Psyllid ID: psy128

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440------
Protein Sequence
MFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTRQTVCRWIGKHPDNVYGKASHRSVRL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccHHHHccccccccccccccccccccccccccHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccEEcccccccccccccccHHHHHHHHHHHHHHHHHcccccHHHHHcccHHHHHHHHHHHHHHHHHccccHHHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccHHHccHcccccccccccccccccccccccccccccEEcccccccccHHHHcccccccccccccHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHcHHHHHcHHHHHHHccccccccccccccccccHHHHccccHHHHHcccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccEEccccccccEcccEccEEccccccccccHHHcccccccccccccccccccccccccccccEEcccccccccccHHHHHHHHHHHHHccccHHHcccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEcc
Coil and Loop (DISEMBL)
mfpfqfspfpsvagpgliprlppmlqhplipqplvhppgtpppskmkdkvspkdktspkekmsskektspkekeyskvkdvelgvtpmvpnivkvtssedlgeikkdksikkdKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKmkedkekpvEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEkersshekevipkltfkfgtdmeektkresspkivikpvkspspppvaaadeydtgdskqvwicpacgvqddgslpmigcdgcdawYHWVCVGLvaepetsdwfcpkcskvdegsrkekkkrgrkkkthqDIIMSTyrferdpselvdksacagsraDLKLCLLEtdcvqvdrktprqclreglapQCEALKNTFFECKRSLLDTRQTVCRWigkhpdnvygkashrsvrl
Flexible Loop (DISEMBL)
mfpfqfspfpsvAGPGLIPRLPPMLQHPLIPQPLVHPPGtpppskmkdkvspkdktspkekmsskektspkekeyskvkdvelgvtpmvpnivkvtssedlgeikkdksikkdkkthkkkekekikkkkdkkdkdkiknkekdkekkekekgkkeekekkeekekkeekefkmkedkekpvekirkeekdsekekkskdkdkklkkeklkkkkkekersshekevipkltfkfgtdmeektkresspkivikpvkspspppVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAepetsdwfcpkcskvdegsrkekkkrgrkkkthqdiimstyrferdpselVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTRQTVCRwigkhpdnvygkashrsvrl
Low Complexity Region (SEG)
MFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDktspkekmsskektspkekeyskVKDVELGVTPMVPNIVKVTSSEDLGeikkdksikkdkkthkkkekekikkkkdkkdkdkiknkekdkekkekekgkkeekekkeekekkeekefkmkedkekPVekirkeekdsekekkskdkdkklkkeklkkkkkekersshekeVIPKLTFKFGTDMEEKTKRESspkivikpvkspspppvaaaDEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSrkekkkrgrkkkTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTRQTVCRWIGKHPDNVYGKASHRSVRL
Disordered region (IsUnstruct)
************************************************************************************V**MV*NI*************************************************************************************************************************************************************************************KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC***************************TY***********KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTRQTVCRWIGKHPDNVY**********
Disordered Region (DISOPRED)
*FPF*****************************************************************************************************************************************************************************************************************************************************************************KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFC********************************RFERDPSELVDKSACAGSRADLKLCLLETDCVQ*********LREGLAPQCEALKNTFFECKRSLLDTRQTVCRWIGKHPDNVYGKA**R****
Disordered Region (DISEMBL)
MFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGT************************************KVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKS******************************************************************************************************************EVIPKLTFKFGTD**********PKIVIKPVK****************DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK*******************QDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTRQTVCRWIGKHPDNVY**********
Disordered Region (DISPRO)
****QFSPFPSVA*************************************************************************************************************************************************************************************************************************************************************EYD*GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK*********************************SELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTRQTVCRWIGKHPDNVYGK*SH*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFPFQFSPFPSVAGPGLIPRLPPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYRFERDPSELVDKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTRQTVCRWIGKHPDNVYGKASHRSVRL
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	446	2.2.26 [Sep-21-2011]
Q5HZG4	932	Transcription initiation	yes	N/A	0.114	0.054	0.641	8e-17
Q5VWG9	929	Transcription initiation	yes	N/A	0.114	0.054	0.641	1e-16
Q5EAW9	845	Transcription initiation	N/A	N/A	0.109	0.057	0.647	2e-15
Q5F489	930	Transcription initiation	yes	N/A	0.114	0.054	0.603	9e-15
Q3ZCK8	74	Cytochrome c oxidase asse	no	N/A	0.121	0.729	0.614	2e-12
Q28CA1	75	Cytochrome c oxidase asse	no	N/A	0.125	0.746	0.610	3e-12
Q8IDX6	3130	Reticulocyte-binding prot	yes	N/A	0.311	0.044	0.236	2e-05
F1QBY1	2876	Nipped-B-like protein B O	no	N/A	0.226	0.035	0.409	0.0002

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

 Score = 89.0 bits (219), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 38/53 (71%), Gaps = 2/53 (3%)

Query: 274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 325
            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 = 87.8 bits (216), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 34/53 (64%), Positives = 38/53 (71%), Gaps = 2/53 (3%)

Query: 274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCSK 325
            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|Q5EAW9|TAF3_XENLA Transcription initiation factor TFIID subunit 3 OS=Xenopus laevis GN=taf3 PE=2 SV=1

 Score = 84.0 bits (206), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 33/51 (64%), Positives = 35/51 (68%), Gaps = 2/51 (3%)

Query: 274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 323
            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|Q5F489|TAF3_CHICK Transcription initiation factor TFIID subunit 3 OS=Gallus gallus GN=TAF3 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 32/53 (60%), Positives = 35/53 (66%), Gaps = 2/53 (3%)

Query: 274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 325
            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|Q3ZCK8|COA5_BOVIN Cytochrome c oxidase assembly factor 5 OS=Bos taurus GN=COA5 PE=3 SV=1

 Score = 74.3 bits (181), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 44/57 (77%), Gaps = 3/57 (5%)

Query: 365 SACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTR 421
            ACAG + DL LCLL++DCV  + K+PRQCL+EG    C+ALK +FFECKRS+LD R
Sbjct: 12  GACAGVKEDLGLCLLQSDCVLKEGKSPRQCLKEG---NCKALKYSFFECKRSMLDAR 65

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

Bos taurus (taxid: 9913)

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

 Score = 73.2 bits (178), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 36/59 (61%), Positives = 46/59 (77%), Gaps = 3/59 (5%)

Query: 363 DKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFECKRSLLDTR 421
           DK  CAG + DLK CLL+TDCV  + K+P++CL+EG    C+AL+ TFFECKRS+LDTR
Sbjct: 11  DKHPCAGVKEDLKSCLLQTDCVLQEGKSPKECLKEGY---CKALQVTFFECKRSILDTR 66

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

Xenopus tropicalis (taxid: 8364)

>sp|Q8IDX6|RBP2A_PLAF7 Reticulocyte-binding protein 2 homolog a OS=Plasmodium falciparum (isolate 3D7) GN=PF13_0198 PE=3 SV=1

 Score = 50.8 bits (120), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/148 (23%), Positives = 91/148 (61%), Gaps = 9/148 (6%)

Query: 114  KKTHKKKEKEKIKKKKDK----KDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEK 169
            ++  ++ +KE+  K++++    ++K +   KE++ +++E+E+ +KEE  K++E+E+ +++
Sbjct: 2741 RQEQERLQKEEELKRQEQERLEREKQEQLQKEEELKRQEQERLQKEEALKRQEQERLQKE 2800

Query: 170  EFKMKEDKEK----PVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEV 225
            E   ++++E+      E+++KEE+   +E++   K++ LK+++ ++ +KE+E    E+E 
Sbjct: 2801 EELKRQEQERLEREKQEQLQKEEELKRQEQERLQKEEALKRQEQERLQKEEELKRQEQER 2860

Query: 226  IPKLTFKFGTDMEE-KTKRESSPKIVIK 252
            + +   +     +  K+K ES    +IK
Sbjct: 2861 LERKKIELAEREQHIKSKLESDMVKIIK 2888

Involved in reticulocyte adhesion.

Plasmodium falciparum (isolate 3D7) (taxid: 36329)

>sp|F1QBY1|NIPLB_DANRE Nipped-B-like protein B OS=Danio rerio GN=nipblb PE=2 SV=1

 Score = 47.4 bits (111), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 43/105 (40%), Positives = 74/105 (70%), Gaps = 4/105 (3%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKE-KKEKEKGKKEEKEKKEEKEKKEEKEFKMKED 176
           + KE+ K + KK  KD +K + K++DKE +K++EK + +E EK  EK++ +E E   ++D
Sbjct: 746 RDKEQVKGRDKKRSKDLEKCREKDQDKELEKDREKNQDKELEKGREKDQDKELEKGREKD 805

Query: 177 KEKPVEKIRKEEKDSEKEK-KSKDKDKKLKK--EKLKKKKKEKER 218
           ++K +EK R++++D E EK + KD+DK+L+K  EK + K +EK+R
Sbjct: 806 RDKEMEKAREKDQDKELEKGREKDQDKELEKGQEKDRDKVREKDR 850

Probably plays a structural role in chromatin. Involved in sister chromatid cohesion, possibly by facilitating the cohesin complex loading, and in transcription regulation.

Danio rerio (taxid: 7955)

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	446
193713718	590	PREDICTED: hypothetical protein LOC10016	0.192	0.145	0.521	7e-20
270015055	865	hypothetical protein TcasGA2_TC014217 [T	0.154	0.079	0.578	9e-20
328700739	906	PREDICTED: hypothetical protein LOC10016	0.152	0.075	0.586	1e-19
189233756	872	PREDICTED: similar to bip2 CG2009-PA [Tr	0.116	0.059	0.685	7e-18
357604267	1167	hypothetical protein KGM_08958 [Danaus p	0.165	0.063	0.5	3e-17
195133998	1094	GI14094 [Drosophila mojavensis] gi|19391	0.125	0.051	0.603	5e-17
353230188	1690	hypothetical protein Smp_127180 [Schisto	0.165	0.043	0.452	9e-17
256072183	1282	hypothetical protein [Schistosoma manson	0.165	0.057	0.452	1e-16
195172552	1497	GL18176 [Drosophila persimilis] gi|19411	0.161	0.048	0.5	1e-16
115711961	1047	PREDICTED: uncharacterized protein LOC59	0.116	0.049	0.615	1e-16

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

 Score =  105 bits (261), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 49/94 (52%), Positives = 60/94 (63%), Gaps = 8/94 (8%)

Query: 250 VIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL 309
           VI PV   +PPP    DE       QVWICP C   DDGS PMIGCDGCD WYHWVCVG+
Sbjct: 503 VIPPVNE-TPPPAFYFDEA----GNQVWICPMCTKPDDGS-PMIGCDGCDVWYHWVCVGI 556

Query: 310 VAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKT 343
              P+ + WFCP+C  + + +++ K KRGR +K 
Sbjct: 557 QCPPDCAVWFCPRC--LAKRAQQPKGKRGRPRKN 588

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  104 bits (259), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 44/76 (57%), Positives = 50/76 (65%), Gaps = 7/76 (9%)

Query: 249 IVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVG 308
           IV  P+  P+PP       Y   D  +VWICP CG QDDGS PMIGCDGCDAWYHWVCVG
Sbjct: 770 IVDVPIVPPAPP-----SRYIDADGNEVWICPGCGSQDDGS-PMIGCDGCDAWYHWVCVG 823

Query: 309 LVAEPETS-DWFCPKC 323
           +   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|328700739|ref|XP_001945181.2| PREDICTED: hypothetical protein LOC100167514 [Acyrthosiphon pisum]

 Score =  103 bits (258), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 44/75 (58%), Positives = 52/75 (69%), Gaps = 7/75 (9%)

Query: 269 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS--KV 326
           D G+  QVWICP CG QDDGS PM+GCDGCDAWYHWVCVG+   P+ + W+CP C   + 
Sbjct: 827 DAGN--QVWICPTCGKQDDGS-PMVGCDGCDAWYHWVCVGIQCPPDCAVWYCPTCLLKRA 883

Query: 327 DEGSRK--EKKKRGR 339
           + 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|189233756|ref|XP_001814148.1| PREDICTED: similar to bip2 CG2009-PA [Tribolium castaneum]

 Score = 98.2 bits (243), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 37/54 (68%), Positives = 41/54 (75%), Gaps = 2/54 (3%)

Query: 271 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETS-DWFCPKC 323
            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

>gi|357604267|gb|EHJ64117.1| hypothetical protein KGM_08958 [Danaus plexippus]

 Score = 96.3 bits (238), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 40/80 (50%), Positives = 49/80 (61%), Gaps = 6/80 (7%)

Query: 268  YDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC--- 323
            Y      ++W+CPACG  D+GS PMIGCDGCD WYHW+CVG+  +P  T DWFC  C   
Sbjct: 1081 YVDEQGNKIWVCPACGRPDNGS-PMIGCDGCDGWYHWICVGITEDPGATEDWFCKSCVAK 1139

Query: 324  -SKVDEGSRKEKKKRGRKKK 342
             + +        KKRGRK K
Sbjct: 1140 RAAMVLAGVTSGKKRGRKPK 1159

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195133998|ref|XP_002011425.1| GI14094 [Drosophila mojavensis] gi|193912048|gb|EDW10915.1| GI14094 [Drosophila mojavensis]

 Score = 95.5 bits (236), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 35/58 (60%), Positives = 41/58 (70%), Gaps = 2/58 (3%)

Query: 267  EYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 323
             Y   D  ++WICPACG  DDGS  MIGCDGCDAWYHW+CVG++  P +  DWFC  C
Sbjct: 1016 SYVDADGYRIWICPACGKVDDGS-AMIGCDGCDAWYHWICVGILVAPNDNEDWFCRVC 1072

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|353230188|emb|CCD76359.1| hypothetical protein Smp_127180 [Schistosoma mansoni]

 Score = 94.7 bits (234), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 38/84 (45%), Positives = 52/84 (61%), Gaps = 10/84 (11%)

Query: 242  KRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAW 301
            +RES+ +IV++          A +  Y   D +Q+W+CP C ++DDG+L MIGCD C  W
Sbjct: 1417 QRESASQIVVES---------AGSSYYFNNDGEQIWLCPICLLEDDGNL-MIGCDNCQDW 1466

Query: 302  YHWVCVGLVAEPETSDWFCPKCSK 325
            YH  C+GL   PE   WFCPKCS+
Sbjct: 1467 YHSTCLGLSKAPEVPQWFCPKCSQ 1490

Source: Schistosoma mansoni

Species: Schistosoma mansoni

Genus: Schistosoma

Family: Schistosomatidae

Order: Strigeidida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|256072183|ref|XP_002572416.1| hypothetical protein [Schistosoma mansoni]

 Score = 94.4 bits (233), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 38/84 (45%), Positives = 52/84 (61%), Gaps = 10/84 (11%)

Query: 242 KRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAW 301
           +RES+ +IV++          A +  Y   D +Q+W+CP C ++DDG+L MIGCD C  W
Sbjct: 926 QRESASQIVVE---------SAGSSYYFNNDGEQIWLCPICLLEDDGNL-MIGCDNCQDW 975

Query: 302 YHWVCVGLVAEPETSDWFCPKCSK 325
           YH  C+GL   PE   WFCPKCS+
Sbjct: 976 YHSTCLGLSKAPEVPQWFCPKCSQ 999

Source: Schistosoma mansoni

Species: Schistosoma mansoni

Genus: Schistosoma

Family: Schistosomatidae

Order: Strigeidida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|195172552|ref|XP_002027061.1| GL18176 [Drosophila persimilis] gi|194112839|gb|EDW34882.1| GL18176 [Drosophila persimilis]

 Score = 94.4 bits (233), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 39/78 (50%), Positives = 47/78 (60%), Gaps = 6/78 (7%)

Query: 251  IKPVKSPSPPP----VAAADEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVC 306
            ++P  SP  PP    +     Y   +  ++WICPACG  DDGS  MIGCDGCDAWYHW C
Sbjct: 1402 VEPTHSPDCPPQIVELNRPSSYVDAEGNRIWICPACGKVDDGSA-MIGCDGCDAWYHWTC 1460

Query: 307  VGLVAEP-ETSDWFCPKC 323
            VG+   P +  DWFC  C
Sbjct: 1461 VGITVAPKDNDDWFCRVC 1478

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|115711961|ref|XP_797041.2| PREDICTED: uncharacterized protein LOC592424 [Strongylocentrotus purpuratus]

 Score = 94.4 bits (233), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 32/52 (61%), Positives = 39/52 (75%)

Query: 272  DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKC 323
            D +++W CPAC   DDG LPMIGCD CD WYHW CVG+  EP T+DW+C +C
Sbjct: 982  DGEKIWYCPACKKADDGVLPMIGCDTCDDWYHWECVGITEEPSTNDWYCKRC 1033

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

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	446
UNIPROTKB|E1BIA9	932	TAF3 "Uncharacterized protein"	0.107	0.051	0.68	1.9e-21
UNIPROTKB|Q5VWG9	929	TAF3 "Transcription initiation	0.109	0.052	0.666	3.2e-20
ZFIN|ZDB-GENE-030131-6406	898	taf3 "TAF3 RNA polymerase II,	0.109	0.054	0.666	1.2e-19
UNIPROTKB|F1RUM5	794	TAF3 "Uncharacterized protein"	0.107	0.060	0.7	1.5e-19
UNIPROTKB|F1NZW0	874	TAF3 "Transcription initiation	0.109	0.056	0.627	2.2e-19
UNIPROTKB|Q5F489	930	TAF3 "Transcription initiation	0.109	0.052	0.627	2.7e-19
UNIPROTKB|F1PI56	932	TAF3 "Uncharacterized protein"	0.109	0.052	0.666	6.7e-19
MGI|MGI:2388097	932	Taf3 "TAF3 RNA polymerase II,	0.109	0.052	0.666	1.7e-18
FB|FBgn0026262	1408	bip2 "bip2" [Drosophila melano	0.118	0.037	0.607	8.5e-16
WB|WBGene00006384	1007	taf-3 [Caenorhabditis elegans	0.134	0.059	0.5	1.2e-14

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

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

Query:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 323
             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|Q5VWG9 TAF3 "Transcription initiation factor TFIID subunit 3" [Homo sapiens (taxid:9606)]

 Score = 216 (81.1 bits), Expect = 3.2e-20, Sum P(3) = 3.2e-20
 Identities = 34/51 (66%), Positives = 38/51 (74%)

Query:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSDWFCPKCS 324
             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

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 = 1.2e-19, Sum P(2) = 1.2e-19
 Identities = 34/51 (66%), Positives = 37/51 (72%)

Query:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 324
             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|F1RUM5 TAF3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

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

Query:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 323
             Q+WICP C   DDGS PMIGCDGCD WYHW CVG+ A P E   WFCPKC
Sbjct:   729 QIWICPGCNKPDDGS-PMIGCDGCDDWYHWPCVGITAAPPEEMQWFCPKC 777

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

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

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

GO:0002039 "p53 binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 203 (76.5 bits), Expect = 2.2e-19, Sum P(2) = 2.2e-19
 Identities = 32/51 (62%), Positives = 35/51 (68%)

Query:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 324
             Q+W CP C   DDGS PMIGCD CD WYHW CVG+ A P E   WFC KC+
Sbjct:   809 QIWFCPGCNKPDDGS-PMIGCDDCDDWYHWPCVGITAAPPEEMQWFCSKCA 858

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0002039 "p53 binding" evidence=IEA

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

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

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

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

 Score = 203 (76.5 bits), Expect = 2.7e-19, Sum P(2) = 2.7e-19
 Identities = 32/51 (62%), Positives = 35/51 (68%)

Query:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 324
             Q+W CP C   DDGS PMIGCD CD WYHW CVG+ A P E   WFC KC+
Sbjct:   865 QIWFCPGCNKPDDGS-PMIGCDDCDDWYHWPCVGITAAPPEEMQWFCSKCA 914

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

Query:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 324
             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

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:   275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCS 324
             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

FB|FBgn0026262 bip2 "bip2" [Drosophila melanogaster (taxid:7227)]

 Score = 212 (79.7 bits), Expect = 8.5e-16, P = 8.5e-16
 Identities = 34/56 (60%), Positives = 41/56 (73%)

Query:   269 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKC 323
             DT +  ++WICPACG  D+GS  MIGCDGCDAWYHW+CVG+   P +  DWFC  C
Sbjct:  1336 DT-EGNRIWICPACGKVDEGSA-MIGCDGCDAWYHWICVGITFAPKDNDDWFCRVC 1389

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

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

GO:0008134 "transcription factor binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0031208 "POZ domain binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0008270 "zinc ion binding" evidence=IEA

GO:0002039 "p53 binding" evidence=IPI

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IGI;IMP

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

 Score = 192 (72.6 bits), Expect = 1.2e-14, Sum P(3) = 1.2e-14
 Identities = 30/60 (50%), Positives = 37/60 (61%)

Query:   266 DEYDTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK 325
             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

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

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	446
pfam10203	68	pfam10203, Pet191_N, Cytochrome c oxidase assembly	2e-18
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-10
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-10
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-10
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-09
smart00249	47	smart00249, PHD, PHD zinc finger	1e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-09
pfam00628	51	pfam00628, PHD, PHD-finger	2e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-09
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-08
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	5e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	1e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	2e-07
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	3e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-07
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	8e-07
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	9e-07
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-06
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	2e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-06
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	3e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-06
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-06
PRK05896	605	PRK05896, PRK05896, DNA polymerase III subunits ga	5e-06
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	6e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-06
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	8e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-05
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	1e-05
pfam05262	489	pfam05262, Borrelia_P83, Borrelia P83/100 protein	1e-05
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	1e-05
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	1e-05
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	1e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	2e-05
CHL00189	742	CHL00189, infB, translation initiation factor 2; P	2e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-05
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	3e-05
COG3064	387	COG3064, TolA, Membrane protein involved in colici	3e-05
COG3064	387	COG3064, TolA, Membrane protein involved in colici	3e-05
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	3e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-05
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	4e-05
pfam05758	832	pfam05758, Ycf1, Ycf1	4e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	6e-05
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	6e-05
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	6e-05
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	7e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	7e-05
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	7e-05
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	8e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	9e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	1e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	1e-04
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	3e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	3e-04
pfam13166	713	pfam13166, AAA_13, AAA domain	3e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	4e-04
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	4e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-04
pfam13166	713	pfam13166, AAA_13, AAA domain	4e-04
pfam09756	189	pfam09756, DDRGK, DDRGK domain	4e-04
COG2176	1444	COG2176, PolC, DNA polymerase III, alpha subunit (	4e-04
smart00935	140	smart00935, OmpH, Outer membrane protein (OmpH-lik	4e-04
pfam09592	228	pfam09592, DUF2031, Protein of unknown function (D	5e-04
pfam13476	204	pfam13476, AAA_23, AAA domain	5e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	5e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	5e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	6e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	7e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	7e-04
pfam06102	168	pfam06102, DUF947, Domain of unknown function (DUF	7e-04
COG1293	564	COG1293, COG1293, Predicted RNA-binding protein ho	7e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	8e-04
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	8e-04
COG5185	622	COG5185, HEC1, Protein involved in chromosome segr	9e-04
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.001
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.001
pfam05087	887	pfam05087, Rota_VP2, Rotavirus VP2 protein	0.001
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.001
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.001
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	0.001
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.001
pfam13476	204	pfam13476, AAA_23, AAA domain	0.001
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.001
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.001
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.001
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.001
PRK00247	429	PRK00247, PRK00247, putative inner membrane protei	0.001
PRK00448	1437	PRK00448, polC, DNA polymerase III PolC; Validated	0.001
COG5034	271	COG5034, TNG2, Chromatin remodeling protein, conta	0.001
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.001
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	0.001
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.002
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	0.002
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.002
smart00435	391	smart00435, TOPEUc, DNA Topoisomerase I (eukaryota	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.002
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
COG0610	962	COG0610, COG0610, Type I site-specific restriction	0.002
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	0.002
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	0.002
PLN02381	1066	PLN02381, PLN02381, valyl-tRNA synthetase	0.002
pfam00012	598	pfam00012, HSP70, Hsp70 protein	0.002
pfam09731	493	pfam09731, Mitofilin, Mitochondrial inner membrane	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.003
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.003
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.003
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.003
PTZ00108	1388	PTZ00108, PTZ00108, DNA topoisomerase 2-like prote	0.003
PTZ00372	413	PTZ00372, PTZ00372, endonuclease 4-like protein; P	0.003
pfam05758	832	pfam05758, Ycf1, Ycf1	0.003
pfam09756	189	pfam09756, DDRGK, DDRGK domain	0.003
pfam12569	516	pfam12569, NARP1, NMDA receptor-regulated protein	0.003
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.003
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	0.003
PRK14907	295	PRK14907, rplD, 50S ribosomal protein L4; Provisio	0.003
PRK00106	535	PRK00106, PRK00106, hypothetical protein; Provisio	0.003
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.003
PRK12705	508	PRK12705, PRK12705, hypothetical protein; Provisio	0.003
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.003
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.004
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	0.004
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.004
pfam03839	217	pfam03839, Sec62, Translocation protein Sec62	0.004
pfam06375	561	pfam06375, BLVR, Bovine leukaemia virus receptor (	0.004
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	0.004
COG5604	523	COG5604, COG5604, Uncharacterized conserved protei	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
PTZ00342	746	PTZ00342, PTZ00342, acyl-CoA synthetase; Provision	0.004
pfam06391	200	pfam06391, MAT1, CDK-activating kinase assembly fa	0.004

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

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 32/63 (50%), Positives = 44/63 (69%), Gaps = 3/63 (4%)

Query: 363 DKSACAGSRADLKLCLLETDCVQVDRKTPRQCLREGLAP---QCEALKNTFFECKRSLLD 419
             S+C G R DL  CLLE+DCV+ +++TPR+CL+E L     +C AL+  FFECKR +LD
Sbjct: 1   MGSSCKGLREDLAECLLESDCVKKEKRTPRECLKEPLKELPEECIALRKAFFECKRGMLD 60

Query: 420 TRQ 422
            R+
Sbjct: 61  MRK 63

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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 63.2 bits (153), Expect = 2e-10
 Identities = 42/122 (34%), Positives = 66/122 (54%)

Query: 103  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEE 162
            E KK    KK  +  KKK  E  K    KK  D+ K K ++K+K ++ K K EE +K +E
Sbjct: 1389 EKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE 1448

Query: 163  KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 222
             +KK E+  K +E K+K  E  + +E   + E+  K  + K K E+ KKK  E ++++  
Sbjct: 1449 AKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEA 1508

Query: 223  KE 224
            K+
Sbjct: 1509 KK 1510

Length = 2084

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

 Score = 60.3 bits (147), Expect = 7e-10
 Identities = 24/76 (31%), Positives = 46/76 (60%)

Query: 129 KDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEE 188
             KK   KIK   +  EKK +E+ K+++K+    K+K+EE+E + ++ +E+  E+  + E
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAE 463

Query: 189 KDSEKEKKSKDKDKKL 204
           ++ E+E++ K K   L
Sbjct: 464 EEKEEEEEKKKKQATL 479

Length = 482

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

 Score = 60.9 bits (147), Expect = 9e-10
 Identities = 35/127 (27%), Positives = 66/127 (51%), Gaps = 5/127 (3%)

Query: 103  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIK----NKEKDKEKKEKEKGKKEE-K 157
            E  K K+    KK  + K+  +  K + +   D+ +      E  ++KKE+ K K +  K
Sbjct: 1325 EEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAK 1384

Query: 158  EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
            +K EEK+K +E + K +EDK+K  E  +      + ++  K  ++K K ++ KKK +E +
Sbjct: 1385 KKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAK 1444

Query: 218  RSSHEKE 224
            ++   K+
Sbjct: 1445 KADEAKK 1451

Length = 2084

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

 Score = 60.0 bits (146), Expect = 1e-09
 Identities = 29/187 (15%), Positives = 61/187 (32%)

