 (17%), Positives = 79/163 (48%), Gaps = 10/163 (6%)

Query: 74  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGK 133
             ++L E+ + +  + +++  ++KE+ +++++ ++ +K+  + +E+  E    +E  K +
Sbjct: 471 HEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEE 530

Query: 134 KEEKEKKEEKEKKEEKEFKMK----------EDKEKPVEKIRKEEKDSEKEKKSKDKDKK 183
            EEK +K E   +E +E K K             E  ++++++  ++    +  K++ ++
Sbjct: 531 LEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEE 590

Query: 184 LKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 226
           L++   + KKK KE      ++   L     ++ E + +    
Sbjct: 591 LRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEE 633

Length = 908

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

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 34/110 (30%), Positives = 51/110 (46%), Gaps = 18/110 (16%)

Query: 90  DKKTHK-----KKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE 144
           DKKT K     +KE E++KK+ D K   ++  +   ++K+I K           K E   
Sbjct: 107 DKKTKKLINELRKELEEVKKELDNKRNGELAIQPI-QDKRIIK-----------KDENSS 154

Query: 145 KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 194
             E ++FK  E++E  +E    E   S   KK K   +KLKK + K  K 
Sbjct: 155 VSEHEDFKQLENEENFLETEYNEITSSNNYKKLKIN-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|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 35/114 (30%), Positives = 57/114 (50%), Gaps = 12/114 (10%)

Query: 87  IKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE-- 144
            K D K   ++EKE+ +  K++K   K+K +E+ K+K++       +K EK K    E  
Sbjct: 545 WKLDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKEL-------EKLEKAKIPPAEFF 597

Query: 145 KKEEKEFKMKEDKEKPVEKIRKEE-KDSEKEKKSK--DKDKKLKKEKLKKKKKE 195
           K++E ++   ++   P      EE    E++K SK  DK  KL +E L K  K 
Sbjct: 598 KRQEDKYSAFDETGLPTHDADGEEISKKERKKLSKEYDKQAKLHEEYLAKGGKS 651

Length = 651

>gnl|CDD|227891 COG5604, COG5604, Uncharacterized conserved protein [Function unknown]

 Score = 39.1 bits (91), Expect = 0.003
 Identities = 25/111 (22%), Positives = 41/111 (36%), Gaps = 11/111 (9%)

Query: 82  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNK----EKDKEKKIDKEKEKGKKEEK 137
           K  K+ KK  K H K   ++ K+    K     KN+    E   E   +   +  +K  K
Sbjct: 3   KASKATKKFTKNHLKNTIDRRKQLARSKKVYGTKNRNSHTENKMESGTNDNNKNKEKLSK 62

Query: 138 EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 188
              +      E+E    E        I K   +S+K   ++   +K +KE 
Sbjct: 63  LYSDVDSSSSEEEEDGSES-------ISKLNVNSKKISLNQVSTQKWRKEL 106

Length = 523

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

 Score = 39.2 bits (91), Expect = 0.004
 Identities = 30/133 (22%), Positives = 68/133 (51%), Gaps = 3/133 (2%)

Query: 71  KVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKE 130
           +    E+L +  K+  IK++ +  ++++ EK+++K ++ +++ +  K+ + E+     K 
Sbjct: 334 EKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

Query: 131 KGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK 190
           K ++ E + +EEKE K   E   +E+      K  K+E+    E+  +  + K  K   +
Sbjct: 394 KEEELELKNEEEKEAKLLLELSEQEEDLL---KEEKKEELKIVEELEESLETKQGKLTEE 450

Query: 191 KKKKEKERSSHEK 203
           K++ EK+     K
Sbjct: 451 KEELEKQALKLLK 463

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|221952 pfam13166, AAA_13, AAA domain

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 34/134 (25%), Positives = 58/134 (43%), Gaps = 14/134 (10%)

Query: 78  LGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEK 137
           LGE   +    + +    KKE +K+++K ++ +  +I+ KE++ EK  +K  +K  K + 
Sbjct: 86  LGEENIEI---EAQIEELKKELKKLEEKIEQLEA-EIEKKEEELEKAKNKFLDKAWK-KL 140

Query: 138 EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
            KK +    E  +    +   K  EK+ KE K       S    ++L       K K K 
Sbjct: 141 AKKYDSNLSEALKGLNYKKNFK--EKLLKELKSVILNASSLLSLEEL-------KAKIKT 191

Query: 198 RSSHEKEVIPKLTF 211
             S  K  +  LT 
Sbjct: 192 LFSSNKPELALLTL 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|221952 pfam13166, AAA_13, AAA domain

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 26/122 (21%), Positives = 51/122 (41%), Gaps = 5/122 (4%)

Query: 119 KDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSK 178
            + E +I+ E +K  K+ +EK E+ E + EK+ +  E  +        ++   + +    
Sbjct: 91  IEIEAQIE-ELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLS 149

Query: 179 DKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKR-ESSPKIVIKPVKSP 237
           +  K L  +K  K+K  KE  S        L+ +   +++ K K   SS K  +  +   
Sbjct: 150 EALKGLNYKKNFKEKLLKELKSVILNASSLLSLE---ELKAKIKTLFSSNKPELALLTLS 206

Query: 238 SP 239
             
Sbjct: 207 VI 208

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|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 99  KEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKE 158
           +E + +    K+  K+   EK  E + +K +    KEE +K + +  + E+     E K 
Sbjct: 5   REALAELA--KELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKP 62

Query: 159 KPVEKIRKEEKDSEKEKKSKDKDKK 183
               +    E++ E+ K    + + 
Sbjct: 63  AASGEGGGGEEEEEEAKAEAAEFRA 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|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 36/120 (30%), Positives = 62/120 (51%), Gaps = 15/120 (12%)

Query: 98  EKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDK 157
           E+ K    + K++ + +  K    EK+++++ E     EK  KE+++ K+E E +M+E K
Sbjct: 500 EQAKTFYGEFKEEINVLIEKLSALEKELEQKNEH---LEKLLKEQEKLKKELEQEMEELK 556

Query: 158 EKPVEKIRKEEKDSEKEKKSKDKDKKLKKE------KLKKKKKEKERSSHEKEVIPKLTF 211
           E      R+  K  E EK++++  K LKKE      +LK+KK  K +     E + KL  
Sbjct: 557 E------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|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 39.0 bits (91), Expect = 0.004
 Identities = 32/127 (25%), Positives = 64/127 (50%), Gaps = 15/127 (11%)

Query: 84  DKSIKKDKKTHKKKEKEKI---------KKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKK 134
              I +  KT   + KE+I          +K+ ++  + ++   K++EK + KE E+  +
Sbjct: 495 PHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEK-LKKELEQEME 553

Query: 135 EEKEKKEEKEKKEEKEF-----KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 189
           E KE++  K+ + EKE       +K++ E  + ++++++    KE KS +   KLK+ K 
Sbjct: 554 ELKERERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQ 613

Query: 190 KKKKKEK 196
           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|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 29/118 (24%), Positives = 61/118 (51%), Gaps = 1/118 (0%)

Query: 82  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKE 141
            + + I+K     +++     ++ K+ ++K++   + K K K+++K  E+ ++  +  +E
Sbjct: 307 DELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEE 366

Query: 142 EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS-KDKDKKLKKEKLKKKKKEKER 198
            K KKEE E   K       EK+ KE ++ EK K+  +++  K+     + KK+ KE 
Sbjct: 367 AKAKKEELERLKKRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKEL 424

Length = 880

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

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 16/52 (30%), Positives = 24/52 (46%)

Query: 147 EEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 198
           +E   K K   EK   K  K+      EKK K+K+K   K++ +  K   +R
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKR 425

Length = 434

>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and secretion]

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 3/100 (3%)

Query: 98  EKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDK 157
           E  K + ++  K KD      KD  +K  +E++  KK E+      E+K ++     E+ 
Sbjct: 60  ELRKFQTREAAKVKDAEAQLLKDPAEKKREERKAAKKIERSTPSLIERKTQEVKDSGEEI 119

Query: 158 EKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 197
               E +R E+    + ++   +   L K++++   +   
Sbjct: 120 ---AEMMRDEKVPIRELEEIPPEFVALYKQEIQSPTRLNL 156

Length = 407

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	410
PF10203	68	Pet191_N: Cytochrome c oxidase assembly protein PE	99.93
KOG4114|consensus	73		99.92
KOG1973|consensus	274		99.1
COG5034	271	TNG2 Chromatin remodeling protein, contains PhD zi	98.88
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	98.87
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	98.76
KOG0825|consensus	1134		98.24
KOG1244|consensus	336		98.15
KOG4299|consensus	613		97.92
KOG1512|consensus	381		97.68
KOG4323|consensus	464		97.65
KOG1844|consensus	508		97.43
KOG0955|consensus	1051		97.32
KOG0954|consensus	893		97.14
PF13831	36	PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.	97.12
KOG1245|consensus	1404		96.84
KOG0383|consensus	696		96.78
COG5141	669	PHD zinc finger-containing protein [General functi	96.58
KOG1632|consensus	345		96.53
KOG0957|consensus	707		96.52
KOG0956|consensus	900		96.33
PTZ00266	1021	NIMA-related protein kinase; Provisional	96.05
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	95.62
KOG4364|consensus	811		95.46
KOG0957|consensus	707		95.36
KOG1632|consensus	345		94.94
KOG4443|consensus	694		94.87
PF07227	446	DUF1423: Protein of unknown function (DUF1423); In	94.39
KOG4364|consensus	811		93.25
KOG1144|consensus	1064		92.03
PF15446	175	zf-PHD-like: PHD/FYVE-zinc-finger like domain	89.9
KOG1144|consensus	1064		88.75
KOG0163|consensus	1259		88.23
PF07649	30	C1_3: C1-like domain; InterPro: IPR011424 This sho	87.95
KOG4443|consensus	694		86.42
KOG2891|consensus	445		85.65
PF07496	50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	83.28
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	81.77
KOG1473|consensus	1414		81.02

>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=99.93  E-value=7.8e-27  Score=185.14  Aligned_cols=64  Identities=47%  Similarity=1.061  Sum_probs=62.1

Q ss_pred             chhhhhHHHHHHHHHhcCcccccCCCChhhhhcCC--Ccc-cHHHHHhHHHHhhcCCcCCcccccCC
Q psy5827         344 KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREG--LAP-QCEALKNTFFECKRSLLDNRTRFRGH  407 (410)
Q Consensus       344 ~ssCa~~r~aL~~Cl~~S~Cv~~~~~t~~eCL~~~--~lp-eC~~l~~~~~eCKRg~lD~r~RfrGn  407 (410)
                      ++||++++.+|+.||++||||+++++||++||+++  ++| +|++|+++||+|||||||||+|||||
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            57999999999999999999999999999999976  899 99999999999999999999999998

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=99.92  E-value=1.4e-26  Score=182.01  Aligned_cols=67  Identities=52%  Similarity=1.045  Sum_probs=64.3

Q ss_pred             chhhhhHHHHHHHHHhcCcccccCCCChhhhhcCCC---cc-cHHHHHhHHHHhhcCCcCCcccccCCCCC
Q psy5827         344 KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGL---AP-QCEALKNTFFECKRSLLDNRTRFRGHKGY  410 (410)
Q Consensus       344 ~ssCa~~r~aL~~Cl~~S~Cv~~~~~t~~eCL~~~~---lp-eC~~l~~~~~eCKRg~lD~r~RfrGn~g~  410 (410)
                      +.||++++.+|+.||++|+||++++++|++||.+++   || +|++|+.+|++|||||||||+||||++||
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            469999999999999999999999999999999764   89 99999999999999999999999999997

>KOG1973|consensus

Probab=99.10  E-value=3.8e-11  Score=118.06  Aligned_cols=55  Identities=38%  Similarity=1.116  Sum_probs=46.4

Q ss_pred             CCCCCCCcccccccCcCCCCCCCeeeccC--CC-CcccceecccCCCCCCCcEEcCCCcCcc
Q psy5827         249 DTGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKVD  307 (410)
Q Consensus       249 eded~~~~~~C~VCg~~ddgd~~mI~CD~--C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~~~  307 (410)
                      ...++++..|| +|+...+|.  ||.||+  |+ .|||+.|||+...+. |.|||+.|....
T Consensus       212 ~~~d~~e~~yC-~Cnqvsyg~--Mi~CDn~~C~~eWFH~~CVGL~~~Pk-gkWyC~~C~~~~  269 (274)
T KOG1973|consen  212 EAVDPDEPTYC-ICNQVSYGK--MIGCDNPGCPIEWFHFTCVGLKTKPK-GKWYCPRCKAEN  269 (274)
T ss_pred             cccCCCCCEEE-Eeccccccc--ccccCCCCCCcceEEEeccccccCCC-Ccccchhhhhhh
Confidence            34456678899 999887887  999999  99 999999999986655 789999998653

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

Probab=98.88  E-value=1.2e-09  Score=105.92  Aligned_cols=49  Identities=39%  Similarity=1.123  Sum_probs=43.1

Q ss_pred             CCCcccccccCcCCCCCCCeeeccC--CC-CcccceecccCCCCCCCcEEcCCCcC
Q psy5827         253 SKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  305 (410)
Q Consensus       253 ~~~~~~C~VCg~~ddgd~~mI~CD~--C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~  305 (410)
                      .++..|| .|+++..|.  ||.||+  |. .|||+.|||+...|. |.|||+.|..
T Consensus       218 e~e~lYC-fCqqvSyGq--MVaCDn~nCkrEWFH~~CVGLk~pPK-G~WYC~eCk~  269 (271)
T COG5034         218 EGEELYC-FCQQVSYGQ--MVACDNANCKREWFHLECVGLKEPPK-GKWYCPECKK  269 (271)
T ss_pred             cCceeEE-Eeccccccc--ceecCCCCCchhheeccccccCCCCC-CcEeCHHhHh
Confidence            4467899 999999998  999998  88 999999999976655 8999999974

>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=98.87  E-value=2.5e-10  Score=84.34  Aligned_cols=46  Identities=48%  Similarity=1.284  Sum_probs=38.9

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC---CCCCcEEcCCCc
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE---PETSDWFCPKCS  304 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~---~~~~~W~Cp~C~  304 (410)
                      +|.+|+..++++ .||+||.|+.|||..|++++..   .....|+|+.|.
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 8999999999999999999876   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 ....

>smart00249 PHD PHD zinc finger

Probab=98.76  E-value=7.2e-09  Score=73.22  Aligned_cols=45  Identities=47%  Similarity=1.305  Sum_probs=38.3

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCC
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKC  303 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C  303 (410)
                      +|.+|+..++++ .||.|+.|+.|||..|+++...  .....|+|+.|
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            478999987555 7999999999999999998766  45579999987

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=98.24  E-value=3.9e-07  Score=99.36  Aligned_cols=52  Identities=27%  Similarity=0.756  Sum_probs=45.5

Q ss_pred             CCcccccccCcCCCCCCCeeeccCCCCc-ccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         254 KQVWICPACGVQDDGSLPMIGCDGCDAW-YHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       254 ~~~~~C~VCg~~ddgd~~mI~CD~C~~W-~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      .+.+.|.+|+.+|..+ .||+||+|+.. ||.+||.++.. .+.+.|||..|.-.
T Consensus       213 ~E~~~C~IC~~~DpEd-VLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL  266 (1134)
T KOG0825|consen  213 QEEVKCDICTVHDPED-VLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLL  266 (1134)
T ss_pred             cccccceeeccCChHH-hheeecccccceeeccccCcccccccccceecCcchhh
Confidence            3567899999998888 89999999977 99999999886 56689999999864

>KOG1244|consensus

Probab=98.15  E-value=7.8e-07  Score=87.48  Aligned_cols=48  Identities=29%  Similarity=0.803  Sum_probs=44.0

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcC
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  305 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~  305 (410)
                      .+|.+||-.++++ .+++||.|++.||++|+.++.. ++.+.|.|-.|..
T Consensus       282 k~csicgtsendd-qllfcddcdrgyhmyclsppm~eppegswsc~KOG~  330 (336)
T KOG1244|consen  282 KYCSICGTSENDD-QLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLE  330 (336)
T ss_pred             ceeccccCcCCCc-eeEeecccCCceeeEecCCCcCCCCCCchhHHHHHH
Confidence            4799999998888 8999999999999999999988 8889999999974

>KOG4299|consensus

Probab=97.92  E-value=4e-06  Score=89.91  Aligned_cols=48  Identities=33%  Similarity=0.780  Sum_probs=40.2

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC---CCCCcEEcCCCcC
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE---PETSDWFCPKCSK  305 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~---~~~~~W~Cp~C~~  305 (410)
                      .+|..|+....-. .+|+||+|+..||++|+.++..   .+.+.|||+.|.-
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            4899999964432 4799999999999999999855   6678999999964

>KOG1512|consensus

Probab=97.68  E-value=1.6e-05  Score=78.84  Aligned_cols=47  Identities=34%  Similarity=0.750  Sum_probs=39.4

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCCCCCCcEEcC-CCcCc
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCP-KCSKV  306 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp-~C~~~  306 (410)
                      .|.+|+.|...+ .|++||.|++.||..|||+...+. |.|+|. .|...
T Consensus       316 lC~IC~~P~~E~-E~~FCD~CDRG~HT~CVGL~~lP~-G~WICD~~C~~~  363 (381)
T KOG1512|consen  316 LCRICLGPVIES-EHLFCDVCDRGPHTLCVGLQDLPR-GEWICDMRCREA  363 (381)
T ss_pred             hhhccCCcccch-heeccccccCCCCccccccccccC-ccchhhhHHHHh
Confidence            588899998777 799999999999999999976654 899997 36544

>KOG4323|consensus

Probab=97.65  E-value=1.8e-05  Score=83.11  Aligned_cols=49  Identities=33%  Similarity=0.922  Sum_probs=38.9

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCC-----CCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~~~  306 (410)
                      ..|| -||.+..++ .||+|++|..|||..|.-+...     ...+.|||..|...
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            3455 566776666 8999999999999999987554     34579999999865

>KOG1844|consensus

Probab=97.43  E-value=0.00025  Score=74.67  Aligned_cols=56  Identities=29%  Similarity=0.796  Sum_probs=47.1