Query: 40  TPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSE 99
           T      +++   K K    +  S    T  + KE  + K         V   +     +
Sbjct: 6   TKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKD 65

Query: 100 DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEK 159
                + D   KK K   K    +   KKK K + D  K  EK     + +     +   
Sbjct: 66  TDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDID 125

Query: 160 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 219
              +   ++ +    +  +  ++    +E D E +      D+  +K++ K+ +K  +  
Sbjct: 126 VLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDD 185

Query: 220 SHEKEVI 226
               +  
Sbjct: 186 DFVWDED 192

Length = 509

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

 Score = 53.4 bits (128), Expect = 1e-09
 Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVG--LVAEPETSDWFCPKC 323
            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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 59.2 bits (144), Expect = 2e-09
 Identities = 21/79 (26%), Positives = 53/79 (67%)

Query: 130 DKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEK 189
            +++ + +   +K  +K +K   K E+K ++E+KEKK++     K+++E+  EK +KEE+
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 190 DSEKEKKSKDKDKKLKKEK 208
             E+E++++++ ++ +++K
Sbjct: 455 KEEEEEEAEEEKEEEEEKK 473

Length = 482

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

 Score = 52.9 bits (127), Expect = 2e-09
 Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 4/50 (8%)

Query: 278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPET---SDWFCPKCS 324
            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|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 58.8 bits (143), Expect = 3e-09
 Identities = 27/81 (33%), Positives = 52/81 (64%)

Query: 133 DKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSE 192
            +++I+     K+  +K K   E+ EKK E+EKKE+K+      K++  E+  KE+K+ E
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 193 KEKKSKDKDKKLKKEKLKKKK 213
           KE++ ++ +++ ++E+ KKKK
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 59.0 bits (142), Expect = 4e-09
 Identities = 36/122 (29%), Positives = 64/122 (52%), Gaps = 2/122 (1%)

Query: 103  EIKKDKSIKKDKKTHKKKEKEKIKKKK--DKKDKDKIKNKEKDKEKKEKEKGKKEEKEKK 160
            E KK     K +      E E  ++K    +K K++ K K    +KK +EK K +E +KK
Sbjct: 1340 EAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKK 1399

Query: 161  EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 220
             E++KK+  E K     +K  ++ +K+ ++ +K  ++K K ++ KK    KKK E+ + +
Sbjct: 1400 AEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKA 1459

Query: 221  HE 222
             E
Sbjct: 1460 EE 1461

Length = 2084

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

 Score = 58.0 bits (141), Expect = 4e-09
 Identities = 33/85 (38%), Positives = 55/85 (64%), Gaps = 10/85 (11%)

Query: 116 THKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKE 175
           T  KK  +KIKK  +K +K      ++++EKKEK+K     K+K+EE+E+++EK    KE
Sbjct: 403 TGSKKATKKIKKIVEKAEK------KREEEKKEKKKKAFAGKKKEEEEEEEKEK----KE 452

Query: 176 DKEKPVEKIRKEEKDSEKEKKSKDK 200
           ++++  E+  +EEK+ E+EKK K  
Sbjct: 453 EEKEEEEEEAEEEKEEEEEKKKKQA 477

Length = 482

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

 Score = 57.1 bits (137), Expect = 1e-08
 Identities = 53/186 (28%), Positives = 98/186 (52%), Gaps = 8/186 (4%)

Query: 71   KEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK-KKEKEKIKKKK 129
            K+ E +K+K  EL         V+    ++  E KK + +KK ++ +K K  +E  K ++
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 130  DKKDKDKIKNKEKDKEK-------KEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVE 182
            DKK  ++ K  E+D++K       + +E  K EE +KKE +EKK+ +E K  E++ K   
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKA 1732

Query: 183  KIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTK 242
            +  K+E + +K+K  + K  + +K+K+   KKE+E+ + E     +   +   D E++ +
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKR 1792

Query: 243  RESSPK 248
            R    K
Sbjct: 1793 RMEVDK 1798

Length = 2084

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

 Score = 56.7 bits (136), Expect = 2e-08
 Identities = 48/181 (26%), Positives = 87/181 (48%), Gaps = 1/181 (0%)

Query: 44   SKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 103
            +   +    K + + K+K  +K+K    +K+  + K  +        +  K    +    
Sbjct: 1356 ADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAA 1415

Query: 104  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEK 163
             KK     K K   KKK  E  KK ++ K  D+ K K ++ +K E+ K K EE +K +E 
Sbjct: 1416 AKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEA 1475

Query: 164  EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 223
            +KK E+  K  E K+K  E+ +K+  +++K  ++K K  + KK +  KK  E +++   K
Sbjct: 1476 KKKAEEAKKADEAKKK-AEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAK 1534

Query: 224  E 224
            +
Sbjct: 1535 K 1535

Length = 2084

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

 Score = 55.5 bits (133), Expect = 4e-08
 Identities = 44/185 (23%), Positives = 94/185 (50%), Gaps = 4/185 (2%)

Query: 44   SKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 103
            ++ K + + K K   K+K  + +K + ++K+  + K            + K  +++   +
Sbjct: 1362 AEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKAD 1421

Query: 104  IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEK 163
              K K+ +K K    KK+ E+ KK  + K K +   K ++ +KK +E  K +E +KK E+
Sbjct: 1422 EAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEE 1481

Query: 164  EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKK----KKKEKERS 219
             KK ++  K  E+ +K  ++ +K  +  +K  ++K  ++  K ++ KK    KK ++ + 
Sbjct: 1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541

Query: 220  SHEKE 224
            + EK+
Sbjct: 1542 AEEKK 1546

Length = 2084

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

 Score = 55.5 bits (133), Expect = 4e-08
 Identities = 35/115 (30%), Positives = 64/115 (55%), Gaps = 4/115 (3%)

Query: 114  KKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKM 173
            KK  +KK+ ++ KK ++KK  D+ K K ++ +K ++ K K EE +KK +  KK+ +E K 
Sbjct: 1284 KKAEEKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKK 1343

Query: 174  KEDKEKPVEKIRKEEKDSEKEKKSKDKDK----KLKKEKLKKKKKEKERSSHEKE 224
              +  K   +   +E ++ +EK    + K    K K +  KKK +EK+++   K+
Sbjct: 1344 AAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKK 1398

Length = 2084

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

 Score = 54.5 bits (131), Expect = 5e-08
 Identities = 39/129 (30%), Positives = 68/129 (52%), Gaps = 3/129 (2%)

Query: 92  IVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEK 151
            VK                 K+ K    KE+EK K++  ++ K K   KEK KE+ +  K
Sbjct: 76  AVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKK---KEKPKEEPKDRK 132

Query: 152 GKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKK 211
            K+E KEK+  KEK++EKE K++E +++  EK R+  +   + KK   K    KK++  +
Sbjct: 133 PKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPE 192

Query: 212 KKKEKERSS 220
           ++K+++ + 
Sbjct: 193 EEKQRQAAR 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|173412 PTZ00121, PTZ00121, MAEBL; Provisional

 Score = 54.0 bits (129), Expect = 1e-07
 Identities = 45/208 (21%), Positives = 93/208 (44%), Gaps = 8/208 (3%)

Query: 49   KVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDK 108
            K     K + + K + +E+ + + +++ + +              +   +++L + ++ K
Sbjct: 1231 KAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKK 1290

Query: 109  SIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEE 168
               + KK  +KK+ ++ KKK ++  K     K+ ++ KK+ +  KK+ +E K+  E  + 
Sbjct: 1291 KADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKA 1350

Query: 169  KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKK-----LKKEKLKKKKKEKERSSHE- 222
            +     ++ E   EK    EK  E+ KK  D  KK      K ++ KKK +E ++ + E 
Sbjct: 1351 EAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADEL 1410

Query: 223  --KEVIPKLTFKFGTDMEEKTKRESSPK 248
                   K   +     EEK K + + K
Sbjct: 1411 KKAAAAKKKADEAKKKAEEKKKADEAKK 1438

Length = 2084

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

 Score = 53.4 bits (129), Expect = 1e-07
 Identities = 27/66 (40%), Positives = 48/66 (72%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
           K  K IKK  +  +KK +E+ K+KK K    K K +E+++EK++KE+ K+EE+E+ EE++
Sbjct: 407 KATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEK 466

Query: 165 KKEEKE 170
           ++EE++
Sbjct: 467 EEEEEK 472

Length = 482

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

 Score = 52.6 bits (127), Expect = 2e-07
 Identities = 29/81 (35%), Positives = 53/81 (65%), Gaps = 1/81 (1%)

Query: 100 DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEK 159
              EI+     KK  K   KK  EK +KK++++ K+K K     K+K+E+E+ +KE+KE+
Sbjct: 395 TEEEIEFLTGSKKATKK-IKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEE 453

Query: 160 KEEKEKKEEKEFKMKEDKEKP 180
           ++E+E++E +E K +E+++K 
Sbjct: 454 EKEEEEEEAEEEKEEEEEKKK 474

Length = 482

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

 Score = 52.1 bits (126), Expect = 3e-07
 Identities = 33/130 (25%), Positives = 73/130 (56%), Gaps = 11/130 (8%)

Query: 108 KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKE---KDKEKKEKEKGKKEEKEKKEEKE 164
           K I + K    ++E ++I ++  K+ +   K      K++  K + + +KE +E++ E +
Sbjct: 26  KKIAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQ 85

Query: 165 KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK- 223
           K E++  + +E+ ++ +E + K E++ EK++K  ++    K+++L+KK++E E    E+ 
Sbjct: 86  KLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQ----KQQELEKKEEELEELIEEQL 141

Query: 224 ---EVIPKLT 230
              E I  LT
Sbjct: 142 QELERISGLT 151

Length = 520

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

 Score = 52.5 bits (125), Expect = 4e-07
 Identities = 44/181 (24%), Positives = 79/181 (43%), Gaps = 2/181 (1%)

Query: 45   KMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEI 104
            K  ++    D+   K +   K+    K+   +K K  E           K   ++   E 
Sbjct: 1385 KKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEA--KKKAEEKKKADEAKKKAEE 1442

Query: 105  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
             K     K K    KK +E  KK ++ K  D+ K K ++ +K ++ K K EE +KK ++ 
Sbjct: 1443 AKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEA 1502

Query: 165  KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 224
            KK  +  K  ++ +K  E  + +E    +E K  D+ KK +++K   + K+ E     +E
Sbjct: 1503 KKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEE 1562

Query: 225  V 225
             
Sbjct: 1563 K 1563

Length = 2084

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

 Score = 52.0 bits (125), Expect = 4e-07
 Identities = 20/133 (15%), Positives = 65/133 (48%), Gaps = 3/133 (2%)

Query: 96  TSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKE 155
               +L E++++    +++    K+E E+++ +     +++++  E + E+ E+   + +
Sbjct: 271 ELKSELEELREELEELQEELLELKEEIEELEGEI-SLLRERLEELENELEELEERLEELK 329

Query: 156 EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK--KEKLKKKK 213
           EK +  ++E +E +    + ++     +  KEE + +     ++ ++  +  +E+L + +
Sbjct: 330 EKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELE 389

Query: 214 KEKERSSHEKEVI 226
            E     +E E +
Sbjct: 390 AELAEIRNELEEL 402

Length = 1163

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

 Score = 51.5 bits (124), Expect = 5e-07
 Identities = 24/83 (28%), Positives = 54/83 (65%)

Query: 97  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEE 156
           + E++  +   K   K  K   +K ++K +++K +K K     K+K++E++E+++ K+EE
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 157 KEKKEEKEKKEEKEFKMKEDKEK 179
           KE++EE+ ++E++E + K+ K+ 
Sbjct: 455 KEEEEEEAEEEKEEEEEKKKKQA 477

Length = 482

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

 Score = 51.7 bits (123), Expect = 7e-07
 Identities = 44/184 (23%), Positives = 89/184 (48%), Gaps = 8/184 (4%)

Query: 49   KVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDK 108
            K     K    +K    +K    +K   K K  EL     +    +   +E+  + ++DK
Sbjct: 1517 KAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDK 1576

Query: 109  SIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEE 168
            ++   K    KK +E   ++  K  +++ K K ++ +K E+ K K EE +K EE++KK E
Sbjct: 1577 NMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVE 1636

Query: 169  KEFKMKEDKEKPVEKIRKEEKDSE--------KEKKSKDKDKKLKKEKLKKKKKEKERSS 220
            +  K + +++K  E+++K E++++        K ++ K K ++ KK +  +KK  +    
Sbjct: 1637 QLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKK 1696

Query: 221  HEKE 224
              +E
Sbjct: 1697 EAEE 1700

Length = 2084

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

 Score = 51.1 bits (123), Expect = 7e-07
 Identities = 26/171 (15%), Positives = 55/171 (32%), Gaps = 3/171 (1%)

Query: 55  KTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDK 114
           K   KE + SK+KT  +  +        +  T                           K
Sbjct: 35  KEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKK 94

Query: 115 KTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMK 174
           K   + +  K  +KK+  DKD   N  KD +   +     ++ +  +  +   + +   +
Sbjct: 95  KLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDE 154

Query: 175 EDKEKPVEKIRKEEKDS---EKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 222
           +D E   +    +E +     KE +    D     ++   +   + R   +
Sbjct: 155 DDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAK 205

Length = 509

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

 Score = 51.1 bits (122), Expect = 8e-07
 Identities = 33/146 (22%), Positives = 78/146 (53%), Gaps = 2/146 (1%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKE 158
           E+   +  D     +++    +E  + ++++ +  K +++ KE++   +  ++ K+EEKE
Sbjct: 223 EEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELE-KEEEILAQVLKENKEEEKE 281

Query: 159 KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
           KK ++E+ +    + +E K + ++  R++  D EK K+S+ K+ K  +++LKK+K+E E 
Sbjct: 282 KKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESE-KELKKLEKELKKEKEEIEE 340

Query: 219 SSHEKEVIPKLTFKFGTDMEEKTKRE 244
              E + +         + E+  K +
Sbjct: 341 LEKELKELEIKREAEEEEEEQLEKLQ 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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 49.3 bits (118), Expect = 9e-07
 Identities = 21/77 (27%), Positives = 42/77 (54%)

Query: 111 KKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKE 170
             D++  KK + ++  + ++ K+++K     +DKE K   + + EE E++ E+E +E  +
Sbjct: 45  AADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSD 104

Query: 171 FKMKEDKEKPVEKIRKE 187
              KE +EK    + KE
Sbjct: 105 ENEKETEEKTESNVEKE 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|234017 TIGR02794, tolA_full, TolA protein

 Score = 49.8 bits (119), Expect = 1e-06
 Identities = 36/141 (25%), Positives = 73/141 (51%), Gaps = 5/141 (3%)

Query: 108 KSIKKDKKTHKKKEKEKIKK---KKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
             I++ KK   KKE+E+ KK   + ++ +K +   + + KE +++   +K  K+ ++  +
Sbjct: 53  NRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAK 112

Query: 165 KKEEKEFKMKEDKEKPV-EKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 223
           + EEK+ + +E K K   E   K E ++EK+ K + K K+ ++E   K   E ++ + E 
Sbjct: 113 QAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAK-KQAEEEAKAKAAAEAKKKAAEA 171

Query: 224 EVIPKLTFKFGTDMEEKTKRE 244
           +   +   K   + + K K E
Sbjct: 172 KKKAEAEAKAKAEAKAKAKAE 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|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 49.4 bits (118), Expect = 2e-06
 Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 10/89 (11%)

Query: 120 KEKEKIKKKKDKKDKDKIK-----NKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMK 174
           K  E++K   D     + +     NK+     K+  + K E    +E + K +E++ K +
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQE 410

Query: 175 EDKEKPVEKIRKEEKDSEKEKKSKDKDKK 203
           E+++K     +KE+ D +KEK+ KD+ KK
Sbjct: 411 ENEKK-----QKEQADEDKEKRQKDERKK 434

Length = 434

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

 Score = 49.8 bits (118), Expect = 3e-06
 Identities = 50/191 (26%), Positives = 94/191 (49%), Gaps = 1/191 (0%)

Query: 59   KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK 118
            +EK  ++E    +E +   ++  E         I +V    +  +  K +  KK ++   
Sbjct: 1561 EEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKI 1620

Query: 119  KKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMK-EDK 177
            K E+ K  +++ KK +   K + ++K+K E+ K  +EE + K  +E K+ +E K K E+ 
Sbjct: 1621 KAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEA 1680

Query: 178  EKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDM 237
            +K  E  +K  +  +KE +   K ++LKK++ ++KKK +E    E+E   K         
Sbjct: 1681 KKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAE 1740

Query: 238  EEKTKRESSPK 248
            E+K K E + K
Sbjct: 1741 EDKKKAEEAKK 1751

Length = 2084

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

 Score = 49.1 bits (117), Expect = 3e-06
 Identities = 48/190 (25%), Positives = 88/190 (46%)

Query: 78  VKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKI 137
           VK VE G +       K          K+++  K+  K  KKK+KEK K++   +   + 
Sbjct: 77  VKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEE 136

Query: 138 KNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS 197
             +++  ++KEKEK KK E+ +  E+EKK E+       K+ P +K   ++K+  +E+K 
Sbjct: 137 AKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQ 196

Query: 198 KDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSP 257
           +   ++  K K ++    +ER   E +   + T     + +E  +     +     +K P
Sbjct: 197 RQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKP 256

Query: 258 SPPPVAAADE 267
            P P  A+ E
Sbjct: 257 DPSPSMASPE 266

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 = 49.1 bits (118), Expect = 3e-06
 Identities = 27/161 (16%), Positives = 65/161 (40%), Gaps = 8/161 (4%)

Query: 96  TSSEDLGEIKKDKSIKKDKKTH------KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEK 149
            SS++L E  K+  I  + K+H      ++  KE+ K++ +++ K + +     + ++E 
Sbjct: 15  VSSKELLEKLKELGI--EVKSHSSTVEEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEA 72

Query: 150 EKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 209
           +         +E  E     E   +  +++         +  + +K +K K     K+K 
Sbjct: 73  KAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAAKKKKGPKPKKKK 132

Query: 210 KKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIV 250
            K+K  +     +     +         ++K K++ + KI 
Sbjct: 133 PKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIP 173

Length = 746

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

 Score = 49.4 bits (117), Expect = 4e-06
 Identities = 40/121 (33%), Positives = 65/121 (53%), Gaps = 5/121 (4%)

Query: 103  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEE 162
            E KK +  KK  +  KK ++ K K ++ KK  +  K  E+ K+K ++ K   E K+K +E
Sbjct: 1455 EAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADE 1514

Query: 163  KEKKEEK----EFKMKEDKEKPVEKIRKEEKDSEKE-KKSKDKDKKLKKEKLKKKKKEKE 217
             +K EE     E K  E+ +K  E  + EEK    E KK+++  K  +K+K ++ KK +E
Sbjct: 1515 AKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEE 1574

Query: 218  R 218
             
Sbjct: 1575 D 1575

Length = 2084

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

 Score = 48.8 bits (116), Expect = 4e-06
 Identities = 32/130 (24%), Positives = 72/130 (55%), Gaps = 2/130 (1%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKE 158
               E K +K   +++K  K K +E+  +  +++ K++ +  E+++   E+E+  KEE+ 
Sbjct: 777 LAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEEL 836

Query: 159 KKEEKEKKEEKEFKMK--EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 216
           ++   E KEE++ +    E+ E+  E+I KEE   E   K ++ +++  K++L+ K++++
Sbjct: 837 EELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKE 896

Query: 217 ERSSHEKEVI 226
           +    E E  
Sbjct: 897 KEEKKELEEE 906

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 = 48.5 bits (116), Expect = 5e-06
 Identities = 26/142 (18%), Positives = 52/142 (36%), Gaps = 8/142 (5%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
              K+    ++  KKK K+   K K K          K++ K+  E  KK  ++  +   
Sbjct: 4   ASTKAELAAEEEAKKKLKKLAAKSKSK------GFITKEEIKEALESKKKTPEQIDQVLI 57

Query: 165 KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 224
                     +  E  + K  K+ K + K   +K   KK  K++L   KK +++++ +K+
Sbjct: 58  FLSGMVKDTDDATESDIPK--KKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKD 115

Query: 225 VIPKLTFKFGTDMEEKTKRESS 246
                        +     +  
Sbjct: 116 DDLNYVKDIDVLNQADDDDDDD 137

Length = 509

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

 Score = 48.3 bits (115), Expect = 5e-06
 Identities = 33/128 (25%), Positives = 56/128 (43%), Gaps = 2/128 (1%)

Query: 101 LGEIKKDKSIKKDKKTHKKKEKEKIKK--KKDKKDKDKIKNKEKDKEKKEKEKGKKEEKE 158
           L   K + SIK +KKT    +    KK    ++ +K+ +      K K    K K  +  
Sbjct: 368 LENKKIEISIKPEKKTINNSQIITTKKINIVEESNKNSVHFDTLYKTKIFYHKKKINQNN 427

Query: 159 KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
           K+++ +K+E  E +  +  EK  +     +     ++K  +KD +L K  L+K  K K  
Sbjct: 428 KEQDIKKEELLEKEFVKKSEKIPKNDELLDNLELAKQKFFNKDIELSKNMLQKFNKFKNE 487

Query: 219 SSHEKEVI 226
            S E   I
Sbjct: 488 ESAENSFI 495

Length = 605

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

 Score = 48.5 bits (116), Expect = 6e-06
 Identities = 42/184 (22%), Positives = 84/184 (45%), Gaps = 2/184 (1%)

Query: 91   NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIK-KKKDKKDKDKIKNKEKDKEKKEK 149
              +K T+ +D+     DK  +  ++  + +EKE  K ++   K K K     K K KK++
Sbjct: 1119 EKLKNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKE 1178

Query: 150  EKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 209
            +K KK   +K ++       +    ++K K  +K   ++ +S    +  D+++K K +K 
Sbjct: 1179 KKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKS 1238

Query: 210  KKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYD 269
              K+ + ++++  K       F    D+ ++ K +++PK V     SP PP      E +
Sbjct: 1239 SVKRLKSKKNNSSKSSEDNDEF-SSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESN 1297

Query: 270  TGDS 273
             G  
Sbjct: 1298 GGSK 1301

Length = 1388

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

 Score = 48.6 bits (115), Expect = 7e-06
 Identities = 49/154 (31%), Positives = 78/154 (50%), Gaps = 7/154 (4%)

Query: 106  KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEK 165
            K K+ +  K    KK+ E+ KKK D+  K     K+ D+ KK +E  K +E +K EE +K
Sbjct: 1476 KKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKK 1535

Query: 166  KEE---KEFKMKEDKEKPVEKIRK-EEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 221
             +E    E K K D+ K  E+++K EEK   +E K  ++DK +   K ++ KK +E    
Sbjct: 1536 ADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIE 1595

Query: 222  EKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVK 255
            E   + KL  +      E+ K+    KI  + +K
Sbjct: 1596 E---VMKLYEEEKKMKAEEAKKAEEAKIKAEELK 1626

Length = 2084

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

 Score = 47.9 bits (115), Expect = 8e-06
 Identities = 32/112 (28%), Positives = 60/112 (53%), Gaps = 10/112 (8%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDK 177
           K +E E + K+ +K  ++  + KEK +E+++K   + E++ ++  KE K+E +  +KE +
Sbjct: 535 KAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELR 594

Query: 178 EKPVEKIRKEEKDSEKEKKSKDKDKKL-----KKEKLKKKKKEKERSSHEKE 224
           +      +K    S K  +  +  K+L     KKEK KKK+KEK+      +
Sbjct: 595 QL-----QKGGYASVKAHELIEARKRLNKANEKKEKKKKKQKEKQEELKVGD 641

Length = 782

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

 Score = 47.2 bits (112), Expect = 1e-05
 Identities = 42/155 (27%), Positives = 77/155 (49%), Gaps = 3/155 (1%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDK 177
            K   ++  K+ +K        K K  ++ + E GK+EEKEK++ KE+K++K+ K KE+ 
Sbjct: 69  SKLSSDEAVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEP 128

Query: 178 EKPVEKIRKEEKDSEKEK---KSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFG 234
           +    K   +EK   KEK   K K  ++   +E+ KK+++ + +S  +K    K   K  
Sbjct: 129 KDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKK 188

Query: 235 TDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYD 269
              EE+ +R+++ + V    + P        +E D
Sbjct: 189 EPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDD 223

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

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

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 22/135 (16%), Positives = 67/135 (49%), Gaps = 1/135 (0%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKE 158
            +  ++K+   ++++   +    K   ++    ++  + + +E +  K+E EK ++   +
Sbjct: 211 LEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQ 270

Query: 159 KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKD-KKLKKEKLKKKKKEKE 217
             +E +++E+++   +E+ +   ++  + + +  K ++ K  D +KLK+ + + KK EKE
Sbjct: 271 VLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKE 330

Query: 218 RSSHEKEVIPKLTFK 232
               ++E+       
Sbjct: 331 LKKEKEEIEELEKEL 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|234017 TIGR02794, tolA_full, TolA protein

 Score = 46.8 bits (111), Expect = 1e-05
 Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 4/111 (3%)

Query: 112 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKK---EEKEKKEE 168
           K K+  + K K+  + K   + + + K KE+ K++ E+E   K   E K    E +KK E
Sbjct: 117 KQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAE 176

Query: 169 KEFKMKED-KEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
            E K K + K K   +  K + ++ K K + +   K + E       E ER
Sbjct: 177 AEAKAKAEAKAKAKAEEAKAKAEAAKAKAAAEAAAKAEAEAAAAAAAEAER 227

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

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

 Score = 47.7 bits (114), Expect = 1e-05
 Identities = 41/219 (18%), Positives = 77/219 (35%), Gaps = 14/219 (6%)

Query: 42   PPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKD----------VELGVTPM--V 89
              SK K K S   K   K+K   K+K+S  + + + V             +L   P    
Sbjct: 1158 LKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKK 1217

Query: 90   PNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEK 149
             N       +D  +  K K     +   KK    K  +  D+   D +  + K K   ++
Sbjct: 1218 SNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPKR 1277

Query: 150  EKGKKEEKE--KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKE 207
                +       K    +           K+K  +++       +K+KKS+ K  + KK 
Sbjct: 1278 VSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKS 1337

Query: 208  KLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 246
            K + K+    +SS       K      ++ ++ ++ + S
Sbjct: 1338 KTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDS 1376

Length = 1388

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

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 34/136 (25%), Positives = 71/136 (52%), Gaps = 12/136 (8%)

Query: 95  VTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKK 154
           V    D+ ++K+ +S +  K+  + KE+   K+    K + K    + + +K+  E  +K
Sbjct: 194 VNFRRDMTDLKERESQEDAKRAQQLKEELDKKQIDADKAQQKADFAQDNADKQRDEVRQK 253

Query: 155 EEKEKKEEK-----EKKEEKEFKMKEDKEKPVEKIRKE-EKDSEKEKKSKDKDKKLKKEK 208
           +++ K   K       KE+K  ++ E++++ +EK + E +K+ E+  K+KD     K   
Sbjct: 254 QQEAKNLPKPADTSSPKEDK--QVAENQKREIEKAQIEIKKNDEEALKAKDH----KAFD 307

Query: 209 LKKKKKEKERSSHEKE 224
           LK++ K  E+ + +KE
Sbjct: 308 LKQESKASEKEAEDKE 323

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

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

 Score = 47.4 bits (113), Expect = 1e-05
 Identities = 23/147 (15%), Positives = 62/147 (42%), Gaps = 14/147 (9%)

Query: 92  IVKVTSSEDLGEIKKDKSIKKDKKTHK--------------KKEKEKIKKKKDKKDKDKI 137
           IV + ++ +  +I     I  D   +               + E+E++K  + ++++  +
Sbjct: 772 IVSLFNNPNAEKILIITEILSDGINNSDINDRPQELIDQIIESEEERLKALRIQREEMLM 831