Q ss_pred             CCcccccccCcCCC-CCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCcccCch
Q psy5827         254 KQVWICPACGVQDD-GSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSR  311 (410)
Q Consensus       254 ~~~~~C~VCg~~dd-gd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~~~~k~  311 (410)
                      .+...| +|+..++ ++ +||+|+.|..|+|..|+|+.....+..|.|..|.+......
T Consensus        84 ~~~~~c-~c~~~~~~~g-~~i~c~~c~~Wqh~~C~g~~~~~~p~~y~c~~c~~~~~~~~  140 (508)
T KOG1844|consen   84 REISRC-DCGLEDDMEG-LMIQCDWCGRWQHKICCGSFKSTKPDKYVCEICTPRNKEVE  140 (508)
T ss_pred             Cccccc-ccccccCCCc-eeeCCcccCcccCceeeeecCCCCchhceeeeeccccccch
Confidence            456789 9999888 66 99999999999999999998774467999999998765443

>KOG0955|consensus

Probab=97.32  E-value=0.00016  Score=82.56  Aligned_cols=53  Identities=28%  Similarity=0.650  Sum_probs=42.1

Q ss_pred             CcccccccCcCCCC-CCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCccc
Q psy5827         255 QVWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDE  308 (410)
Q Consensus       255 ~~~~C~VCg~~ddg-d~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~~~  308 (410)
                      ++..|.||...+.. ...+|+||+|+..+|..|+|++..+. +.|+|..|.....
T Consensus       218 ~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipe-g~WlCr~Cl~s~~  271 (1051)
T KOG0955|consen  218 EDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPE-GQWLCRRCLQSPQ  271 (1051)
T ss_pred             CCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCC-CcEeehhhccCcC
Confidence            45579999886533 13899999999999999999766544 8999999986544

>KOG0954|consensus

Probab=97.14  E-value=0.00017  Score=79.04  Aligned_cols=50  Identities=32%  Similarity=0.806  Sum_probs=41.5

Q ss_pred             CcccccccCcCCCCC-CCeeeccCCCCcccceecccCCCCCCCcEEcCCCcC
Q psy5827         255 QVWICPACGVQDDGS-LPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  305 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd-~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~  305 (410)
                      +...|.||..+|... ..||+||.|+.-.|..|+||...+. +.|.|..|.-
T Consensus       270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~-gpWlCr~Cal  320 (893)
T KOG0954|consen  270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE-GPWLCRTCAL  320 (893)
T ss_pred             ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC-CCeeehhccc
Confidence            446799999986332 3799999999999999999987755 8999999864

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

Probab=97.12  E-value=6.5e-05  Score=52.98  Aligned_cols=34  Identities=35%  Similarity=1.055  Sum_probs=19.8

Q ss_pred             CeeeccCCCCcccceecccCCCCCCCcEEcCCCc
Q psy5827         271 PMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS  304 (410)
Q Consensus       271 ~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~  304 (410)
                      .||.|++|..++|..|.|+...+....|+|..|.
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            5899999999999999999888665679998773

>KOG1245|consensus

Probab=96.84  E-value=0.00019  Score=84.31  Aligned_cols=52  Identities=27%  Similarity=0.722  Sum_probs=44.6

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCccc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  308 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~~  308 (410)
                      ...|.+|..-.+.. .|+.||.|..|||+.|+.+... .+.++|+|+.|+....
T Consensus      1108 ~~~c~~cr~k~~~~-~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKKQDE-KMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKEHR 1160 (1404)
T ss_pred             hhhhhhhhhcccch-hhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchhhh
Confidence            35799998876665 7999999999999999998777 6668999999998765

>KOG0383|consensus

Probab=96.78  E-value=0.00063  Score=75.04  Aligned_cols=50  Identities=26%  Similarity=0.689  Sum_probs=39.6

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCccc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  308 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~~  308 (410)
                      ....|.+|+.  +|.  .|+||.|..|||.+|++++.. .+.+.|.|+.|.....
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            4457989987  555  899999999999999999887 4445599999954443

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

Probab=96.58  E-value=0.00081  Score=71.10  Aligned_cols=49  Identities=33%  Similarity=0.754  Sum_probs=40.3

Q ss_pred             ccccccCcCCCCC-CCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         257 WICPACGVQDDGS-LPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       257 ~~C~VCg~~ddgd-~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      ..|.+|...+.+. +.+|.||+|+...|..|.||.-.+. |.|+|..|.-.
T Consensus       194 ~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe-G~WlCrkCi~~  243 (669)
T COG5141         194 DICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE-GFWLCRKCIYG  243 (669)
T ss_pred             hhhHhccccccCCcceEEEecCcchhhhhhcccceecCc-chhhhhhhccc
Confidence            4799998876532 3799999999999999999987655 89999999743

>KOG1632|consensus

Probab=96.53  E-value=0.0018  Score=66.24  Aligned_cols=51  Identities=31%  Similarity=0.732  Sum_probs=43.9

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCccccee--cccCCC--CCCCcEEcCCCcCccc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVC--VGLVAE--PETSDWFCPKCSKVDE  308 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~C--lgi~~~--~~~~~W~Cp~C~~~~~  308 (410)
                      .+| .|..+++.+.+|+.||.|..|||..|  +|++..  +....|+|..|.....
T Consensus        61 ~~~-~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~  115 (345)
T KOG1632|consen   61 RYC-KCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQD  115 (345)
T ss_pred             chh-hcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchhhh
Confidence            378 88888877658999999999999999  999877  6678999999987754

>KOG0957|consensus

Probab=96.52  E-value=0.008  Score=63.96  Aligned_cols=49  Identities=27%  Similarity=0.691  Sum_probs=40.8

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-----CCCCcEEcCCCcCc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  306 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~~~  306 (410)
                      ..|.||.+..+.- .+++||.|..-||+.|+.+++.     ...+.|.|..|...
T Consensus       545 ysCgiCkks~dQH-ll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~  598 (707)
T KOG0957|consen  545 YSCGICKKSTDQH-LLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKN  598 (707)
T ss_pred             eeeeeeccchhhH-HHhhcchhhceeeccccCCccccCcccccCcceeecccccc
Confidence            4699999865544 7899999999999999999887     33678999999554

>KOG0956|consensus

Probab=96.33  E-value=0.0015  Score=71.38  Aligned_cols=48  Identities=35%  Similarity=0.908  Sum_probs=38.1

Q ss_pred             ccccCcCC-CCCCCeeeccC--CCCcccceecccCCCCCCCcEEcCCCcCcc
Q psy5827         259 CPACGVQD-DGSLPMIGCDG--CDAWYHWVCVGLVAEPETSDWFCPKCSKVD  307 (410)
Q Consensus       259 C~VCg~~d-dgd~~mI~CD~--C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~~  307 (410)
                      |-||..-. +.+..+|.||+  |..+.|..|+||...+. +.|||..|....
T Consensus         8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt-GpWfCrKCesqe   58 (900)
T KOG0956|consen    8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT-GPWFCRKCESQE   58 (900)
T ss_pred             eeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC-Cchhhhhhhhhh
Confidence            55996632 33458999997  99999999999987654 899999997543

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=96.05  E-value=0.14  Score=59.32  Aligned_cols=7  Identities=29%  Similarity=0.311  Sum_probs=4.3

Q ss_pred             CCCCCCC
Q psy5827           1 MLQHPLI    7 (410)
Q Consensus         1 ~~~~~~~    7 (410)
                      +|+||+|
T Consensus       292 lL~h~~i  298 (1021)
T PTZ00266        292 CLGYQII  298 (1021)
T ss_pred             HhccHHH
Confidence            3567666

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

Probab=95.62  E-value=0.0071  Score=55.30  Aligned_cols=28  Identities=25%  Similarity=0.680  Sum_probs=23.9

Q ss_pred             cccceecccCCC-CCCCcEEcCCCcCccc
Q psy5827         281 WYHWVCVGLVAE-PETSDWFCPKCSKVDE  308 (410)
Q Consensus       281 W~H~~Clgi~~~-~~~~~W~Cp~C~~~~~  308 (410)
                      .||+.|+.++.. .+.++|+||.|.....
T Consensus         1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~   29 (148)
T cd04718           1 GFHLCCLRPPLKEVPEGDWICPFCEVEKS   29 (148)
T ss_pred             CcccccCCCCCCCCCCCCcCCCCCcCCCC
Confidence            489999999998 6779999999986543

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.

>KOG4364|consensus

Probab=95.46  E-value=0.094  Score=57.68  Aligned_cols=19  Identities=11%  Similarity=-0.109  Sum_probs=10.5

Q ss_pred             HHHHHHHHHhcCcccccCC
Q psy5827         350 SRADLKLCLLETDCVQVDR  368 (410)
Q Consensus       350 ~r~aL~~Cl~~S~Cv~~~~  368 (410)
                      +++.++.|+--..|+.+..
T Consensus       610 ~~A~~ah~a~d~ak~~~~~  628 (811)
T KOG4364|consen  610 LQALTAHAAKDTAKLIICN  628 (811)
T ss_pred             HHHHHHHHhhhhHHHhhhh
Confidence            4555555666666655543

>KOG0957|consensus

Probab=95.36  E-value=0.01  Score=63.14  Aligned_cols=47  Identities=32%  Similarity=0.748  Sum_probs=34.3

Q ss_pred             cccccCc--CCCCCCCeeeccCCCCcccceecccCCC------C---CCCcEEcCCCcC
Q psy5827         258 ICPACGV--QDDGSLPMIGCDGCDAWYHWVCVGLVAE------P---ETSDWFCPKCSK  305 (410)
Q Consensus       258 ~C~VCg~--~ddgd~~mI~CD~C~~W~H~~Clgi~~~------~---~~~~W~Cp~C~~  305 (410)
                      .|.||..  .++.+ .+|+||.|+.-.|-.|+|+...      .   ....|||.-|.-
T Consensus       121 iCcVClg~rs~da~-ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~  178 (707)
T KOG0957|consen  121 ICCVCLGQRSVDAG-EILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLY  178 (707)
T ss_pred             EEEEeecCcccccc-ceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhc
Confidence            4669944  23333 5999999999999999998632      1   236899988864

>KOG1632|consensus

Probab=94.94  E-value=0.0032  Score=64.50  Aligned_cols=57  Identities=28%  Similarity=0.675  Sum_probs=44.2

Q ss_pred             CCCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCc----EEcCCCcCccc
Q psy5827         252 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSD----WFCPKCSKVDE  308 (410)
Q Consensus       252 d~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~----W~Cp~C~~~~~  308 (410)
                      ++....+|..||..+....+||+|+.|..|||..|+.+...  .-+..    |+|++|.....
T Consensus       235 ~~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~~~  297 (345)
T KOG1632|consen  235 PDYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVLKF  297 (345)
T ss_pred             cccccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeeccc
Confidence            33345679999987765469999999999999999998776  22234    99999987543

>KOG4443|consensus

Probab=94.87  E-value=0.012  Score=64.27  Aligned_cols=49  Identities=31%  Similarity=0.840  Sum_probs=39.1

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      ..|..|+...+.. .++.|+.|+..||.+|..+... ...+.|+|+.|...
T Consensus        69 rvCe~c~~~gD~~-kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c  118 (694)
T KOG4443|consen   69 RVCEACGTTGDPK-KFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRC  118 (694)
T ss_pred             eeeeeccccCCcc-cccccccccccccccccCCccccccCcccccHHHHhh
Confidence            3566778655555 5779999999999999999877 66689999988654

>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=94.39  E-value=0.032  Score=58.88  Aligned_cols=50  Identities=32%  Similarity=0.787  Sum_probs=35.9

Q ss_pred             ccccccCcCCCC--CCCeeeccCCCCcccceec--------ccCCC----CCCCcEEcCCCcCc
Q psy5827         257 WICPACGVQDDG--SLPMIGCDGCDAWYHWVCV--------GLVAE----PETSDWFCPKCSKV  306 (410)
Q Consensus       257 ~~C~VCg~~ddg--d~~mI~CD~C~~W~H~~Cl--------gi~~~----~~~~~W~Cp~C~~~  306 (410)
                      +-|.+|++.|+.  .-.||.||.|+-|-|..|.        |++..    ..+..|+|..|...
T Consensus       129 C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~  192 (446)
T PF07227_consen  129 CMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT  192 (446)
T ss_pred             CCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence            457778875432  2379999999999999995        33222    23569999999865

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.

>KOG4364|consensus

Probab=93.25  E-value=0.85  Score=50.53  Aligned_cols=14  Identities=29%  Similarity=0.441  Sum_probs=9.8

Q ss_pred             hhhhhHHHHHHHHH
Q psy5827         345 SACAGSRADLKLCL  358 (410)
Q Consensus       345 ssCa~~r~aL~~Cl  358 (410)
                      ..|++.+.-+..|.
T Consensus       615 ah~a~d~ak~~~~~  628 (811)
T KOG4364|consen  615 AHAAKDTAKLIICN  628 (811)
T ss_pred             HHHhhhhHHHhhhh
Confidence            46777777777776

>KOG1144|consensus

Probab=92.03  E-value=0.58  Score=52.74  Aligned_cols=6  Identities=17%  Similarity=0.063  Sum_probs=3.3

Q ss_pred             hhhhhc
Q psy5827         371 PRQCLR  376 (410)
Q Consensus       371 ~~eCL~  376 (410)
                      +-+||+
T Consensus       491 lld~ir  496 (1064)
T KOG1144|consen  491 LLDKIR  496 (1064)
T ss_pred             HHHHhh
Confidence            455665

>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain

Probab=89.90  E-value=0.21  Score=46.76  Aligned_cols=48  Identities=27%  Similarity=0.807  Sum_probs=35.2

Q ss_pred             cccccCcCC---CCCCCeeeccCCCCcccceecccCCC---------CCCCcEEcCCCcCc
Q psy5827         258 ICPACGVQD---DGSLPMIGCDGCDAWYHWVCVGLVAE---------PETSDWFCPKCSKV  306 (410)
Q Consensus       258 ~C~VCg~~d---dgd~~mI~CD~C~~W~H~~Clgi~~~---------~~~~~W~Cp~C~~~  306 (410)
                      .|.+|+...   .-+ .||.|-+|...||-.|+|+...         ...+...|..|...
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            378886532   223 7999999999999999998664         34456668888744

>KOG1144|consensus

Probab=88.75  E-value=1.5  Score=49.51  Aligned_cols=14  Identities=64%  Similarity=0.729  Sum_probs=5.9

Q ss_pred             hhhhhHHHHHHHHh
Q psy5827          91 KKTHKKKEKEKIKK  104 (410)
Q Consensus        91 ~~~~~~~~~~~~~~  104 (410)
                      +|...|+++++.+.
T Consensus       157 kKkkeKkek~~~~~  170 (1064)
T KOG1144|consen  157 KKKKEKKEKEKKKE  170 (1064)
T ss_pred             hhhhhhhhhhhhhh
Confidence            33334444444444

>KOG0163|consensus

Probab=88.23  E-value=2.8  Score=47.45  Aligned_cols=13  Identities=23%  Similarity=0.406  Sum_probs=5.5

Q ss_pred             HHhhhHHHHHHHH
Q psy5827         129 KEKGKKEEKEKKE  141 (410)
Q Consensus       129 ~e~~e~~~k~k~~  141 (410)
                      .|.+|.+++++++
T Consensus       930 qE~~E~ER~rrEa  942 (1259)
T KOG0163|consen  930 QELAEAERKRREA  942 (1259)
T ss_pred             HHHHHHHHHhhhh
Confidence            3334444444444

>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines

Probab=87.95  E-value=0.2  Score=33.51  Aligned_cols=29  Identities=38%  Similarity=0.703  Sum_probs=13.1

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceec
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCV  287 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Cl  287 (410)
                      .|.+|+.+.+++ .+-.|..|+.+.|..|+
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            588999987774 67889999999999884

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.

>KOG4443|consensus

Probab=86.42  E-value=0.14  Score=56.25  Aligned_cols=48  Identities=31%  Similarity=0.776  Sum_probs=38.5

Q ss_pred             ccccccCcCCCCC--CCeeeccCCCCcccceecccCCC-----CCCCcEEcCCCc
Q psy5827         257 WICPACGVQDDGS--LPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCS  304 (410)
Q Consensus       257 ~~C~VCg~~ddgd--~~mI~CD~C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~  304 (410)
                      .+|++|...+...  ..|++|+.|.+|.|..|-|+...     ..+-.|-|..|+
T Consensus       146 ~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR  200 (694)
T KOG4443|consen  146 SYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR  200 (694)
T ss_pred             ccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence            6899998876443  35699999999999999998765     233489999998

>KOG2891|consensus

Probab=85.65  E-value=7.4  Score=39.60  Aligned_cols=16  Identities=38%  Similarity=0.538  Sum_probs=8.6

Q ss_pred             hhhhHHHHHHHHHHHH
Q psy5827         178 KDKDKKLKKEKLKKKK  193 (410)
Q Consensus       178 k~~e~k~kkek~kkKK  193 (410)
                      .+++.+++.+.++-+.
T Consensus       396 qkeeeklk~e~qkike  411 (445)
T KOG2891|consen  396 QKEEEKLKAEEQKIKE  411 (445)
T ss_pred             hhHHHHHHHHHHHHHH
Confidence            3455566666555444

>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=83.28  E-value=0.48  Score=35.51  Aligned_cols=32  Identities=22%  Similarity=0.593  Sum_probs=17.2

Q ss_pred             CeeeccCCCCcccceecccCC--CCCCCcEEcCCC
Q psy5827         271 PMIGCDGCDAWYHWVCVGLVA--EPETSDWFCPKC  303 (410)
Q Consensus       271 ~mI~CD~C~~W~H~~Clgi~~--~~~~~~W~Cp~C  303 (410)
                      .||+||.|..|-.+. .++..  ...++.|+|..-
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            599999999998876 44433  222348999763

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.

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=81.77  E-value=0.79  Score=35.44  Aligned_cols=31  Identities=35%  Similarity=0.807  Sum_probs=25.9

Q ss_pred             ccccccCcCCC-CCCCeeeccCCCCcccceecc
Q psy5827         257 WICPACGVQDD-GSLPMIGCDGCDAWYHWVCVG  288 (410)
Q Consensus       257 ~~C~VCg~~dd-gd~~mI~CD~C~~W~H~~Clg  288 (410)
                      ..|.+|+.+.. ++ ..|.|..|..-||-.|..
T Consensus         6 ~~C~~Cg~~~~~~d-DiVvCp~CgapyHR~C~~   37 (54)
T PF14446_consen    6 CKCPVCGKKFKDGD-DIVVCPECGAPYHRDCWE   37 (54)
T ss_pred             ccChhhCCcccCCC-CEEECCCCCCcccHHHHh
Confidence            47999999873 33 599999999999999983

>KOG1473|consensus

Probab=81.02  E-value=0.89  Score=52.97  Aligned_cols=45  Identities=24%  Similarity=0.482  Sum_probs=37.2

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcC
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  305 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~  305 (410)
                      ..|.+|..  .++  .+||+.|++.||+.|+.++.. .+...|-|..|..
T Consensus       345 dhcrf~~d--~~~--~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~  390 (1414)
T KOG1473|consen  345 DHCRFCHD--LGD--LLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNI  390 (1414)
T ss_pred             ccccccCc--ccc--eeecccCCceEEeeecCCccccCCCccchhhhhhh
Confidence            46888876  454  899999999999999998877 5557899999873

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	410
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: 253 SKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 305
             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 = 41.6 bits (96), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 4/37 (10%)
Query: 272 MIGCDGCDA---WYHWVCVGLVAEPETSDWFCPKCSK 305
           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	410
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	1e-17
1we9_A	64	PHD finger family protein; structural genomics, PH	2e-16
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	9e-14
1wee_A	72	PHD finger family protein; structural genomics, PH	7e-13
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	1e-12
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	2e-12
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	2e-12
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	1e-11
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	5e-11
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	9e-11
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	1e-09
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	3e-08
1wem_A	76	Death associated transcription factor 1; structura	9e-11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-10
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-09
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	8e-08
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-05
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	1e-10
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	2e-10
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	4e-10
3kv5_D	488	JMJC domain-containing histone demethylation prote	6e-09
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	6e-09
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	7e-09
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-05
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,	7e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-04
1weu_A	91	Inhibitor of growth family, member 4; structural g	3e-08
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	4e-08
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	4e-08
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	9e-08
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	3e-07
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	3e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	4e-07
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	7e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	2e-04
1b6a_A	478	Methionine aminopeptidase; angiogenesis inhibitor;	4e-07
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	5e-07
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	6e-07
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	6e-07
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	6e-07
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	7e-07
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	8e-07
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	1e-06
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	1e-06
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	1e-06
1wew_A	78	DNA-binding family protein; structural genomics, P	1e-06
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	1e-06
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	2e-06
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	4e-06
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	7e-05
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	5e-06
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	5e-06
2yt5_A	66	Metal-response element-binding transcription facto	5e-06
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	5e-06
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	1e-05
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	1e-05
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	5e-05
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	7e-04
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	1e-05
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	1e-05
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	2e-05
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	3e-05
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	4e-05
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	4e-05
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	1e-04
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	2e-04
3lu0_C	1342	DNA-directed RNA polymerase subunit beta; E. coli	3e-04
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	3e-04
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	4e-04
2zuo_A	861	MVP, major vault protein; repeat domains, protein-	6e-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 = 76.0 bits (187), Expect = 1e-17
 Identities = 35/62 (56%), Positives = 40/62 (64%), Gaps = 2/62 (3%)

Query: 252 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCSKVDEGS 310
              Q+WICP C   DDGS PMIGCD CD WYHW CVG+  A PE   WFCPKC+   +  
Sbjct: 14  WGNQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKKD 72

Query: 311 RK 312
           +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 = 72.2 bits (177), Expect = 2e-16
 Identities = 19/62 (30%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 251 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDE 308
           G S     C ACG         I CD C+ W+H  CV +          + CP CS    
Sbjct: 1   GSSGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKSG 60

Query: 309 GS 310
            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 = 64.6 bits (157), Expect = 9e-14
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 258 ICPA--CGVQDDGSLPMIGCDG-CDAWYHWVCVGLVAEP-ETSDWFCPKCS 304
           +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 = 62.6 bits (152), Expect = 7e-13
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 4/65 (6%)

Query: 244 AADEYDTGDSKQVWI--CPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFC 300
           ++           W   C  CG +DD    M+ CDGC  W+H  C+G+  A+   S + C
Sbjct: 2   SSGSSGMERGVDNWKVDCK-CGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLC 60

Query: 301 PKCSK 305
            +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 = 61.8 bits (150), Expect = 1e-12
 Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 2/62 (3%)

Query: 244 AADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC 303
            +   +    + +  C  C     G  PMI C+ C  W H  C  +        + C KC
Sbjct: 7   HSSGRENLYFQGLVTCF-CMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKC 64

Query: 304 SK 305
             
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 = 61.5 bits (149), Expect = 2e-12
 Identities = 24/62 (38%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 262 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKKKRGR 319
           C +  D +  MI CD C  W+H  CVG+  E  P+   + CP C K   G    KKKR  
Sbjct: 15  CRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEK-THGKSTLKKKRTW 73

Query: 320 KK 321
            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 = 60.5 bits (147), Expect = 2e-12
 Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 1/42 (2%)

Query: 262 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC 303
           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 = 60.3 bits (145), Expect = 1e-11
 Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 8/70 (11%)

Query: 256 VWICPACGVQDDGSLPMIGCDG-CDAWYHWVCVGL-------VAEPETSDWFCPKCSKVD 307
           V+ C AC  + +     I C+  C  W+H  C G+       +    ++ W C  C K  
Sbjct: 3   VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK 62

Query: 308 EGSRKEKKKR 317
           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 = 57.3 bits (138), Expect = 5e-11
 Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 262 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKKKRGR 319
           C    + +  MI C  C  W+H  CVG+  E   +   + CP C  V  G    K     
Sbjct: 17  CRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV-FGPSIMKNWHSG 75

Query: 320 KKK 322
              
Sbjct: 76  PSS 78

>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 = 62.8 bits (153), Expect = 9e-11
 Identities = 14/126 (11%), Positives = 38/126 (30%), Gaps = 7/126 (5%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDK----EKEKGKKE 135
             ++K   I K  +     +   +   +       ++ K K+ E    +    E +     
Sbjct: 887  LLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDL 946

Query: 136  EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
                 +  E       ++ E K+       ++    +   ++       + E+L+K +  
Sbjct: 947  LSILAQLTELNYNGVPELTERKD---TFFAQQWTGVKSSAETYKNTLLAELERLQKIEDL 1003

Query: 196  KERSSH 201
                 H
Sbjct: 1004 HHHHHH 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 = 59.3 bits (144), Expect = 1e-09
 Identities = 10/120 (8%), Positives = 33/120 (27%), Gaps = 3/120 (2%)

Query: 76   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKE 135
              L +++   + K       +        +   K+ +    + +  E + + +      +
Sbjct: 893  RILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQ 952

Query: 136  EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
              E       +  +       ++       K   ++ K     + ++  K E L      
Sbjct: 953  LTELNYNGVPELTERKDTFFAQQW---TGVKSSAETYKNTLLAELERLQKIEDLHHHHHH 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 = 55.1 bits (133), Expect = 3e-08
 Identities = 14/130 (10%), Positives = 41/130 (31%), Gaps = 7/130 (5%)

Query: 81  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKG------KK 134
           IK++  +     T  + +      +K +++  +    E  ++KKI    +K        +
Sbjct: 840 IKREPFVAPAGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLLQKYNRILKKLE 899

Query: 135 EEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 194
                K       E         +  ++ +   + + +  +   + D      +L +   
Sbjct: 900 NWATTKSVYLGSNETG-DSITAVQAKLKNLEAFDGECQSLEGQSNSDLLSILAQLTELNY 958

Query: 195 EKERSSHEKE 204
                  E++
Sbjct: 959 NGVPELTERK 968

>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 = 56.5 bits (136), Expect = 9e-11
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 7/69 (10%)

Query: 243 AAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL------VAEPETS 296
           ++    +        +   C    +    MI CD C+ W+H  CVG+      + E    
Sbjct: 2   SSGSSGECEVYDPNALYCICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGE 60

Query: 297 DWFCPKCSK 305
           D+ CP C+ 
Sbjct: 61  DYICPNCTI 69

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 62.8 bits (153), Expect = 1e-10
 Identities = 30/152 (19%), Positives = 63/152 (41%), Gaps = 5/152 (3%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
                     K     +   +  + K++ KK K + ++ E+ K+  I  E +  + + K  
Sbjct: 879  ARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKID 938

Query: 140  KEEKEKKEEKEF--KMKEDKEKPVEKIRKEEKD---SEKEKKSKDKDKKLKKEKLKKKKK 194
            ++ KE K   E    ++       EK+R + +    SE+E K+        +E++ K +K
Sbjct: 939  EQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRK 998

Query: 195  EKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 226
            E  ++  EK+ I +   K+  + E+       
Sbjct: 999  ELHQTQTEKKTIEEWADKYKHETEQLVSELKE 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 = 2e-09
 Identities = 25/137 (18%), Positives = 60/137 (43%), Gaps = 9/137 (6%)

Query: 76   EDLGEIKKDKSIKKDK-KTHKKKEKEKIKKKKDK-----KDKDKIKNKEKDKEKKIDKEK 129
            ++  +  K    K +  +     E EK++   ++     ++     N+    +++I K +
Sbjct: 938  DEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLR 997

Query: 130  EKGKKEEKEKK--EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 187
            ++  + + EKK  EE   K + E +    + K    + K EK+ E  ++  D+ K++ + 
Sbjct: 998  KELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKE-ELNRRIHDQAKEITET 1056

Query: 188  KLKKKKKEKERSSHEKE 204
              KK  +E ++   +  
Sbjct: 1057 MEKKLVEETKQLELDLN 1073

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 57.0 bits (138), Expect = 6e-09
 Identities = 24/138 (17%), Positives = 60/138 (43%), Gaps = 9/138 (6%)

Query: 74   SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGK 133
            S E   ++      K  +   K  E+ K  K   +K  + ++     + +K+  + E+ +
Sbjct: 915  SVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEK-MNNLEITYSTETEKLRSDVERLR 973

Query: 134  KEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS-----KDKDKKLKKE- 187
              E+E K    +    + ++ + +++ + + + E+K  E+         +    +LK++ 
Sbjct: 974  MSEEEAKNATNRVLSLQEEIAKLRKE-LHQTQTEKKTIEEWADKYKHETEQLVSELKEQN 1032

Query: 188  -KLKKKKKEKERSSHEKE 204
              LK +K+E  R  H++ 
Sbjct: 1033 TLLKTEKEELNRRIHDQA 1050

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 55.5 bits (134), Expect = 2e-08
 Identities = 20/136 (14%), Positives = 48/136 (35%), Gaps = 5/136 (3%)

Query: 74   SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGK 133
                L         K D++  + K   +     +     + +    D E+    E+E   
Sbjct: 922  LHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKN 981

Query: 134  KEEKEKKEEKEKKE-----EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 188
               +    ++E  +      +    K+  E+  +K + E +    E K ++   K +KE+
Sbjct: 982  ATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEE 1041

Query: 189  LKKKKKEKERSSHEKE 204
            L ++  ++ +   E  
Sbjct: 1042 LNRRIHDQAKEITETM 1057

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 54.0 bits (130), Expect = 7e-08
 Identities = 23/126 (18%), Positives = 57/126 (45%), Gaps = 5/126 (3%)

Query: 85   KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE 144
            +S+++ KK H   E + ++ ++   +++K      +K   ++      + E+     E+ 
Sbjct: 914  RSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYST-ETEKLRSDVERL 972

Query: 145  KKEEKEFKMKEDKEKPV-EKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 203
            +  E+E K   ++   + E+I K  K+  + +    + K +++   K K + ++  S  K
Sbjct: 973  RMSEEEAKNATNRVLSLQEEIAKLRKELHQTQT---EKKTIEEWADKYKHETEQLVSELK 1029

Query: 204  EVIPKL 209
            E    L
Sbjct: 1030 EQNTLL 1035

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 53.6 bits (129), Expect = 8e-08
 Identities = 19/125 (15%), Positives = 45/125 (36%), Gaps = 1/125 (0%)

Query: 80  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
           + +      K     K       +    +  K  +  +   +     +E +K K E +  
Sbjct: 857 KYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSV 916

Query: 140 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
           +  K+     E K+ + + K +++  KE K   ++  + +     + EKL+   +    S
Sbjct: 917 ERYKKLHIGLENKIMQLQRK-IDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMS 975

Query: 200 SHEKE 204
             E +
Sbjct: 976 EEEAK 980

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 51.3 bits (123), Expect = 4e-07
 Identities = 17/112 (15%), Positives = 53/112 (47%), Gaps = 1/112 (0%)

Query: 76   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKE 135
            E L   +++     ++    ++E  K++K+  +    + K  E+  +K   + ++   + 
Sbjct: 970  ERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQT-EKKTIEEWADKYKHETEQLVSEL 1028

Query: 136  EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 187
            +++    K +KEE   ++ +  ++  E + K+  +  K+ +    D++L+ +
Sbjct: 1029 KEQNTLLKTEKEELNRRIHDQAKEITETMEKKLVEETKQLELDLNDERLRYQ 1080

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 45.1 bits (107), Expect = 4e-05
 Identities = 19/117 (16%), Positives = 51/117 (43%), Gaps = 8/117 (6%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDK-KDKDKIKNKEKDKEKKIDKEKEKGKKE--- 135
            +++ D    +  +   K    ++   +++     K  ++ + ++K I++  +K K E   
Sbjct: 964  KLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQ 1023

Query: 136  --EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK 190
               + K++    K EKE   +   ++   K   E  + +  +++K  +  L  E+L+
Sbjct: 1024 LVSELKEQNTLLKTEKEELNRRIHDQ--AKEITETMEKKLVEETKQLELDLNDERLR 1078

>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 = 55.9 bits (134), Expect = 1e-10
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 8/60 (13%)

Query: 252 DSKQVWICPACGVQDDGSLPMIGCDG-CDAWYHWVCVGL-------VAEPETSDWFCPKC 303
            S  V+ C  C  + +     I C+  C  W+H +C G+       +    ++ W C  C
Sbjct: 4   SSDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 63

>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 = 55.6 bits (134), Expect = 2e-10
 Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 7/63 (11%)

Query: 262 CGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRG 318
           C     G   M+GCD  D    W+H+ CVGL   P+   W+CP+C+      R  + K G
Sbjct: 11  CNQVSYG--EMVGCDNQDCPIEWFHYGCVGLTEAPK-GKWYCPQCTA-AMKRRGSRHKSG 66

Query: 319 RKK 321
              
Sbjct: 67  PSS 69

>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 = 60.5 bits (145), Expect = 4e-10
 Identities = 27/121 (22%), Positives = 38/121 (31%), Gaps = 3/121 (2%)

Query: 216 DMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGC 275
            ME+KT +ES                 A  +E      K +                IGC
Sbjct: 3   HMEQKTPKESDRCGGCGKFTHEDDLI-ALEEEKKKEKEKPLMSKKKSHHHKKNDFQWIGC 61

Query: 276 DGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYR 333
           D C  WYH++C GL          +FCPKC      S + K     + + +         
Sbjct: 62  DSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSIRYKVVAPHRYRWYSPNEKHLGI 121

Query: 334 F 334
            
Sbjct: 122 E 122

>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 = 57.0 bits (136), Expect = 6e-09
 Identities = 24/166 (14%), Positives = 50/166 (30%), Gaps = 4/166 (2%)

Query: 221 TKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDA 280
               +          + +    A            V+ C  C    D +  MI CD C  
Sbjct: 3   GAAAAVAAGAAAGAAAAAVSVAAPGRASAPPPPPPVY-C-VCRQPYDVNRFMIECDICKD 60

Query: 281 WYHWVCVGL--VAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDP 338
           W+H  CVG+      +   + CP C+ +   S  +K++   +    +    S        
Sbjct: 61  WFHGSCVGVEEHHAVDIDLYHCPNCAVLHGSSLMKKRRNWHRHDYTEIDDGSKPVQAGTR 120

Query: 339 SELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCE 384
           + + +  +     AD  +  +    +              + P+ +
Sbjct: 121 TFIKELRSRVFPSADEIIIKMHGSQLTQRYLEKHGFDVPIMVPKLD 166

>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 = 51.0 bits (122), Expect = 6e-09
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 257 WICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWFCPKCSK 305
             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 = 51.4 bits (123), Expect = 7e-09
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%)

Query: 258 ICPACG-VQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC 303
           +C  C   +   S  ++ CD C+   H  C G+   PE   W C  C
Sbjct: 18  VCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEG-QWLCRHC 63

>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 = 55.2 bits (133), Expect = 3e-08
 Identities = 26/142 (18%), Positives = 64/142 (45%)

Query: 85   KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE 144
            + +++++   +K + EK+      K  +      +D+  K+ KE++  ++   +      
Sbjct: 962  EQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLA 1021

Query: 145  KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 204
            ++EEK   + + K K    I + E   +KE+KS+ + +K+K++   +     E+ +  + 
Sbjct: 1022 EEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQA 1081

Query: 205  VIPKLTFKFGTDMEEKTKRESS 226
             I +L  +     EE     + 
Sbjct: 1082 QIAELKAQLAKKEEELQAALAR 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 = 54.8 bits (132), Expect = 3e-08
 Identities = 22/125 (17%), Positives = 59/125 (47%), Gaps = 4/125 (3%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            + + ++ + + +   +++E+   + + +KK   K++ +  D E+++++E+   +K + EK
Sbjct: 922  KQELEEILHEMEARIEEEEERSQQLQAEKK---KMQQQMLDLEEQLEEEEAARQKLQLEK 978

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
                 K ++ E  +   +++   K+ KE K  E+       +   ++EK K   K K + 
Sbjct: 979  VTADGKIKKMEDDILIMEDQ-NNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKH 1037

Query: 200  SHEKE 204
                 
Sbjct: 1038 ESMIS 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 = 54.1 bits (130), Expect = 5e-08
 Identities = 19/147 (12%), Positives = 75/147 (51%), Gaps = 1/147 (0%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E K  +  ++     +K + E     + ++ + ++  K+++ E+ + + + + ++EE+  
Sbjct: 884  EQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERS 943