Query: 138 KNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS 197
           + +E +   +E++  K+E K +  E ++ EE+   + E+K + VE     +K ++     
Sbjct: 832 RPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNINENKNEFVEFKNDPKKLNKLIIAK 891

Query: 198 KDKDKKLKKEKLKKKKKEKERSSHEKE 224
               K +      K+ ++  +   +  
Sbjct: 892 DVLIKLVISSDEIKQDEKTTKKKKKDL 918

Length = 925

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

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 22/118 (18%), Positives = 43/118 (36%), Gaps = 1/118 (0%)

Query: 96  TSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKE 155
           T    L  I    S              + + K       K K ++K+ E K+K + KK+
Sbjct: 16  TQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKK 75

Query: 156 EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 213
           +K++K+E + + E +   K  K+    K +  +     E      +K  +  +     
Sbjct: 76  KKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKP-NEDVDNAFNKIAELAEKSNVY 132

Length = 413

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

 Score = 46.5 bits (111), Expect = 1e-05
 Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 7/83 (8%)

Query: 115 KTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMK 174
           K    K   ++ +K DK  +++ +   K  E++ +E    E +EKKEEK+K+E +    K
Sbjct: 247 KLANLKLSPEVLRKVDKTREEEEEKILKAAEEERQE----EAQEKKEEKKKEEREA---K 299

Query: 175 EDKEKPVEKIRKEEKDSEKEKKS 197
             K  P E+ + EEK+ +K+ + 
Sbjct: 300 LAKLSPEEQRKLEEKERKKQARK 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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 46.8 bits (111), Expect = 2e-05
 Identities = 48/231 (20%), Positives = 95/231 (41%), Gaps = 20/231 (8%)

Query: 35  VHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVK 94
           V   G+  P+            S KE+   KE+   ++K+                   K
Sbjct: 80  VEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKK-------------------K 120

Query: 95  VTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKK 154
               ++  + +K K   K+K+  K+KEKEK KK ++ +D+++ K +E+ + K   +K  K
Sbjct: 121 KEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPK 180

Query: 155 EEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 214
           ++   K+++  +EEK+ +   +  K   +     ++ EKE+    KD++     +++ + 
Sbjct: 181 KKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEED-DGKDRETTTSPMEEDES 239

Query: 215 EKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAA 265
            +      +             M     RESS +   +P  S  PP    A
Sbjct: 240 RQSSEISRRSSSSLKKPDPSPSMASPETRESSKRTETRPRTSLRPPSARPA 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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 46.9 bits (111), Expect = 2e-05
 Identities = 38/166 (22%), Positives = 81/166 (48%)

Query: 59  KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK 118
           +E++ S ++   KE+E       E         + +        E ++ KS     +  K
Sbjct: 251 QEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRK 310

Query: 119 KKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKE 178
             ++EK+K+ + +  K + + K++ +E +E EK  KE + K+E +E++EE+  K++E  E
Sbjct: 311 VDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLE 370

Query: 179 KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 224
           +  E++  ++K   +   S  K K+ + E   +++KE +      E
Sbjct: 371 QLEEELLAKKKLESERLSSAAKLKEEELELKNEEEKEAKLLLELSE 416

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

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

 Score = 46.0 bits (109), Expect = 2e-05
 Identities = 27/111 (24%), Positives = 51/111 (45%), Gaps = 2/111 (1%)

Query: 104 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEK 163
            K+ +     +K    K+ E+  K+ ++K K   + K K   + + +   + EK+ KEE 
Sbjct: 91  QKELEQRAAAEK--AAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEA 148

Query: 164 EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 214
           +K+ E+E K K   E   +    ++K   + K   +   K K E+ K K +
Sbjct: 149 KKQAEEEAKAKAAAEAKKKAAEAKKKAEAEAKAKAEAKAKAKAEEAKAKAE 199

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

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

 Score = 46.7 bits (111), Expect = 2e-05
 Identities = 24/106 (22%), Positives = 45/106 (42%), Gaps = 3/106 (2%)

Query: 112 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEF 171
            +KK H+K +K+  K  K    KD  K K K K+K +K+    ++ +        +    
Sbjct: 48  INKKLHEKLDKKNKKFNKTDDLKDSKKTKLKQKKKIKKKLHIDDDYD---NFFDSKNNSK 104

Query: 172 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
           +        + +  K + +  K+K + +K    KK+K+   K E  
Sbjct: 105 QFAGPLAISLMRKPKPKTEKLKKKITVNKSTNKKKKKVLSSKDELI 150

Length = 742

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

 Score = 46.1 bits (110), Expect = 3e-05
 Identities = 22/75 (29%), Positives = 44/75 (58%)

Query: 154 KEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 213
           +EE E     +K  +K  K+ E  EK  E+ +KE+K      K K+++++ +KEK +++K
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 214 KEKERSSHEKEVIPK 228
           +E+E  + E++   +
Sbjct: 456 EEEEEEAEEEKEEEE 470

Length = 482

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

 Score = 45.9 bits (109), Expect = 3e-05
 Identities = 24/129 (18%), Positives = 68/129 (52%), Gaps = 4/129 (3%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
           + + ++   K    +KE E+++++  + +++  + +E+ +E +++ +  K E E+  E+ 
Sbjct: 224 ELELALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREEL 283

Query: 165 KKEEKEF----KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSS 220
           ++ ++E     +  E+ E  +  +R+  ++ E E +  ++  +  KEK++  K+E E   
Sbjct: 284 EELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERE 343

Query: 221 HEKEVIPKL 229
              E + +L
Sbjct: 344 TLLEELEQL 352

Length = 1163

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

 Score = 46.5 bits (110), Expect = 3e-05
 Identities = 24/126 (19%), Positives = 60/126 (47%), Gaps = 4/126 (3%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDK----IKNKEKDKEKKEKEKGKKEEKE 158
            I   + +K  +   K++ K+ ++  + K+  +     +   +  K  +E+    +E   
Sbjct: 189 LIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLR 248

Query: 159 KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
            ++E+ +  ++E + +E+    V K  KEE+  +K ++ + K    ++E+LK +  + ER
Sbjct: 249 DEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLER 308

Query: 219 SSHEKE 224
              + E
Sbjct: 309 RKVDDE 314

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

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

 Score = 46.0 bits (110), Expect = 3e-05
 Identities = 38/132 (28%), Positives = 66/132 (50%), Gaps = 21/132 (15%)

Query: 115 KTHKKKEKEK----IKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEE-------- 162
           K    ++KEK    I   ++ + + + K +E +   KE EK K+E +EKKE+        
Sbjct: 508 KKLIGEDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKL 567

Query: 163 KEKKEEK-EFKMKEDKEKPVEKIR------KEEKDSEKEKKSKDKDKKLKK--EKLKKKK 213
            E+ E++ +  +KE K++  E I+      K    S K  +  +  K+L K  EK +KKK
Sbjct: 568 LEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKANEKKEKKK 627

Query: 214 KEKERSSHEKEV 225
           K+++    E +V
Sbjct: 628 KKQKEKQEELKV 639

Length = 782

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

 Score = 46.1 bits (109), Expect = 3e-05
 Identities = 32/133 (24%), Positives = 63/133 (47%), Gaps = 2/133 (1%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKE--EKEKKEEKEKKEEKEFKMKE 175
           K+ EKE++K ++ +K  ++ + + + ++K+++E+ +K   E++KK E  K +      K 
Sbjct: 104 KQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKL 163

Query: 176 DKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGT 235
                 +K  +E   + +E K+K +    KK+   + K   E++  E E   K   K   
Sbjct: 164 KAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKAKAEAEAKAKAEKKAEA 223

Query: 236 DMEEKTKRESSPK 248
             EEK   E    
Sbjct: 224 AAEEKAAAEKKKA 236

Length = 387

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

 Score = 45.7 bits (108), Expect = 3e-05
 Identities = 26/117 (22%), Positives = 49/117 (41%), Gaps = 3/117 (2%)

Query: 112 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEF 171
           + KK    K K   +  K K   +  K  E+  +  E+ K K E    K++ E + +   
Sbjct: 145 QKKKAEAAKAKAAAEAAKLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAA 204

Query: 172 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK---KLKKEKLKKKKKEKERSSHEKEV 225
           +  + + +   K  K+ + + +EK + +K K   K K +K     K  ER +    +
Sbjct: 205 EKAKAEAEAKAKAEKKAEAAAEEKAAAEKKKAAAKAKADKAAAAAKAAERKAAAAAL 261

Length = 387

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

 Score = 46.1 bits (109), Expect = 3e-05
 Identities = 26/99 (26%), Positives = 55/99 (55%), Gaps = 5/99 (5%)

Query: 134 KDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEK-KEEKEFKMKEDKEKPVEKIRKEE--KD 190
             +  N   +   +EK+  K+++K + E KEK  ++KE  + ++ + PV++   +E  K 
Sbjct: 5   NRREANINNNDRMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLKI 64

Query: 191 SEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE--KEVIP 227
           +++ KKS  ++ K   E LK K++ ++   +E  ++ IP
Sbjct: 65  ADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIP 103

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

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

 Score = 45.9 bits (108), Expect = 4e-05
 Identities = 41/131 (31%), Positives = 78/131 (59%), Gaps = 6/131 (4%)

Query: 98   SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEK 157
            +++  + ++ K   + KK  + K+ ++ KK ++KK  D++K  E+   KK +EK K EE 
Sbjct: 1512 ADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEE--LKKAEEKKKAEEA 1569

Query: 158  EKKEEKE----KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 213
            +K EE +    +K E+  K +E + + V K+ +EEK  + E+  K ++ K+K E+LKK +
Sbjct: 1570 KKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAE 1629

Query: 214  KEKERSSHEKE 224
            +EK++    K+
Sbjct: 1630 EEKKKVEQLKK 1640

Length = 2084

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

 Score = 45.4 bits (108), Expect = 4e-05
 Identities = 27/94 (28%), Positives = 49/94 (52%), Gaps = 6/94 (6%)

Query: 115 KTHKK---KEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKK---EEKEKKEEKEKKEE 168
           KTH+K   K +EKIK  K +  + K      +     K K K     + EK + + K+++
Sbjct: 273 KTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKK 332

Query: 169 KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK 202
           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|218734 pfam05758, Ycf1, Ycf1

 Score = 45.8 bits (109), Expect = 4e-05
 Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 5/88 (5%)

Query: 146 KKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK 205
           KK KE  + EE+E  EE + + E   + K  K++      ++     +EK+  DK + L 
Sbjct: 224 KKLKETSETEERE--EETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLD 281

Query: 206 KEKLKKKKKEKERSSHEKEVIPKLTFKF 233
           K ++ K+KK++E    EK   P  T  F
Sbjct: 282 KLEILKEKKDEELFWFEK---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|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain

 Score = 45.3 bits (107), Expect = 5e-05
 Identities = 28/138 (20%), Positives = 72/138 (52%), Gaps = 4/138 (2%)

Query: 91  NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKE 150
              K+   E+  E  + K  +++++  +   KEK   ++++K +     +EK+++ K +E
Sbjct: 742 LEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQE 801

Query: 151 KGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKD----SEKEKKSKDKDKKLKK 206
           +  +  +E+ +E+ +  E+E  + E +EK  E+  +E        +K +K  +++ +  +
Sbjct: 802 EELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEELERLE 861

Query: 207 EKLKKKKKEKERSSHEKE 224
           E++ K++  +E    E+E
Sbjct: 862 EEITKEELLQELLLKEEE 879

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 = 45.5 bits (107), Expect = 6e-05
 Identities = 38/109 (34%), Positives = 66/109 (60%), Gaps = 5/109 (4%)

Query: 105  KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
            K+ +  KK ++  KK+ +EK K ++ KK +++ K K ++ +K+ +E  KK E+ KK+E+E
Sbjct: 1696 KEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEE 1755

Query: 165  KKEEKEFKMKEDKE-----KPVEKIRKEEKDSEKEKKSKDKDKKLKKEK 208
            KK+    K +E+K+     K  E + +EE D E EK+  + DKK+K   
Sbjct: 1756 KKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVDKKIKDIF 1804

Length = 2084

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

 Score = 45.2 bits (107), Expect = 6e-05
 Identities = 36/117 (30%), Positives = 61/117 (52%), Gaps = 12/117 (10%)

Query: 121 EKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKP 180
           E+ K    + K++ + +  K    EK+ ++K +  EK  KE+++ K+E E +M+E KE  
Sbjct: 500 EQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKE-- 557

Query: 181 VEKIRKEEKDSEKEKKSKDKDKKLKKE------KLKKKKKEKERSSHEKEVIPKLTF 231
               R+  K  E EK++++  K LKKE      +LK+KK  K +     E + KL  
Sbjct: 558 ----RERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKE 610

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

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

 Score = 45.5 bits (108), Expect = 6e-05
 Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 10/98 (10%)

Query: 121  EKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKM-KEDKEK 179
              E + KK ++K K  I + EK        K  + E   +EEKE   + E +  KE K  
Sbjct: 1494 GNENVNKKINQKKKGFIPSNEK--------KSIEIENRNQEEKEPAGQGELESDKEKKGN 1545

Query: 180  PVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
                +  +EK+ E++    D  KK K +K  K   E E
Sbjct: 1546 LESVLSNQEKNIEEDYAESDI-KKRKNKKQYKSNTEAE 1582

Length = 1832

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

 Score = 44.9 bits (107), Expect = 7e-05
 Identities = 23/80 (28%), Positives = 52/80 (65%)

Query: 143 DKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK 202
           ++E +     KK  K+ K+  EK E+K  + K++K+K     +K+E++ E+EK+ K+++K
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 203 KLKKEKLKKKKKEKERSSHE 222
           + ++E+ +++K+E+E    +
Sbjct: 456 EEEEEEAEEEKEEEEEKKKK 475

Length = 482

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

 Score = 44.4 bits (105), Expect = 7e-05
 Identities = 30/122 (24%), Positives = 60/122 (49%), Gaps = 9/122 (7%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKK-- 160
             KK +   ++ +  +  E+ + K+ + +    +   K+ ++  K+ E+ +K+ +E K  
Sbjct: 69  RQKKLEQQAEEAEKQRAAEQARQKELEQRA-AAEKAAKQAEQAAKQAEEKQKQAEEAKAK 127

Query: 161 ---EEKEKKEEK-EFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 216
              E K K E + E K KE+ +K  E+  K +  +E +KK+ +  KK + E   K K E 
Sbjct: 128 QAAEAKAKAEAEAEKKAKEEAKKQAEEEAKAKAAAEAKKKAAEAKKKAEAE--AKAKAEA 185

Query: 217 ER 218
           + 
Sbjct: 186 KA 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|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein

 Score = 44.9 bits (106), Expect = 7e-05
 Identities = 41/147 (27%), Positives = 72/147 (48%), Gaps = 10/147 (6%)

Query: 44  SKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGE 103
               D++  KD     EK   K +   KEK   K ++V   VT  V + VK  SS++   
Sbjct: 11  INNNDRMQEKDD----EKQDQKNRMELKEKVLDKKEEV---VTDNVDSPVKEQSSQE--N 61

Query: 104 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKE-KEKGKKEEKEKKEE 162
           +K    +KK  K   K+  E +K K++ + + + +  +K     E KE   K+ ++ K E
Sbjct: 62  LKIADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPSFEPKESILKKLEDIKPE 121

Query: 163 KEKKEEKEFKMKEDKEKPVEKIRKEEK 189
           + KK+ K F++ E K+ P+ +   E++
Sbjct: 122 QAKKQTKLFRLFEPKQLPIYRANGEKE 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|214395 CHL00204, ycf1, Ycf1; Provisional

 Score = 45.1 bits (107), Expect = 8e-05
 Identities = 27/100 (27%), Positives = 46/100 (46%), Gaps = 4/100 (4%)

Query: 138  KNKEKDKEKKEKEKGKKEEKEKKE---EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKE 194
             N+  +K+  +K+KG     EKK    E   +EEKE   + + E   EK    E     +
Sbjct: 1494 GNENVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQ 1553

Query: 195  KKSKDKD-KKLKKEKLKKKKKEKERSSHEKEVIPKLTFKF 233
            +K+ ++D  +   +K K KK+ K  +  E +   K   +F
Sbjct: 1554 EKNIEEDYAESDIKKRKNKKQYKSNTEAELDFFLKRYLRF 1593

Length = 1832

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

 Score = 44.7 bits (106), Expect = 9e-05
 Identities = 35/117 (29%), Positives = 69/117 (58%), Gaps = 11/117 (9%)

Query: 112 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKK-EEKEKKEEKE 170
           K++    +KE E ++  K +K ++KI+  E+  E+ +KE  + EEK K+ +E ++K E+ 
Sbjct: 237 KEEIEELEKELESLEGSK-RKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEY 295

Query: 171 FKMKEDKEKPVEKIRKEEKDSEK---------EKKSKDKDKKLKKEKLKKKKKEKER 218
            K+ E  E+ ++++R+ EK   +         E+  + ++K+ + E+LKKK KE E+
Sbjct: 296 IKLSEFYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEK 352

Length = 880

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

 Score = 44.2 bits (105), Expect = 1e-04
 Identities = 22/132 (16%), Positives = 44/132 (33%), Gaps = 1/132 (0%)

Query: 86  TPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE 145
           T            E   ++KK  +  K K    K+E ++  + K K  + +I        
Sbjct: 2   TTASTKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPE-QIDQVLIFLS 60

Query: 146 KKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK 205
              K+     E +  ++K K   K    K   +K ++      K +EK+      D    
Sbjct: 61  GMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNY 120

Query: 206 KEKLKKKKKEKE 217
            + +    +  +
Sbjct: 121 VKDIDVLNQADD 132

Length = 509

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

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 25/127 (19%), Positives = 68/127 (53%), Gaps = 5/127 (3%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKE 158
           E+L E++++    + +    K E E+++++ ++  ++ ++ KE+  E+ E E     E+ 
Sbjct: 253 EELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEE-IEELEGEISLLRERL 311

Query: 159 KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
           ++ E E +E +E      +E   +    +E+  E+E   ++ ++ L + +  K++ E++ 
Sbjct: 312 EELENELEELEE----RLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKL 367

Query: 219 SSHEKEV 225
           S+  +E+
Sbjct: 368 SALLEEL 374

Length = 1163

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

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 29/136 (21%), Positives = 67/136 (49%), Gaps = 6/136 (4%)

Query: 114 KKTHKKKEK--EKIKKKKDKKDK--DKIKNKEKDKEKKEKEKGKKEE-KEKKEEKEKKEE 168
            K  ++KE+   K+++ ++  ++  D ++  EK  EK E++  K E  +E K E  + E 
Sbjct: 168 SKYKERKEEAERKLERTEENLERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELEL 227

Query: 169 KEFKMK-EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIP 227
                K ++  K +E++ +E    E+E +   ++ +  ++++++ K E E    E E + 
Sbjct: 228 ALLLAKLKELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQ 287

Query: 228 KLTFKFGTDMEEKTKR 243
           +   +   ++EE    
Sbjct: 288 EELLELKEEIEELEGE 303

Length = 1163

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

 Score = 44.2 bits (104), Expect = 1e-04
 Identities = 35/179 (19%), Positives = 83/179 (46%), Gaps = 3/179 (1%)

Query: 71  KEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIK---K 127
           K +   + ++++     +   + K+   ++     K +  +       K  ++KIK   +
Sbjct: 692 KNEILRRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEE 751

Query: 128 KKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKE 187
           +++K    K + +E+  E   KEK   EE+EK E+ + +EEKE K+K  +E+      + 
Sbjct: 752 EEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEEL 811

Query: 188 EKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESS 246
           ++++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|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 23/113 (20%), Positives = 53/113 (46%), Gaps = 1/113 (0%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
           +K     ++++  K++++ +  ++K   +++++K  EK++   +++K + EE  K+   +
Sbjct: 71  QKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALK 130

Query: 165 KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
           +K+ +E   K        K   E K +    K    + K K E    KK   E
Sbjct: 131 QKQAEEAAAKA-AAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAE 182

Length = 387

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

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 35/147 (23%), Positives = 69/147 (46%), Gaps = 11/147 (7%)

Query: 97  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEE 156
           S E+  E    K++ + K   +  EKE   KK  K++K++ K K++  E++E E  ++ +
Sbjct: 407 SDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKKESDEEEELEDEEEAK 466

Query: 157 KEKKEEKEKKEEKEFKMKEDKEKPVE-----------KIRKEEKDSEKEKKSKDKDKKLK 205
            EK   K  K  ++ + +E++E+  E               +++DS+K+  SK      K
Sbjct: 467 VEKVANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKKKSSSKLDKAANK 526

Query: 206 KEKLKKKKKEKERSSHEKEVIPKLTFK 232
             K   K K+K++     ++   L  +
Sbjct: 527 ISKAAVKVKKKKKKEKSIDLDDDLIDE 553

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|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 43.2 bits (103), Expect = 2e-04
 Identities = 41/151 (27%), Positives = 83/151 (54%), Gaps = 23/151 (15%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKK--KDKKDK-DKIKNKEK---DKEKKEKEKGKKEEKE 158
           K+ ++IKK+     K+E  K++ +  K+ +++ ++++  EK    KE+    K +  EK 
Sbjct: 49  KEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKR 108

Query: 159 KKEEKEKKEEKEFKMK--EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK--KK 214
           ++E ++K++E E K +  E KE+ +E++ +E+   E E+ S      L  E+ K+   +K
Sbjct: 109 EEELEKKEKELEQKQQELEKKEEELEELIEEQLQ-ELERIS-----GLTAEEAKEILLEK 162

Query: 215 EKERSSHEKEVIPKLTFKFGTDMEEKTKRES 245
            +E + HE  V+ K       ++EE+ K E+
Sbjct: 163 VEEEARHEAAVLIK-------EIEEEAKEEA 186

Length = 520

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

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 30/128 (23%), Positives = 58/128 (45%), Gaps = 8/128 (6%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEE 162
             KK++  K  ++T    E   I  ++ K  + K+K + K   +  + K +K E E++  
Sbjct: 170 RKKKERLKKLIEETENLAELI-IDLEELKLQELKLKEQAKKALEYYQLK-EKLELEEENL 227

Query: 163 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEK------EKKSKDKDKKLKKEKLKKKKKEK 216
                 K  + + D  + + +  +EE +S K      E+      K+ K+E+ +KK +E+
Sbjct: 228 LYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEE 287

Query: 217 ERSSHEKE 224
           E     KE
Sbjct: 288 ELKLLAKE 295

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 = 43.2 bits (101), Expect = 3e-04
 Identities = 39/144 (27%), Positives = 75/144 (52%), Gaps = 3/144 (2%)

Query: 103  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEK--- 159
            + KK +  KK ++  KK  +   K+ ++ K  +++K KE +++KK +E  K EE+ K   
Sbjct: 1673 DKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKA 1732

Query: 160  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 219
            +E K++ EE + K +E K+   EK +      E+EKK+++  K+ +    ++  +E E+ 
Sbjct: 1733 EEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKR 1792

Query: 220  SHEKEVIPKLTFKFGTDMEEKTKR 243
              E +   K  F    ++ E  K 
Sbjct: 1793 RMEVDKKIKDIFDNFANIIEGGKE 1816

Length = 2084

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

 Score = 42.8 bits (100), Expect = 3e-04
 Identities = 43/182 (23%), Positives = 84/182 (46%), Gaps = 17/182 (9%)

Query: 103  EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKI------KNKEKDKEKKEKEKGKKEE 156
             +KK +  KKD +  KK E+E+  ++  K ++ ++      +   K +E ++ ++ KK E
Sbjct: 1228 AVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAE 1287

Query: 157  KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEE--KDSEKEKKSKDKDKKLKKEKLK---- 210
            ++KK ++ KK E++ K  E K+K  E  + +E  K +E+ KK  D  KK  +E  K    
Sbjct: 1288 EKKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEA 1347

Query: 211  -----KKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAA 265
                 +   ++  ++ EK    +   +      +  K+++  K      K  +      A
Sbjct: 1348 AKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKA 1407

Query: 266  DE 267
            DE
Sbjct: 1408 DE 1409

Length = 2084

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

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 21/117 (17%), Positives = 52/117 (44%), Gaps = 5/117 (4%)

Query: 106 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEK--DKEKKEKEKGKKEEKEKKEEK 163
            D+ I+ +++  K    ++ +     ++ + I  ++K   +E K +    +E +E+ +  
Sbjct: 808 IDQIIESEEERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLELSEIQEAEEEIQNI 867

Query: 164 EKKEEKEFKMKEDKEKPVEKI---RKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
            + + +  + K D +K  + I       K      + K  +K  KK+K   +K ++E
Sbjct: 868 NENKNEFVEFKNDPKKLNKLIIAKDVLIKLVISSDEIKQDEKTTKKKKKDLEKTDEE 924

Length = 925

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

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 29/139 (20%), Positives = 63/139 (45%), Gaps = 13/139 (9%)

Query: 99   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEK-----EKGK 153
            E++ +I +D S   ++K   +  +E + + + K ++    N E D   KE      E   
Sbjct: 3890 EEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKD 3949

Query: 154  KEEKEKKEEKE----KKEEKEFKMKEDKEKPVEKIRK----EEKDSEKEKKSKDKDKKLK 205
            ++EKE +EE        +E +  ++E+  +P  +       E+   ++++    KD  L+
Sbjct: 3950 RQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDSDLE 4009

Query: 206  KEKLKKKKKEKERSSHEKE 224
               ++   + KE +  EK+
Sbjct: 4010 DMDMEAADENKEEADAEKD 4028

Length = 4600

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

 Score = 42.7 bits (101), Expect = 3e-04
 Identities = 32/132 (24%), Positives = 58/132 (43%), Gaps = 6/132 (4%)

Query: 102 GEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEK-K 160
           GEIK   ++ ++    + + +E  K+ K  ++K +    E +K+++E EK K +  +K  
Sbjct: 78  GEIKGVFTLGEENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAW 137

Query: 161 EEKEKKEEKEFKMKEDKEKPVEKIRKEEKD-SEKEKKSKDKDKKLKKEKLKKKKKEKERS 219
           ++  KK +      E  +    K   +EK   E +    +    L  E+L  K K K   
Sbjct: 138 KKLAKKYDSNL--SEALKGLNYKKNFKEKLLKELKSVILNASSLLSLEEL--KAKIKTLF 193

Query: 220 SHEKEVIPKLTF 231
           S  K  +  LT 
Sbjct: 194 SSNKPELALLTL 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|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 42.1 bits (99), Expect = 4e-04
 Identities = 29/103 (28%), Positives = 56/103 (54%), Gaps = 7/103 (6%)

Query: 77  KVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDK 136
            + D +L +  +     +V S+ DL   K+ + +K+  K  +   K K+ + KD+ D   
Sbjct: 338 NLDDNDLTLLALTKLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTK-KLGEVKDETDAS- 395

Query: 137 IKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEK 179
               E+ + K ++EK K+EE E K++KE+ +E + K ++D+ K
Sbjct: 396 ----EEAEAKAKEEKLKQEENE-KKQKEQADEDKEKRQKDERK 433

Length = 434

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

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 36/137 (26%), Positives = 55/137 (40%), Gaps = 15/137 (10%)

Query: 57  SPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKT 116
           S     + K K  P    YS V  +   +           ++      KKDK   K+ ++
Sbjct: 10  SFFSGTTQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTS---TKKDKKEDKNNES 66

Query: 117 HKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKED 176
            KKK ++K KKKK+KK+            K E E     +  KK +K KK+  + K  ED
Sbjct: 67  -KKKSEKKKKKKKEKKE-----------PKSEGETKLGFKTPKKSKKTKKKPPKPKPNED 114