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
            ++ + +K++ + +M + +E+ +E+     +  + EK + D   K  ++ +   + +  + 
Sbjct: 944  QQLQAEKKKMQQQMLDLEEQ-LEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKL 1002

Query: 200  SHEKEVIPKLTFKFGTDMEEKTKRESS 226
            + E++++ +      T++ E+ ++  +
Sbjct: 1003 TKERKLLEERVSDLTTNLAEEEEKAKN 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 = 50.2 bits (120), Expect = 9e-07
 Identities = 24/123 (19%), Positives = 57/123 (46%), Gaps = 4/123 (3%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            +++++++ ++  +  K     KIKK +D     + +N +  KE+K+ +E+         +
Sbjct: 963  QLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAE 1022

Query: 140  KEEKEKKEEKEF----KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 195
            +EEK K   K       M  + E  ++K  K  ++ EK K+  + +     E++ + + +
Sbjct: 1023 EEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQ 1082

Query: 196  KER 198
               
Sbjct: 1083 IAE 1085

>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 = 50.2 bits (120), Expect = 9e-07
 Identities = 31/147 (21%), Positives = 69/147 (46%), Gaps = 12/147 (8%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            E+  +    + +   KK+E E+I  + + + ++     E+++ +++  EK+K +++  + 
Sbjct: 906  ELYAEAEEMRVRLAAKKQELEEILHEMEARIEE-----EEERSQQLQAEKKKMQQQMLDL 960

Query: 140  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 199
            +E+ E++E    K++ +K     KI+K E D    +   +K  K +K   ++        
Sbjct: 961  EEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNL 1020

Query: 200  SHEKEVIPKLTFKFGTDMEEKTKRESS 226
            + E+E    LT       + K K ES 
Sbjct: 1021 AEEEEKAKNLT-------KLKNKHESM 1040

>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 = 49.8 bits (119), Expect = 1e-06
 Identities = 27/120 (22%), Positives = 50/120 (41%), Gaps = 4/120 (3%)

Query: 85   KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKE 144
              I   +  + K  KE+   ++   D      +E++K K + K K K     +    E E
Sbjct: 990  DDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNK----HESMISELE 1045

Query: 145  KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 204
             + +KE K +++ EK   K+  E  D  ++           K +L KK++E + +    E
Sbjct: 1046 VRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLE 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 = 48.3 bits (115), Expect = 3e-06
 Identities = 24/134 (17%), Positives = 62/134 (46%), Gaps = 3/134 (2%)

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            + ++ K+  + K+  +K  +   +K   ++          + E+   +   K ++ E+  
Sbjct: 870  KERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEIL 929

Query: 140  KEEKEKKEEKE---FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 196
             E + + EE+E    +++ +K+K  +++   E+  E+E+ ++ K +  K     K KK +
Sbjct: 930  HEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKME 989

Query: 197  ERSSHEKEVIPKLT 210
            +     ++   KLT
Sbjct: 990  DDILIMEDQNNKLT 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 = 48.3 bits (115), Expect = 3e-06
 Identities = 25/128 (19%), Positives = 64/128 (50%), Gaps = 4/128 (3%)

Query: 81   IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKK 140
            I++++   +  +  KKK ++++   +++ ++++   ++   EK     K K  +++    
Sbjct: 936  IEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIM 995

Query: 141  EEKEKKEEKEFK-MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE---KLKKKKKEK 196
            E++  K  KE K ++E        + +EE+ ++   K K+K + +  E   +LKK++K +
Sbjct: 996  EDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSR 1055

Query: 197  ERSSHEKE 204
            +     K 
Sbjct: 1056 QELEKIKR 1063

>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 = 47.9 bits (114), Expect = 4e-06
 Identities = 27/133 (20%), Positives = 60/133 (45%), Gaps = 1/133 (0%)

Query: 73   TSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKG 132
               ++L EI  +   + +++  + ++ +  KKK  ++  D  +  E+++  +   + EK 
Sbjct: 920  AKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKV 979

Query: 133  KKEEKEKKEEKEKKEEKEFKMKEDKE-KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKK 191
              + K KK E +    ++   K  KE K +E+   +   +  E++ K K+    K K + 
Sbjct: 980  TADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHES 1039

Query: 192  KKKEKERSSHEKE 204
               E E    ++E
Sbjct: 1040 MISELEVRLKKEE 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 = 46.4 bits (110), Expect = 1e-05
 Identities = 20/120 (16%), Positives = 64/120 (53%), Gaps = 6/120 (5%)

Query: 91  KKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKE 150
           ++T ++++K + + K+ ++   ++  ++   ++K+  E E   + E+ +     KK+E E
Sbjct: 867 QRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELE 926

Query: 151 FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKD-----KKLKKEKLKKKKKEKERSSHEKEV 205
             + E + + +E+  +  +  + EKK   +      ++L++E+  ++K + E+ + + ++
Sbjct: 927 EILHEMEAR-IEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKI 985

>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 = 2e-05
 Identities = 28/142 (19%), Positives = 63/142 (44%), Gaps = 25/142 (17%)

Query: 88   KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKE------ 141
            +   +   + E+E+ + ++ + +K K++ +  D E+++++E+   +K + EK        
Sbjct: 927  EILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIK 986

Query: 142  ----------------EKEKK--EEKEFKMKEDKEKPVEKIRKEEKDSEK-EKKSKDKDK 182
                             KE+K  EE+   +  +  +  EK +   K   K E    + + 
Sbjct: 987  KMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEV 1046

Query: 183  KLKKEKLKKKKKEKERSSHEKE 204
            +LKKE+  +++ EK +   E E
Sbjct: 1047 RLKKEEKSRQELEKIKRKLEGE 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 = 45.2 bits (107), Expect = 3e-05
 Identities = 22/138 (15%), Positives = 67/138 (48%)

Query: 67  PNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKID 126
           P +        L ++ + +   + K    ++ KE+ +K + +  + + K+ +  +EK + 
Sbjct: 838 PWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLL 897

Query: 127 KEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK 186
           +EK + + E   + EE   +   + +  E+    +E   +EE++  ++ +++ K  + + 
Sbjct: 898 QEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQM 957

Query: 187 EKLKKKKKEKERSSHEKE 204
             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 = 44.1 bits (104), Expect = 7e-05
 Identities = 37/204 (18%), Positives = 89/204 (43%), Gaps = 22/204 (10%)

Query: 22   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTS-----SE 76
            KM+ ++   ++   +E+ + ++    K     K+K +E  +  M     K+T       E
Sbjct: 952  KMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEE 1011

Query: 77   DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEE 136
             + ++  + + +++K  +  K K K +    +  + ++K +EK +++ ++K K K + E 
Sbjct: 1012 RVSDLTTNLAEEEEKAKNLTKLKNKHESMISEL-EVRLKKEEKSRQE-LEKIKRKLEGES 1069

Query: 137  KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKK------------- 183
             +  E+  + + +  ++K    K  E+++      E E   K+   K             
Sbjct: 1070 SDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHISDLQ 1129

Query: 184  --LKKEKLKKKKKEKERSSHEKEV 205
              L+ EK  + K EK++    +E+
Sbjct: 1130 EDLESEKAARNKAEKQKRDLSEEL 1153

>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 = 41.0 bits (96), Expect = 6e-04
 Identities = 21/120 (17%), Positives = 59/120 (49%), Gaps = 3/120 (2%)

Query: 86  SIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEK 145
            + K  +  ++ + +  + ++ K+ + K + + K+ E+K  +  E+    +++ + E E 
Sbjct: 848 PLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETEL 907

Query: 146 KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 205
             E E        K   K   EE   E E + ++++++ ++ + +KKK +++    E+++
Sbjct: 908 YAEAEEMRVRLAAK---KQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQL 964

>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 = 49.7 bits (118), Expect = 3e-08
 Identities = 28/88 (31%), Positives = 37/88 (42%), Gaps = 9/88 (10%)

Query: 221 TKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG--- 277
           +    SP+  +  V   S  P    D     D  +   C  C     G   MIGCD    
Sbjct: 3   SGSSGSPEYGMPSVTFGSVHPSDVLDM--PVDPNEPTYCL-CHQVSYGE--MIGCDNPDC 57

Query: 278 CDAWYHWVCVGLVAEPETSDWFCPKCSK 305
              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 = 48.7 bits (116), Expect = 4e-08
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 9/57 (15%)

Query: 252 DSKQVWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWFCPKCSK 305
           +     +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 = 48.8 bits (116), Expect = 4e-08
 Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 7/66 (10%)

Query: 243 AAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWF 299
           + +      D  +   C  C     G   MIGCD       W+H+ CVGL  +P    WF
Sbjct: 3   SGSSGDMPVDPNEPTYCL-CHQVSYGE--MIGCDNPDCSIEWFHFACVGLTTKPR-GKWF 58

Query: 300 CPKCSK 305
           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 = 48.5 bits (115), Expect = 9e-08
 Identities = 16/73 (21%), Positives = 24/73 (32%), Gaps = 4/73 (5%)

Query: 232 KPVKSPSPPPVAAADEYDTGDSKQVWICPACG-VQDDGSLPMIGCDGCDAWYHWVCVGLV 290
               +      ++       D   V  C  C   +   S  ++ CD C+   H  C G+ 
Sbjct: 3   TKQTARKSTGGSSGSSQSLIDEDAV--CSICMDGESQNSNVILFCDMCNLAVHQECYGVP 60

Query: 291 AEPETSDWFCPKC 303
             PE   W C  C
Sbjct: 61  YIPEG-QWLCRHC 72

>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 = 46.3 bits (110), Expect = 3e-07
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 259 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 305
           C  CG + D     + CD CD  +H  C+   L + P   +W+CP+C  
Sbjct: 21  CHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN 68

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus} Length = 62

 Score = 46.0 bits (109), Expect = 3e-07
 Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 8/67 (11%)

Query: 245 ADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCP 301
             E+    ++  + C  C     G   MIGCD       W+H+ CV L  +P+   W+CP
Sbjct: 1   GSEFAIDPNEPTY-CL-CNQVSYGE--MIGCDNEQCPIEWFHFSCVSLTYKPK-GKWYCP 55

Query: 302 KCSKVDE 308
           KC   +E
Sbjct: 56  KCRGDNE 62

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 49.0 bits (116), Expect = 4e-07
 Identities = 15/74 (20%), Positives = 34/74 (45%), Gaps = 11/74 (14%)

Query: 95  KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKK----------EEKEKKEEKE 144
             +E E I+K ++++ K +++  +   +    + +EK KK          E+ EK +   
Sbjct: 80  LTQEPESIRKWREEQRK-RLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINN 138

Query: 145 KKEEKEFKMKEDKE 158
           +  +K F  + D +
Sbjct: 139 RIADKAFYQQPDAD 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 = 45.5 bits (107), Expect = 7e-06
 Identities = 11/87 (12%), Positives = 43/87 (49%), Gaps = 9/87 (10%)

Query: 121 KEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDK 180
           +  ++ +E E  +K  +E+++  ++ +     M+++         +E+   + E+ ++ +
Sbjct: 76  QADRLTQEPESIRKWREEQRKRLQELDAASKVMEQEW--------REKAKKDLEEWNQRQ 127

Query: 181 DKKLKKEKLKKKKKEKE-RSSHEKEVI 206
            ++++K K+  +  +K      + ++I
Sbjct: 128 SEQVEKNKINNRIADKAFYQQPDADII 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 = 40.9 bits (95), Expect = 2e-04
 Identities = 9/58 (15%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 82  KKDKSI-KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKE 138
           ++ K + + D  +   +++ + K KKD ++ ++ ++++ +K K  ++  +K   ++ +
Sbjct: 93  EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPD 150

>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 = 50.7 bits (121), Expect = 4e-07
 Identities = 21/102 (20%), Positives = 39/102 (38%)

Query: 95  KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKEFKMK 154
                  +    D  D+++      ++  K  + K+K  K      E++  KE      +
Sbjct: 7   VAASGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDE 66

Query: 155 EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 196
             ++     +  +E+D + E    D D    K+K KKKKK  
Sbjct: 67  VARQLERSALEDKERDEDDEDGDGDGDGATGKKKKKKKKKRG 108

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A* Length = 90

 Score = 46.7 bits (110), Expect = 5e-07
 Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 233 PVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGL 289
           P+ S          +   G++ Q  +   C     G   M+ CD       W+H+ CVGL
Sbjct: 2   PLGSHMASEFINQGDVTEGNNNQEEVYCFCRNVSYGP--MVACDNPACPFEWFHYGCVGL 59

Query: 290 VAEPETSDWFCPKCSKVDEGSRKEKKKRGRKK 321
              P+   W+C K  K     R + K++ R+K
Sbjct: 60  KQAPK-GKWYCSKDCKEIANQRSKSKRQKRRK 90

>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 = 45.4 bits (108), Expect = 6e-07
 Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 7/59 (11%)

Query: 249 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 305
            +G S     C  C         ++ CD C   YH  C+   L   P+   W CP+C  
Sbjct: 2   SSGSSGHEDFCSVCRKSGQ----LLMCDTCSRVYHLDCLDPPLKTIPK-GMWICPRCQD 55

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens} Length = 77

 Score = 46.0 bits (109), Expect = 6e-07
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 259 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 305
           C  CG + D     + CD CD  +H  C+   L + P   +W+CP+C  
Sbjct: 29  CHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN 76

>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 = 49.0 bits (116), Expect = 6e-07
 Identities = 25/129 (19%), Positives = 46/129 (35%), Gaps = 5/129 (3%)

Query: 179 DKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPS 238
           D +   K+E    ++        +  +            + +   E SP +     +   
Sbjct: 99  DAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSG 158

Query: 239 PPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETS 296
           P      D+ +     +V  C  CG + D     + CD CD  +H  C+   L + P   
Sbjct: 159 PSCKHCKDDVN--RLCRVCACHLCGGRQDPDK-QLMCDECDMAFHIYCLDPPLSSVPSED 215

Query: 297 DWFCPKCSK 305
           +W+CP+C  
Sbjct: 216 EWYCPECRN 224

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group} Length = 68

 Score = 45.4 bits (107), Expect = 7e-07
 Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 11/68 (16%)

Query: 249 DTGDSKQVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVGLVAEPETSD-----WFCP 301
           D+   +    C  C         MI C+   C  W H  CV +  +P  S      ++C 
Sbjct: 3   DSFQPEAKVRCI-CSSTMVND-SMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCE 60

Query: 302 KC--SKVD 307
            C  S+ D
Sbjct: 61  LCRLSRAD 68

>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 = 45.6 bits (108), Expect = 8e-07
 Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 259 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 305
           C  CG + + ++  + CD C+  YH  C+   L   PE   W+CP C  
Sbjct: 29  CRVCGGKHEPNM-QLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT 76

>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 = 44.3 bits (105), Expect = 1e-06
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 7/50 (14%)

Query: 257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCS 304
             C  C   D G L  + CD C + YH  C+   L   P   +W CP+C+
Sbjct: 10  EFCRVCK--DGGEL--LCCDTCPSSYHIHCLNPPLPEIPN-GEWLCPRCT 54

>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 = 49.2 bits (116), Expect = 1e-06
 Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKEKK 315
           +   C +  D +  MI CD C  W+H  CVG+  E   +   + CP C  +   S  +K+
Sbjct: 6   VYCLCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPSIMKKR 65

Query: 316 KRGRKKKTHQDIIMS 330
           +   K          
Sbjct: 66  RGSSKGHDTHKGKPV 80

>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 = 47.7 bits (112), Expect = 1e-06
 Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 8/56 (14%)

Query: 257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCS 304
            +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 = 45.1 bits (106), Expect = 1e-06
 Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 11/69 (15%)

Query: 243 AAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVGLVAEPETSD--- 297
            ++ E       +V  C  CG   +    MI C+   C  W H  CV L  +P   +   
Sbjct: 4   GSSGEDPFQPEIKVR-CV-CGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPL 60

Query: 298 ---WFCPKC 303
              ++C  C
Sbjct: 61  PESFYCEIC 69

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2 Length = 51

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 4/48 (8%)

Query: 259 CPACGVQDDGSLPMIGCDGCDAWYHWVCV--GLVAEPETSDWFCPKCS 304
           C  C  + +    +I CD C+  +H  C+   L   P+  +W CP C 
Sbjct: 3   CKVCRKKGEDDK-LILCDECNKAFHLFCLRPALYEVPD-GEWQCPACQ 48

>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 = 43.6 bits (103), Expect = 2e-06
 Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 7/49 (14%)

Query: 259 CPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSK 305
           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 = 48.3 bits (114), Expect = 4e-06
 Identities = 40/216 (18%), Positives = 80/216 (37%), Gaps = 43/216 (19%)

Query: 27  VSPKDKTSPKEKMSSKEKTS----PKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIK 82
           +   D+  PK +M+   K      P+  E +  K+VE      V   V  T+        
Sbjct: 772 IRGSDQAIPKFQMNCYAKEDAFSYPRMYEEASGKEVE-----KVATAVLSTT-------- 818

Query: 83  KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEE 142
                 + K   KK +KEK   +++KK + + K KE++  KK  KE ++  +E  + K  
Sbjct: 819 -----ARAKARAKKTKKEKGPNEEEKKKEHEEKEKERETNKKGIKETKENDEEFYKNKYS 873

Query: 143 K-----------EKKEEKEFKMKEDKE-KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK 190
                         ++ +     +D    PV K +     +      +D++ K     ++
Sbjct: 874 SKPYKVDNMTRILPQQSRYISFIKDDRFVPVRKFKG----NNGVVVLRDREPKEPVALIE 929

Query: 191 KKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 226
             ++ K     +        FK   +++  +  + S
Sbjct: 930 TVRQMK-----DVNAPLPTPFKVDDNVDFPSALQPS 960

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} Length = 963

 Score = 44.0 bits (103), Expect = 7e-05
 Identities = 31/171 (18%), Positives = 60/171 (35%), Gaps = 39/171 (22%)

Query: 115 KNKEKDKEKKIDKEKEK-----GKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEK 169
           +  E+   K+++K          + + + KK +KEK   +E K KE +EK         +
Sbjct: 797 RMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEK---------E 847

Query: 170 DSEKEKKSKDKDKKLKKEKLKKKKKEK--ERSSHEKEVIPK----LTF------------ 211
              +  K   K+ K   E+  K K      +  +   ++P+    ++F            
Sbjct: 848 KERETNKKGIKETKENDEEFYKNKYSSKPYKVDNMTRILPQQSRYISFIKDDRFVPVRKF 907