Query: 177 KEKPVEKIRKEEKDSEK 193
            +    KI +  + S  
Sbjct: 115 VDNAFNKIAELAEKSNV 131

Length = 413

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

 Score = 42.7 bits (101), Expect = 4e-04
 Identities = 29/137 (21%), Positives = 75/137 (54%), Gaps = 3/137 (2%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKE 158
           ++L E+ ++ +    +    ++E EK++K+  + ++ K + +E +KE +  E  K++ +E
Sbjct: 200 KELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEE 259

Query: 159 KKEEKEK---KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 215
           K  E E+   + +KE +  E+K K +++++++ ++  K  +  ++     +E  K+  + 
Sbjct: 260 KIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKRLSRL 319

Query: 216 KERSSHEKEVIPKLTFK 232
           +E  +  +E I +L  K
Sbjct: 320 EEEINGIEERIKELEEK 336

Length = 880

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

 Score = 42.3 bits (100), Expect = 4e-04
 Identities = 26/123 (21%), Positives = 52/123 (42%), Gaps = 4/123 (3%)

Query: 138 KNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS 197
           +N E + + +E +K  K+ +EK E+ E + EK+ +  E  +        ++   + +   
Sbjct: 89  ENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNL 148

Query: 198 KDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKR-ESSPKIVIKPVKS 256
            +  K L  +K  K+K  KE  S        L+ +   +++ K K   SS K  +  +  
Sbjct: 149 SEALKGLNYKKNFKEKLLKELKSVILNASSLLSLE---ELKAKIKTLFSSNKPELALLTL 205

Query: 257 PSP 259
              
Sbjct: 206 SVI 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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 26/84 (30%), Positives = 55/84 (65%), Gaps = 3/84 (3%)

Query: 127 KKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRK 186
           KK   K + K++ K+  ++++E E+ ++EE++K EEK + E KE   +E+ E+  EK ++
Sbjct: 1   KKIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKE---EEELEEEREKKKE 57

Query: 187 EEKDSEKEKKSKDKDKKLKKEKLK 210
           EE+  E+E++++ + ++ +K K  
Sbjct: 58  EEERKEREEQARKEQEEYEKLKSS 81

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

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

 Score = 42.7 bits (101), Expect = 4e-04
 Identities = 26/116 (22%), Positives = 48/116 (41%), Gaps = 6/116 (5%)

Query: 108 KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKE 167
           KS+    K   K     I++  +  + D  KNK  + +KK +  G  +   + E  +  E
Sbjct: 113 KSLLNKLKLKVKGNNILIEQVLNNPEFDHFKNKSPELQKKLQSFGFPQLLIEFEVNDISE 172

Query: 168 EKEFKMK------EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
           E+EF+        E ++   E +  E+K   +  K +        +K +K K  +E
Sbjct: 173 EQEFEKFEEAINEEVEKAAQEALEAEKKLKAESPKVEKPKPLFDGQKGRKIKSTEE 228

Length = 1444

>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like)

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 23/92 (25%), Positives = 53/92 (57%), Gaps = 7/92 (7%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEE------KE 158
           K+ +   K ++   +K +++++K K+K  KD     E  +EKKEKE  KK +      ++
Sbjct: 21  KQLEKEFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKELQKKVQEFQRKQQK 80

Query: 159 KKEEKEKKEEKEFKMKEDK-EKPVEKIRKEEK 189
            +++ +K++++E +   DK  K ++++ K++ 
Sbjct: 81  LQQDLQKRQQEELQKILDKINKAIKEVAKKKG 112

This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery. Length = 140

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

 Score = 41.2 bits (97), Expect = 5e-04
 Identities = 32/107 (29%), Positives = 48/107 (44%), Gaps = 15/107 (14%)

Query: 113 DKKTHK-----KKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKE 167
           DKKT K     +KE E++KK+ D K   ++  +    ++  K         K E     E
Sbjct: 107 DKKTKKLINELRKELEEVKKELDNKRNGELAIQPIQDKRIIK---------KDENSSVSE 157

Query: 168 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 214
            ++FK  E++E  +E    E   S   KK K   +KLKK + K  K 
Sbjct: 158 HEDFKQLENEENFLETEYNEITSSNNYKKLKIN-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|222160 pfam13476, AAA_23, AAA domain

 Score = 41.0 bits (96), Expect = 5e-04
 Identities = 29/124 (23%), Positives = 62/124 (50%), Gaps = 9/124 (7%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEE------ 156
             + +K   K +   + +E  K K KK KK   +I   ++ +E  ++     +E      
Sbjct: 79  TFENNKGKLKLRLIEESRELTKKKGKKVKKSILEIVEIDELQEFIDELLKSDKEILPLLL 138

Query: 157 ---KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 213
              +E+ EE + K +++ +  E+ EK +E++  E+   EK  + K+K K+L++ K + ++
Sbjct: 139 YLGQERLEELKFKRKEKKERLEELEKELEELEDEKDLLEKLLEEKEKKKELEELKEELEE 198

Query: 214 KEKE 217
             +E
Sbjct: 199 LLEE 202

Length = 204

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

 Score = 41.8 bits (99), Expect = 5e-04
 Identities = 38/157 (24%), Positives = 78/157 (49%), Gaps = 33/157 (21%)

Query: 119 KKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEK---GKKE--------EKEKKEEKE--K 165
           K+  EK     ++  K  I+  +K+ E  +KE     K+E        E+E KE +   +
Sbjct: 20  KRIAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQ 79

Query: 166 KEEKEFKMKEDK-EKPVEKIRKEEKDSEK-EKKSKDKDKKLKK------EKLKKKKKEKE 217
           + E+    +E+  ++ +E + K+E++ EK EK+  +K+K L +      E + ++++E E
Sbjct: 80  RLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELE 139

Query: 218 RSS-----HEKEVIPKLTFKFGTDMEEKTKRESSPKI 249
           R S       KE++ +       ++EE+ + E++  I
Sbjct: 140 RISGLTQEEAKEILLE-------EVEEEARHEAAKLI 169

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

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 20/78 (25%), Positives = 47/78 (60%), Gaps = 2/78 (2%)

Query: 130 DKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEK 189
            +K+    K++  +++  ++ + K+E+K K+E+ E +E ++ ++ ED E+      K E+
Sbjct: 1   MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEE--SNEVKIEE 58

Query: 190 DSEKEKKSKDKDKKLKKE 207
             ++  K K+++KKL+ E
Sbjct: 59  LKDENNKLKEENKKLENE 76

Length = 211

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

 Score = 41.8 bits (99), Expect = 6e-04
 Identities = 23/125 (18%), Positives = 47/125 (37%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEE 162
           E K +       +  ++ + E       ++  +     E      E E  +  E   +  
Sbjct: 55  EAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRP 114

Query: 163 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 222
           K KK  K+ K  + K+K  ++         K  K + + +  ++ + KKKK++       
Sbjct: 115 KAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIPR 174

Query: 223 KEVIP 227
           + VIP
Sbjct: 175 EVVIP 179

Length = 746

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

 Score = 41.8 bits (99), Expect = 6e-04
 Identities = 40/157 (25%), Positives = 87/157 (55%), Gaps = 24/157 (15%)

Query: 103 EIKKD-KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKG-----KKEE 156
           E KK+ +++KK+     K+E  K++ + +++ K++ +N+ +  E++  ++      K E 
Sbjct: 40  EAKKEAETLKKEALLEAKEEVHKLRAELERELKER-RNELQRLERRLLQREETLDRKMES 98

Query: 157 KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKK---LKKEKLKKK- 212
            +KKEE  +K+EKE     +KEK +++  KEE+  E   + +++ ++   L +E+ K+  
Sbjct: 99  LDKKEENLEKKEKEL---SNKEKNLDE--KEEELEELIAEQREELERISGLTQEEAKEIL 153

Query: 213 -KKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPK 248
            ++ +E + HE   + K       ++EE+ K E+  K
Sbjct: 154 LEEVEEEARHEAAKLIK-------EIEEEAKEEADKK 183

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

 Score = 41.9 bits (98), Expect = 7e-04
 Identities = 31/150 (20%), Positives = 75/150 (50%), Gaps = 4/150 (2%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKI-KKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEK 157
           E   E K +K  +++ +  +++  ++   ++   K+++  + K KD+ + ++EK K+E+K
Sbjct: 842 ELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESKEEKEKEEKK 901

Query: 158 EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK---EKLKKKKK 214
           E +EE +K    E K  E +E+  E+     K   + ++   ++   K+   +  +++++
Sbjct: 902 ELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEE 961

Query: 215 EKERSSHEKEVIPKLTFKFGTDMEEKTKRE 244
             +R    KE +  +      + EEK +R 
Sbjct: 962 RNKRLLLAKEELGNVNLMAIAEFEEKEERY 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|235401 PRK05306, infB, translation initiation factor IF-2; Validated

 Score = 41.8 bits (99), Expect = 7e-04
 Identities = 16/119 (13%), Positives = 41/119 (34%)

Query: 106 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEK 165
               + +  K      KE ++K K+   + K  +   ++E+  KE+ K+E +E+ + + +
Sbjct: 2   SKVRVYELAKELGVSSKELLEKLKELGIEVKSHSSTVEEEEARKEEAKREAEEEAKAEAE 61

Query: 166 KEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 224
           +       +E K +       EE                 +     +   +   + +  
Sbjct: 62  EAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARRPKAKKAA 120

Length = 746

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

 Score = 41.8 bits (99), Expect = 7e-04
 Identities = 15/124 (12%), Positives = 47/124 (37%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEE 162
           E  K ++ +      +++ K +       ++  +     +   +  +++  +  +     
Sbjct: 54  EEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPAEDEAARPAEAAARR 113

Query: 163 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 222
            + K+  + K     +K   K +        +     + ++ ++ + KKKKK+K      
Sbjct: 114 PKAKKAAKKKKGPKPKKKKPKRKAARGGKRGKGGKGRRRRRGRRRRRKKKKKQKPTEKIP 173

Query: 223 KEVI 226
           +EV+
Sbjct: 174 REVV 177

Length = 746

>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947)

 Score = 40.0 bits (94), Expect = 7e-04
 Identities = 26/103 (25%), Positives = 55/103 (53%), Gaps = 2/103 (1%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDK 177
            ++ ++ +KK KD ++K+++K   +  + + K    K+ + +  ++ KK+EKE   +  K
Sbjct: 65  IEELEKALKKTKDSEEKEELKRTLQSMKSRLKTLKNKDREREILKEHKKQEKELIKEGKK 124

Query: 178 EKPVEKIRKEEKDSEKEKKSKDKDKKLKK--EKLKKKKKEKER 218
              ++K   ++   +K+     K K+L K  EK +KK   KE+
Sbjct: 125 PYYLKKSEIKKLVLKKKFDELKKSKQLDKALEKKRKKNAGKEK 167

Family of eukaryotic proteins with unknown function. Length = 168

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

 Score = 41.6 bits (98), Expect = 7e-04
 Identities = 29/115 (25%), Positives = 52/115 (45%), Gaps = 15/115 (13%)

Query: 110 IKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE-KKEKEKGKKEEKEKKEEKEKKEE 168
           I++  K+ +  +    ++ K + DK K  ++   +  KK K+    +    ++  E KE 
Sbjct: 333 IEEGLKSVRLADFYGNEEIKIELDKSKTPSENAQRYFKKYKKLKGAKVNLDRQLSELKEA 392

Query: 169 -------KEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 216
                  K    K + +K +E+IR+E  + E   KSK K +K      KK+  EK
Sbjct: 393 IAYYESAKTALEKAEGKKAIEEIREELIE-EGLLKSKKKKRK------KKEWFEK 440

Length = 564

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

 Score = 41.6 bits (98), Expect = 8e-04
 Identities = 18/128 (14%), Positives = 65/128 (50%), Gaps = 1/128 (0%)

Query: 98  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEK 157
            E+L E+K++   + + +    +E+ +  + + ++ +++++  ++  E  ++E  ++E  
Sbjct: 287 QEELLELKEEIE-ELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETL 345

Query: 158 EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
            ++ E+   E +E K + +++        EE      ++  + + +L + + + ++ ++E
Sbjct: 346 LEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKRE 405

Query: 218 RSSHEKEV 225
             S E+ +
Sbjct: 406 IESLEERL 413

Length = 1163

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

 Score = 40.7 bits (95), Expect = 8e-04
 Identities = 33/170 (19%), Positives = 72/170 (42%), Gaps = 12/170 (7%)

Query: 59  KEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHK 118
           KEK +S+    P+E E    ++ +L V      + +        E+K+      +K    
Sbjct: 68  KEKSTSEPTVPPEEAEPHAEEEGQLAVRKTKQKVEE--------EVKEQLQSLLEKIVVS 119

Query: 119 KKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKE 178
           K+E++   K+    +   +  ++ D  ++  E GK  E    E ++    +E   ++ K+
Sbjct: 120 KQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGKVHE----ETEDSYHVEETASEQYKQ 175

Query: 179 KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPK 228
              EK  ++E +  KE   K +  K + + + ++  ++E +  E     K
Sbjct: 176 DMKEKASEQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIK 225

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

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 41.5 bits (98), Expect = 8e-04
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 120 KEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEK 179
           +E+E         ++ K++ K++  EKK +    KEE EK   K+K E    K K    +
Sbjct: 397 EEEEGENGNLSPAERKKLRKKQRKAEKKAE----KEEAEKAAAKKKAEAAAKKAKGPDGE 452

Query: 180 P 180
            
Sbjct: 453 T 453

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

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

 Score = 41.1 bits (96), Expect = 9e-04
 Identities = 41/195 (21%), Positives = 88/195 (45%), Gaps = 17/195 (8%)

Query: 62  MSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKE 121
           +  ++   P E+E       +LG    V  I    ++         + I++  K  +K +
Sbjct: 245 LKLEDNYEPSEQEL------KLGFEKFVHIINTDIANLKTQNDNLYEKIQEAMKISQKIK 298

Query: 122 KEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPV 181
             + K +  K D +K +N     ++K +E   K EK  K E E KEE+   ++ + ++  
Sbjct: 299 TLREKWRALKSDSNKYENYVNAMKQKSQEWPGKLEK-LKSEIELKEEEIKALQSNIDELH 357

Query: 182 EKIRK--------EEKDSEKEKKSKDKDK-KLKKEKLKKKKKEKERSSHEK-EVIPKLTF 231
           +++RK        E  + E+EK +++ DK  ++ +KL K  K ++  +    + + K   
Sbjct: 358 KQLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLTKSVKSRKLEAQGIFKSLEKTLR 417

Query: 232 KFGTDMEEKTKRESS 246
           ++ + ++  T+  S 
Sbjct: 418 QYDSLIQNITRSRSQ 432

Length = 622

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 8/92 (8%)

Query: 125 IKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKI 184
            K  ++ K    +   ++ +  KE  K  K +   K+  E K+E       D  +  E  
Sbjct: 350 TKLYEEVKSNTDLSGDKRQELLKEYNK--KLQDYTKKLGEVKDET------DASEEAEAK 401

Query: 185 RKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 216
            KEEK  ++E + K K++  + ++ ++K + K
Sbjct: 402 AKEEKLKQEENEKKQKEQADEDKEKRQKDERK 433

Length = 434

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 27/108 (25%), Positives = 49/108 (45%), Gaps = 1/108 (0%)

Query: 116 THKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKE 175
           T +K + + I            +      E++ K      +K+KKE+K  + +K+   K+
Sbjct: 15  TTQKSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKK-SEKK 73

Query: 176 DKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 223
            K+K  +K  K E +++   K+  K KK KK+  K K  E   ++  K
Sbjct: 74  KKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNK 121

Length = 413

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

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 22/97 (22%), Positives = 48/97 (49%), Gaps = 13/97 (13%)

Query: 137 IKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKK 196
                ++      ++ ++++ EK+++K + E KE K+ + KE+ V     +  DS  +++
Sbjct: 2   AYRNRREANINNNDRMQEKDDEKQDQKNRMELKE-KVLDKKEEVVT----DNVDSPVKEQ 56

Query: 197 SKDKDKKLKKEKLKKKKKE--------KERSSHEKEV 225
           S  ++ K+  E  K  K+E        K +  H+KE+
Sbjct: 57  SSQENLKIADEVKKSTKEESKQLLEVLKTKEEHQKEI 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|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 35/126 (27%), Positives = 62/126 (49%), Gaps = 16/126 (12%)

Query: 107 DKSIKKDKKTHKKKEKEK----IKKKKDKKDKDKIKNKEKDKEKKEKEKGKKE------- 155
              I +  KT   + KE+    I+K    + + + KN+  +K  KE+EK KKE       
Sbjct: 495 PHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEE 554

Query: 156 EKEKKEEKEKKEEKEF-----KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK 210
            KE++  K+ + EKE       +K++ E  + ++++++    KE KS +   KLK+ K K
Sbjct: 555 LKERERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQK 614

Query: 211 KKKKEK 216
             +K  
Sbjct: 615 IPQKPT 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|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 3/103 (2%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEE---KEKKEEKEKKEEKEFKMK 174
           K+ EKE++  ++ KK  ++   +   K+K+ +E   K     K K E + K+     K  
Sbjct: 104 KQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKA 163

Query: 175 EDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
             + K   +    +K + + KK  + +   K     KKK E E
Sbjct: 164 AAEAKKKAEAEAAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAE 206

Length = 387

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

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 29/124 (23%), Positives = 48/124 (38%), Gaps = 11/124 (8%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKD------KEKKEKEKGKKEE 156
           E KK       +   K+K+ E+   K     K K + + K       K   E +K  + E
Sbjct: 115 EQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAE 174

Query: 157 KEKKEEKEKKEEKE----FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK 212
             KK   E K++ E     K   + +K  E   K++  +E +KK+   + K    K   +
Sbjct: 175 AAKKAAAEAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKA-AAEAKAAAAKAAAE 233

Query: 213 KKEK 216
            K  
Sbjct: 234 AKAA 237

Length = 387

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

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 38/154 (24%), Positives = 78/154 (50%), Gaps = 4/154 (2%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDK-KDKDKIKNKEKDKEKKEKEKGKKEEK 157
            ++ E++++   +++    + +E  K    + K   ++  K  E  K KKE +   KE+K
Sbjct: 392 AEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKK 451

Query: 158 EKKEEKEKKEEKEFKMKEDKEKPV---EKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKK 214
           E  EE+E ++E+E K+++   K +   EK +KEE++ E ++++          K  KK+ 
Sbjct: 452 ESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQD 511

Query: 215 EKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPK 248
            K++SS + +       K    +++K K+E S  
Sbjct: 512 SKKKSSSKLDKAANKISKAAVKVKKKKKKEKSID 545

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|222160 pfam13476, AAA_23, AAA domain

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 30/141 (21%), Positives = 62/141 (43%), Gaps = 12/141 (8%)

Query: 97  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEE 156
            S+  G +K D  I+KD+   K   +   +  K K     I+   +  +KK K+  K   
Sbjct: 52  KSKGRGIVKGDIEIEKDEGKKKTYVEITFENNKGKLKLRLIEESRELTKKKGKKVKKSIL 111

Query: 157 KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK----------- 205
           +  + ++ ++   E    + +  P+     +E+  E + K K+K ++L+           
Sbjct: 112 EIVEIDELQEFIDELLKSDKEILPLLLYLGQERLEELKFKRKEKKERLEELEKELEELED 171

Query: 206 -KEKLKKKKKEKERSSHEKEV 225
            K+ L+K  +EKE+    +E+
Sbjct: 172 EKDLLEKLLEEKEKKKELEEL 192

Length = 204

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

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 28/94 (29%), Positives = 52/94 (55%), Gaps = 3/94 (3%)

Query: 121 EKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEK---KEEKEFKMKEDK 177
            +    KKK K+  ++I+  +K+ E+K+K K KK++ +KK++K+K    ++K+ K ++  
Sbjct: 55  AEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKD 114

Query: 178 EKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKK 211
           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|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742)

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 5/88 (5%)

Query: 112 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEF 171
           K KK    +E EK+KK+ ++K K K       K+K +K+K K ++K+  ++ +K E+K+ 
Sbjct: 61  KKKKKELAEEIEKVKKEYEEKQKWK-----WKKKKSKKKKDKDKDKKDDKKDDKSEKKDE 115

Query: 172 KMKEDKEKPVEKIRKEEKDSEKEKKSKD 199
           K  EDK + + K   E   +  E K + 
Sbjct: 116 KEAEDKLEDLTKSYSETLSTLSELKPRK 143

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

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

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 101 LGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKK 160
           + E  K + I + +   K    EK   K  KK   K   K++ +++K K K +  + +  
Sbjct: 364 IEEPLKARVIDELRPKTKA-PSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNI 422

Query: 161 EEKEKKEEKE 170
            ++ K     
Sbjct: 423 GKRRKPSGTS 432

Length = 434

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

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 17/72 (23%), Positives = 34/72 (47%)

Query: 154 KEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 213
            E ++ K  K+K   + +     ++K +EK +   K    E+  K   ++ K+EK K KK
Sbjct: 16  LESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKK 75

Query: 214 KEKERSSHEKEV 225
           K+     +  ++
Sbjct: 76  KKVPLQVNPAQL 87

Length = 217

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

 Score = 41.0 bits (96), Expect = 0.001
 Identities = 25/141 (17%), Positives = 49/141 (34%), Gaps = 14/141 (9%)

Query: 113 DKKTHKKKEKEKIKKKKDKKD-----KDKIKNKEKDKEKKEKEKGKKEEK-EKKEEKEKK 166
            +K  +KK      ++   +      +    + E  + KK +   K E K  KKE  +K+
Sbjct: 295 REKQKEKKAFLWTLRRNRLRMIITPWRAPELHAENAEIKKTRTAEKNEAKARKKEIAQKR 354

Query: 167 EEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVI 226
              E ++  ++E   E+     +   +    K K K L  +    +    E    +    
Sbjct: 355 RAAEREI--NREARQERAAAMARARARRAAVKAKKKGL-IDASPNEDTPSENEESKGSP- 410

Query: 227 PKLTFKFGTDMEEKTKRESSP 247
           P++          +  RE S 
Sbjct: 411 PQVE----ATTTAEPNREPSQ 427

Length = 429

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

 Score = 41.4 bits (98), Expect = 0.001
 Identities = 30/120 (25%), Positives = 59/120 (49%), Gaps = 2/120 (1%)

Query: 108 KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKE 167
           KS+ K +K   +  K  IK   ++ ++D +K K   K  K+ EK      +   E +  +
Sbjct: 111 KSLLKKQKVEVEGNKLIIKVN-NEIERDHLKKKHLPKLIKQYEKFGFGILKIDFEIDDSK 169

Query: 168 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIP 227
           E+  K +  KE+  EK+ KE  ++ K+ +++ K K+ K    K+   +  +   ++E+ P
Sbjct: 170 EELEKFEAQKEEEDEKLAKEALEAMKKLEAE-KKKQSKNFDPKEGPVQIGKKIDKEEITP 228

Length = 1437

>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 = 15/38 (39%), Positives = 21/38 (55%), Gaps = 4/38 (10%)

Query: 291 PMIGCDGCDA---WYHWVCVGLVAEPETSDWFCPKCSK 325
            M+ CD  +    W+H  CVGL   P+   W+CP+C K
Sbjct: 233 QMVACDNANCKREWFHLECVGLKEPPKGK-WYCPECKK 269

Length = 271

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 26/77 (33%), Positives = 44/77 (57%)

Query: 138 KNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKS 197
            NK    ++K K +  KE++ K+ E+E KEEK+ K K  +   +++I KE    EK +  
Sbjct: 269 INKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARAR 328

Query: 198 KDKDKKLKKEKLKKKKK 214
           K + +K + EK K K++
Sbjct: 329 KKEQRKERGEKKKLKRR 345

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 25/147 (17%), Positives = 71/147 (48%), Gaps = 5/147 (3%)

Query: 101 LGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE--KKEKEKGKKEEKE 158
           L E+ K+   K ++   +  E  +  +   +  ++++K  +K +E  ++++E+  ++E E
Sbjct: 176 LKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIE 235

Query: 159 KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
             EE+  + E+E +  E+ +  + +I   E ++ K ++ + ++ +     L++ +++ ER
Sbjct: 236 ALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELE---RLLEELEEKIER 292

Query: 219 SSHEKEVIPKLTFKFGTDMEEKTKRES 245
               +  I +L  +         + E 
Sbjct: 293 LEELEREIEELEEELEGLRALLEELEE 319

Length = 908

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

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 19/112 (16%), Positives = 59/112 (52%)

Query: 113 DKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFK 172
           +++  +  E E+  K++ ++  +K++N  ++ E+ +++   ++ KE+  + E + ++  +
Sbjct: 514 EEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKE 573

Query: 173 MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 224
           + E+      +  + E+  E+ K+ K K K+L++   + ++  +     E E
Sbjct: 574 LLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAE 625

Length = 908

>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 25/126 (19%), Positives = 58/126 (46%), Gaps = 5/126 (3%)

Query: 104 IKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEK 163
           I + K  K       K+ +  ++ +  K +  ++ N EKDKE +  EK   E  ++ +++
Sbjct: 74  INQKKEQKNLFNEQIKQFELALQDEIAKLEALELLNLEKDKELELLEKELDELSKELQKQ 133

Query: 164 EKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK-----EKLKKKKKEKER 218
            +   +  + K +  K  E+++ E +   +E    +++K  ++       L+ K+ E++R
Sbjct: 134 LQNTAEIIEKKRENNKNEERLKFENEKKLEESLELEREKFEEQLHEANLDLEFKENEEQR 193

Query: 219 SSHEKE 224
            S    
Sbjct: 194 ESKWAI 199

Length = 438

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

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 31/145 (21%), Positives = 64/145 (44%), Gaps = 12/145 (8%)

Query: 92  IVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEK 151
           I  +   ++    + DK  +   +   KK+K+K+ K K K D DK   +  D +  E + 
Sbjct: 215 IKDLEGDDEDDGDESDKGGEDGDEEKSKKKKKKLAKNKKKLDDDKKGKRGGDDDADEYDS 274

Query: 152 GKKEEKEKKE---------EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKD- 201
              +++ ++E           + +E ++    E   KP  +  ++ ++SE+EK  ++   
Sbjct: 275 DDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGL 334

Query: 202 --KKLKKEKLKKKKKEKERSSHEKE 224
             K  K +KLK KK   ++   +  
Sbjct: 335 SKKGKKLKKLKGKKNGLDKDDSDSG 359

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

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

 Score = 40.3 bits (94), Expect = 0.002
 Identities = 34/97 (35%), Positives = 55/97 (56%), Gaps = 2/97 (2%)

Query: 126 KKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIR 185
           + K    +  K   K   K    K K  KE K  +  KE+++EKE ++KE+K+K  EK +
Sbjct: 68  ESKLSSDEAVKRVEKGGSKGPAAKTKPAKEPK-NESGKEEEKEKE-QVKEEKKKKKEKPK 125

Query: 186 KEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 222
           +E KD + ++++K+K    +KEK K+KK E+ R   E
Sbjct: 126 EEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREE 162

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

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

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 32/152 (21%), Positives = 72/152 (47%), Gaps = 11/152 (7%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDK-KDKDKIKNKEKDKEKKE-------KEKGKKEE 156
           K +K +KK+K+  ++ EKE  + +  +  ++++ +  EK +EK E        +K  + E
Sbjct: 326 KLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESE 385

Query: 157 KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEK---LKKKK 213
           +     K K+EE E K +E+KE  +     E+++   +++ K++ K +++ +     K+ 
Sbjct: 386 RLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQG 445

Query: 214 KEKERSSHEKEVIPKLTFKFGTDMEEKTKRES 245
           K  E     ++   KL        + +   + 
Sbjct: 446 KLTEEKEELEKQALKLLKDKLELKKSEDLLKE 477

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 = 40.3 bits (94), Expect = 0.002
 Identities = 31/152 (20%), Positives = 71/152 (46%), Gaps = 14/152 (9%)