Query: 212 -KFGTDMEEKTKRESSPKIVIKPVKS------PSPPPVAAADEYDTGDSKQ 255
                 +  + +    P  +I+ V+       P P P    D  D   + Q
Sbjct: 908 KGNNGVVVLRDREPKEPVALIETVRQMKDVNAPLPTPFKVDDNVDFPSALQ 958

>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 = 42.8 bits (101), Expect = 5e-06
 Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 8/64 (12%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCSKVDEGSRKEKKK 316
            C  C   D G L  I CDGC   +H  C+     E  +  W C  C    + + +E + 
Sbjct: 10  ECAVCR--DGGEL--ICCDGCPRAFHLACLSPPLREIPSGTWRCSSCL---QATVQEVQP 62

Query: 317 RGRK 320
           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 = 43.8 bits (103), Expect = 5e-06
 Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSKVDEGSRKEK 314
           IC  C   D+    ++ CDGCD  YH  C+   L   P    W CPKC   +     E 
Sbjct: 18  ICQVCSRGDEDD-KLLFCDGCDDNYHIFCLLPPLPEIPRG-IWRCPKCILAECKQPPEA 74

>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 = 42.9 bits (101), Expect = 5e-06
 Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 5/66 (7%)

Query: 251 GDSKQVWICPACGVQDDGSL-PMIGCDGCDAWYHWVC----VGLVAEPETSDWFCPKCSK 305
           G S    +C  C  +   +   M+ CD C   YH +C    +          W C +C  
Sbjct: 1   GSSGSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVF 60

Query: 306 VDEGSR 311
                R
Sbjct: 61  ATTTKR 66

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens} Length = 60

 Score = 42.8 bits (101), Expect = 5e-06
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 9/59 (15%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCSKVDEGSRKEK 314
            C  C         ++ CD C   YH  C+   L   P+   W CP+C   D+  +KE+
Sbjct: 7   FCSVCRKSGQ----LLMCDTCSRVYHLDCLDPPLKTIPK-GMWICPRC--QDQMLKKEE 58

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A Length = 112

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 3/49 (6%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKCS 304
            C +C  Q   +  M+ CD CD  +H  C    L   P+   W C  C 
Sbjct: 63  TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPK-GMWICQICR 110

>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 = 46.5 bits (109), Expect = 1e-05
 Identities = 20/117 (17%), Positives = 54/117 (46%), Gaps = 3/117 (2%)

Query: 91  KKTHKKKEKEKIKKKKDKKDKDKIKNKEK---DKEKKIDKEKEKGKKEEKEKKEEKEKKE 147
           +K  + +E  +   K  +   D I   ++   +KEK+I+ E+ K +  +   K   E + 
Sbjct: 452 RKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQR 511

Query: 148 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 204
           + E  M++ +    E +++  +  E ++    K+++       +++++  +   +KE
Sbjct: 512 KNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKE 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 = 44.6 bits (104), Expect = 5e-05
 Identities = 15/113 (13%), Positives = 58/113 (51%), Gaps = 1/113 (0%)

Query: 88  KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKE 147
            +     +K+ + +  K +  +   K+ ++ + K +++ ++KE+   +E  K+  ++ + 
Sbjct: 479 DQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKER-SYQEHLKQLTEKMEN 537

Query: 148 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 200
           ++   +KE +     K++++E+  ++  + + +  K + + L+ K + ++  +
Sbjct: 538 DRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRKACT 590

>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 = 40.7 bits (94), Expect = 7e-04
 Identities = 21/125 (16%), Positives = 56/125 (44%), Gaps = 3/125 (2%)

Query: 81  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKK 140
           I+ ++ ++   K+ +      ++  +   +K+K    E+ K +      +    E + K 
Sbjct: 455 IQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKM-LHEMQRKN 513

Query: 141 EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 200
           E+  +++E+ ++    +    EK+  +     KE++     K  ++E+L K+  +KE   
Sbjct: 514 EQMMEQKERSYQEHLKQLT--EKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRI 571

Query: 201 HEKEV 205
            + E+
Sbjct: 572 MKNEI 576

>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 = 44.5 bits (105), Expect = 1e-05
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 2/75 (2%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL--VAEPETSDWFCPKCSKVDEGSRKEKK 315
           +   C   +D S   IGCD C  WYH  CVG+         ++ CP+C   ++       
Sbjct: 9   LYCICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDAMTVLTP 68

Query: 316 KRGRKKKTHQDIIMS 330
              +  +  + ++ S
Sbjct: 69  LTEKDYEGLKRVLRS 83

>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 = 43.1 bits (101), Expect = 1e-05
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 252 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG-LVAEPETSDWFCPKCSKVDEG 309
              +   C  CG  ++    ++ CD CD  YH  C+   VAEP    W C  C ++ + 
Sbjct: 54  QCIECKSCILCGTSENDD-QLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKE 111

>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 = 44.3 bits (104), Expect = 2e-05
 Identities = 12/79 (15%), Positives = 16/79 (20%), Gaps = 26/79 (32%)

Query: 238 SPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSD 297
           +   +         +   V  CP C V                        +V      D
Sbjct: 3   TRESIDKRAGRRGPNLNIVLTCPECKVYPP--------------------KIVERFSEGD 42

Query: 298 WFCPKCSKV------DEGS 310
             C  C  V      D  S
Sbjct: 43  VVCALCGLVLSDKLVDTRS 61

>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 = 44.5 bits (105), Expect = 3e-05
 Identities = 19/128 (14%), Positives = 48/128 (37%), Gaps = 3/128 (2%)

Query: 76  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE-KKIDKEKEKGKK 134
             L  I + +   +      K+ ++++++ + + +  +   K + KE   ++KEKEK  K
Sbjct: 153 AKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKEESLKARLKEMSNLEKEKEKLTK 212

Query: 135 --EEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK 192
             E  +K      +   +  ++E     ++K   E         S  +  K  + ++   
Sbjct: 213 FVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAP 272

Query: 193 KKEKERSS 200
                  +
Sbjct: 273 NGVLTIDN 280

>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 = 41.9 bits (98), Expect = 4e-05
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG-LVAEPETSDWFCPKCSK 305
           +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 = 41.5 bits (97), Expect = 4e-05
 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCP---KCSKVDEGSRKE 313
            C  C    D       C  C   YH +C+ +   P + + W CP    C    +     
Sbjct: 9   NCAVCDSPGDLL-DQFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDS 67

Query: 314 K 314
           K
Sbjct: 68  K 68

>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 = 39.7 bits (92), Expect = 1e-04
 Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 6/68 (8%)

Query: 259 CPACGVQDDGSL-PMIGCDGCDAWYHWVCVG-----LVAEPETSDWFCPKCSKVDEGSRK 312
           C  C      S   ++ C  C   YH  C                W+C +C++  +   +
Sbjct: 19  CVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRMAQ 78

Query: 313 EKKKRGRK 320
           + +K G  
Sbjct: 79  KNQKSGPS 86

>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 = 39.1 bits (91), Expect = 2e-04
 Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 5/47 (10%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 303
           IC  C    D    ++ C+ C+  +H  C    + +    +W C  C
Sbjct: 27  ICRVCQKPGD----LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLC 69

>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 = 42.0 bits (99), Expect = 3e-04
 Identities = 40/170 (23%), Positives = 74/170 (43%), Gaps = 24/170 (14%)

Query: 26   KVSPKDKT--SPKEKMSSK---EKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 80
            KV+PK +T  +P+EK+      EK S        VKD  L V   V   V          
Sbjct: 886  KVTPKGETQLTPEEKLLRAIFGEKAS-------DVKDSSLRVPNGVSGTVIDVQVFTRDG 938

Query: 81   IKKDKSIKKDKKTHKKKEKEKIKKKKDKKD-KDKIKNKEKDKEKKIDKEKEKGKKEEKEK 139
            ++KDK         +  E E+++ K+ KKD  ++++  E     +I          E EK
Sbjct: 939  VEKDK---------RALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVL-VAGGVEAEK 988

Query: 140  KEEKEKKEEKEFKMK-EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 188
             ++  +    E  +  E+K+  +E++ ++  + + E + K + K+ K  +
Sbjct: 989  LDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQ 1038

>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 = 40.2 bits (93), Expect = 3e-04
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 303
           IC  C  Q  G L  + C+ C+  +H  C    + +    +W C  C
Sbjct: 4   ICRVC--QKPGDL--VMCNQCEFCFHLDCHLPALQDVPGEEWSCSLC 46

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 41.7 bits (97), Expect = 4e-04
 Identities = 24/138 (17%), Positives = 50/138 (36%), Gaps = 2/138 (1%)

Query: 68  NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDK 127
           N + V+S +       D+  +   +   +   E     ++   K + +  E++   ++++
Sbjct: 631 NGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLER 690

Query: 128 EKEKGKKE-EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK 186
           +K   + E EK +KE  E +            K   + R E    E E        K  +
Sbjct: 691 QKILDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLK-AQ 749

Query: 187 EKLKKKKKEKERSSHEKE 204
               + + E ER    +E
Sbjct: 750 ALAIETEAELERVKKVRE 767

>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex, cytoplasm, ribonucleoprotein, structural protein; 3.50A {Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A Length = 861

 Score = 41.3 bits (96), Expect = 6e-04
 Identities = 17/117 (14%), Positives = 45/117 (38%), Gaps = 1/117 (0%)

Query: 91  KKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKEKEKGKKEEKEKKEEKEKKEEKE 150
           +K   + E EK +K+  + +   +  +     K   + + +  + E E    + K + + 
Sbjct: 691 QKILDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQA 750

Query: 151 FKMKEDKEKPVEKIRKE-EKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVI 206
             ++ + E    K  +E E    + +   +  K  +   ++ KK ++   +     I
Sbjct: 751 LAIETEAELERVKKVREMELIYARAQLELEVSKAQQLANVEAKKFKEMTEALGPGTI 807

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	410
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	99.43
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	99.4
1weu_A	91	Inhibitor of growth family, member 4; structural g	99.38
1wee_A	72	PHD finger family protein; structural genomics, PH	99.34
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	99.32
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	99.32
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	99.31
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	99.29
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	99.29
1wew_A	78	DNA-binding family protein; structural genomics, P	99.28
1we9_A	64	PHD finger family protein; structural genomics, PH	99.26
1wem_A	76	Death associated transcription factor 1; structura	99.26
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	99.25
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	99.19
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	99.18
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	99.17
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	99.16
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	99.15
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	99.11
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	99.11
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	99.06
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	99.01
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	98.99
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	98.97
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	98.97
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	98.96
3kv5_D	488	JMJC domain-containing histone demethylation prote	98.95
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	98.94
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	98.93
2yt5_A	66	Metal-response element-binding transcription facto	98.92
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	98.91
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	98.9
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	98.87
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	98.86
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	98.86
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	98.84
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	98.82
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	98.81
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	98.77
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	98.76
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	98.75
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	98.69
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	98.68
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	98.63
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	98.6
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	98.58
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	98.54
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.46
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	98.43
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	98.36
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.09
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	98.05
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	97.67
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	97.6
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	97.58
3rsn_A	177	SET1/ASH2 histone methyltransferase complex subun;	97.55
4bbq_A	117	Lysine-specific demethylase 2A; oxidoreductase, ub	97.5
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	97.36
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	96.33
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	91.22
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	89.82
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	85.63
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	82.52
2lq6_A	87	Bromodomain-containing protein 1; PHD finger, meta	81.46

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=99.43  E-value=4.6e-14  Score=117.85  Aligned_cols=61  Identities=26%  Similarity=0.679  Sum_probs=49.8

Q ss_pred             CCCCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCcccCchhh
Q psy5827         251 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKE  313 (410)
Q Consensus       251 ed~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~~~~k~k~  313 (410)
                      ..++++++| +|+.+++++ .||+||.|+.|||+.|+|++....++.|+|+.|.+......+.
T Consensus        23 ~~~~d~vrC-iC~~~~~~~-~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~~~~~~~~   83 (98)
T 2lv9_A           23 SYGTDVTRC-ICGFTHDDG-YMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPRNLDKERA   83 (98)
T ss_dssp             CCCCCBCCC-TTSCCSCSS-CEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSSCCCHHHH
T ss_pred             CCCCCCEEe-ECCCccCCC-cEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCCCCCHHHH
Confidence            344567889 999998777 8999999999999999999877445689999999776554443

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=99.40  E-value=5.3e-14  Score=111.34  Aligned_cols=55  Identities=62%  Similarity=1.550  Sum_probs=46.7

Q ss_pred             CCCCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         251 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       251 ed~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      ++++...+|.+|+.+++++ +||+||.|+.|||+.|+|++.. .+.+.|||+.|...
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            3345667899999998876 8999999999999999999887 44589999999854

>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=99.38  E-value=7.8e-13  Score=109.58  Aligned_cols=54  Identities=43%  Similarity=1.120  Sum_probs=44.5

Q ss_pred             CCCCCCCcccccccCcCCCCCCCeeeccC--CC-CcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         249 DTGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       249 eded~~~~~~C~VCg~~ddgd~~mI~CD~--C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      ...++++..|| +|+.++++  +||+||+  |+ .|||+.|||++..+. +.|||+.|...
T Consensus        29 ~~~d~~e~~yC-iC~~~~~g--~MI~CD~~dC~~~WfH~~CVgl~~~p~-g~W~Cp~C~~~   85 (91)
T 1weu_A           29 MPVDPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQE   85 (91)
T ss_dssp             CCCCSCCCBCS-TTCCBCCS--CCCCCSCSSCSCCCCCSTTTTCSSCCC-SSCCCTTTCCC
T ss_pred             CCcCCCCCcEE-ECCCCCCC--CEeEecCCCCCCCCEecccCCcCcCCC-CCEECcCccCc
Confidence            34455677899 99999875  5999999  77 799999999987654 89999999854

>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=2.2e-13  Score=107.39  Aligned_cols=57  Identities=32%  Similarity=0.798  Sum_probs=46.6

Q ss_pred             CCCCCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCcc
Q psy5827         250 TGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  307 (410)
Q Consensus       250 ded~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~  307 (410)
                      .+++++..+| +|+.+++++.+||+||.|..|||+.|+|++.. ..++.|+|+.|....
T Consensus        10 ~~~~~~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~   67 (72)
T 1wee_A           10 RGVDNWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             CSSCSSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             CCCCCcceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCC
Confidence            3455678999 99998754448999999999999999999865 445899999998543

>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=3.5e-13  Score=105.78  Aligned_cols=54  Identities=26%  Similarity=0.612  Sum_probs=45.9

Q ss_pred             CCCCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         251 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       251 ed~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      .++.+..|| +|+.+++++ +||+||.|..|||+.|+|++....++.|+|+.|...
T Consensus        14 ~~~~~~~~C-iC~~~~~~~-~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~s   67 (68)
T 3o70_A           14 LYFQGLVTC-FCMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRDS   67 (68)
T ss_dssp             CTTTTCCCS-TTCCCCTTC-CEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHTC
T ss_pred             CCCCCceEe-ECCCcCCCC-CEEECCCCCccccccccCcCcccCCCcEECCCCCCC
Confidence            334567899 999998877 899999999999999999988744579999999743

>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=99.32  E-value=1.4e-12  Score=103.22  Aligned_cols=54  Identities=43%  Similarity=1.120  Sum_probs=44.3

Q ss_pred             CCCCCCCcccccccCcCCCCCCCeeeccC--CC-CcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         249 DTGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       249 eded~~~~~~C~VCg~~ddgd~~mI~CD~--C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      .+.++++..|| +|+.++++  +||+||+  |+ .|||+.|||++..+. +.|||+.|...
T Consensus         9 ~~~d~~~~~~C-~C~~~~~g--~MI~CD~~~C~~~wfH~~Cvgl~~~p~-g~w~Cp~C~~~   65 (71)
T 1wen_A            9 MPVDPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQE   65 (71)
T ss_dssp             CCCCTTSCCCS-TTCCCSCS--SEECCSCSSCSCCCEETTTTTCSSCCS-SCCCCTTTSSC
T ss_pred             cccCCCCCCEE-ECCCCCCC--CEeEeeCCCCCCccEecccCCcCcCCC-CCEECCCCCcc
Confidence            34455567899 99998775  5999999  77 799999999977654 89999999865

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A*

Probab=99.31  E-value=1.4e-13  Score=113.76  Aligned_cols=51  Identities=33%  Similarity=0.979  Sum_probs=41.4

Q ss_pred             CCCCCcccccccCcCCCCCCCeeeccCCC---CcccceecccCCCCCCCcEEcCC-CcC
Q psy5827         251 GDSKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPK-CSK  305 (410)
Q Consensus       251 ed~~~~~~C~VCg~~ddgd~~mI~CD~C~---~W~H~~Clgi~~~~~~~~W~Cp~-C~~  305 (410)
                      .++++..|| +|+.++++.  ||+||+|+   .|||+.|||++..+. +.|||+. |..
T Consensus        21 ~~~~~~~yC-iC~~~~~g~--MI~CD~c~C~~eWfH~~CVgl~~~p~-~~W~Cp~cC~~   75 (90)
T 2jmi_A           21 NNNQEEVYC-FCRNVSYGP--MVACDNPACPFEWFHYGCVGLKQAPK-GKWYCSKDCKE   75 (90)
T ss_dssp             ---CCSCCS-TTTCCCSSS--EECCCSSSCSCSCEETTTSSCSSCTT-SCCCSSHHHHH
T ss_pred             CCCCCCcEE-EeCCCCCCC--EEEecCCCCccccCcCccCCCCcCCC-CCccCChhhcc
Confidence            344567899 999988765  99999977   899999999987654 7999999 974

>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=99.29  E-value=1.7e-13  Score=108.89  Aligned_cols=56  Identities=32%  Similarity=0.758  Sum_probs=46.2