Query: 117 HKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKED 176
            K+K+KE++KK  ++ +       + ++ K ++ K K++ K+  E  + K EK    +E+
Sbjct: 168 EKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLK-EKLELEEEN 226

Query: 177 -------------KEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 223
                         +   E +R E+++ E  K+  +K++++  + LK+ K+E++    ++
Sbjct: 227 LLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQE 286

Query: 224 EVIPKLTFKFGTDMEEKTKRESSPKIVIKPVK 255
           E +  L  +      E  K E       + +K
Sbjct: 287 EELKLLAKEEEELKSELLKLERRKVDDEEKLK 318

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

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 22/93 (23%), Positives = 47/93 (50%), Gaps = 1/93 (1%)

Query: 91  NIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKE 150
            +   +S  D     + ++ K D +   + E+ K ++K+    +DK    + +KE +E E
Sbjct: 33  QLFFPSSPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESE 92

Query: 151 KGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEK 183
           +  +EE E+  ++ +KE +E K + + EK +  
Sbjct: 93  EENEEEDEESSDENEKETEE-KTESNVEKEITN 124

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|226894 COG4499, COG4499, Predicted membrane protein [Function unknown]

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 147 KEKEKGKKEEK---EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKK 203
           K  E+ K       +K++E  K+  K+ +    K   V    K+E D+ +E ++K K++K
Sbjct: 351 KLYEEVKSNTDLSGDKRQELLKEYNKKLQDYTKKLGEV----KDETDASEEAEAKAKEEK 406

Query: 204 LKKEKLKKKKKEKERSSHEKE 224
           LK+E+ +KK+KE+     EK 
Sbjct: 407 LKQEENEKKQKEQADEDKEKR 427

Length = 434

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

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 27/155 (17%), Positives = 54/155 (34%), Gaps = 2/155 (1%)

Query: 40   TPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSE 99
             P  S +K   S K+ +S   + + +  +    KE       +      V       S  
Sbjct: 1234 KPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGKPKNAPK--RVSAVQYSPPPPSKR 1291

Query: 100  DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEK 159
              GE           K   KK  E       KK K + K   K K K   ++    +  +
Sbjct: 1292 PDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTRVKQASASQSSR 1351

Query: 160  KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKE 194
               + +K++ +   ++D +  V+    E+ + +++
Sbjct: 1352 LLRRPRKKKSDSSSEDDDDSEVDDSEDEDDEDDED 1386

Length = 1388

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

 Score = 39.6 bits (93), Expect = 0.002
 Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 7/87 (8%)

Query: 138 KNKEKDKEK-KEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKK 196
           K+ EK +EK K  +   K  K+     E   + + K+K   E+  EK+  E K+ +KEKK
Sbjct: 277 KSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKK 336

Query: 197 SKDKDKKL------KKEKLKKKKKEKE 217
            ++K KK       + EKL+ +  +KE
Sbjct: 337 KEEKKKKQIERLEERIEKLEVQATDKE 363

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

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

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 38/142 (26%), Positives = 78/142 (54%), Gaps = 13/142 (9%)

Query: 96  TSSEDLGEIKK--DKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEK---- 149
            + ++LGE+ K   + I++ +K  K+ E  +   K+ +K+ +++  +  +   +      
Sbjct: 162 NAYKNLGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELRE 221

Query: 150 -----EKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRK-EEKDSEKEKKSKDKDKK 203
                EK  KE +E KEE E+ E++   ++  K K  EKIR+ EE+  E +K+ ++ ++K
Sbjct: 222 ELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEK 281

Query: 204 LKK-EKLKKKKKEKERSSHEKE 224
           +K+ ++LK+K +E  + S   E
Sbjct: 282 VKELKELKEKAEEYIKLSEFYE 303

Length = 880

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

 Score = 40.3 bits (95), Expect = 0.002
 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 112 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEK 163
            +KKT K  +K   K+ + KK+K+K K K K + +  K  GK+ +     E+
Sbjct: 384 SEKKTGKPSKKVLAKRAE-KKEKEKEKPKVKKRHRDTKNIGKRRKPSGTSEE 434

Length = 434

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

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 106 KDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKK----EKEKGKKEEKEKKE 161
           +     KDK   +   K   + K  +K K  IK +  ++ KK    EK++ KK+ K+KK 
Sbjct: 19  EKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPKKKKV 78

Query: 162 EKEKKEEKEFKMKE 175
             +    + F   E
Sbjct: 79  PLQVNPAQLFVDDE 92

Length = 217

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

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 24/127 (18%), Positives = 69/127 (54%), Gaps = 1/127 (0%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEK-EKGKKEEK 157
            +L E++++    +++    + ++  I +     +K  +  +E  +E +++  +  + E 
Sbjct: 424 RELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELEL 483

Query: 158 EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKE 217
           E+ EE+  +E++E +++E+ E+  +++R+ E++  +  + ++  K+  +EKL+K +   E
Sbjct: 484 EELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLE 543

Query: 218 RSSHEKE 224
                KE
Sbjct: 544 ELEELKE 550

Length = 908

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

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 30/140 (21%), Positives = 72/140 (51%), Gaps = 14/140 (10%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKE--- 155
           E+L  ++      ++     K  +E+++K ++K +K + + +E  +EK E  K  +E   
Sbjct: 305 EELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLK 364

Query: 156 ---------EKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKK 206
                    EKE ++  E+ ++ E  ++E KE+  E     E+  E+ ++ + + ++L++
Sbjct: 365 ELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELER 424

Query: 207 --EKLKKKKKEKERSSHEKE 224
             E+L+++ K+ E   ++ E
Sbjct: 425 ELEELEEEIKKLEEQINQLE 444

Length = 908

>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 21/115 (18%), Positives = 49/115 (42%), Gaps = 4/115 (3%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKD--KKDKDKIKNKEKDKEKKEKEKGKKEEKEKK 160
           +    +S+K+  +   K+  E +++KK   ++  + I      K    ++  +     KK
Sbjct: 828 KNGAYESLKELIERIIKEWIEDLRQKKKLIERLIEAINQYRAKKLDTAEKLEELYILAKK 887

Query: 161 EEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 215
           EE+ K+  +E  + E++              +  +   +  +KL KEK  ++K +
Sbjct: 888 EEEFKQFAEEEGLNEEELA--FYDDLALNGGKLPENGTELVEKLAKEKSLREKNK 940

Length = 962

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 3/91 (3%)

Query: 123 EKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVE 182
           E  + +K    K+  +   K+  +    + ++E K+K  EK +++EK  +  E  +  +E
Sbjct: 285 ENYRTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELE--QNLIE 342

Query: 183 KIR-KEEKDSEKEKKSKDKDKKLKKEKLKKK 212
           + +    K  E +KK +D +K+L+K K  K 
Sbjct: 343 ERKELNSKLEEIQKKLEDLEKRLEKLKSNKS 373

Length = 373

>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 29/133 (21%), Positives = 64/133 (48%), Gaps = 2/133 (1%)

Query: 86  TPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE 145
             ++   VKV S++   +  K+ + +K +     K      K+   K  + + +  K K 
Sbjct: 169 KSIMSPEVKVKSAKKTQDTSKETTTEKTEGKTSVKAASL--KRNPPKKSNIMSSFFKKKT 226

Query: 146 KKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK 205
           K++KEK +  E   KEE E++  K   + ED+      + ++E + E +   +  D + +
Sbjct: 227 KEKKEKKEASESTVKEESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEE 286

Query: 206 KEKLKKKKKEKER 218
            E+ +K+K+++ +
Sbjct: 287 TEEKEKEKRKRLK 299

This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. Length = 427

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

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 27/103 (26%), Positives = 52/103 (50%)

Query: 150 EKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 209
           E   +++   +EE E+K++KE K KE + K ++  +KE K   + +++ D     KK + 
Sbjct: 5   ESEAEKKILTEEELERKKKKEEKAKEKELKKLKAAQKEAKAKLQAQQASDGTNVPKKSEK 64

Query: 210 KKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIK 252
           K +K++ E  + E  + P   F     +  +  ++ SP  V K
Sbjct: 65  KSRKRDVEDENPEDFIDPDTPFGQKKRLSSQMAKQYSPSAVEK 107

Length = 1066

>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein

 Score = 40.3 bits (95), Expect = 0.002
 Identities = 30/112 (26%), Positives = 55/112 (49%), Gaps = 19/112 (16%)

Query: 112 KDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEF 171
           KDK T  K++K  I       D       E ++  K+ E+   E+K++KE  E K E E 
Sbjct: 483 KDKGT-GKEQKITITASSGLSDD------EIERMVKDAEEYAAEDKKRKERIEAKNEAEE 535

Query: 172 -------KMKEDKEKP----VEKIRKEEKDSEKEKKSKDKDK-KLKKEKLKK 211
                   +KE+ +K      +K+ +  +  ++E + +DK++ + K E+L+K
Sbjct: 536 YVYSLEKSLKEEGDKLPEADKKKVEEAIEWLKEELEGEDKEEIEAKTEELQK 587

Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. Length = 598

>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 40/223 (17%), Positives = 93/223 (41%), Gaps = 30/223 (13%)

Query: 37  PPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDVELGVTPMVPNIVKVT 96
                     +  +S +   +  +  S   + +  +     V+ +E     ++  ++K T
Sbjct: 77  DEPKQVKIPRQSGLSEEVAEAEAKATSVAAEATTPKSIQELVEALE----ELLEELLKET 132

Query: 97  SSE-----------DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKE 145
           +S+           DL +  K+ ++K D ++     KE++ +   K  +      E+++E
Sbjct: 133 ASDPVVQELVSIFNDLIDSIKEDNLKDDLESLIASAKEELDQLSKKLAE---LKAEEEEE 189

Query: 146 KKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLK 205
            +   K K+EE   K E+E     E K    +++      + E + EKE+  K  ++KL+
Sbjct: 190 LERALKEKREELLSKLEEELLARLESKEAALEKQ-----LRLEFEREKEELRKKYEEKLR 244

Query: 206 KEKLKKKKKEKERSSHEKEVIP----KLTFKFGTDMEEKTKRE 244
           +E    +++ +      K  +     +L  +F  +++EK + E
Sbjct: 245 QE---LERQAEAHEQKLKNELALQAIELQREFNKEIKEKVEEE 284

Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains. Length = 493

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

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 27/165 (16%), Positives = 64/165 (38%), Gaps = 4/165 (2%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
           +    + K ++   + E    + ++        K    +KE +E ++ + + KE+ +  E
Sbjct: 795 EIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYL-EKEIQELQEQRIDLKEQIKSIE 853

Query: 165 KKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 224
           K+ E     KE+ E+ +E++    +D E       K++   + +L++ +++ E    + E
Sbjct: 854 KEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIE 913

Query: 225 VIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYD 269
              K   +    +E   +  S    +  P       P       D
Sbjct: 914 KKRKRLSELKAKLEALEEELSE---IEDPKGEDEEIPEEELSLED 955

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

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

 Score = 40.1 bits (94), Expect = 0.003
 Identities = 30/142 (21%), Positives = 69/142 (48%), Gaps = 20/142 (14%)

Query: 102 GEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKE 161
           GEI   +   ++ +   ++ +E++++ K+K +  K + +E++   +E E+   E +E KE
Sbjct: 302 GEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKE 361

Query: 162 EKEK---------KEEKE----------FKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDK 202
           E E+         +E  E           ++ E + + +E++++E +  E+  +   +  
Sbjct: 362 ELEEKLSALLEELEELFEALREELAELEAELAEIRNE-LEELKREIESLEERLERLSERL 420

Query: 203 KLKKEKLKKKKKEKERSSHEKE 224
           +  KE+LK+ + E E    E E
Sbjct: 421 EDLKEELKELEAELEELQTELE 442

Length = 1163

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

 Score = 40.1 bits (94), Expect = 0.003
 Identities = 21/128 (16%), Positives = 55/128 (42%), Gaps = 6/128 (4%)

Query: 99  EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEK- 157
           E+   + ++      +    K+E E+      ++ ++  +   ++  + E E  +   + 
Sbjct: 340 EERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNEL 399

Query: 158 -EKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEK 216
            E K E E  EE+     E   + +E +++E K+ E E +    + +   E+L++ +++ 
Sbjct: 400 EELKREIESLEER----LERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQL 455

Query: 217 ERSSHEKE 224
           E      +
Sbjct: 456 EELRDRLK 463

Length = 1163

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

 Score = 40.0 bits (93), Expect = 0.003
 Identities = 29/164 (17%), Positives = 68/164 (41%), Gaps = 24/164 (14%)

Query: 99   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEK--------- 149
             +  ++K +   K++K+  +KKE E+  +K +  ++ + + +E+  E+            
Sbjct: 880  LEEQKLKDELESKEEKEKEEKKELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPE 939

Query: 150  --------EKGKKEEKEKKEEKEKKEEKEFKMKEDKEKP------VEKIRKEEKDSEKEK 195
                    EK K+E+ +++EE+  K     K +             EK  +  KD  K++
Sbjct: 940  ELLLEEADEKEKEEDNKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKE 999

Query: 196  KSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEE 239
            + +++ K+L +E +++  +  +    E  V             E
Sbjct: 1000 RLEEEKKELLREIIEETCQRFKE-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|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510)

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 127 KKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVE-KIR 185
              D+   D+ + K+ D ++  + +  KEE+++    E KE+K    KED+E   E +  
Sbjct: 39  SPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEE 98

Query: 186 KEEKDSEKEKKSKDKD 201
            EE   E EK++++K 
Sbjct: 99  DEESSDENEKETEEKT 114

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

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 113 DKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFK 172
                   ++++ KK  D++  +  + KE++KE    E  + +   +KE++E +EE E +
Sbjct: 39  SPSDQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENE-E 97

Query: 173 MKEDKEKPVEKIRKEEKDSEKEKKS 197
             E+     EK   EEK     +K 
Sbjct: 98  EDEESSDENEKE-TEEKTESNVEKE 121

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

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

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
           K D     + +  K++EKE    +  +   D  K  E+ +E+ E+E  +  ++ +KE +E
Sbjct: 53  KSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEE 112

Query: 165 KKEEKEFKMKEDKE-KPV 181
           K E    K   +   KPV
Sbjct: 113 KTESNVEKEITNPSWKPV 130

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

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 27/177 (15%), Positives = 57/177 (32%), Gaps = 3/177 (1%)

Query: 99   EDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKE 158
             +  EI K++ +K   K    K ++   KKK+K  K K  + +K K+       K+ + +
Sbjct: 1147 VEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEK--KKKKSSADKSKKASVVGNSKRVDSD 1204

Query: 159  KKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
            +K + + K + +       ++  ++ +K +      K+ K K     K      +     
Sbjct: 1205 EKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFS-SD 1263

Query: 219  SSHEKEVIPKLTFKFGTDMEEKTKRESSPKIVIKPVKSPSPPPVAAADEYDTGDSKQ 275
               ++        +              P         PS P      +   G    
Sbjct: 1264 DLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAA 1320

Length = 1388

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

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 43/204 (21%), Positives = 76/204 (37%), Gaps = 29/204 (14%)

Query: 92   IVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKD-------- 143
            ++     +DL +  K     + K   KKK ++   ++++  ++D   + E D        
Sbjct: 1027 VITNAKKKDLVKELKKLGYVRFKDIIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAV 1086

Query: 144  --------------KEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKI----R 185
                          KEK EK   + E+KEK+ EK K    +    ED +K  E +     
Sbjct: 1087 SYDYLLSMPIWSLTKEKVEKLNAELEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEE 1146

Query: 186  KEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRES 245
             EEK+  KE++ K K K    +  K K K+KE+   +                   + +S
Sbjct: 1147 VEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVV---GNSKRVDS 1203

Query: 246  SPKIVIKPVKSPSPPPVAAADEYD 269
              K  +           + +D+ D
Sbjct: 1204 DEKRKLDDKPDNKKSNSSGSDQED 1227

Length = 1388

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

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 25/116 (21%), Positives = 42/116 (36%), Gaps = 1/116 (0%)

Query: 136 KIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEK 195
           K K +             KE      E+E K       K+ KE    + +K+ +  +K+K
Sbjct: 18  KSKLQPISYIYSNVLVLSKEILSTFSEEENKVATTSTKKDKKEDKNNESKKKSEKKKKKK 77

Query: 196 KSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEE-KTKRESSPKIV 250
           K K + K   + KL  K  +K + + +K   PK          +     E S   +
Sbjct: 78  KEKKEPKSEGETKLGFKTPKKSKKTKKKPPKPKPNEDVDNAFNKIAELAEKSNVYI 133

Length = 413

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 4/76 (5%)

Query: 116 THKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKE 175
           T K KE  + ++++++ D +     E    K+E+E   +E+     E+++  +K     E
Sbjct: 223 TKKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKT----E 278

Query: 176 DKEKPVEKIRKEEKDS 191
           D +K      K++++ 
Sbjct: 279 DLDKLEILKEKKDEEL 294

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 24/81 (29%), Positives = 52/81 (64%), Gaps = 8/81 (9%)

Query: 118 KKKEKEKIKKKKDKKDKD-KIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKED 176
           + K +EK  +++ ++ ++ + + ++K +EK+E E+ ++EE E++ EK+K+EE+  + +E 
Sbjct: 8   RAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQ 67

Query: 177 KEKPVEKIRKEEKDSEKEKKS 197
                   RKE+++ EK K S
Sbjct: 68  A-------RKEQEEYEKLKSS 81

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 10/87 (11%)

Query: 127 KKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRK 186
             + ++++ +  N    + KK ++K +K EK+ ++E+ +K           +K  E   K
Sbjct: 393 LAEGEEEEGENGNLSPAERKKLRKKQRKAEKKAEKEEAEKAA--------AKKKAEAAAK 444

Query: 187 EEKDSEKEKKSKDKDKKLKKEKLKKKK 213
           + K  + E K  D D     EKL + +
Sbjct: 445 KAKGPDGETKKVDPD--PLGEKLARTE 469

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam07719, pfam00515. There is a single completely conserved residue L that may be functionally important. NARP1 is the mammalian homologue of a yeast N-terminal acetyltransferase that regulates entry into the G(0) phase of the cell cycle. Length = 516

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

 Score = 39.5 bits (93), Expect = 0.003
 Identities = 16/52 (30%), Positives = 24/52 (46%)

Query: 167 EEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
           +E   K K   EK   K  K+      EKK K+K+K   K++ +  K   +R
Sbjct: 374 DELRPKTKAPSEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKR 425

Length = 434

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

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 27/113 (23%), Positives = 64/113 (56%), Gaps = 2/113 (1%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDK 177
           + +E  + K +  K  ++++K  E+  E+ EKE  K  E+ K+ E+  +E KE   +   
Sbjct: 344 ELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELSA 403

Query: 178 EKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLT 230
              +E+I++E ++ EKE +  +++ +  +E++KK +++  +   ++ +I +L 
Sbjct: 404 A--LEEIQEELEELEKELEELERELEELEEEIKKLEEQINQLESKELMIAELA 454

Length = 908

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

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 25/127 (19%), Positives = 66/127 (51%), Gaps = 7/127 (5%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEK-----EK 159
           + ++ I++ ++  ++ E+ + + +  +   ++++   +  +  E+   K EEK      +
Sbjct: 285 ELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESE 344

Query: 160 KEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERS 219
            EE  +++ +  K+ E++ K +E  R EE + E EK  +   K+L++   + K++  E S
Sbjct: 345 LEELAEEKNELAKLLEERLKELE-ERLEELEKELEKALERL-KQLEEAIQELKEELAELS 402

Query: 220 SHEKEVI 226
           +  +E+ 
Sbjct: 403 AALEEIQ 409

Length = 908

>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 27/135 (20%), Positives = 67/135 (49%), Gaps = 5/135 (3%)

Query: 113 DKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFK 172
           +K+ ++K+ + +  KKK+    ++    +K ++K    +  K+ +   +++  K E    
Sbjct: 48  EKEANEKRAQYRSAKKKELSQLEEQLINQKKEQKNLFNEQIKQFELALQDEIAKLEALEL 107

Query: 173 MKEDKEKPVEKIRKE--EKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLT 230
           +  +K+K +E + KE  E   E +K+ ++  + ++K++   K +E+ +  +EK++   L 
Sbjct: 108 LNLEKDKELELLEKELDELSKELQKQLQNTAEIIEKKRENNKNEERLKFENEKKLEESLE 167

Query: 231 F---KFGTDMEEKTK 242
               KF   + E   
Sbjct: 168 LEREKFEEQLHEANL 182

Length = 438

>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 7/84 (8%)

Query: 122 KEKIKKKKDKKD-KDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEF------KMK 174
            EK+   K+  +   K  ++ +  E++ + K K  EK +++EK  +E ++       ++ 
Sbjct: 289 TEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKELN 348

Query: 175 EDKEKPVEKIRKEEKDSEKEKKSK 198
              E+  +K+   EK  EK K +K
Sbjct: 349 SKLEEIQKKLEDLEKRLEKLKSNK 372

Length = 373

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

 Score = 39.2 bits (91), Expect = 0.003
 Identities = 33/111 (29%), Positives = 47/111 (42%), Gaps = 1/111 (0%)

Query: 114 KKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKE-EKEKKEEKEKKEEKEFK 172
           KKT KKK  E+ K    K    K   K K   K    K  K+  K KK +  K   K+  
Sbjct: 5   KKTTKKKTTEEKKPAAKKATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVT 64

Query: 173 MKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEK 223
           +K +K + V+K    +K  +KE  S +  +   K      K  K+  + EK
Sbjct: 65  VKFEKTESVKKESVAKKTVKKEAVSAEVFEASNKLFKNTSKLPKKLFASEK 115

Length = 295

>gnl|CDD|178867 PRK00106, PRK00106, hypothetical protein; Provisional

 Score = 39.5 bits (92), Expect = 0.003
 Identities = 27/98 (27%), Positives = 52/98 (53%), Gaps = 3/98 (3%)

Query: 113 DKKTHKKKEKEKIKKKKDKKDKDKIKN-KEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEF 171
           D+K      KEK  + K++   DK K+  E++++ ++ E+ KK E E+     + E +E 
Sbjct: 114 DRKDENLSSKEKTLESKEQSLTDKSKHIDEREEQVEKLEEQKKAELERVAALSQAEAREI 173

Query: 172 KMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKL 209
            + E + K   +I    +++E+E   KD+  K+ K+ L
Sbjct: 174 ILAETENKLTHEIATRIREAERE--VKDRSDKMAKDLL 209

Length = 535

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 39.1 bits (92), Expect = 0.003
 Identities = 19/100 (19%), Positives = 65/100 (65%), Gaps = 1/100 (1%)

Query: 120 KEKEKIKKKKDK-KDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKE 178
           +E+EK ++++ + + +++ +  E  +  +E+++ + +EK +K++K ++E  EF  +  + 
Sbjct: 81  EEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIER 140

Query: 179 KPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKER 218
           K  EK R+ E++ +  +  ++K ++ ++ + +++++++E+
Sbjct: 141 KEEEKEREREEELKILEYQREKAEREEEREAERRERKEEK 180

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 26/123 (21%), Positives = 64/123 (52%), Gaps = 4/123 (3%)

Query: 114 KKTHKKKEKEKIKKKKDKKDKDKIK---NKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKE 170
           K+    KE E+I ++  K+ ++K++    + K+   +E+ + ++E + ++EE +++EE+ 
Sbjct: 27  KRQRLAKEAERILQEAQKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERL 86

Query: 171 FKMKEDKEKPVEKIR-KEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKL 229
            + +E  +   EK+   E +  E+EK    ++ +L++ + +   +    +    E   KL
Sbjct: 87  VQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQARKL 146

Query: 230 TFK 232
             K
Sbjct: 147 LLK 149

Length = 508

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

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 15/87 (17%), Positives = 39/87 (44%)

Query: 137 IKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKK 196
           +K   +   +  KE  K  E EK  E E+++ +   +KE+ +K   +I + E+  ++ + 
Sbjct: 1   LKELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEA 60

Query: 197 SKDKDKKLKKEKLKKKKKEKERSSHEK 223
                 +    + ++++ + E +    
Sbjct: 61  KPAASGEGGGGEEEEEEAKAEAAEFRA 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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 39.2 bits (92), Expect = 0.004
 Identities = 26/147 (17%), Positives = 52/147 (35%), Gaps = 5/147 (3%)

Query: 126 KKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIR 185
             K +   +++ K K K    K K KG   ++E KE  E K++   ++ +        + 
Sbjct: 5   STKAELAAEEEAKKKLKKLAAKSKSKGFITKEEIKEALESKKKTPEQIDQVLIF----LS 60

Query: 186 KEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRES 245
              KD++   +S    KK K        K   +   + E+      +   +  +K    +
Sbjct: 61  GMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAE-KKNALDKDDDLN 119

Query: 246 SPKIVIKPVKSPSPPPVAAADEYDTGD 272
             K +    ++         D+ D  D
Sbjct: 120 YVKDIDVLNQADDDDDDDDDDDLDDDD 146

Length = 509

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

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 9/83 (10%)

Query: 135 DKIKN---KEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDS 191
           DK+ N     +   K +K + ++EEK  K  +E+++E+  + KE+K+K  E+  K  K S
Sbjct: 246 DKLANLKLSPEVLRKVDKTREEEEEKILKAAEEERQEEAQEKKEEKKK-EEREAKLAKLS 304

Query: 192 EKEKKSKDKDKKLKKEKLKKKKK 214
            +E++     K  +KE+ K+ +K
Sbjct: 305 PEEQR-----KLEEKERKKQARK 322

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

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

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 27/98 (27%), Positives = 54/98 (55%), Gaps = 1/98 (1%)

Query: 122 KEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPV 181
           +E+IK+ ++K+++ +   K+  + +K  E+ ++  +  +E K KKEE E   K       
Sbjct: 327 EERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGLTP 386

Query: 182 EKIRKEEKDSEKEKKS-KDKDKKLKKEKLKKKKKEKER 218
           EK+ KE ++ EK K+  +++  K+     + KK+ KE 
Sbjct: 387 EKLEKELEELEKAKEEIEEEISKITARIGELKKEIKEL 424

Length = 880

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

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 40/171 (23%), Positives = 86/171 (50%), Gaps = 15/171 (8%)

Query: 65  KEKTSPKEKEYSKVKDVELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEK 124
            E+   K +EY K+K+  + +   + ++ K    E L E+KK  +  + K    ++E  +
Sbjct: 517 LEELEKKAEEYEKLKEKLIKLKGEIKSLKK--ELEKLEELKKKLAELEKKLDELEEELAE 574

Query: 125 IKKKKDKK-------DKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKE----FKM 173
           + K+ ++         ++++K  E    +  + K  ++E E++E++ KK E+E    F+ 
Sbjct: 575 LLKELEELGFESVEELEERLKELEPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEE 634

Query: 174 KEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHEKE 224
             + EK +E++RKE +  E EKK  +++ +  +E+  +  +E      E E
Sbjct: 635 LAETEKRLEELRKELE--ELEKKYSEEEYEELREEYLELSRELAGLRAELE 683

Length = 880

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

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 9/86 (10%)

Query: 136 KIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEK 195
               K+K +  +E EK KKE     EEK+K + K+ K K+ K+K      K++KD +K+ 
Sbjct: 58  TEAKKKKKELAEEIEKVKKE----YEEKQKWKWKKKKSKKKKDKD-----KDKKDDKKDD 108

Query: 196 KSKDKDKKLKKEKLKKKKKEKERSSH 221
           KS+ KD+K  ++KL+   K    +  
Sbjct: 109 KSEKKDEKEAEDKLEDLTKSYSETLS 134

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

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

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 9/82 (10%)

Query: 114 KKTHKKKEKEKIKKKKDKK-----DKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEE 168
           K+  +  E EK K  KDK      +K   ++K  +K K   +    E  +K   +EKKEE
Sbjct: 10  KRVVRALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEE 69