Q ss_pred             CCCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCCC--CCCcEEcCCCcCccc
Q psy5827         252 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP--ETSDWFCPKCSKVDE  308 (410)
Q Consensus       252 d~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~--~~~~W~Cp~C~~~~~  308 (410)
                      .+++..|| +|+.+++++.+||+||.|..|||+.|+|++...  ..+.|+|+.|.....
T Consensus         6 ~~~~~~yC-iC~~~~~~~~~MI~Cd~C~~WfH~~Cvg~~~~~~~~~~~~~C~~C~~~~~   63 (75)
T 3kqi_A            6 MATVPVYC-VCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHG   63 (75)
T ss_dssp             TCCCCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCTTTGGGBSSCCCHHHHHHHC
T ss_pred             CCCCeeEE-ECCCcCCCCCCEEEcCCCCCCEecccccccccccCCCCEEECCCCcccCC
Confidence            34567899 999997755589999999999999999998773  336899999987644

>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=99.29  E-value=1.3e-12  Score=104.75  Aligned_cols=55  Identities=29%  Similarity=0.626  Sum_probs=45.4

Q ss_pred             CCcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCCcCcccC
Q psy5827         254 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEG  309 (410)
Q Consensus       254 ~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C~~~~~~  309 (410)
                      .+..|| +|+.+++++.+||+||.|..|||+.|+|++..  ...+.|+|+.|......
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~~   66 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFGP   66 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSCS
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccCC
Confidence            356799 99999864448999999999999999999776  33579999999976543

>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=8.3e-13  Score=105.80  Aligned_cols=55  Identities=27%  Similarity=0.643  Sum_probs=45.7

Q ss_pred             CCCCCCcccccccCcCCCCCCCeeecc--CCCCcccceecccCCCC------CCCcEEcCCCcCc
Q psy5827         250 TGDSKQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAEP------ETSDWFCPKCSKV  306 (410)
Q Consensus       250 ded~~~~~~C~VCg~~ddgd~~mI~CD--~C~~W~H~~Clgi~~~~------~~~~W~Cp~C~~~  306 (410)
                      ..++++.+|| +|+.+++++ +||+||  .|..|||+.|||++..+      .+..|||+.|...
T Consensus        10 ~~~~~~~~~C-iC~~~~~~g-~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T 1wew_A           10 PFQPEIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             SSSCCCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             ccCCCCCEEe-ECCCcCCCC-CEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcc
Confidence            3445578899 999996666 899999  99999999999998763      3579999999854

>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=99.26  E-value=1.2e-12  Score=100.61  Aligned_cols=52  Identities=31%  Similarity=0.700  Sum_probs=43.8

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCCcCc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  306 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C~~~  306 (410)
                      +..+|++|+++++++.+||+||.|..|||+.|+|++..  .....|+|+.|...
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            45689999999864448999999999999999999876  22479999999854

>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=99.26  E-value=4e-13  Score=106.77  Aligned_cols=51  Identities=31%  Similarity=0.897  Sum_probs=43.4

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCCC------CCCcEEcCCCcCcc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP------ETSDWFCPKCSKVD  307 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~------~~~~W~Cp~C~~~~  307 (410)
                      +..|| +|+.+++++ +||+||.|..|||+.|+|++...      ....|+|+.|....
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            45899 999998876 89999999999999999997652      34789999998553

>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=99.25  E-value=8.7e-13  Score=98.01  Aligned_cols=49  Identities=29%  Similarity=0.751  Sum_probs=42.6

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcC
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  305 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~  305 (410)
                      +..+| +|+.+++++ +||+||.|..|||+.|+|++....++.|+|+.|..
T Consensus         3 d~~~C-~C~~~~~~~-~MI~Cd~C~~W~H~~Cvgi~~~~~~~~~~C~~C~~   51 (52)
T 3o7a_A            3 DLVTC-FCMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   51 (52)
T ss_dssp             TCBCS-TTCCBCTTC-CEEECTTTCCEEETTTTTCCGGGCCSSCCCHHHHT
T ss_pred             cCeEE-EeCCcCCCC-CEEEcCCCCccccccccCCCcccCCCcEECcCCCC
Confidence            35689 999998876 89999999999999999998874457999999964

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=99.19  E-value=3.4e-12  Score=99.70  Aligned_cols=52  Identities=23%  Similarity=0.620  Sum_probs=42.4

Q ss_pred             CCCCcccccccCcCCCCCCCeeeccC--CCCcccceecccCCC-----CCCCcEEcCCCcC
Q psy5827         252 DSKQVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVGLVAE-----PETSDWFCPKCSK  305 (410)
Q Consensus       252 d~~~~~~C~VCg~~ddgd~~mI~CD~--C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~~  305 (410)
                      +++..++| +|+.+++++ +||+||+  |..|||+.|+|++..     ..+..|||+.|+.
T Consensus         6 ~~e~~v~C-~C~~~~~~g-~mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr~   64 (68)
T 2rsd_A            6 QPEAKVRC-ICSSTMVND-SMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRL   64 (68)
T ss_dssp             CSSCEECC-TTCCCSCCS-CEEECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHHH
T ss_pred             CCCCCEEe-ECCCCcCCC-CEEEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCccC
Confidence            34466899 999987777 8999995  999999999999765     2235899999974

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=99.18  E-value=2.6e-12  Score=99.18  Aligned_cols=51  Identities=41%  Similarity=1.103  Sum_probs=40.5

Q ss_pred             CCCCCcccccccCcCCCCCCCeeeccC--CC-CcccceecccCCCCCCCcEEcCCCcC
Q psy5827         251 GDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  305 (410)
Q Consensus       251 ed~~~~~~C~VCg~~ddgd~~mI~CD~--C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~  305 (410)
                      .++++..|| +|+.+++|  +||+||+  |+ .|||+.|||++..+ .+.|||+.|..
T Consensus         6 ~d~~e~~yC-~C~~~~~g--~MI~CD~c~C~~~WfH~~Cvgl~~~p-~~~w~Cp~C~~   59 (62)
T 2g6q_A            6 IDPNEPTYC-LCNQVSYG--EMIGCDNEQCPIEWFHFSCVSLTYKP-KGKWYCPKCRG   59 (62)
T ss_dssp             ----CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSCC-SSCCCCHHHHT
T ss_pred             cCCCCCcEE-ECCCCCCC--CeeeeeCCCCCcccEecccCCcCcCC-CCCEECcCccc
Confidence            345567899 99998776  4999999  55 99999999998765 48999999974

>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=99.17  E-value=2.9e-12  Score=97.98  Aligned_cols=50  Identities=42%  Similarity=1.177  Sum_probs=40.5

Q ss_pred             CCCCcccccccCcCCCCCCCeeeccC--CC-CcccceecccCCCCCCCcEEcCCCcC
Q psy5827         252 DSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  305 (410)
Q Consensus       252 d~~~~~~C~VCg~~ddgd~~mI~CD~--C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~  305 (410)
                      ++++..|| +|+.+++|  .||+||+  |+ .|||+.|+|++..+. +.|||+.|..
T Consensus         5 d~~e~~yC-~C~~~~~g--~mi~CD~~~C~~~wfH~~Cvgl~~~p~-~~w~Cp~C~~   57 (59)
T 3c6w_A            5 GSNEPTYC-LCHQVSYG--EMIGCDNPDCPIEWFHFACVDLTTKPK-GKWFCPRCVQ   57 (59)
T ss_dssp             ---CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSCCS-SCCCCHHHHC
T ss_pred             CCCCCcEE-ECCCCCCC--CeeEeeCCCCCCCCEecccCCcccCCC-CCEECcCccC
Confidence            44567899 99999875  4999999  77 799999999987654 7999999974

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.16  E-value=6.4e-12  Score=99.17  Aligned_cols=50  Identities=40%  Similarity=1.097  Sum_probs=42.1

Q ss_pred             CCCcccccccCcCCCCCCCeeeccCCC---CcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         253 SKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       253 ~~~~~~C~VCg~~ddgd~~mI~CD~C~---~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      +++..|| +|+.++++  +||+||+|+   .|||+.|||++..+ .+.|||+.|...
T Consensus         3 ~~~~~yC-~C~~~~~g--~MI~CD~cdC~~~WfH~~Cvgl~~~p-~~~w~Cp~C~~~   55 (70)
T 1x4i_A            3 SGSSGYC-ICNQVSYG--EMVGCDNQDCPIEWFHYGCVGLTEAP-KGKWYCPQCTAA   55 (70)
T ss_dssp             CSCCCCS-TTSCCCCS--SEECCSCTTCSCCCEEHHHHTCSSCC-SSCCCCHHHHHH
T ss_pred             CCCCeEE-EcCCCCCC--CEeEeCCCCCCccCCcccccccCcCC-CCCEECCCCCcc
Confidence            4466799 99999766  599999975   89999999998764 589999999854

>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=99.15  E-value=4e-12  Score=97.37  Aligned_cols=50  Identities=46%  Similarity=1.263  Sum_probs=40.2

Q ss_pred             CCCCcccccccCcCCCCCCCeeeccC--CC-CcccceecccCCCCCCCcEEcCCCcC
Q psy5827         252 DSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  305 (410)
Q Consensus       252 d~~~~~~C~VCg~~ddgd~~mI~CD~--C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~  305 (410)
                      ++++..|| +|+.+++|  .||+||+  |+ .|||+.|+|++..+. +.|||+.|..
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--EMIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQ   58 (60)
T ss_dssp             ---CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSCCS-SCCCCHHHHC
T ss_pred             CCCCCCEE-ECCCcCCC--CEEEeCCCCCCCceEehhcCCCCcCCC-CCEECcCccC
Confidence            45567899 99998775  4999999  66 899999999877654 8999999974

>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=99.11  E-value=5.6e-12  Score=98.23  Aligned_cols=50  Identities=26%  Similarity=0.824  Sum_probs=41.8

Q ss_pred             CcccccccCcCCCCCCCeeecc-CCCCcccceecccCCC-------CCCCcEEcCCCc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-------PETSDWFCPKCS  304 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD-~C~~W~H~~Clgi~~~-------~~~~~W~Cp~C~  304 (410)
                      .+..|.+|+++++++.+||+|| .|..|||+.|+|++..       .+...|+|+.|.
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            4457999999987767999999 9999999999999874       244699999985

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=99.11  E-value=2.7e-11  Score=89.14  Aligned_cols=48  Identities=25%  Similarity=0.751  Sum_probs=41.1

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      +|.+|+..++++ .||.||+|+.|||+.|++++.. .+.+.|||+.|...
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~~   50 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQPA   50 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSCC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCcccc
Confidence            589999987666 7999999999999999987665 55689999999753

>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=99.06  E-value=1.8e-11  Score=90.99  Aligned_cols=47  Identities=36%  Similarity=0.957  Sum_probs=38.8

Q ss_pred             cccccCcCCCCCCCeeecc-CCCCcccceecccCCC-CCCCcEEcCCCc
Q psy5827         258 ICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-PETSDWFCPKCS  304 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD-~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~  304 (410)
                      .|.+|++|++++.+||+|| .|+.|||+.|+|++.. ...+.|+|+.|.
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            4669999987655899999 8999999999999865 223789999995

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=99.01  E-value=1.3e-10  Score=89.13  Aligned_cols=48  Identities=35%  Similarity=0.805  Sum_probs=40.3

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      +..+|.+|+.  .+  .||+||.|+.|||+.|++++.. .+.+.|||+.|...
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            4458999997  33  4999999999999999999765 55689999999854

>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=98.99  E-value=3.2e-10  Score=86.88  Aligned_cols=48  Identities=27%  Similarity=0.805  Sum_probs=39.9

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      +..+|.+|+.  .+  .||+||.|+.+||+.|++++.. .+.+.|||+.|...
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            4457999986  33  4999999999999999998766 55689999999865

>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=98.97  E-value=1.4e-10  Score=95.82  Aligned_cols=50  Identities=34%  Similarity=0.798  Sum_probs=42.4

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      ...|.+|+..++.+ .||+||.|+.|||+.|++++.. .+.+.|||+.|...
T Consensus        16 ~~~C~vC~~~~~~~-~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           16 SYICQVCSRGDEDD-KLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCSSSCCSGGGG-GCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             CCCCccCCCcCCCC-CEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            34799999977655 7999999999999999998766 55689999999743

>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=4.4e-11  Score=107.69  Aligned_cols=52  Identities=35%  Similarity=0.915  Sum_probs=42.8

Q ss_pred             CCcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCCcCc
Q psy5827         254 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  306 (410)
Q Consensus       254 ~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C~~~  306 (410)
                      ++..+| +|+.+++++.+||+||.|+.|||+.|+|++..  ...+.|+|+.|...
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            356799 99998764448999999999999999998765  34579999999854

>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=98.96  E-value=7.9e-11  Score=99.49  Aligned_cols=53  Identities=30%  Similarity=0.823  Sum_probs=43.1

Q ss_pred             cccccccCcCCCCCCCeeecc-CCCCcccceecccCCC-------CCCCcEEcCCCcCccc
Q psy5827         256 VWICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVDE  308 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD-~C~~W~H~~Clgi~~~-------~~~~~W~Cp~C~~~~~  308 (410)
                      ++.|.+|+++++++..||+|| .|..|||+.|+|++..       .+...|+|+.|.....
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~   63 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKE   63 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCC
Confidence            467999999965544799998 9999999999999863       2347999999986543

>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=98.95  E-value=4.6e-11  Score=124.44  Aligned_cols=57  Identities=28%  Similarity=0.672  Sum_probs=46.1

Q ss_pred             CCCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCCC--CCCcEEcCCCcCcccC
Q psy5827         252 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP--ETSDWFCPKCSKVDEG  309 (410)
Q Consensus       252 d~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~--~~~~W~Cp~C~~~~~~  309 (410)
                      .+....|| +|+.+++++.+||+||.|+.|||+.|+|++...  ..+.|+|+.|......
T Consensus        33 ~~~~~~yC-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~~   91 (488)
T 3kv5_D           33 PPPPPVYC-VCRQPYDVNRFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCAVLHGS   91 (488)
T ss_dssp             CCCCCEET-TTTEECCTTSCEEEBTTTCCEEEHHHHTCCGGGGGGEEEBCCHHHHHHHCS
T ss_pred             CCCCCeEE-eCCCcCCCCCCeEEccCCCCceeeeecCcCcccccCCCEEECCCCcCCcCc
Confidence            34466899 999997644489999999999999999998772  2468999999876543

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=98.94  E-value=1.5e-10  Score=89.89  Aligned_cols=47  Identities=28%  Similarity=0.725  Sum_probs=39.3

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      ..+|.+|+.  .+  .||+||.|+.|||+.|++++.. .+.+.|||+.|...
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  4999999999999999998766 55589999999854

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.93  E-value=3.1e-10  Score=85.29  Aligned_cols=47  Identities=28%  Similarity=0.791  Sum_probs=39.0

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcC
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  305 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~  305 (410)
                      ...+|.+|+..  +  .||.||.|+.|||+.|++++.. .+.+.|||+.|..
T Consensus         8 ~~~~C~vC~~~--g--~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS--G--QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS--S--CCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC--C--eEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            34579999983  3  4999999999999999998766 5568999999963

>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=98.92  E-value=1.9e-10  Score=88.66  Aligned_cols=53  Identities=23%  Similarity=0.599  Sum_probs=42.2

Q ss_pred             CcccccccCcCC--CCCCCeeeccCCCCcccceecccCCC----CCCCcEEcCCCcCccc
Q psy5827         255 QVWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAE----PETSDWFCPKCSKVDE  308 (410)
Q Consensus       255 ~~~~C~VCg~~d--dgd~~mI~CD~C~~W~H~~Clgi~~~----~~~~~W~Cp~C~~~~~  308 (410)
                      ....|.+|+..+  +++ .||+||.|+.|||+.|++++..    .+.+.|||+.|.....
T Consensus         5 ~~~~C~vC~~~~~~~~~-~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPN-EMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCBSSSCCCCCBTTB-CEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCC-CEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            345799999863  224 7999999999999999999765    1568999999985543

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=98.91  E-value=3.3e-10  Score=92.95  Aligned_cols=49  Identities=22%  Similarity=0.601  Sum_probs=40.5

Q ss_pred             cccccccCcCC--CCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~d--dgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      ...|.+|+..+  +++ .||+||.|+.|||+.|++++.. +.+.|||+.|...
T Consensus        25 ~~~C~vC~~~~s~~~~-~ll~CD~C~~~fH~~Cl~p~~v-P~g~W~C~~C~~~   75 (88)
T 2l43_A           25 DAVCSICMDGESQNSN-VILFCDMCNLAVHQECYGVPYI-PEGQWLCRHCLQS   75 (88)
T ss_dssp             CCCCSSCCSSSSCSEE-EEEECSSSCCCCCHHHHTCSSC-CSSCCCCHHHHHH
T ss_pred             CCcCCcCCCCCCCCCC-CEEECCCCCchhhcccCCCCcc-CCCceECccccCc
Confidence            35799999864  333 7999999999999999999864 4589999999854

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

Probab=98.90  E-value=8.8e-10  Score=86.02  Aligned_cols=46  Identities=26%  Similarity=0.598  Sum_probs=38.9

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      ..|.+|+.  .+  .||+||.|+.|||++|++++.. .+.+.|||+.|...
T Consensus        13 ~~C~vC~~--~~--~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           13 ARCGVCGD--GT--DVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             CCCTTTSC--CT--TCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCcCCCCC--CC--eEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            46999985  34  4999999999999999998876 55689999999854

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=98.87  E-value=4e-10  Score=89.14  Aligned_cols=49  Identities=22%  Similarity=0.601  Sum_probs=40.4

Q ss_pred             cccccccCcCC--CCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~d--dgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      ...|.+|+..+  +++ .||+||+|+.|||+.|++++.. +.+.|||+.|...
T Consensus        16 ~~~C~vC~~~~s~~~~-~ll~CD~C~~~~H~~Cl~~~~v-P~g~W~C~~C~~~   66 (71)
T 2ku3_A           16 DAVCSICMDGESQNSN-VILFCDMCNLAVHQECYGVPYI-PEGQWLCRHCLQS   66 (71)
T ss_dssp             SCSCSSSCCCCCCSSS-CEEECSSSCCEEEHHHHTCSSC-CSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCC-CEEECCCCCCccccccCCCCcC-CCCCcCCccCcCc
Confidence            34799999864  344 7999999999999999999864 4589999999743

>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=8.2e-10  Score=86.96  Aligned_cols=47  Identities=30%  Similarity=0.882  Sum_probs=39.4