Query: 169 KEFKMKEDKEKPVEKIRKEEKD 190
           K    K+ K+K V       + 
Sbjct: 70  K----KKPKKKKVPLQVNPAQL 87

Length = 217

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

 Score = 39.3 bits (91), Expect = 0.004
 Identities = 42/160 (26%), Positives = 67/160 (41%), Gaps = 26/160 (16%)

Query: 115 KTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMK 174
           + H+  E  K  +K D    +K   K K KEKKEKEK +  +K+KK+E E  +     + 
Sbjct: 176 QKHRNAETSKSPEKGDVPAVEKKSKKPKKKEKKEKEKER--DKDKKKEVEGFKSLLLALD 233

Query: 175 ED------------------------KEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLK 210
           +                           +P E    E ++++K  K K K ++ +KE+ K
Sbjct: 234 DSPASAASVAEADEASLANTVSGTAPDSEPDEPKDAEAEETKKSPKHKKKKQRKEKEEKK 293

Query: 211 KKKKEKERSSHEKEVIPKLTFKFGTDMEEKTKRESSPKIV 250
           KKKK      H  +   +   + G   EE     SS K++
Sbjct: 294 KKKKHHHHRCHHSDGGAEQPVQNGAVEEEPLPPMSSYKLL 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|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 33/96 (34%), Positives = 56/96 (58%), Gaps = 9/96 (9%)

Query: 134 KDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEE-KDSE 192
           +DK       +EK+E+++ +KEEKE+KEEKEK+  K    KE++EK +E++ K + K   
Sbjct: 5   RDKSGRIIDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEELEKAKNKPLA 64

Query: 193 KEKKSKDKDKKLKKE--------KLKKKKKEKERSS 220
           +    +D D++LK++        +  +KKKEK    
Sbjct: 65  RYADDEDYDEELKEQERWDDPMAQFLRKKKEKTDKK 100

This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. Length = 141

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

 Score = 39.1 bits (91), Expect = 0.004
 Identities = 27/105 (25%), Positives = 44/105 (41%), Gaps = 2/105 (1%)

Query: 105 KKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKE 164
           K  K+ KK  K H K   ++ K+    K     KN+    E K  E G  +  + KE+  
Sbjct: 3   KASKATKKFTKNHLKNTIDRRKQLARSKKVYGTKNRNSHTENK-MESGTNDNNKNKEKLS 61

Query: 165 KKEEKEFKMKEDKEKP-VEKIRKEEKDSEKEKKSKDKDKKLKKEK 208
           K          ++E+   E I K   +S+K   ++   +K +KE 
Sbjct: 62  KLYSDVDSSSSEEEEDGSESISKLNVNSKKISLNQVSTQKWRKEL 106

Length = 523

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 25/131 (19%), Positives = 68/131 (51%), Gaps = 4/131 (3%)

Query: 98  SEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEK 157
           + ++  +++ K I +++  + +++ E+++ + ++ +    +  E+  E +EK +  KEE 
Sbjct: 294 ANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEEL 353

Query: 158 EKKEEKEKKEEKEFKM----KEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKK 213
           E  E + ++ E E +      E+ E+ +E +R +    E +  S + + +  + +L++ +
Sbjct: 354 ESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLE 413

Query: 214 KEKERSSHEKE 224
             +ER   E E
Sbjct: 414 DRRERLQQEIE 424

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|240370 PTZ00342, PTZ00342, acyl-CoA synthetase; Provisional

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 27/111 (24%), Positives = 41/111 (36%), Gaps = 13/111 (11%)

Query: 131 KKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKD 190
           K  +  I  +EK+        G K  KE     E+K        ED      +  KE+  
Sbjct: 212 KSKEININKEEKNNGSNVNNNGNKNNKE-----EQKGNDLSNELEDISLGPLEYDKEK-- 264

Query: 191 SEKEKKSKDKDKKLKK------EKLKKKKKEKERSSHEKEVIPKLTFKFGT 235
            EK K  K+K KKL        +  K K    +  + + + I  + +  GT
Sbjct: 265 LEKIKDLKEKAKKLGISIILFDDMTKNKTTNYKIQNEDPDFITSIVYTSGT 315

Length = 746

>gnl|CDD|115072 pfam06391, MAT1, CDK-activating kinase assembly factor MAT1

 Score = 37.8 bits (88), Expect = 0.004
 Identities = 26/105 (24%), Positives = 58/105 (55%), Gaps = 5/105 (4%)

Query: 118 KKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKEEKEFKM--KE 175
           ++K  +  K+ KD   ++K +   + +E ++  + +KE KE+K    +KEE+E KM  ++
Sbjct: 67  EEKVDQYEKENKDSIMRNKRRLTREQEELEQALEEEKEMKEEKRLHLQKEEQEQKMAKEK 126

Query: 176 DKEKPVEKIRKEEKDSEK---EKKSKDKDKKLKKEKLKKKKKEKE 217
           DK++ ++++      +     + K + K  + + EKL++KK+   
Sbjct: 127 DKQEIIDELETSNLPANVIIAQHKKQSKQLESQVEKLERKKRVTF 171

MAT1 is an assembly/targeting factor for cyclin-dependent kinase-activating kinase (CAK), which interacts with the transcription factor TFIIH. The domain found to the N-terminal side of this domain is a C3HC4 RING finger. Length = 200

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	446
PF10203	68	Pet191_N: Cytochrome c oxidase assembly protein PE	99.85
KOG4114|consensus	73		99.84
KOG1973|consensus	274		99.05
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	98.88
COG5034	271	TNG2 Chromatin remodeling protein, contains PhD zi	98.78
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	98.75
KOG0825|consensus	1134		98.27
KOG1244|consensus	336		98.1
KOG4323|consensus	464		97.83
KOG4299|consensus	613		97.75
KOG1844|consensus	508		97.74
KOG1512|consensus	381		97.73
KOG1632|consensus	345		97.11
KOG0955|consensus	1051		96.97
KOG1245|consensus	1404		96.91
KOG0383|consensus	696		96.91
PF13831	36	PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.	96.77
KOG0957|consensus	707		96.73
KOG0954|consensus	893		96.36
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	95.89
PTZ00266	1021	NIMA-related protein kinase; Provisional	95.67
PF07227	446	DUF1423: Protein of unknown function (DUF1423); In	95.42
KOG0957|consensus	707		95.24
COG5141	669	PHD zinc finger-containing protein [General functi	95.22
KOG1632|consensus	345		95.21
KOG0956|consensus	900		94.81
KOG4364|consensus	811		94.76
KOG4443|consensus	694		94.74
KOG4364|consensus	811		92.83
KOG0163|consensus	1259		91.52
KOG1029|consensus	1118		91.21
KOG1144|consensus	1064		91.05
KOG2891|consensus	445		90.18
KOG3054|consensus	299		88.87
PF05262	489	Borrelia_P83: Borrelia P83/100 protein; InterPro:	88.27
PF15446	175	zf-PHD-like: PHD/FYVE-zinc-finger like domain	88.02
KOG1029|consensus	1118		87.09
PF07649	30	C1_3: C1-like domain; InterPro: IPR011424 This sho	86.9
KOG1144|consensus	1064		85.79
KOG2752|consensus	345		85.64
PF07496	50	zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zi	82.78
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	82.47
KOG4443|consensus	694		81.2
KOG1473|consensus	1414		80.98

>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=99.85  E-value=4.8e-22  Score=159.50  Aligned_cols=64  Identities=44%  Similarity=1.021  Sum_probs=60.3

Q ss_pred             cchhhhhHHhHHHHhhhccccccCCCChhhhhcCC---ChhhHHHHHhHHHhccccCcccccccccccCC
Q psy128          364 KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREG---LAPQCEALKNTFFECKRSLLDTRQTVCRWIGK  430 (446)
Q Consensus       364 ~~SC~~iredLa~CLleSdC~~~~~~t~keCL~~~---lp~eC~~l~~~f~eCKR~llD~r~Rfrr~rGn  430 (446)
                      ++||++++++|+.||++||||+++++||+|||+++   ||.+|++|+++||+|||||||||+   |||||
T Consensus         2 ~~sC~~~~~~L~~Cl~~SdCv~~~~~t~~~Cl~~~~~~~p~eC~~lr~~f~eCKrg~lDmr~---RfRGn   68 (68)
T PF10203_consen    2 SKSCKGIREALAECLQESDCVKKEKRTPKDCLKDPSDELPEECQQLRKAFFECKRGMLDMRK---RFRGN   68 (68)
T ss_pred             CchHHHHHHHHHHHHhhChhhccCCCCHHHHHcCCCCcCCHHHHHHHHHHHHHhcccccccc---cccCc
Confidence            57999999999999999999999999999999987   899999999999999999999999   55555

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=99.84  E-value=7.9e-22  Score=156.97  Aligned_cols=67  Identities=43%  Similarity=0.886  Sum_probs=63.1

Q ss_pred             cchhhhhHHhHHHHhhhccccccCCCChhhhhcCC----ChhhHHHHHhHHHhccccCcccccccccccCC
Q psy128          364 KSACAGSRADLKLCLLETDCVQVDRKTPRQCLREG----LAPQCEALKNTFFECKRSLLDTRQTVCRWIGK  430 (446)
Q Consensus       364 ~~SC~~iredLa~CLleSdC~~~~~~t~keCL~~~----lp~eC~~l~~~f~eCKR~llD~r~Rfrr~rGn  430 (446)
                      +.||.+++++|+.||++|||+++++++|++||+++    ||.+|++|+.+|++|||+|||||+|||+.+|.
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            57999999999999999999999999999999974    89999999999999999999999988887763

>KOG1973|consensus

Probab=99.05  E-value=6.4e-11  Score=117.73  Aligned_cols=54  Identities=37%  Similarity=1.067  Sum_probs=45.5

Q ss_pred             CCCCCCCcccccccccCCCCCCCeeecCC--CC-CcccccccccCCCCCCCcEEcCCCCCc
Q psy128          269 DTGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       269 eeed~~~~~~C~VCg~pdd~~~~mIqCD~--C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      ...++++..|| +|....+|.  ||.||+  |. .|||+.|||+... +.+.|||+.|...
T Consensus       212 ~~~d~~e~~yC-~Cnqvsyg~--Mi~CDn~~C~~eWFH~~CVGL~~~-PkgkWyC~~C~~~  268 (274)
T KOG1973|consen  212 EAVDPDEPTYC-ICNQVSYGK--MIGCDNPGCPIEWFHFTCVGLKTK-PKGKWYCPRCKAE  268 (274)
T ss_pred             cccCCCCCEEE-Eeccccccc--ccccCCCCCCcceEEEeccccccC-CCCcccchhhhhh
Confidence            34556678899 999877777  999998  99 9999999999966 5568999999854

>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=98.88  E-value=2.9e-10  Score=84.94  Aligned_cols=46  Identities=48%  Similarity=1.284  Sum_probs=39.2

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC---CCCCcEEcCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE---PETSDWFCPKCS  324 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~---~~~~~w~Cp~C~  324 (446)
                      +|.+|+..++++ .||+||.|+.|||..|++++..   .....|+|+.|.
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            588999966666 8999999999999999999987   223489999986

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

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

Probab=98.78  E-value=2.5e-09  Score=104.77  Aligned_cols=51  Identities=35%  Similarity=1.025  Sum_probs=43.5

Q ss_pred             CCCCCcccccccccCCCCCCCeeecCC--CC-CcccccccccCCCCCCCcEEcCCCCC
Q psy128          271 GDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       271 ed~~~~~~C~VCg~pdd~~~~mIqCD~--C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      .+.++..|| .|++..+|.  ||.||+  |. .|||+.|||+... +.+.|||+.|..
T Consensus       216 ~se~e~lYC-fCqqvSyGq--MVaCDn~nCkrEWFH~~CVGLk~p-PKG~WYC~eCk~  269 (271)
T COG5034         216 NSEGEELYC-FCQQVSYGQ--MVACDNANCKREWFHLECVGLKEP-PKGKWYCPECKK  269 (271)
T ss_pred             cccCceeEE-Eeccccccc--ceecCCCCCchhheeccccccCCC-CCCcEeCHHhHh
Confidence            334567899 999999998  999997  88 9999999999765 668999999973

>smart00249 PHD PHD zinc finger

Probab=98.75  E-value=8.8e-09  Score=73.57  Aligned_cols=45  Identities=47%  Similarity=1.305  Sum_probs=38.5

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKC  323 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C  323 (446)
                      +|.+|+..++++ .||+||.|+.|||..|+++...  .....|+|+.|
T Consensus         1 ~C~~C~~~~~~~-~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~~C~~C   47 (47)
T smart00249        1 YCSVCGKPDDGG-ELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC   47 (47)
T ss_pred             CcccCCCcCCCC-CEEECCCCCchhhhhhCCCcccCCCCCCCEECcCC
Confidence            377899887555 8999999999999999998877  45678999987

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

>KOG0825|consensus

Probab=98.27  E-value=3.2e-07  Score=100.98  Aligned_cols=55  Identities=27%  Similarity=0.728  Sum_probs=47.4

Q ss_pred             CCCcccccccccCCCCCCCeeecCCCCCc-ccccccccCCC-CCCCcEEcCCCCCccc
Q psy128          273 SKQVWICPACGVQDDGSLPMIGCDGCDAW-YHWVCVGLVAE-PETSDWFCPKCSKVDE  328 (446)
Q Consensus       273 ~~~~~~C~VCg~pdd~~~~mIqCD~C~~W-fH~~Cvg~~~~-~~~~~w~Cp~C~~k~~  328 (446)
                      ....+.|.||+.+|..+ .||+||.|+.. ||.+||++++. .+.+.|||..|.-...
T Consensus       212 ~~E~~~C~IC~~~DpEd-VLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL~~  268 (1134)
T KOG0825|consen  212 SQEEVKCDICTVHDPED-VLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLLEI  268 (1134)
T ss_pred             ccccccceeeccCChHH-hheeecccccceeeccccCcccccccccceecCcchhhhh
Confidence            34567899999998888 99999999977 99999999987 7778999999986443

>KOG1244|consensus

Probab=98.10  E-value=1e-06  Score=87.48  Aligned_cols=47  Identities=30%  Similarity=0.812  Sum_probs=43.5

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCC
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCS  324 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~  324 (446)
                      .+|.|||..++++ .++.||.|++.||.+|+.++.. ++.+.|.|-.|.
T Consensus       282 k~csicgtsendd-qllfcddcdrgyhmyclsppm~eppegswsc~KOG  329 (336)
T KOG1244|consen  282 KYCSICGTSENDD-QLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCL  329 (336)
T ss_pred             ceeccccCcCCCc-eeEeecccCCceeeEecCCCcCCCCCCchhHHHHH
Confidence            4799999988888 8999999999999999999998 888999999997

>KOG4323|consensus

Probab=97.83  E-value=7e-06  Score=87.04  Aligned_cols=50  Identities=32%  Similarity=0.899  Sum_probs=40.1

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-----CCCCcEEcCCCCCcc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKVD  327 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~~k~  327 (446)
                      ..|| .|+.+..++ .||+|+.|+.|||..|..+...     .....|||..|..+.
T Consensus       171 c~vC-~~g~~~~~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~  225 (464)
T KOG4323|consen  171 CSVC-YCGGPGAGN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP  225 (464)
T ss_pred             eeee-ecCCcCccc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence            4456 567776666 8999999999999999988766     456789999999654

>KOG4299|consensus

Probab=97.75  E-value=1.3e-05  Score=87.06  Aligned_cols=49  Identities=33%  Similarity=0.752  Sum_probs=41.2

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccCCC---CCCCcEEcCCCCCc
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE---PETSDWFCPKCSKV  326 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~---~~~~~w~Cp~C~~k  326 (446)
                      .+|..|++.+.-. .+|+||+|+..||+.|+.++..   .+.+.|+|+.|.-.
T Consensus       254 ~fCsaCn~~~~F~-~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k  305 (613)
T KOG4299|consen  254 DFCSACNGSGLFN-DIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK  305 (613)
T ss_pred             HHHHHhCCccccc-cceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence            3899999865442 5799999999999999999966   78889999999653

>KOG1844|consensus

Probab=97.74  E-value=4.5e-05  Score=81.06  Aligned_cols=59  Identities=27%  Similarity=0.759  Sum_probs=49.5

Q ss_pred             CCcccccccccCCC-CCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCcccCchhhH
Q psy128          274 KQVWICPACGVQDD-GSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEK  334 (446)
Q Consensus       274 ~~~~~C~VCg~pdd-~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k~~~~~K~k  334 (446)
                      .....| +|+..++ ++ +||+|+.|..|+|..|+|+.....+..|.|..|.++........
T Consensus        84 ~~~~~c-~c~~~~~~~g-~~i~c~~c~~Wqh~~C~g~~~~~~p~~y~c~~c~~~~~~~~~~~  143 (508)
T KOG1844|consen   84 REISRC-DCGLEDDMEG-LMIQCDWCGRWQHKICCGSFKSTKPDKYVCEICTPRNKEVERAL  143 (508)
T ss_pred             Cccccc-ccccccCCCc-eeeCCcccCcccCceeeeecCCCCchhceeeeeccccccchhhh
Confidence            456779 9999888 66 99999999999999999998874467899999999877665443

>KOG1512|consensus

Probab=97.73  E-value=1.3e-05  Score=80.32  Aligned_cols=46  Identities=33%  Similarity=0.702  Sum_probs=39.2

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcC-CCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCP-KCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp-~C~~  325 (446)
                      .|.||++|...+ .|+.||.|++.||+.|||+... +.|.|+|. .|..
T Consensus       316 lC~IC~~P~~E~-E~~FCD~CDRG~HT~CVGL~~l-P~G~WICD~~C~~  362 (381)
T KOG1512|consen  316 LCRICLGPVIES-EHLFCDVCDRGPHTLCVGLQDL-PRGEWICDMRCRE  362 (381)
T ss_pred             hhhccCCcccch-heeccccccCCCCccccccccc-cCccchhhhHHHH
Confidence            588999998777 8999999999999999999766 55799998 3543

>KOG1632|consensus

Probab=97.11  E-value=0.00031  Score=72.61  Aligned_cols=51  Identities=33%  Similarity=0.786  Sum_probs=43.6

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccc--cccCCC--CCCCcEEcCCCCCcccC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVC--VGLVAE--PETSDWFCPKCSKVDEG  329 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~C--vg~~~~--~~~~~w~Cp~C~~k~~~  329 (446)
                      +| .|..+.+.+.+|+.||.|..|||+.|  +|++..  +....|+|..|.....+
T Consensus        62 ~~-~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~~  116 (345)
T KOG1632|consen   62 YC-KCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQDG  116 (345)
T ss_pred             hh-hcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchhhhh
Confidence            78 88888877558999999999999999  999887  66789999999875543

>KOG0955|consensus

Probab=96.97  E-value=0.00061  Score=78.75  Aligned_cols=128  Identities=18%  Similarity=0.259  Sum_probs=74.8

Q ss_pred             CcccccccccCCCC-CCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCcccCchhhHhhhcccccccccccccccc
Q psy128          275 QVWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKRGRKKKTHQDIIMSTYR  353 (446)
Q Consensus       275 ~~~~C~VCg~pdd~-~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k~~~~~K~kr~kkRkkk~~qs~~mstYr  353 (446)
                      ++..|.||...+-. .+..|+||.|+..+|..|+|++.. +.+.|+|..|........          ... -....+-+
T Consensus       218 ~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~i-peg~WlCr~Cl~s~~~~v----------~c~-~cp~~~gA  285 (1051)
T KOG0955|consen  218 EDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFI-PEGQWLCRRCLQSPQRPV----------RCL-LCPSKGGA  285 (1051)
T ss_pred             CCccceeecccccCCCceEEEcCCCcchhhhhccCCCCC-CCCcEeehhhccCcCccc----------ceE-eccCCCCc
Confidence            34578899865422 238999999999999999996655 668999999986654321          000 00111222


Q ss_pred             eecCCccccccchhhhh--------------------HHhHHHHhhhccccccCCCChhhhhcCCChhhHHHHHhHHHhc
Q psy128          354 FERDPSELVDKSACAGS--------------------RADLKLCLLETDCVQVDRKTPRQCLREGLAPQCEALKNTFFEC  413 (446)
Q Consensus       354 fErdpeeLk~~~SC~~i--------------------redLa~CLleSdC~~~~~~t~keCL~~~lp~eC~~l~~~f~eC  413 (446)
                      |......-|-...|+-.                    --..+-=|-++.|-..+-++..+|-.-    .|.+.....-.-
T Consensus       286 Fkqt~dgrw~Hv~caiwipev~F~nt~~~E~I~~i~~i~~aRwkL~cy~cK~~~~gaciqcs~~----~c~~a~hvtca~  361 (1051)
T KOG0955|consen  286 FKQTDDGRWAHVVCAIWIPEVSFANTVFLEPIDSIENIPPARWKLTCYICKQKGLGACIQCSKA----NCYTAFHVTCAR  361 (1051)
T ss_pred             ceeccCCceeeeehhhcccccccccchhhccccchhcCcHhhhhceeeeeccCCCCcceecchh----hhhhhhhhhhHh
Confidence            33322222222233211                    011123456677766665677777654    577666666666


Q ss_pred             cccCc
Q psy128          414 KRSLL  418 (446)
Q Consensus       414 KR~ll  418 (446)
                      +.||.
T Consensus       362 ~agl~  366 (1051)
T KOG0955|consen  362 RAGLY  366 (1051)
T ss_pred             hcCce
Confidence            66655

>KOG1245|consensus

Probab=96.91  E-value=0.00019  Score=85.21  Aligned_cols=52  Identities=27%  Similarity=0.722  Sum_probs=45.4

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCccc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  328 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~~  328 (446)
                      ...|.+|....+.. .|+.||.|+.|||..|+.+... .+.++|+|+.|+....
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            45799999877665 7999999999999999999988 7888999999997654

>KOG0383|consensus

Probab=96.91  E-value=0.00046  Score=76.89  Aligned_cols=51  Identities=27%  Similarity=0.720  Sum_probs=40.2

Q ss_pred             CCcccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCccc
Q psy128          274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  328 (446)
Q Consensus       274 ~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~~  328 (446)
                      .....|.||+   +++ ..|+||.|..|||.+|++++.. .+.+.|.|+.|.....
T Consensus        45 ~~~e~c~ic~---~~g-~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~   96 (696)
T KOG0383|consen   45 AEQEACRICA---DGG-ELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPKN   96 (696)
T ss_pred             hhhhhhhhhc---CCC-cEEEeccccHHHHHHccCCCCCcCCccceeeeeeccCCC
Confidence            3455798999   344 5899999999999999999988 5555699999954443

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

Probab=96.77  E-value=0.00021  Score=50.99  Aligned_cols=34  Identities=35%  Similarity=1.055  Sum_probs=19.8

Q ss_pred             CeeecCCCCCcccccccccCCCCCCCcEEcCCCC
Q psy128          291 PMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS  324 (446)
Q Consensus       291 ~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~  324 (446)
                      .||.|+.|+.+.|..|.|+........|+|..|.
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            5999999999999999999988666579998773

>KOG0957|consensus

Probab=96.73  E-value=0.0096  Score=64.06  Aligned_cols=49  Identities=27%  Similarity=0.691  Sum_probs=41.2

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-----CCCCcEEcCCCCC
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSK  325 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~~  325 (446)
                      ...|.||.+..+-. .+++||.|+.-||+.|+.+++.     ....-|.|..|..
T Consensus       544 ~ysCgiCkks~dQH-ll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk  597 (707)
T KOG0957|consen  544 NYSCGICKKSTDQH-LLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDK  597 (707)
T ss_pred             ceeeeeeccchhhH-HHhhcchhhceeeccccCCccccCcccccCcceeeccccc
Confidence            34699999876666 8999999999999999999998     2356799999943

>KOG0954|consensus

Probab=96.36  E-value=0.0016  Score=72.43  Aligned_cols=51  Identities=27%  Similarity=0.698  Sum_probs=41.5

Q ss_pred             CcccccccccCCCC-CCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCc
Q psy128          275 QVWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       275 ~~~~C~VCg~pdd~-~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      +...|.+|..+|.+ .+.||.||.|+.-.|..|.||... +.+.|.|..|.-.
T Consensus       270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~-p~gpWlCr~Calg  321 (893)
T KOG0954|consen  270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEV-PEGPWLCRTCALG  321 (893)
T ss_pred             ccceeceecCCCccccceeEEeccchhHHHHhhhceeec-CCCCeeehhcccc
Confidence            35679999988632 247999999999999999999876 4478999998654

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

Probab=95.89  E-value=0.0048  Score=57.01  Aligned_cols=30  Identities=27%  Similarity=0.710  Sum_probs=25.4

Q ss_pred             cccccccccCCC-CCCCcEEcCCCCCcccCc
Q psy128          301 WYHWVCVGLVAE-PETSDWFCPKCSKVDEGS  330 (446)
Q Consensus       301 WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~~~~  330 (446)
                      .||+.|+.+++. .+.++|+|+.|.....+.
T Consensus         1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~   31 (148)
T cd04718           1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQ   31 (148)
T ss_pred             CcccccCCCCCCCCCCCCcCCCCCcCCCCCC
Confidence            489999999999 788999999998755443

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.

>PTZ00266 NIMA-related protein kinase; Provisional

Probab=95.67  E-value=0.089  Score=61.53  Aligned_cols=6  Identities=33%  Similarity=0.412  Sum_probs=2.8

Q ss_pred             cCCCCC
Q psy128           25 LQHPLI   30 (446)
Q Consensus        25 ~~~~~~   30 (446)
                      |+||+|
T Consensus       293 L~h~~i  298 (1021)
T PTZ00266        293 LGYQII  298 (1021)
T ss_pred             hccHHH
Confidence            445544

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

Probab=95.42  E-value=0.011  Score=62.90  Aligned_cols=51  Identities=31%  Similarity=0.759  Sum_probs=36.4

Q ss_pred             cccccccccCCCC--CCCeeecCCCCCccccccc--------ccCCC----CCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDG--SLPMIGCDGCDAWYHWVCV--------GLVAE----PETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~--~~~mIqCD~C~~WfH~~Cv--------g~~~~----~~~~~w~Cp~C~~k  326 (446)
                      .+.|.||++-|++  .-.||.||.|+.|-|+.|.        |++..    ..+..|+|..|...
T Consensus       128 ~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~  192 (446)
T PF07227_consen  128 RCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT  192 (446)
T ss_pred             cCCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence            4457788875422  2389999999999999993        33332    23568999999854

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.

>KOG0957|consensus

Probab=95.24  E-value=0.012  Score=63.21  Aligned_cols=50  Identities=30%  Similarity=0.664  Sum_probs=36.8

Q ss_pred             ccccccc--CCCCCCCeeecCCCCCcccccccccCCC------C---CCCcEEcCCCCCccc
Q psy128          278 ICPACGV--QDDGSLPMIGCDGCDAWYHWVCVGLVAE------P---ETSDWFCPKCSKVDE  328 (446)
Q Consensus       278 ~C~VCg~--pdd~~~~mIqCD~C~~WfH~~Cvg~~~~------~---~~~~w~Cp~C~~k~~  328 (446)
                      +|.||-.  .++.+ .+|+||.|+.-.|-.|.|+...      .   ....|||..|.-...
T Consensus       121 iCcVClg~rs~da~-ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs  181 (707)
T KOG0957|consen  121 ICCVCLGQRSVDAG-EILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVS  181 (707)
T ss_pred             EEEEeecCcccccc-ceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCCC
Confidence            5669953  33444 6999999999999999998843      1   235799998875443

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

Probab=95.22  E-value=0.0079  Score=64.55  Aligned_cols=50  Identities=30%  Similarity=0.695  Sum_probs=40.4

Q ss_pred             ccccccccCCC-CCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCcc
Q psy128          277 WICPACGVQDD-GSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVD  327 (446)
Q Consensus       277 ~~C~VCg~pdd-~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k~  327 (446)
                      ..|.+|...+. +.+.+|.||+|+..-|..|.||... +.|.|+|..|.-..
T Consensus       194 ~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~-peG~WlCrkCi~~~  244 (669)
T COG5141         194 DICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFL-PEGFWLCRKCIYGE  244 (669)
T ss_pred             hhhHhccccccCCcceEEEecCcchhhhhhcccceec-Ccchhhhhhhcccc
Confidence            36989987664 2247999999999999999999866 56799999997543

>KOG1632|consensus

Probab=95.21  E-value=0.0021  Score=66.61  Aligned_cols=56  Identities=29%  Similarity=0.716  Sum_probs=43.6

Q ss_pred             CCCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCC----cEEcCCCCCc
Q psy128          271 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETS----DWFCPKCSKV  326 (446)
Q Consensus       271 ed~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~----~w~Cp~C~~k  326 (446)
                      .++.....|..||..+....+||+|+.|..|||+.|+.+...  .-..    .|+|+.|...
T Consensus       234 ~~~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~  295 (345)
T KOG1632|consen  234 APDYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVL  295 (345)
T ss_pred             ccccccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeec
Confidence            334445678889987765469999999999999999999877  2223    4999999863

>KOG0956|consensus

Probab=94.81  E-value=0.013  Score=65.06  Aligned_cols=48  Identities=35%  Similarity=0.823  Sum_probs=38.1

Q ss_pred             cccccccC-CCCCCCeeecCC--CCCcccccccccCCCCCCCcEEcCCCCCc
Q psy128          278 ICPACGVQ-DDGSLPMIGCDG--CDAWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       278 ~C~VCg~p-dd~~~~mIqCD~--C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      -|.||... .+.++.+|.||+  |..+.|..|+||... +.+.|||..|...
T Consensus         7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqV-PtGpWfCrKCesq   57 (900)
T KOG0956|consen    7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQV-PTGPWFCRKCESQ   57 (900)
T ss_pred             ceeeecCcCCCccCceeeecCCCceeeeehhcceeEec-CCCchhhhhhhhh
Confidence            36699732 244568999996  999999999999765 6689999999754

>KOG4364|consensus

Probab=94.76  E-value=0.18  Score=56.07  Aligned_cols=16  Identities=13%  Similarity=-0.124  Sum_probs=9.5

Q ss_pred             HhHHHHhhhccccccC
Q psy128          372 ADLKLCLLETDCVQVD  387 (446)
Q Consensus       372 edLa~CLleSdC~~~~  387 (446)
                      ..++.|+..+-|.++.
T Consensus       612 A~~ah~a~d~ak~~~~  627 (811)
T KOG4364|consen  612 ALTAHAAKDTAKLIIC  627 (811)
T ss_pred             HHHHHHhhhhHHHhhh
Confidence            4456666666665554

>KOG4443|consensus

Probab=94.74  E-value=0.014  Score=64.45  Aligned_cols=47  Identities=32%  Similarity=0.887  Sum_probs=38.9

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      .|..|+...|.. ..+.|+.|+..||++|..|.+. .+.+.|+|+.|..
T Consensus        70 vCe~c~~~gD~~-kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~  117 (694)
T KOG4443|consen   70 VCEACGTTGDPK-KFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTR  117 (694)
T ss_pred             eeeeccccCCcc-cccccccccccccccccCCccccccCcccccHHHHh
Confidence            576788665655 6778999999999999999988 7788999998754

>KOG4364|consensus

Probab=92.83  E-value=0.82  Score=51.18  Aligned_cols=22  Identities=32%  Similarity=0.211  Sum_probs=11.0

Q ss_pred             CCCCCCCCCCchhhccccccCC
Q psy128           48 DKVSPKDKTSPKEKMSSKEKTS   69 (446)
Q Consensus        48 ~~~~~~~~~~~~~~~~~~~~~~   69 (446)
                      -+.++.|-.|..++|+----||
T Consensus       198 l~s~~~~~sSs~~~~~~~sdts  219 (811)
T KOG4364|consen  198 LKSWRSDLSSSAEKLGKISDTS  219 (811)
T ss_pred             HhhccccchhhHhhhhccCCcc
Confidence            3445555555555555444443

>KOG0163|consensus

Probab=91.52  E-value=1.2  Score=50.81  Aligned_cols=6  Identities=33%  Similarity=0.999  Sum_probs=2.9

Q ss_pred             CCCccc
Q psy128          298 CDAWYH  303 (446)
Q Consensus       298 C~~WfH  303 (446)
                      |..-||
T Consensus      1091 CreEFh 1096 (1259)
T KOG0163|consen 1091 CREEFH 1096 (1259)
T ss_pred             HHHHHH
Confidence            554444

>KOG1029|consensus

Probab=91.21  E-value=2.3  Score=48.68  Aligned_cols=19  Identities=11%  Similarity=0.268  Sum_probs=11.5

Q ss_pred             ccceeecccchhccchhhc
Q psy128           89 VPNIVKVTSSEDLGEIKKD  107 (446)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~  107 (446)
                      -|+.+.+.|..-+-+++-.
T Consensus       277 pp~~r~~rs~~sis~~~p~  295 (1118)
T KOG1029|consen  277 PPSFRSSRSANSISGLEPG  295 (1118)
T ss_pred             CcccccccCCCCccccccC
Confidence            3577777776555555443

>KOG1144|consensus

Probab=91.05  E-value=0.38  Score=54.69  Aligned_cols=6  Identities=17%  Similarity=0.063  Sum_probs=2.8

Q ss_pred             hhhhhc
Q psy128          391 PRQCLR  396 (446)
Q Consensus       391 ~keCL~  396 (446)
                      .-+||+
T Consensus       491 lld~ir  496 (1064)
T KOG1144|consen  491 LLDKIR  496 (1064)
T ss_pred             HHHHhh
Confidence            444554

>KOG2891|consensus

Probab=90.18  E-value=2.5  Score=43.29  Aligned_cols=67  Identities=36%  Similarity=0.407  Sum_probs=34.1

Q ss_pred             hhhhhhhHHHHHHhhhchhhH-----HHHhhhhhHHHHHHHHhhhHHH-HHHHHHHHHHHHHHHhhhhhhcch
Q psy128          114 KKTHKKKEKEKIKKKKDKKDK-----DKIKNKEKDKEKKEKEKGKKEE-KEKKEEKEKKEEKEFKMKEDKEKP  180 (446)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~-----~~~~~~e~~ke~~e~e~~e~~~-k~~~~~~~~~~~~~~~~~~~k~~~  180 (446)
                      +-.+|+-+-=+|+-.=|-+|+     +--+-+=.+.+++|.|+..+.. +|.+++.+++..+++++++..+..
T Consensus       296 elnikk~e~~kikqe~ddkdk~~ed~e~kkrqlerqekqeleqmaeeekkr~eeaeerqraeekeq~eaee~~  368 (445)
T KOG2891|consen  296 ELNIKKAEACKIKQEFDDKDKHLEDAEIKKRQLERQEKQELEQMAEEEKKREEEAEERQRAEEKEQKEAEELE  368 (445)
T ss_pred             hhhhhHHHhhchhhhcCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            334555555566654443333     2222233344667777654443 555555566666665555554444

>KOG3054|consensus

Probab=88.87  E-value=2.1  Score=43.09  Aligned_cols=15  Identities=20%  Similarity=0.184  Sum_probs=6.3

Q ss_pred             chhccchhhccccch
Q psy128           98 SEDLGEIKKDKSIKK  112 (446)
Q Consensus        98 ~~~~~~~~~~~~~~~  112 (446)
                      .++-|-+--+...+-
T Consensus        81 ~ee~~~~dg~ee~~e   95 (299)
T KOG3054|consen   81 VEEEGSGDGDEEEPE   95 (299)
T ss_pred             ccccccccccccccc
Confidence            344444444443333

>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins

Probab=88.27  E-value=2  Score=46.85  Aligned_cols=23  Identities=35%  Similarity=0.398  Sum_probs=11.6

Q ss_pred             cccccccceeecc-cchhccchhh
Q psy128           84 GVTPMVPNIVKVT-SSEDLGEIKK  106 (446)
Q Consensus        84 ~~~~~~~~~~~~~-~~~~~~~~~~  106 (446)
                      =|.|++-|+...+ |.-+.++|..
T Consensus       156 I~IPL~~~~~~~~~s~vdt~~i~~  179 (489)
T PF05262_consen  156 IVIPLSDNILSGSLSDVDTDEISD  179 (489)
T ss_pred             EEEeccccccCCCccccchhhccc
Confidence            3556664444422 4445666643

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

Probab=88.02  E-value=0.36  Score=45.81  Aligned_cols=47  Identities=28%  Similarity=0.825  Sum_probs=35.5

Q ss_pred             ccccccC---CCCCCCeeecCCCCCcccccccccCCC---------CCCCcEEcCCCCCc
Q psy128          279 CPACGVQ---DDGSLPMIGCDGCDAWYHWVCVGLVAE---------PETSDWFCPKCSKV  326 (446)
Q Consensus       279 C~VCg~p---dd~~~~mIqCD~C~~WfH~~Cvg~~~~---------~~~~~w~Cp~C~~k  326 (446)
                      |.+|+..   ..-+ .||.|-+|...||-.|+|+...         ...+...|..|...
T Consensus         2 C~~C~~~g~~~~kG-~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~   60 (175)
T PF15446_consen    2 CDTCGYEGDDRNKG-PLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGI   60 (175)
T ss_pred             cccccCCCCCccCC-CeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcCh
Confidence            7788542   2334 7999999999999999999876         23456678888854

>KOG1029|consensus

Probab=87.09  E-value=2.4  Score=48.45  Aligned_cols=43  Identities=26%  Similarity=0.390  Sum_probs=18.1

Q ss_pred             HhhhhhhcchHHHHHHHHHHHHHHH-hchhhHHHHHHHHHHhhH
Q psy128          171 FKMKEDKEKPVEKIRKEEKDSEKEK-KSKDKDKKLKKEKLKKKK  213 (446)
Q Consensus       171 ~~~~~~k~~~~e~~rke~~~~e~ek-k~k~~~~k~kkek~kkkK  213 (446)
                      .+...+-+++.|++|.=++.+|+++ ++.+..+++++|=++.++
T Consensus       367 rk~qlElekqLerQReiE~qrEEerkkeie~rEaar~ElEkqRq  410 (1118)
T KOG1029|consen  367 RKAQLELEKQLERQREIERQREEERKKEIERREAAREELEKQRQ  410 (1118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555333333333 333333333444333343

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

Probab=86.90  E-value=0.26  Score=33.37  Aligned_cols=29  Identities=38%  Similarity=0.703  Sum_probs=13.0

Q ss_pred             cccccccCCCCCCCeeecCCCCCccccccc
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCV  307 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cv  307 (446)
                      .|.+|+.+.+++ .+-.|..|+.+.|..|+
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.

>KOG1144|consensus

Probab=85.79  E-value=1.9  Score=49.35  Aligned_cols=11  Identities=18%  Similarity=0.039  Sum_probs=6.6

Q ss_pred             HHhHHHHhhhc
Q psy128          371 RADLKLCLLET  381 (446)
Q Consensus       371 redLa~CLleS  381 (446)
                      ..-|.+||..+
T Consensus       488 KTKlld~ir~t  498 (1064)
T KOG1144|consen  488 KTKLLDKIRGT  498 (1064)
T ss_pred             chHHHHHhhcc
Confidence            45566666655

>KOG2752|consensus

Probab=85.64  E-value=0.37  Score=49.65  Aligned_cols=32  Identities=25%  Similarity=0.681  Sum_probs=25.3

Q ss_pred             cccccccccCCCC-----CCCeeecCCCCCccc-ccccc
Q psy128          276 VWICPACGVQDDG-----SLPMIGCDGCDAWYH-WVCVG  308 (446)
Q Consensus       276 ~~~C~VCg~pdd~-----~~~mIqCD~C~~WfH-~~Cvg  308 (446)
                      ..+| .|..++++     +..|+||-.|..||| -.|+.
T Consensus       128 G~~C-~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~  165 (345)
T KOG2752|consen  128 GLFC-KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQ  165 (345)
T ss_pred             ceeE-EecCCCCCccccccceeeeEEeccchhcccccCc
Confidence            4579 99988755     348999999999999 66653

>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=82.78  E-value=0.66  Score=35.18  Aligned_cols=32  Identities=22%  Similarity=0.593  Sum_probs=16.9

Q ss_pred             CeeecCCCCCcccccccccCC--CCCCCcEEcCCC
Q psy128          291 PMIGCDGCDAWYHWVCVGLVA--EPETSDWFCPKC  323 (446)
Q Consensus       291 ~mIqCD~C~~WfH~~Cvg~~~--~~~~~~w~Cp~C  323 (446)
                      .|||||.|..|=.+. .++..  ...++.|+|..-
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            599999999998776 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=82.47  E-value=0.9  Score=35.58  Aligned_cols=32  Identities=31%  Similarity=0.649  Sum_probs=26.3

Q ss_pred             cccccccccCC--CCCCCeeecCCCCCccccccccc
Q psy128          276 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGL  309 (446)
Q Consensus       276 ~~~C~VCg~pd--d~~~~mIqCD~C~~WfH~~Cvg~  309 (446)
                      ...|.+|+.+.  .+  ..|.|..|..-||-.|...
T Consensus         5 ~~~C~~Cg~~~~~~d--DiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGD--DIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCC--CEEECCCCCCcccHHHHhh
Confidence            34799999877  44  4999999999999999843

>KOG4443|consensus

Probab=81.20  E-value=0.32  Score=54.18  Aligned_cols=49  Identities=31%  Similarity=0.773  Sum_probs=38.1

Q ss_pred             cccccccccCCCCC--CCeeecCCCCCcccccccccCCC-----CCCCcEEcCCCC
Q psy128          276 VWICPACGVQDDGS--LPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCS  324 (446)
Q Consensus       276 ~~~C~VCg~pdd~~--~~mIqCD~C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~  324 (446)
                      ..+|++|...+...  ..|++|+.|.+|.|..|-++...     ..+-.|-|.-|+
T Consensus       145 ~~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR  200 (694)
T KOG4443|consen  145 LSYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR  200 (694)
T ss_pred             cccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence            36899998766333  25699999999999999998766     223489999998

>KOG1473|consensus

Probab=80.98  E-value=0.93  Score=53.36  Aligned_cols=46  Identities=24%  Similarity=0.442  Sum_probs=37.7

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      ...|.+|..  .+  ..+||+.|+.-||+.|+.++.. .+...|-|..|..
T Consensus       344 ddhcrf~~d--~~--~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~  390 (1414)
T KOG1473|consen  344 DDHCRFCHD--LG--DLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNI  390 (1414)
T ss_pred             cccccccCc--cc--ceeecccCCceEEeeecCCccccCCCccchhhhhhh
Confidence            346888873  34  4899999999999999999988 6677899999973

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	446
2k16_A	75	Solution Structure Of The Free Taf3 Phd Domain Leng		2e-13
2ri7_A	174	Crystal Structure Of Phd Finger-Linker-Bromodomain		9e-04

>pdb|2K16|A Chain A, Solution Structure Of The Free Taf3 Phd Domain Length = 75

Iteration: 1
 Score = 73.6 bits (179), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/54 (62%), Positives = 38/54 (70%), Gaps = 2/54 (3%)
Query: 273 SKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK 325
             Q+WICP C   DDGS PMIGCD CD WYHW CVG++A  PE   WFCPKC+ 
Sbjct: 15  GNQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCAN 67

>pdb|2RI7|A Chain A, Crystal Structure Of Phd Finger-Linker-Bromodomain Y17e Mutant From Human Bptf In The H3(1-9)k4me2 Bound State Length = 174

Iteration: 1
 Score = 41.6 bits (96), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 282 CGVQDDGSLPMIGCDGCDAWYHWVCVGLV-AEPETSD-WFCPKCSKVDEG 329
           C   +D S   IGCD C  WYH  CVG++ +E E  D + CP+C   ++ 
Sbjct: 13  CKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTEDA 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	446
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	99.45
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	99.4
1weu_A	91	Inhibitor of growth family, member 4; structural g	99.37
1wee_A	72	PHD finger family protein; structural genomics, PH	99.36
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	99.34
1wew_A	78	DNA-binding family protein; structural genomics, P	99.31
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	99.3
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	99.3
1wem_A	76	Death associated transcription factor 1; structura	99.29
1we9_A	64	PHD finger family protein; structural genomics, PH	99.29
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	99.26
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	99.25
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	99.24
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	99.23
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	99.16
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	99.15
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	99.14
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	99.13
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	99.12
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	99.11
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	99.09
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	98.98
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
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	98.95
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	98.94
3kv5_D	488	JMJC domain-containing histone demethylation prote	98.93
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	98.91
2yt5_A	66	Metal-response element-binding transcription facto	98.89
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	98.88
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	98.86
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	98.86
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	98.86
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	98.84
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	98.84
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	98.83
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	98.81
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	98.77
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	98.75
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	98.75
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	98.7
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	98.68
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	98.65
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	98.62
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	98.58
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	98.53
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	98.48
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.44
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	98.38
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	98.32
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.02
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	97.95
3rsn_A	177	SET1/ASH2 histone methyltransferase complex subun;	97.78
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	97.78
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	97.54
4bbq_A	117	Lysine-specific demethylase 2A; oxidoreductase, ub	97.5
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	97.45
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	97.21
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	95.87
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	92.19
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	91.11
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	85.6
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	83.65
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	82.95
2ect_A	78	Ring finger protein 126; metal binding protein, st	82.61

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=99.45  E-value=4.2e-14  Score=119.36  Aligned_cols=65  Identities=25%  Similarity=0.615  Sum_probs=52.3

Q ss_pred             CCCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCcccCchhhHhhh
Q psy128          271 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVDEGSRKEKKKR  337 (446)
Q Consensus       271 ed~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k~~~~~K~kr~k  337 (446)
                      ..+.+++.| ||+.+++++ .||+||.|+.|||+.|++++....++.|+|+.|.+......+....+
T Consensus        23 ~~~~d~vrC-iC~~~~~~~-~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~~~~~~~~~~~q   87 (98)
T 2lv9_A           23 SYGTDVTRC-ICGFTHDDG-YMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPRNLDKERAVLLQ   87 (98)
T ss_dssp             CCCCCBCCC-TTSCCSCSS-CEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSSCCCHHHHHHHH
T ss_pred             CCCCCCEEe-ECCCccCCC-cEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCCCCCHHHHHHHH
Confidence            344557789 999988877 89999999999999999998875556899999998776655544433

>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=5.2e-14  Score=112.62  Aligned_cols=55  Identities=62%  Similarity=1.560  Sum_probs=47.2

Q ss_pred             CCCCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          270 TGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       270 eed~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      +++++...+|.+|+.+++++ +||+||.|+.|||+.||+++.. .+.+.|||+.|..
T Consensus        12 ~~~~~~~~~C~~C~~~~~~~-~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~   67 (75)
T 2k16_A           12 DEWGNQIWICPGCNKPDDGS-PMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCAN   67 (75)
T ss_dssp             CSSSCEEECBTTTTBCCSSC-CEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHH
T ss_pred             cccCCCCcCCCCCCCCCCCC-CEEEcCCCCcccccccCCCCccCCCCCCEEChhccC
Confidence            34455677899999998876 8999999999999999999988 4557999999984

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.37  E-value=1.1e-12  Score=109.84  Aligned_cols=55  Identities=42%  Similarity=1.079  Sum_probs=44.7

Q ss_pred             CCCCCCCCcccccccccCCCCCCCeeecCC--CC-CcccccccccCCCCCCCcEEcCCCCCc
Q psy128          268 YDTGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       268 ~eeed~~~~~~C~VCg~pdd~~~~mIqCD~--C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      ....++++..|| +|+.++++  +||+||.  |. .|||+.||+++..+ .+.|||+.|...
T Consensus        28 ~~~~d~~e~~yC-iC~~~~~g--~MI~CD~~dC~~~WfH~~CVgl~~~p-~g~W~Cp~C~~~   85 (91)
T 1weu_A           28 DMPVDPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTKP-RGKWFCPRCSQE   85 (91)
T ss_dssp             SCCCCSCCCBCS-TTCCBCCS--CCCCCSCSSCSCCCCCSTTTTCSSCC-CSSCCCTTTCCC
T ss_pred             cCCcCCCCCcEE-ECCCCCCC--CEeEecCCCCCCCCEecccCCcCcCC-CCCEECcCccCc
Confidence            344556678899 99998775  5999999  76 79999999987663 478999999854

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=99.36  E-value=1.7e-13  Score=109.17  Aligned_cols=56  Identities=32%  Similarity=0.815  Sum_probs=46.4

Q ss_pred             CCCCCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          269 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       269 eeed~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      +.+++.+..+| +|+.+++++.+||+||.|..|||+.||+++.. ..++.|+|+.|..
T Consensus         9 e~~~~~~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~   65 (72)
T 1wee_A            9 ERGVDNWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIE   65 (72)
T ss_dssp             SCSSCSSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHH
T ss_pred             cCCCCCcceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccC
Confidence            34456678899 99998754448999999999999999999875 4567999999984

>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=99.34  E-value=2.7e-13  Score=107.63  Aligned_cols=54  Identities=26%  Similarity=0.621  Sum_probs=45.6

Q ss_pred             CCCCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCC
Q psy128          270 TGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       270 eed~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      ..++.+..+| +|+++++++ +||+||.|..|||+.|+|++....++.|+|+.|..
T Consensus        13 ~~~~~~~~~C-iC~~~~~~~-~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           13 NLYFQGLVTC-FCMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             -CTTTTCCCS-TTCCCCTTC-CEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             cCCCCCceEe-ECCCcCCCC-CEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            3344567899 999998877 89999999999999999999874457999999974

>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=99.31  E-value=4.4e-13  Score=108.57  Aligned_cols=56  Identities=29%  Similarity=0.659  Sum_probs=46.4

Q ss_pred             CCCCCCCcccccccccCCCCCCCeeecC--CCCCcccccccccCCCC------CCCcEEcCCCCCc
Q psy128          269 DTGDSKQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAEP------ETSDWFCPKCSKV  326 (446)
Q Consensus       269 eeed~~~~~~C~VCg~pdd~~~~mIqCD--~C~~WfH~~Cvg~~~~~------~~~~w~Cp~C~~k  326 (446)
                      +..++++..+| +|+.+++++ +||+||  .|..|||+.|||++...      .+..|||+.|...
T Consensus         9 d~~~~~~~~~C-iC~~~~~~g-~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T 1wew_A            9 DPFQPEIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CSSSCCCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             cccCCCCCEEe-ECCCcCCCC-CEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcc
Confidence            34455678899 999997666 899999  99999999999998762      3579999999853

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A*

Probab=99.30  E-value=2.2e-13  Score=113.86  Aligned_cols=51  Identities=33%  Similarity=0.972  Sum_probs=40.9

Q ss_pred             CCCCCcccccccccCCCCCCCeeecCCCC---CcccccccccCCCCCCCcEEcCC-CCC
Q psy128          271 GDSKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPK-CSK  325 (446)
Q Consensus       271 ed~~~~~~C~VCg~pdd~~~~mIqCD~C~---~WfH~~Cvg~~~~~~~~~w~Cp~-C~~  325 (446)
                      .++++..|| +|+.++++.  ||+||.|+   .|||+.|||++..+ .+.|||+. |..
T Consensus        21 ~~~~~~~yC-iC~~~~~g~--MI~CD~c~C~~eWfH~~CVgl~~~p-~~~W~Cp~cC~~   75 (90)
T 2jmi_A           21 NNNQEEVYC-FCRNVSYGP--MVACDNPACPFEWFHYGCVGLKQAP-KGKWYCSKDCKE   75 (90)
T ss_dssp             ---CCSCCS-TTTCCCSSS--EECCCSSSCSCSCEETTTSSCSSCT-TSCCCSSHHHHH
T ss_pred             CCCCCCcEE-EeCCCCCCC--EEEecCCCCccccCcCccCCCCcCC-CCCccCChhhcc
Confidence            344557799 999987765  99999977   99999999998763 47999999 973

>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=99.30  E-value=2.5e-12  Score=102.88  Aligned_cols=56  Identities=39%  Similarity=1.007  Sum_probs=44.8

Q ss_pred             CCCCCCCCCcccccccccCCCCCCCeeecCC--CC-CcccccccccCCCCCCCcEEcCCCCCc
Q psy128          267 EYDTGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       267 e~eeed~~~~~~C~VCg~pdd~~~~mIqCD~--C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      +..+.++++..+| +|+.++++  +||+||.  |. .|||+.||+++.. +.+.|||+.|...
T Consensus         7 ~~~~~d~~~~~~C-~C~~~~~g--~MI~CD~~~C~~~wfH~~Cvgl~~~-p~g~w~Cp~C~~~   65 (71)
T 1wen_A            7 GDMPVDPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTK-PRGKWFCPRCSQE   65 (71)
T ss_dssp             SCCCCCTTSCCCS-TTCCCSCS--SEECCSCSSCSCCCEETTTTTCSSC-CSSCCCCTTTSSC
T ss_pred             cccccCCCCCCEE-ECCCCCCC--CEeEeeCCCCCCccEecccCCcCcC-CCCCEECCCCCcc
Confidence            3344555667899 99998775  5999999  77 7999999998765 3478999999854

>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=99.29  E-value=2.4e-13  Score=109.25  Aligned_cols=50  Identities=32%  Similarity=0.911  Sum_probs=42.8

Q ss_pred             CcccccccccCCCCCCCeeecCCCCCcccccccccCCCC------CCCcEEcCCCCCc
Q psy128          275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP------ETSDWFCPKCSKV  326 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~------~~~~w~Cp~C~~k  326 (446)
                      +..|| +|+++++++ +||+||.|..|||+.|||++...      ....|+|+.|...
T Consensus        15 ~~~~C-~C~~~~~~~-~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~   70 (76)
T 1wem_A           15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCCEE-ECCCccCCC-CEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCc
Confidence            46889 999998876 89999999999999999998652      3568999999843

>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=99.29  E-value=7.5e-13  Score=102.81  Aligned_cols=52  Identities=31%  Similarity=0.700  Sum_probs=43.5

Q ss_pred             CcccccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCCCCc
Q psy128          275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  326 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C~~k  326 (446)
                      +..+|.+|+++++++.+||+||.|..|||+.|+|++..  .....|+|+.|..+
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            45689999999864448999999999999999999877  23578999999854

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=99.26  E-value=9.3e-13  Score=98.94  Aligned_cols=48  Identities=29%  Similarity=0.763  Sum_probs=42.2

Q ss_pred             CcccccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCC
Q psy128          275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCS  324 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~  324 (446)
                      +..+| +|+++++++ +||+||.|..|||+.|+|++....++.|+|+.|.
T Consensus         3 d~~~C-~C~~~~~~~-~MI~Cd~C~~W~H~~Cvgi~~~~~~~~~~C~~C~   50 (52)
T 3o7a_A            3 DLVTC-FCMKPFAGR-PMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCR   50 (52)
T ss_dssp             TCBCS-TTCCBCTTC-CEEECTTTCCEEETTTTTCCGGGCCSSCCCHHHH
T ss_pred             cCeEE-EeCCcCCCC-CEEEcCCCCccccccccCCCcccCCCcEECcCCC
Confidence            35689 999998876 8999999999999999999987445799999996

>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=99.25  E-value=3.2e-13  Score=108.54  Aligned_cols=55  Identities=33%  Similarity=0.776  Sum_probs=45.3