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCC-cEEcCCCcC
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  305 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~-~W~Cp~C~~  305 (410)
                      .|.+|+..++++ .||+||+|+.|||+.|++++.. .+.+ .|||+.|..
T Consensus        20 ~C~~C~~~~~~~-~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   68 (70)
T 3asl_A           20 ACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   68 (70)
T ss_dssp             SBTTTCCCSCGG-GEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSC
T ss_pred             CCcCCCCcCCCC-CEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccC
Confidence            456788877666 7999999999999999998766 4456 999999984

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=98.86  E-value=5.4e-10  Score=85.00  Aligned_cols=47  Identities=28%  Similarity=0.772  Sum_probs=39.1

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      ..+|.+|+..  +  .||.||.|+.|||+.|++++.. .+.+.|||+.|...
T Consensus         5 ~~~C~vC~~~--g--~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   52 (60)
T 2puy_A            5 EDFCSVCRKS--G--QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQ   52 (60)
T ss_dssp             CSSCTTTCCC--S--SCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHH
T ss_pred             CCCCcCCCCC--C--cEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccCh
Confidence            3579999983  4  4999999999999999998766 55689999999743

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.84  E-value=1.4e-09  Score=87.36  Aligned_cols=47  Identities=28%  Similarity=0.818  Sum_probs=40.3

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCC-cEEcCCCcC
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  305 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~-~W~Cp~C~~  305 (410)
                      .|.+|+..++++ .||+||.|+.+||+.|++++.. .+.+ .|||+.|..
T Consensus        28 ~C~vC~~~~~~~-~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           28 SCRVCGGKHEPN-MQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SCSSSCCCCCST-TEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCcCcCCcCCCC-CEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            688999887666 7999999999999999998766 4456 999999974

>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=98.82  E-value=1.3e-09  Score=101.25  Aligned_cols=50  Identities=22%  Similarity=0.640  Sum_probs=41.3

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCccc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  308 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~~  308 (410)
                      ...+|.+|+.  +|+  ||+||+|+.|||+.|++++.. .+.+.|+|+.|.....
T Consensus         6 ~~~~C~~C~~--~g~--ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~~   56 (207)
T 3u5n_A            6 NEDWCAVCQN--GGD--LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGK   56 (207)
T ss_dssp             SCSSBTTTCC--CEE--EEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCCCCCCCC--CCc--eEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCccc
Confidence            3457999996  344  999999999999999998776 5668999999997643

>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=1.7e-10  Score=119.09  Aligned_cols=56  Identities=32%  Similarity=0.729  Sum_probs=45.9

Q ss_pred             CCcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCCcCcccCc
Q psy5827         254 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGS  310 (410)
Q Consensus       254 ~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C~~~~~~k  310 (410)
                      ++..|| +|+.+++++.+||+||.|+.|||+.|+|++..  ...+.|+|+.|......+
T Consensus         3 ~~~~yC-iC~~~~d~~~~MIqCD~C~~WfH~~CVgi~~~~~~~~~~y~C~~C~~~~~~~   60 (447)
T 3kv4_A            3 SVPVYC-LCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGPS   60 (447)
T ss_dssp             CCCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTEEECCCHHHHHHHCCC
T ss_pred             CCCeEE-eCCCcCCCCCCeEEcCCCCcccccccCCcCcccccCCCEEECCCCccccCCc
Confidence            356799 99999764448999999999999999999876  334789999998765544

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=98.77  E-value=7.2e-09  Score=85.34  Aligned_cols=47  Identities=23%  Similarity=0.678  Sum_probs=39.8

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      ..+|.+|+.  .++  +|+||.|+.+||+.|+.++.. .+.+.|+|+.|...
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  999999999999999988776 56689999999855

>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=98.76  E-value=1.3e-09  Score=89.20  Aligned_cols=51  Identities=20%  Similarity=0.588  Sum_probs=41.9

Q ss_pred             cccccccCcCCCC-CCCeeeccCCCCcccceecccCCC-----CCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddg-d~~mI~CD~C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~~~  306 (410)
                      ..+|.+|+..+.. +..||+||.|+.+||+.|++++..     .+.+.|||+.|...
T Consensus        16 ~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~   72 (88)
T 1wev_A           16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             CCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccch
Confidence            4579999986542 126999999999999999999876     46789999999854

>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=98.75  E-value=1.1e-09  Score=100.88  Aligned_cols=52  Identities=33%  Similarity=0.788  Sum_probs=42.2

Q ss_pred             cccccCcCCCCCC---CeeeccCCCCcccceecccCCC--------CCCCcEEcCCCcCcccC
Q psy5827         258 ICPACGVQDDGSL---PMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVDEG  309 (410)
Q Consensus       258 ~C~VCg~~ddgd~---~mI~CD~C~~W~H~~Clgi~~~--------~~~~~W~Cp~C~~~~~~  309 (410)
                      +|++|+++++++.   .||+||.|+.|||..|+|++..        +....|+|+.|......
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            7999999987653   4999999999999999999753        11237999999977543

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=98.69  E-value=4.9e-09  Score=84.17  Aligned_cols=48  Identities=31%  Similarity=0.871  Sum_probs=39.4

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCc-EEcCCCcC
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSD-WFCPKCSK  305 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~-W~Cp~C~~  305 (410)
                      ..|.+|+..++++ .||+||.|+.+||++|++++.. .+.+. |||+.|..
T Consensus        27 C~C~vC~~~~d~~-~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           27 CACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             TSBTTTCCCSCGG-GEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             CcCCccCCCCCCc-ceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            3577788877666 7999999999999999998776 44466 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=98.68  E-value=7.2e-09  Score=94.29  Aligned_cols=47  Identities=21%  Similarity=0.671  Sum_probs=39.8

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCcc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  307 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~  307 (410)
                      .+|.+|+.  +|+  +|+||+|+.|||..|++++.. .+.+.|+|+.|....
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  344  999999999999999988776 556899999998654

>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=98.63  E-value=1e-08  Score=97.44  Aligned_cols=48  Identities=29%  Similarity=0.857  Sum_probs=37.6

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCC-cEEcCCCcC
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  305 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~-~W~Cp~C~~  305 (410)
                      ..|.+|+..++++ .||+||+|+.|||+.|++++.. .+.+ .|+|+.|..
T Consensus       175 c~C~vC~~~~~~~-~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~  224 (226)
T 3ask_A          175 CACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN  224 (226)
T ss_dssp             TSCSSSCCCCC---CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC-
T ss_pred             CCCcCCCCCCCCC-CeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcC
Confidence            4699999987776 7999999999999999998777 4556 999999974

>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=98.60  E-value=9.1e-09  Score=87.60  Aligned_cols=47  Identities=30%  Similarity=0.824  Sum_probs=40.5

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcC
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  305 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~  305 (410)
                      +|.+|+..++++ .||.||.|+.|||+.|++++.. .+.+.|||+.|..
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            588888877666 7999999999999999998766 5668999999974

>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=98.58  E-value=1.9e-08  Score=85.55  Aligned_cols=45  Identities=33%  Similarity=0.828  Sum_probs=36.5

Q ss_pred             CcccccccCcCCCCCCCeeecc--CCCCcccceecccCCCCCCCcEEcCCCc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAEPETSDWFCPKCS  304 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD--~C~~W~H~~Clgi~~~~~~~~W~Cp~C~  304 (410)
                      +..+|.+|+.  +|+  ||+||  .|+.|||+.|+++...+ .+.|||+.|.
T Consensus        14 ~~~~C~~C~~--~G~--ll~CD~~~Cp~~fH~~Cl~L~~~P-~g~W~Cp~c~   60 (107)
T 4gne_A           14 HEDYCFQCGD--GGE--LVMCDKKDCPKAYHLLCLNLTQPP-YGKWECPWHQ   60 (107)
T ss_dssp             SCSSCTTTCC--CSE--EEECCSTTCCCEECTGGGTCSSCC-SSCCCCGGGB
T ss_pred             CCCCCCcCCC--CCc--EeEECCCCCCcccccccCcCCcCC-CCCEECCCCC
Confidence            3457999984  444  99999  89999999999976544 5899999875

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=98.54  E-value=3.9e-08  Score=83.35  Aligned_cols=48  Identities=27%  Similarity=0.654  Sum_probs=38.7

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcC
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  305 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~  305 (410)
                      +|.+|+..++++..||+||.|+.+||+.|++++.. .+.+.|||+.|.+
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            57788875332226999999999999999988766 5668999999985

>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=98.46  E-value=4.5e-08  Score=82.40  Aligned_cols=50  Identities=32%  Similarity=0.747  Sum_probs=41.7

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCccc
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  308 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~~  308 (410)
                      +|.+|+..++++ .||.||.|+.|||+.|++++.. .+.+.|||+.|.....
T Consensus        56 ~C~~C~~~~~~~-~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~c~~  106 (111)
T 2ysm_A           56 VCQNCKQSGEDS-KMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRICIS  106 (111)
T ss_dssp             CCTTTCCCSCCT-TEEECSSSCCEEEGGGSSSCCSSCCSSCCCCHHHHCCSC
T ss_pred             cccccCccCCCC-CeeECCCCCcHHhHHhcCCccccCCCCCcCCcCCcCcCC
Confidence            577888877666 7999999999999999998766 5568999999976543

>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=8e-08  Score=88.45  Aligned_cols=46  Identities=24%  Similarity=0.712  Sum_probs=39.0

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCcc
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  307 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~  307 (410)
                      +|.+|+.  +|+  +|+||+|+.+||+.|+.++.. .+.+.|+|+.|....
T Consensus         4 ~C~~C~~--~g~--ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            4 ICRVCQK--PGD--LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CBTTTCC--CSS--CCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             cCccCCC--CCc--eeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            6999996  344  999999999999999987766 556899999998653

>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=98.36  E-value=6.5e-08  Score=101.40  Aligned_cols=50  Identities=34%  Similarity=0.804  Sum_probs=38.2

Q ss_pred             cCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCCcCcccCch
Q psy5827         262 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSR  311 (410)
Q Consensus       262 Cg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C~~~~~~k~  311 (410)
                      +..+.+.+.+||+||.|+.|||+.|+|++..  ...+.|+||.|......+.
T Consensus        48 ~~~~~n~~~~mI~CD~C~~WfH~~CVgi~~~~a~~~~~y~Cp~C~~~~gps~   99 (528)
T 3pur_A           48 SHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPHTGHSI   99 (528)
T ss_dssp             TTTTTTSTTSEEECTTTCCEEEGGGTTCCGGGTTTEEECCCTTTHHHHCSCE
T ss_pred             cccCCCcCCCEEECCCCCcCCCCcCCCCChhHhcCCCeEECcCCcCCCCCcc
Confidence            3333334459999999999999999999876  3347999999997654433

>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=98.09  E-value=1.8e-06  Score=72.55  Aligned_cols=47  Identities=26%  Similarity=0.712  Sum_probs=39.2

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCS  304 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~  304 (410)
                      .+|.+|+...+.. .||.|+.|++.||..|++++.. ...+.|+|+.|.
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            4799999965543 5899999999999999999876 345799999986

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=98.05  E-value=1.5e-06  Score=77.30  Aligned_cols=48  Identities=25%  Similarity=0.559  Sum_probs=40.2

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--------CCCCcEEcCCCcCc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKV  306 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--------~~~~~W~Cp~C~~~  306 (410)
                      ...+|.+|+.  +|+  +|+||.|++.||..|+.++..        .+.+.|+|+.|...
T Consensus        62 ~~d~C~vC~~--GG~--LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           62 MDEQCRWCAE--GGN--LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             CBCSCSSSCC--CSS--EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCeecccCC--CCc--EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            4468999997  555  999999999999999997664        35689999999865

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=97.67  E-value=7e-06  Score=69.07  Aligned_cols=37  Identities=35%  Similarity=0.872  Sum_probs=30.5

Q ss_pred             eeeccCCCCcccceecccCCC--------CCCCcEEcCCCcCccc
Q psy5827         272 MIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVDE  308 (410)
Q Consensus       272 mI~CD~C~~W~H~~Clgi~~~--------~~~~~W~Cp~C~~~~~  308 (410)
                      ||+||.|..|||..|++++..        +....|.|+.|.....
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        3345899999986543

>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=97.60  E-value=1.4e-05  Score=69.96  Aligned_cols=49  Identities=24%  Similarity=0.543  Sum_probs=39.1

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--------CCCCcEEcCCCcCcc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVD  307 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--------~~~~~W~Cp~C~~~~  307 (410)
                      ...+|.+|+.  +|+  +|+||.|++.||..|+.+...        .+.+.|+|..|....
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            4467999996  454  999999999999999986532        246899999998653

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=97.58  E-value=1.2e-05  Score=68.09  Aligned_cols=48  Identities=25%  Similarity=0.571  Sum_probs=36.9

Q ss_pred             ccccccCcCC------CCCCCeeeccCCCCcccceecccCCC----CCCCcEEcCCCcC
Q psy5827         257 WICPACGVQD------DGSLPMIGCDGCDAWYHWVCVGLVAE----PETSDWFCPKCSK  305 (410)
Q Consensus       257 ~~C~VCg~~d------dgd~~mI~CD~C~~W~H~~Clgi~~~----~~~~~W~Cp~C~~  305 (410)
                      .+|.+|...+      .++ .||.|++|+.+||.+|+++...    ...+.|+|+.|..
T Consensus         6 ~~C~~C~~~~~~~~~g~~~-~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~~   63 (112)
T 3v43_A            6 PICSFCLGTKEQNREKKPE-ELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECKT   63 (112)
T ss_dssp             SSBTTTCCCTTCCTTSCCC-CCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTCC
T ss_pred             ccccccCCchhhCcCCCch-hceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCCc
Confidence            4799997642      233 6999999999999999986422    3357999999973

>3rsn_A SET1/ASH2 histone methyltransferase complex subun; PHD domain, winged helix domain, binding, transcription; 2.10A {Homo sapiens} PDB: 3s32_A

Probab=97.55  E-value=4.4e-05  Score=70.09  Aligned_cols=51  Identities=12%  Similarity=0.240  Sum_probs=36.6

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCC-----CCCCcEEcCCCcCcc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKVD  307 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~~~~  307 (410)
                      ..|| -||.+.+-+..|++|+.|..|||..|++....     .....|.|..|...+
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            4589 99998776679999999999999999986443     234578899998765

>4bbq_A Lysine-specific demethylase 2A; oxidoreductase, ubiquitin, ligase, ubiquitination, demethyla ZF-CXXC DNA binding domain, CPG island, chromatin; 2.24A {Homo sapiens}

Probab=97.50  E-value=2.8e-05  Score=65.53  Aligned_cols=38  Identities=29%  Similarity=0.627  Sum_probs=29.5

Q ss_pred             CCeeeccCCCCcccceecccCCC-----CCCCcEEcCCCcCcc
Q psy5827         270 LPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKVD  307 (410)
Q Consensus       270 ~~mI~CD~C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~~~~  307 (410)
                      ..||+|+.|+.|||..|+++...     ..+..|+|+.|.+.+
T Consensus        73 ~~m~~C~~C~~~~H~~C~~~~~~~~~~~~~~~~~~C~~C~~~~  115 (117)
T 4bbq_A           73 KKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQED  115 (117)
T ss_dssp             GSCEEETTTCCEECGGGCCSCCCCEECSSSSSEEECTTTC---
T ss_pred             cceEEeeecCCeEECCCCCCCccccccccCCCCeECCCCcCCC
Confidence            37999999999999999998754     223569999998764

>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=97.36  E-value=2.3e-05  Score=66.49  Aligned_cols=46  Identities=22%  Similarity=0.573  Sum_probs=35.9

Q ss_pred             cccccCcCC-------CCCCCeeeccCCCCcccceecccCCC----CCCCcEEcCCCc
Q psy5827         258 ICPACGVQD-------DGSLPMIGCDGCDAWYHWVCVGLVAE----PETSDWFCPKCS  304 (410)
Q Consensus       258 ~C~VCg~~d-------dgd~~mI~CD~C~~W~H~~Clgi~~~----~~~~~W~Cp~C~  304 (410)
                      +|.+|...+       +++ .||.|+.|+..||.+|+++...    ...+.|+|+.|.
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            688997643       223 6999999999999999998632    334689999985

>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=96.33  E-value=0.0017  Score=53.13  Aligned_cols=50  Identities=22%  Similarity=0.585  Sum_probs=38.5

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccC------------CC-CCCCcEEcCCCcCccc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV------------AE-PETSDWFCPKCSKVDE  308 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~------------~~-~~~~~W~Cp~C~~~~~  308 (410)
                      ..|.||..-..++  ++.|..|.+.||..|+...            .. .....|.|+.|...+.
T Consensus        16 ~~C~VC~~~t~~~--l~pCRvC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T~~GWSC~~CenL~l   78 (89)
T 1wil_A           16 EMCDVCEVWTAES--LFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNINL   78 (89)
T ss_dssp             CCCTTTCCCCSSC--CSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCCCS
T ss_pred             cccCccccccccc--eeccccccccccHhhcccccccccHHHHHHHHccCCCCCccccccchhhh
Confidence            3699999865555  8999999999999998642            11 3557899999976543

>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=91.22  E-value=0.065  Score=48.33  Aligned_cols=49  Identities=20%  Similarity=0.509  Sum_probs=38.2

Q ss_pred             CcccccccCcCCCCCCCeeecc--CCCCcccceecccCCC-------CCCCcEEcCCCcCcc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVD  307 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD--~C~~W~H~~Clgi~~~-------~~~~~W~Cp~C~~~~  307 (410)
                      -..||.+|+.  ++  .+|.||  .|.+.|-..|+.....       ...+.|.|-.|.+..
T Consensus        78 ~~~yC~wC~~--Gg--~l~~Cdn~~C~r~FC~~CI~~nvG~~~~~~i~~~d~W~Cy~C~P~~  135 (159)
T 3a1b_A           78 YQSYCTICCG--GR--EVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKG  135 (159)
T ss_dssp             SBSSCTTTSC--CS--EEEECSSTTTCCEEEHHHHHHHTCTTHHHHHHTSSSCCCTTTCSSC
T ss_pred             CcceeeEecC--CC--eEEeeCCCCCCCchhHHHHHHhcCHhHHHHHhccCCCEEEecCCcc
Confidence            3468999996  44  499999  7999999999754332       345799999999764

>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=89.82  E-value=0.087  Score=53.55  Aligned_cols=49  Identities=22%  Similarity=0.611  Sum_probs=38.9

Q ss_pred             CcccccccCcCCCCCCCeeecc--CCCCcccceecccCCC-------CCCCcEEcCCCcCcc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVD  307 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD--~C~~W~H~~Clgi~~~-------~~~~~W~Cp~C~~~~  307 (410)
                      ...||.+|+.  +++  +|+||  .|.+.|-..|+.....       ...+.|.|-.|.+..
T Consensus        92 ~~~yCr~C~~--Gg~--l~~Cdn~~C~r~FC~~Ci~~n~g~~~~~~i~~~d~W~Cf~C~p~p  149 (386)
T 2pv0_B           92 YQSYCSICCS--GET--LLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSS  149 (386)
T ss_dssp             SBCSCTTTCC--CSS--CEECCSTTCCCEECHHHHHHHTCTTHHHHHHHCSSCCCTTTSSCC
T ss_pred             CcccceEcCC--CCe--EEEeCCCCCCcchHHHHHHHhcChhHHHHhhccCCceEEEcCCcc
Confidence            4578999997  444  99999  8999999999865443       234789999999764

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

Probab=85.63  E-value=0.71  Score=34.33  Aligned_cols=47  Identities=21%  Similarity=0.457  Sum_probs=31.8

Q ss_pred             cccccccCcCCCCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      ...|.||......-  ++.  .|+-.||..|+..-.........||.|...
T Consensus        20 ~~~C~IC~~~~~~~--~~~--~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~   66 (73)
T 2ysl_A           20 EVICPICLDILQKP--VTI--DCGHNFCLKCITQIGETSCGFFKCPLCKTS   66 (73)
T ss_dssp             CCBCTTTCSBCSSE--EEC--TTCCEEEHHHHHHHCSSSCSCCCCSSSCCC
T ss_pred             CCEeccCCcccCCe--EEc--CCCChhhHHHHHHHHHcCCCCCCCCCCCCc
Confidence            45799998865433  333  788889999986543322246789999865

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

Probab=82.52  E-value=0.88  Score=31.99  Aligned_cols=47  Identities=21%  Similarity=0.347  Sum_probs=31.9

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      ..|.||......+...+....|+-.||..|+..-..   ....||.|+..
T Consensus         6 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~---~~~~CP~Cr~~   52 (55)
T 1iym_A            6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLG---SHSTCPLCRLT   52 (55)
T ss_dssp             CCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTT---TCCSCSSSCCC
T ss_pred             CcCccCCccccCCCceEECCCCCCcccHHHHHHHHH---cCCcCcCCCCE
Confidence            359999886544323445557999999999865433   24579999753

>2lq6_A Bromodomain-containing protein 1; PHD finger, metal binding protein; NMR {Homo sapiens}

Probab=81.46  E-value=0.54  Score=38.01  Aligned_cols=32  Identities=25%  Similarity=0.563  Sum_probs=25.6

Q ss_pred             CcccccccCcCCCCCCCeeeccC--CCCcccceecc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVG  288 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~--C~~W~H~~Clg  288 (410)
                      |...|.+|+....|.  .|+|..  |..+||..|.-
T Consensus        16 ~~l~C~iC~~~~~GA--ciqC~~~~C~~~fHv~CA~   49 (87)
T 2lq6_A           16 WKLTCYLCKQKGVGA--SIQCHKANCYTAFHVTCAQ   49 (87)
T ss_dssp             CCCCBTTTTBCCSSC--EEECSCTTTCCEEEHHHHH
T ss_pred             hcCCCcCCCCCCCcE--eEecCCCCCCCcCcHHHHH
Confidence            556799998754455  899986  99999999963

---

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	410
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	1e-13
d1wepa_	79	g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus mus	2e-11
d1weea_	72	g.50.1.2 (A:) PHD finger protein At1g33420 {Thale	9e-11
d1wema_	76	g.50.1.2 (A:) Death associated transcription facto	2e-10
d1f62a_	51	g.50.1.2 (A:) Williams-Beuren syndrome transcripti	1e-08
d1mm2a_	61	g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens	9e-08
d1wewa_	78	g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale c	1e-07
d1fp0a1	70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	3e-07
d2pnxa1	51	g.50.1.2 (A:195-245) Inhibitor of growth protein 4	4e-07
d1weva_	88	g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu	8e-07
d1wesa_	71	g.50.1.2 (A:) PHD Inhibitor of growth protein 2, I	2e-06
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	0.001

>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 = 63.1 bits (153), Expect = 1e-13
 Identities = 18/57 (31%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 251 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSK 305
           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 = 57.4 bits (138), Expect = 2e-11
 Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 3/69 (4%)

Query: 256 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKE 313
           V +   C    + +  MI C  C  W+H  CVG+  E   +   + CP C +   G    
Sbjct: 11  VPVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDC-EAVFGPSIM 69

Query: 314 KKKRGRKKK 322
           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 = 55.4 bits (133), Expect = 9e-11
 Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 262 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCSK 305
           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 = 54.7 bits (131), Expect = 2e-10
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)

Query: 262 CGVQDDGSLPMIGCDGCDAWYHWVCVGL------VAEPETSDWFCPKCS 304
           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 = 48.4 bits (115), Expect = 1e-08
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 259 CPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 303
           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 = 46.5 bits (110), Expect = 9e-08
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 5/55 (9%)

Query: 251 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCS 304
           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 = 46.7 bits (110), Expect = 1e-07
 Identities = 12/62 (19%), Positives = 18/62 (29%), Gaps = 6/62 (9%)

Query: 249 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP------ETSDWFCPK 302
           D    +    C      +  S+       C  W H  CV L  +P          ++C  
Sbjct: 9   DPFQPEIKVRCVCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEI 68

Query: 303 CS 304
           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 = 45.4 bits (107), Expect = 3e-07
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCSKVDEGSRKEKKK 316
           IC  C    D    ++ C+ C+  +H  C    + +    +W C  C  + +   ++   
Sbjct: 9   ICRVCQKPGD----LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDVDL 64

Query: 317 RGRK 320
           +  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 = 44.1 bits (104), Expect = 4e-07
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 262 CGVQDDGSLPMI-GCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK 305
           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 = 44.8 bits (105), Expect = 8e-07
 Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 259 CPACG-VQDDGSLPMIGCDGCDAWYHWVCVG-----LVAEPETSDWFCPKCSKVDEGSRK 312
           C  C  +       ++ C  C   YH  C                W+C +C++  +   +
Sbjct: 19  CVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRMAQ 78

Query: 313 EKKKRG 318
           + +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 = 43.0 bits (101), Expect = 2e-06
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 262 CGVQDDGSLPMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKC 303
           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 = 38.7 bits (89), Expect = 0.001
 Identities = 28/172 (16%), Positives = 60/172 (34%), Gaps = 3/172 (1%)

Query: 20   PSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLG 79
                 +  + K  T   E     +  S    E  ++  +   +            S  L 
Sbjct: 1133 IRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLL 1192

Query: 80   EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKIDKE--KEKGKKEEK 137
             ++ D++   DK     +  E+I K+  K D   I +++ D++  I     + K    E 
Sbjct: 1193 RLELDRAAMNDKDLTMGQVGERI-KQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAET 1251

Query: 138  EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 189
            E +E+   K+ +   ++    + VE I +        K      + +K+ + 
Sbjct: 1252 EAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEW 1303

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	410
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	99.24
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	99.21
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	99.11
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	99.1
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	99.06
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	99.05
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	99.03
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	99.01
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	99.0
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	98.98
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	98.89
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	89.11
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	88.86
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	86.85
d1weqa_	85	PHD finger protein 7 (NYD-SP6) {Mouse (Mus musculu	86.84

>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=99.24  E-value=1.7e-12  Score=102.28  Aligned_cols=53  Identities=30%  Similarity=0.673  Sum_probs=44.1

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCCcCccc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDE  308 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C~~~~~  308 (410)
                      ..+|| +|+.+++.+.+||+||.|+.|||..|+|++..  ...+.|+|+.|.....
T Consensus        11 ~pv~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             CCeEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            34689 99998765558999999999999999999765  4556899999987544

>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=99.21  E-value=1.5e-12  Score=100.46  Aligned_cols=54  Identities=31%  Similarity=0.821  Sum_probs=45.1

Q ss_pred             CCCcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCcc
Q psy5827         253 SKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  307 (410)
Q Consensus       253 ~~~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~  307 (410)
                      ++|.++| +|+.+++++..||+||.|+.|||+.|+|++.. .+.+.|+|+.|....
T Consensus        13 ~~~~~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~   67 (72)
T d1weea_          13 DNWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             CSSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             CCCeEEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcC
Confidence            3567889 99998766658999999999999999999766 445799999998553

>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=99.11  E-value=2.1e-11  Score=94.62  Aligned_cols=55  Identities=29%  Similarity=0.825  Sum_probs=40.5

Q ss_pred             CCCCcccccccCcCCCCCCCeeeccCCC-CcccceecccCCCCCCCcEEcCCCcCccc
Q psy5827         252 DSKQVWICPACGVQDDGSLPMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKCSKVDE  308 (410)
Q Consensus       252 d~~~~~~C~VCg~~ddgd~~mI~CD~C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~~~~  308 (410)
                      ++++..|| ||+.+++++.+|+.|+.|. .|||+.||+++..+. +.|||+.|.....
T Consensus        12 d~~e~~~C-iC~~~~~~~~i~c~~~~C~~~wfH~~Cvgl~~~p~-~~w~C~~C~~~~g   67 (71)
T d1wesa_          12 DPNEPTYC-LCNQVSYGEMIGCDNEQCPIEWFHFSCVSLTYKPK-GKWYCPKCRGDSG   67 (71)
T ss_dssp             CSSSCCCS-TTCCCCCSSEECCSCTTCSCCCEETTTTTCSSCCS-SCCCCTTTSSCCS
T ss_pred             CCCCCCEE-EeCCCCCCCEEEEECCCCCCcCccCccCCCCcCCC-CcEECcCCccccC
Confidence            34455799 9999877762333355675 799999999976654 7999999986543

>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=99.10  E-value=1.4e-11  Score=88.96  Aligned_cols=48  Identities=25%  Similarity=0.751  Sum_probs=42.0

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCc
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  306 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~  306 (410)
                      .|.+|+..++++ .||.||.|+.|||+.|++++.. .+.+.|+|+.|...
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 7999999999999999999876 55579999999854

>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=99.06  E-value=1.6e-11  Score=92.53  Aligned_cols=51  Identities=31%  Similarity=0.722  Sum_probs=43.3

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC--CCCCcEEcCCCcCcc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVD  307 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~--~~~~~W~Cp~C~~~~  307 (410)
                      ..|.+|+.+++++.+||+||.|+.|||..|++++..  .....|+|+.|....
T Consensus         7 ~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~~   59 (64)
T d1we9a_           7 GQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             CCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCcC
Confidence            469999998766658999999999999999999776  345789999998653

>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=99.05  E-value=6.8e-12  Score=97.14  Aligned_cols=51  Identities=31%  Similarity=0.897  Sum_probs=41.9

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC------CCCCcEEcCCCcCcc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE------PETSDWFCPKCSKVD  307 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~------~~~~~W~Cp~C~~~~  307 (410)
                      ...+| +|+.+++++ .||+||.|+.|||..|+|++..      .....|+|+.|....
T Consensus        15 ~~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CcCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            45679 999998777 8999999999999999998653      234679999997553

>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=99.03  E-value=7.6e-11  Score=88.28  Aligned_cols=47  Identities=28%  Similarity=0.801  Sum_probs=38.9

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCcc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  307 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~  307 (410)
                      .+|.+|+.  ++  .||+||+|+.|||+.|++++.. .+.+.|+|+.|....
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            47999986  34  4999999999999999998766 445799999998654

>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=99.01  E-value=3.8e-11  Score=94.05  Aligned_cols=53  Identities=28%  Similarity=0.696  Sum_probs=41.9

Q ss_pred             CCCcccccccCcCCCCCCCeeecc--CCCCcccceecccCCC------CCCCcEEcCCCcCcc
Q psy5827         253 SKQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE------PETSDWFCPKCSKVD  307 (410)
Q Consensus       253 ~~~~~~C~VCg~~ddgd~~mI~CD--~C~~W~H~~Clgi~~~------~~~~~W~Cp~C~~~~  307 (410)
                      +++.++| +|+.+++++ .||+|+  .|..|||+.|+|++..      .....|+|+.|....
T Consensus        13 ~~~~~~C-~C~~~~~~~-~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          13 PEIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             CCCccEe-ECCCccCCC-cEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            4456799 999987766 799987  6999999999999754      223479999997553

>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=99.00  E-value=2.1e-11  Score=88.77  Aligned_cols=46  Identities=46%  Similarity=1.209  Sum_probs=38.9

Q ss_pred             cccccccCcCCCCCCCeeeccC---CCCcccceecccCCCCCCCcEEcCCCcC
Q psy5827         256 VWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWFCPKCSK  305 (410)
Q Consensus       256 ~~~C~VCg~~ddgd~~mI~CD~---C~~W~H~~Clgi~~~~~~~~W~Cp~C~~  305 (410)
                      ..|| +|+.+++++  ||.||.   |..|||+.|+|++..+. ++|||+.|..
T Consensus         2 ~~yC-~C~~~~~~~--mi~Cd~~~C~~~WfH~~Cvgl~~~p~-~~w~C~~C~~   50 (51)
T d2pnxa1           2 PTYC-LCHQVSYGE--MIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQ   50 (51)
T ss_dssp             CEET-TTTEECCSE--EEECSCTTCSSCEEEGGGGTCSSCCS-SCCCCHHHHC
T ss_pred             CcEE-EcCCCCCCC--EEEEecCCCCCCCEeCCccCCCcCCC-CcEECcCCCC
Confidence            3589 999988776  999997   57899999999977654 7999999974

>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=98.98  E-value=2.7e-11  Score=96.45  Aligned_cols=51  Identities=20%  Similarity=0.588  Sum_probs=40.5

Q ss_pred             cccccccCcCCCC-CCCeeeccCCCCcccceecccCCC-----CCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddg-d~~mI~CD~C~~W~H~~Clgi~~~-----~~~~~W~Cp~C~~~  306 (410)
                      ..+|.+|+..... ...||+||.|..|||..|++++..     .+.+.|||+.|...
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            3569999986432 237999999999999999998764     34568999999854

>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=98.89  E-value=5.8e-10  Score=85.60  Aligned_cols=50  Identities=22%  Similarity=0.652  Sum_probs=40.1

Q ss_pred             CcccccccCcCCCCCCCeeeccCCCCcccceecccCCC-CCCCcEEcCCCcCccc
Q psy5827         255 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  308 (410)
Q Consensus       255 ~~~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~-~~~~~W~Cp~C~~~~~  308 (410)
                      ...+|.+|+.  .++  ||+||+|+.|||..|++++.. .+.+.|+|+.|.....
T Consensus         6 ~c~~C~~C~~--~~~--ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           6 SATICRVCQK--PGD--LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSSCCSSSCS--SSC--CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCC--cCE--EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            3456888876  344  999999999999999998766 5567999999986544

>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=89.11  E-value=0.14  Score=39.74  Aligned_cols=50  Identities=22%  Similarity=0.619  Sum_probs=36.4

Q ss_pred             ccccccCcCCCCCCCeeeccCCCCcccceecccC----CC---------CCCCcEEcCCCcCccc
Q psy5827         257 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV----AE---------PETSDWFCPKCSKVDE  308 (410)
Q Consensus       257 ~~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~----~~---------~~~~~W~Cp~C~~~~~  308 (410)
                      ..|.||.....+.  ++.|-.|.+.||..|+.--    ..         .....|.|..|...+.
T Consensus        16 ~mC~vC~v~t~~~--l~pCRvCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~nl~~   78 (89)
T d1wila_          16 EMCDVCEVWTAES--LFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNINL   78 (89)
T ss_dssp             CCCTTTCCCCSSC--CSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCCCS
T ss_pred             ccccccCcccccc--eecceeecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcchhh
Confidence            3699997754444  7799999999999997321    10         2346899999987643

>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=88.86  E-value=0.022  Score=40.59  Aligned_cols=50  Identities=22%  Similarity=0.386  Sum_probs=33.0

Q ss_pred             cccccccCcCCCCC-CCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         256 VWICPACGVQDDGS-LPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       256 ~~~C~VCg~~ddgd-~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      ...|.||...+++. .....|.+|..+||..|+..=... .+.+.||.|+..
T Consensus         6 ~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~-~~~~~CP~Cr~~   56 (60)
T d1vyxa_           6 VPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTI-SRNTACQICGVV   56 (60)
T ss_dssp             CCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHH-HTCSBCTTTCCB
T ss_pred             CCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhh-CCCCCCcccCCe
Confidence            34699998765544 122357788899999998642110 134689999865

>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=86.85  E-value=0.2  Score=35.21  Aligned_cols=46  Identities=20%  Similarity=0.361  Sum_probs=33.5

Q ss_pred             cccccCcCCCCCCCeeeccCCCCcccceecccCCCCCCCcEEcCCCcCc
Q psy5827         258 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  306 (410)
Q Consensus       258 ~C~VCg~~ddgd~~mI~CD~C~~W~H~~Clgi~~~~~~~~W~Cp~C~~~  306 (410)
                      .|.||......+...+.+..|+-.||..|+..-...   .-.||.|+..
T Consensus         7 ~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~---~~~CP~CR~~   52 (55)
T d1iyma_           7 ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS---HSTCPLCRLT   52 (55)
T ss_dssp             CCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT---CCSCSSSCCC
T ss_pred             CCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHh---CCcCCCCCCE
Confidence            499998876544356667789999999998764432   3469999853

>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=86.84  E-value=0.55  Score=36.26  Aligned_cols=36  Identities=25%  Similarity=0.601  Sum_probs=29.1

Q ss_pred             CeeeccCCC-CcccceecccCCCCCCCcEEcCCCcCccc
Q psy5827         271 PMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKCSKVDE  308 (410)
Q Consensus       271 ~mI~CD~C~-~W~H~~Clgi~~~~~~~~W~Cp~C~~~~~  308 (410)
                      .||.|..|. ..-|..|..+...  ...|.|..|.....
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 8899999776543  35899999987644