Q ss_pred             CCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCCC--CCCcEEcCCCCCcc
Q psy128          272 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP--ETSDWFCPKCSKVD  327 (446)
Q Consensus       272 d~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~--~~~~w~Cp~C~~k~  327 (446)
                      .+.+..|| +|+.+++++.+||+||.|..|||+.|+|++...  ..+.|+|+.|....
T Consensus         6 ~~~~~~yC-iC~~~~~~~~~MI~Cd~C~~WfH~~Cvg~~~~~~~~~~~~~C~~C~~~~   62 (75)
T 3kqi_A            6 MATVPVYC-VCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTH   62 (75)
T ss_dssp             TCCCCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCTTTGGGBSSCCCHHHHHHH
T ss_pred             CCCCeeEE-ECCCcCCCCCCEEEcCCCCCCEecccccccccccCCCCEEECCCCcccC
Confidence            34567899 999997654489999999999999999999872  34689999998653

>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=99.24  E-value=3.6e-12  Score=103.27  Aligned_cols=53  Identities=30%  Similarity=0.664  Sum_probs=44.1

Q ss_pred             CCcccccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCCCCcc
Q psy128          274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVD  327 (446)
Q Consensus       274 ~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C~~k~  327 (446)
                      .+..+| +|+.+++++.+||+||.|..|||+.||+++..  ...+.|+|+.|....
T Consensus        10 ~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           10 LVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            346789 99999864348999999999999999999876  335799999999654

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=99.23  E-value=2.1e-12  Score=102.05  Aligned_cols=52  Identities=23%  Similarity=0.620  Sum_probs=42.7

Q ss_pred             CCCCcccccccccCCCCCCCeeecCC--CCCcccccccccCCC-----CCCCcEEcCCCCC
Q psy128          272 DSKQVWICPACGVQDDGSLPMIGCDG--CDAWYHWVCVGLVAE-----PETSDWFCPKCSK  325 (446)
Q Consensus       272 d~~~~~~C~VCg~pdd~~~~mIqCD~--C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~~  325 (446)
                      +++..++| +|+.+++++ +||+||.  |..|||+.|||++..     ..+..|||+.|+.
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            44557899 999987777 8999995  999999999999765     1235899999973

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=99.16  E-value=4e-12  Score=99.18  Aligned_cols=52  Identities=38%  Similarity=1.034  Sum_probs=40.2

Q ss_pred             CCCCCCcccccccccCCCCCCCeeecCC--CC-CcccccccccCCCCCCCcEEcCCCCC
Q psy128          270 TGDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       270 eed~~~~~~C~VCg~pdd~~~~mIqCD~--C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      +.++++..|| +|++++++  +||+||.  |. .|||+.|||++.. +.+.|||+.|..
T Consensus         5 ~~d~~e~~yC-~C~~~~~g--~MI~CD~c~C~~~WfH~~Cvgl~~~-p~~~w~Cp~C~~   59 (62)
T 2g6q_A            5 AIDPNEPTYC-LCNQVSYG--EMIGCDNEQCPIEWFHFSCVSLTYK-PKGKWYCPKCRG   59 (62)
T ss_dssp             -----CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSC-CSSCCCCHHHHT
T ss_pred             ccCCCCCcEE-ECCCCCCC--CeeeeeCCCCCcccEecccCCcCcC-CCCCEECcCccc
Confidence            3455667899 99998775  4999999  55 9999999999866 457999999974

>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=99.15  E-value=5.2e-12  Score=97.58  Aligned_cols=50  Identities=42%  Similarity=1.170  Sum_probs=39.9

Q ss_pred             CCCCcccccccccCCCCCCCeeecCC--CC-CcccccccccCCCCCCCcEEcCCCCC
Q psy128          272 DSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       272 d~~~~~~C~VCg~pdd~~~~mIqCD~--C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      |+++..+| +|++++++  .||+||+  |. .|||+.|||++..+ .+.|||+.|..
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--EMIGCDNPDCPIEWFHFACVDLTTKP-KGKWFCPRCVQ   57 (59)
T ss_dssp             ---CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSCC-SSCCCCHHHHC
T ss_pred             CCCCCcEE-ECCCCCCC--CeeEeeCCCCCCCCEecccCCcccCC-CCCEECcCccC
Confidence            44567799 99998765  5999999  77 79999999987763 47999999974

>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=99.14  E-value=6e-12  Score=97.42  Aligned_cols=51  Identities=43%  Similarity=1.160  Sum_probs=39.7

Q ss_pred             CCCCCcccccccccCCCCCCCeeecCC--CC-CcccccccccCCCCCCCcEEcCCCCC
Q psy128          271 GDSKQVWICPACGVQDDGSLPMIGCDG--CD-AWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       271 ed~~~~~~C~VCg~pdd~~~~mIqCD~--C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      .++++..+| +|++++++  .||+||+  |. .|||+.|||++.. +.+.|||+.|..
T Consensus         5 ~d~~e~~~C-~C~~~~~g--~mi~CD~cdC~~~wfH~~Cvgl~~~-p~g~w~C~~C~~   58 (60)
T 2vnf_A            5 VDPNEPTYC-LCHQVSYG--EMIGCDNPDCSIEWFHFACVGLTTK-PRGKWFCPRCSQ   58 (60)
T ss_dssp             ----CCEET-TTTEECCS--EEEECSCTTCSSCEEETGGGTCSSC-CSSCCCCHHHHC
T ss_pred             cCCCCCCEE-ECCCcCCC--CEEEeCCCCCCCceEehhcCCCCcC-CCCCEECcCccC
Confidence            345567899 99998765  5999999  55 8999999998765 447999999974

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.13  E-value=1.2e-11  Score=98.69  Aligned_cols=49  Identities=39%  Similarity=1.064  Sum_probs=41.2

Q ss_pred             CCCcccccccccCCCCCCCeeecCCCC---CcccccccccCCCCCCCcEEcCCCCC
Q psy128          273 SKQVWICPACGVQDDGSLPMIGCDGCD---AWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       273 ~~~~~~C~VCg~pdd~~~~mIqCD~C~---~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      +++..|| +|++++++  +||+||.|+   .|||+.||+++.. +.+.|||+.|..
T Consensus         3 ~~~~~yC-~C~~~~~g--~MI~CD~cdC~~~WfH~~Cvgl~~~-p~~~w~Cp~C~~   54 (70)
T 1x4i_A            3 SGSSGYC-ICNQVSYG--EMVGCDNQDCPIEWFHYGCVGLTEA-PKGKWYCPQCTA   54 (70)
T ss_dssp             CSCCCCS-TTSCCCCS--SEECCSCTTCSCCCEEHHHHTCSSC-CSSCCCCHHHHH
T ss_pred             CCCCeEE-EcCCCCCC--CEeEeCCCCCCccCCcccccccCcC-CCCCEECCCCCc
Confidence            3456799 99998766  599999985   8999999999875 467999999984

>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=99.12  E-value=8.5e-12  Score=93.76  Aligned_cols=48  Identities=35%  Similarity=0.931  Sum_probs=39.4

Q ss_pred             ccccccccCCCCCCCeeecC-CCCCcccccccccCCC-CCCCcEEcCCCC
Q psy128          277 WICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-PETSDWFCPKCS  324 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD-~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~  324 (446)
                      ..|.+|++|++++.+||+|| .|+.|||+.|+|++.. ...+.|+|+.|.
T Consensus         3 c~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            3 CAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             CSCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             ccCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            34669999987655999999 8999999999999876 223789999994

>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=6.7e-12  Score=98.85  Aligned_cols=50  Identities=26%  Similarity=0.824  Sum_probs=41.8

Q ss_pred             CcccccccccCCCCCCCeeecC-CCCCcccccccccCCC-------CCCCcEEcCCCC
Q psy128          275 QVWICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-------PETSDWFCPKCS  324 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD-~C~~WfH~~Cvg~~~~-------~~~~~w~Cp~C~  324 (446)
                      ....|.+|+++++++.+||+|| .|..|||+.|||++..       .+...|+|+.|.
T Consensus         7 ~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvglt~~~~~~l~~e~~~~w~C~~C~   64 (65)
T 2vpb_A            7 PVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCM   64 (65)
T ss_dssp             --CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTCCHHHHHHHHHCTTEEECCHHHH
T ss_pred             CcCcCccCCCccCCCCCeEecccCccccCchhccCCCHHHHHHhhccCCCcEECcCcc
Confidence            3457999999987666999999 9999999999999975       245689999985

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=99.09  E-value=4.1e-11  Score=89.10  Aligned_cols=47  Identities=26%  Similarity=0.767  Sum_probs=41.4

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      +|.+|+..++++ .||.||.|+.|||+.|++++.. .+.+.|+|+.|..
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588999887666 8999999999999999998777 6678999999974

>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=98.98  E-value=3.8e-10  Score=87.42  Aligned_cols=49  Identities=27%  Similarity=0.789  Sum_probs=40.8

Q ss_pred             CcccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCcc
Q psy128          275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  327 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~  327 (446)
                      +..+|.+|+.   ++ .||.||.|+.+||+.|+++++. .+.+.|+|+.|....
T Consensus         8 ~~~~C~vC~~---~g-~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            8 HMEFCRVCKD---GG-ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCC---CS-SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCCCC---CC-CEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            3457999995   33 5999999999999999998777 677899999998643

>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=4.9e-11  Score=108.55  Aligned_cols=52  Identities=35%  Similarity=0.915  Sum_probs=42.7

Q ss_pred             CCcccccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCCCCc
Q psy128          274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  326 (446)
Q Consensus       274 ~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C~~k  326 (446)
                      ++..+| +|+.+++++.+||+||.|..|||+.|+|++..  ...+.|+|+.|...
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            346789 99998764448999999999999999998765  34679999999853

>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=8.8e-11  Score=100.28  Aligned_cols=51  Identities=29%  Similarity=0.829  Sum_probs=42.0

Q ss_pred             cccccccccCCCCCCCeeecC-CCCCcccccccccCCC-------CCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDGSLPMIGCD-GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD-~C~~WfH~~Cvg~~~~-------~~~~~w~Cp~C~~k  326 (446)
                      +..|.+|+++++++..||+|| .|..|||+.|||++..       .+...|+|+.|...
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~   61 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKT   61 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCc
Confidence            457999999964444799998 9999999999999963       24479999999854

>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=98.95  E-value=2e-10  Score=95.96  Aligned_cols=49  Identities=35%  Similarity=0.814  Sum_probs=42.6

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      ...|.||+..++.+ .||+||.|+.|||+.|+++++. .+.+.|||+.|..
T Consensus        16 ~~~C~vC~~~~~~~-~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~   65 (92)
T 2e6r_A           16 SYICQVCSRGDEDD-KLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCIL   65 (92)
T ss_dssp             CCCCSSSCCSGGGG-GCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCccCCCcCCCC-CEEEcCCCCchhccccCCCCcccCCCCCcCCccCcC
Confidence            34699999877655 7999999999999999998877 6778999999974

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=98.94  E-value=3.6e-10  Score=87.53  Aligned_cols=47  Identities=36%  Similarity=0.835  Sum_probs=40.0

Q ss_pred             CcccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      +..+|.+|+.  ++  .||.||.|+.|||+.|++++.. .+.+.|+|+.|..
T Consensus        10 ~~~~C~vC~~--~g--~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A           10 HQDYCEVCQQ--GG--EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCSSCTTTSC--CS--SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCccCCC--CC--cEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            3457999996  33  5999999999999999999876 6778999999984

>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=98.93  E-value=4.4e-11  Score=125.90  Aligned_cols=56  Identities=29%  Similarity=0.681  Sum_probs=45.4

Q ss_pred             CCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCCC--CCCcEEcCCCCCccc
Q psy128          272 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP--ETSDWFCPKCSKVDE  328 (446)
Q Consensus       272 d~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~--~~~~w~Cp~C~~k~~  328 (446)
                      .+....+| +|+.+++++.+||+||.|+.|||+.|+|++...  ..+.|+|+.|.....
T Consensus        33 ~~~~~~yC-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~   90 (488)
T 3kv5_D           33 PPPPPVYC-VCRQPYDVNRFMIECDICKDWFHGSCVGVEEHHAVDIDLYHCPNCAVLHG   90 (488)
T ss_dssp             CCCCCEET-TTTEECCTTSCEEEBTTTCCEEEHHHHTCCGGGGGGEEEBCCHHHHHHHC
T ss_pred             CCCCCeEE-eCCCcCCCCCCeEEccCCCCceeeeecCcCcccccCCCEEECCCCcCCcC
Confidence            34557889 999997633489999999999999999998872  346899999986543

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

Probab=98.91  E-value=9e-10  Score=86.91  Aligned_cols=47  Identities=26%  Similarity=0.562  Sum_probs=39.8

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k  326 (446)
                      ...|.+|+.  ++  .||+||.|+.|||++|+++++. .+.+.|||+.|...
T Consensus        12 ~~~C~vC~~--~~--~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           12 GARCGVCGD--GT--DVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             TCCCTTTSC--CT--TCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCCcCCCCC--CC--eEEECCCCCCceecccCCCccCcCCCCCEECccccCC
Confidence            346999984  33  4999999999999999998887 67789999999854

>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=98.89  E-value=3.1e-10  Score=88.41  Aligned_cols=52  Identities=23%  Similarity=0.618  Sum_probs=42.0

Q ss_pred             CcccccccccCC--CCCCCeeecCCCCCcccccccccCCCC----CCCcEEcCCCCCcc
Q psy128          275 QVWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEP----ETSDWFCPKCSKVD  327 (446)
Q Consensus       275 ~~~~C~VCg~pd--d~~~~mIqCD~C~~WfH~~Cvg~~~~~----~~~~w~Cp~C~~k~  327 (446)
                      ....|.+|+..+  +++ .||+||.|+.|||+.|++++...    +.+.|||+.|....
T Consensus         5 ~~~~C~vC~~~~~~~~~-~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~   62 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPN-EMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFAT   62 (66)
T ss_dssp             CCCCBSSSCCCCCBTTB-CEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTT
T ss_pred             CCCCCCCCCCCCCCCCC-CEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCcc
Confidence            345799999763  234 79999999999999999998762    67899999998543

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=98.88  E-value=4.2e-10  Score=88.31  Aligned_cols=47  Identities=26%  Similarity=0.681  Sum_probs=39.6

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k  326 (446)
                      ..+|.+|+.  . + .||.||.|+.|||+.|+++++. .+.+.|+|+.|...
T Consensus         8 ~~~C~vC~~--~-g-~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            8 EDECAVCRD--G-G-ELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCSBSSSSC--C-S-SCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCccCCC--C-C-CEEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            347999995  3 3 5999999999999999998877 67789999999843

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=98.86  E-value=4.7e-10  Score=93.01  Aligned_cols=49  Identities=22%  Similarity=0.602  Sum_probs=40.5

Q ss_pred             cccccccccCC--CCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pd--d~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      ...|.+|+..+  +++ .||+||.|+.|||+.|++++. .+.+.|||+.|...
T Consensus        25 ~~~C~vC~~~~s~~~~-~ll~CD~C~~~fH~~Cl~p~~-vP~g~W~C~~C~~~   75 (88)
T 2l43_A           25 DAVCSICMDGESQNSN-VILFCDMCNLAVHQECYGVPY-IPEGQWLCRHCLQS   75 (88)
T ss_dssp             CCCCSSCCSSSSCSEE-EEEECSSSCCCCCHHHHTCSS-CCSSCCCCHHHHHH
T ss_pred             CCcCCcCCCCCCCCCC-CEEECCCCCchhhcccCCCCc-cCCCceECccccCc
Confidence            34699999764  333 799999999999999999986 46689999999843

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.86  E-value=8.2e-10  Score=83.91  Aligned_cols=45  Identities=29%  Similarity=0.814  Sum_probs=38.7

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCC
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCS  324 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~  324 (446)
                      ..+|.+|+..  +  .||.||.|+.|||+.|+++++. .+.+.|+|+.|.
T Consensus         9 ~~~C~vC~~~--g--~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~   54 (56)
T 2yql_A            9 EDFCSVCRKS--G--QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQ   54 (56)
T ss_dssp             CCSCSSSCCS--S--CCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHH
T ss_pred             CCCCccCCCC--C--eEEEcCCCCcceECccCCCCcCCCCCCceEChhhh
Confidence            4579999963  3  5999999999999999998877 677899999996

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=98.86  E-value=1.1e-09  Score=87.28  Aligned_cols=47  Identities=30%  Similarity=0.882  Sum_probs=40.5

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCC-cEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~-~w~Cp~C~~  325 (446)
                      .|.+|++.++++ .||.||.|+.|||+.|+++++. .+.+ .|+|+.|..
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            466889877666 8999999999999999998877 5667 999999984

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=98.84  E-value=6.5e-10  Score=88.89  Aligned_cols=48  Identities=23%  Similarity=0.621  Sum_probs=40.2

Q ss_pred             cccccccccCC--CCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCC
Q psy128          276 VWICPACGVQD--DGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       276 ~~~C~VCg~pd--d~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      ...|.+|+..+  +++ .||+||.|+.|||+.|++++. .+.+.|||+.|..
T Consensus        16 ~~~C~vC~~~~s~~~~-~ll~CD~C~~~~H~~Cl~~~~-vP~g~W~C~~C~~   65 (71)
T 2ku3_A           16 DAVCSICMDGESQNSN-VILFCDMCNLAVHQECYGVPY-IPEGQWLCRHCLQ   65 (71)
T ss_dssp             SCSCSSSCCCCCCSSS-CEEECSSSCCEEEHHHHTCSS-CCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCC-CEEECCCCCCccccccCCCCc-CCCCCcCCccCcC
Confidence            34699999764  344 799999999999999999986 4668999999974

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=98.84  E-value=3.6e-10  Score=86.97  Aligned_cols=46  Identities=28%  Similarity=0.800  Sum_probs=39.2

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      ..+|.+|+..  +  .||.||.|+.|||+.|++++.. .+.+.|+|+.|..
T Consensus         5 ~~~C~vC~~~--g--~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~   51 (60)
T 2puy_A            5 EDFCSVCRKS--G--QLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   51 (60)
T ss_dssp             CSSCTTTCCC--S--SCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHH
T ss_pred             CCCCcCCCCC--C--cEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccC
Confidence            3469999963  3  5999999999999999998877 6678999999974

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.83  E-value=2e-09  Score=87.33  Aligned_cols=47  Identities=28%  Similarity=0.818  Sum_probs=41.2

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCC-cEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~-~w~Cp~C~~  325 (446)
                      .|.+|+..++++ .||.||.|+.+||+.|+++++. .+.+ .|||+.|..
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            688999887776 8999999999999999998877 5667 999999973

>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=120.41  Aligned_cols=55  Identities=31%  Similarity=0.729  Sum_probs=44.7

Q ss_pred             CCcccccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCCCCcccC
Q psy128          274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEG  329 (446)
Q Consensus       274 ~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C~~k~~~  329 (446)
                      .+..|| +|+++++++.+||+||.|+.|||+.|+|++..  ...+.|+|+.|......
T Consensus         3 ~~~~yC-iC~~~~d~~~~MIqCD~C~~WfH~~CVgi~~~~~~~~~~y~C~~C~~~~~~   59 (447)
T 3kv4_A            3 SVPVYC-LCRLPYDVTRFMIECDMCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLHGP   59 (447)
T ss_dssp             CCCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTEEECCCHHHHHHHCC
T ss_pred             CCCeEE-eCCCcCCCCCCeEEcCCCCcccccccCCcCcccccCCCEEECCCCccccCC
Confidence            346789 99999764348999999999999999999877  34478999999865443

>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=98.77  E-value=2.9e-09  Score=99.90  Aligned_cols=48  Identities=23%  Similarity=0.646  Sum_probs=40.7

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCcc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  327 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~  327 (446)
                      ..+|.+|+.  +|  .+|+||+|+.|||+.|++++.. .+.+.|+|+.|....
T Consensus         7 ~~~C~~C~~--~g--~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            7 EDWCAVCQN--GG--DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             CSSBTTTCC--CE--EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCC--CC--ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            456999994  33  4999999999999999998887 677899999999654

>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=1.3e-09  Score=101.67  Aligned_cols=52  Identities=33%  Similarity=0.788  Sum_probs=41.9

Q ss_pred             cccccccCCCCCC---CeeecCCCCCcccccccccCCC--------CCCCcEEcCCCCCcccC
Q psy128          278 ICPACGVQDDGSL---PMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVDEG  329 (446)
Q Consensus       278 ~C~VCg~pdd~~~---~mIqCD~C~~WfH~~Cvg~~~~--------~~~~~w~Cp~C~~k~~~  329 (446)
                      +|++|+++++++.   .||+||.|+.|||+.|+|++..        +....|+|+.|......
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            6999999886653   4999999999999999999763        11237999999976554

>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=98.75  E-value=1.7e-09  Score=89.51  Aligned_cols=52  Identities=19%  Similarity=0.570  Sum_probs=42.6

Q ss_pred             CcccccccccCCCC-CCCeeecCCCCCcccccccccCCC-----CCCCcEEcCCCCCc
Q psy128          275 QVWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  326 (446)
Q Consensus       275 ~~~~C~VCg~pdd~-~~~mIqCD~C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~~k  326 (446)
                      ...+|.+|+..+.. +..||+||.|+.+||+.|+++++.     .+.+.|||+.|...
T Consensus        15 ~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~   72 (88)
T 1wev_A           15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             CCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccch
Confidence            34579999986542 126999999999999999999886     57889999999843

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=98.70  E-value=1.6e-08  Score=84.26  Aligned_cols=47  Identities=23%  Similarity=0.673  Sum_probs=40.1

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k  326 (446)
                      ..+|.+|+..  +  .+|+||.|+..||+.|+.++.. .+.+.|+|+.|...
T Consensus        25 ~~~C~vC~~~--g--~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           25 ATICRVCQKP--G--DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSCCSSSCSS--S--CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCcCcCcCCC--C--CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            3479999953  3  4999999999999999998887 67889999999854

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=98.68  E-value=7.3e-09  Score=84.11  Aligned_cols=47  Identities=32%  Similarity=0.897  Sum_probs=40.3

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCc-EEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSD-WFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~-w~Cp~C~~  325 (446)
                      .|.+|+..++++ .||+||.|+.+||++|+++++. .+.+. |+|+.|..
T Consensus        28 ~C~vC~~~~d~~-~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCSCGG-GEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCCCCc-ceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            577888877766 8999999999999999998887 56667 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=98.65  E-value=1.5e-08  Score=93.25  Aligned_cols=47  Identities=21%  Similarity=0.666  Sum_probs=40.1

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCcc
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  327 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~  327 (446)
                      .+|.+|+.  +|  .+|+||.|+.|||..|++++.. .+.+.|+|+.|....
T Consensus         5 ~~C~~C~~--~g--~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            5 DWCAVCQN--GG--ELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SSCTTTCC--CS--SCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CccccCCC--CC--eeeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            46999994  34  4999999999999999998887 677899999999654

>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=98.62  E-value=1.1e-08  Score=98.08  Aligned_cols=49  Identities=31%  Similarity=0.863  Sum_probs=38.7

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCC-cEEcCCCCC
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETS-DWFCPKCSK  325 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~-~w~Cp~C~~  325 (446)
                      .+.|.+|+..++++ .||+||.|+.|||+.|+++++. .+.+ .|+|+.|..
T Consensus       174 ~c~C~vC~~~~~~~-~lL~CD~C~~~yH~~CL~PPL~~vP~G~~W~Cp~C~~  224 (226)
T 3ask_A          174 VCACHLCGGRQDPD-KQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN  224 (226)
T ss_dssp             TTSCSSSCCCCC---CCEECSSSCCEECSCC--CCCCSCCSSSCCCCGGGC-
T ss_pred             CCCCcCCCCCCCCC-CeEEcCCCCcceeCccCCCCcccCCCCCCCCCcCCcC
Confidence            34699999887776 8999999999999999999888 5667 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=98.58  E-value=1.3e-08  Score=87.54  Aligned_cols=47  Identities=30%  Similarity=0.824  Sum_probs=41.2

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      +|.+|+..++++ .||.||.|+.|||+.|+++++. .+.+.|+|+.|..
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            588899877666 7999999999999999998877 6778999999973

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=98.53  E-value=5.2e-08  Score=83.52  Aligned_cols=48  Identities=27%  Similarity=0.654  Sum_probs=39.5

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      +|.+|+..++++..+|.||.|+.+||++|+++++. .+.+.|+|+.|..
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            57788865332227999999999999999998877 6778999999985

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=98.48  E-value=5.2e-08  Score=83.71  Aligned_cols=45  Identities=33%  Similarity=0.823  Sum_probs=36.2

Q ss_pred             CcccccccccCCCCCCCeeecC--CCCCcccccccccCCCCCCCcEEcCCCC
Q psy128          275 QVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAEPETSDWFCPKCS  324 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD--~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~  324 (446)
                      +..+|.+|+.  +|  .||+||  .|+.|||+.|+++.. .+.+.|||+.|.
T Consensus        14 ~~~~C~~C~~--~G--~ll~CD~~~Cp~~fH~~Cl~L~~-~P~g~W~Cp~c~   60 (107)
T 4gne_A           14 HEDYCFQCGD--GG--ELVMCDKKDCPKAYHLLCLNLTQ-PPYGKWECPWHQ   60 (107)
T ss_dssp             SCSSCTTTCC--CS--EEEECCSTTCCCEECTGGGTCSS-CCSSCCCCGGGB
T ss_pred             CCCCCCcCCC--CC--cEeEECCCCCCcccccccCcCCc-CCCCCEECCCCC
Confidence            3457988982  44  499999  899999999999654 466899999875

>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=98.44  E-value=5.9e-08  Score=82.58  Aligned_cols=48  Identities=33%  Similarity=0.803  Sum_probs=41.4

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCc
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  326 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k  326 (446)
                      +|.+|+..++++ .||.||.|+.|||+.|+++++. .+.+.|+|+.|...
T Consensus        56 ~C~~C~~~~~~~-~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~c  104 (111)
T 2ysm_A           56 VCQNCKQSGEDS-KMLVCDTCDKGYHTFCLQPVMKSVPTNGWKCKNCRIC  104 (111)
T ss_dssp             CCTTTCCCSCCT-TEEECSSSCCEEEGGGSSSCCSSCCSSCCCCHHHHCC
T ss_pred             cccccCccCCCC-CeeECCCCCcHHhHHhcCCccccCCCCCcCCcCCcCc
Confidence            577898877666 8999999999999999998877 67789999999754

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=98.38  E-value=1.6e-07  Score=87.43  Aligned_cols=46  Identities=24%  Similarity=0.703  Sum_probs=39.5

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCcc
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVD  327 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~  327 (446)
                      +|.+|+.  +|  .+|+||+|+.+||..|+.++.. .+.+.|+|+.|....
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--PG--DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CBTTTCC--CS--SCCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             cCccCCC--CC--ceeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            6999994  33  4999999999999999998877 677899999998654

>3pur_A Lysine-specific demethylase 7 homolog; oxidoreductase-oxidoreductase inhibitor complex; HET: 2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A* 3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A*

Probab=98.32  E-value=1.4e-07  Score=99.99  Aligned_cols=45  Identities=36%  Similarity=0.911  Sum_probs=36.1

Q ss_pred             cccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCCCCc
Q psy128          282 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  326 (446)
Q Consensus       282 Cg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C~~k  326 (446)
                      +..+.+++.+||+||.|+.|||+.|||++..  ...+.|+||.|...
T Consensus        48 ~~~~~n~~~~mI~CD~C~~WfH~~CVgi~~~~a~~~~~y~Cp~C~~~   94 (528)
T 3pur_A           48 SHHHKKNDFQWIGCDSCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPH   94 (528)
T ss_dssp             TTTTTTSTTSEEECTTTCCEEEGGGTTCCGGGTTTEEECCCTTTHHH
T ss_pred             cccCCCcCCCEEECCCCCcCCCCcCCCCChhHhcCCCeEECcCCcCC
Confidence            3333344559999999999999999999987  34579999999864

>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=98.02  E-value=3.6e-06  Score=71.49  Aligned_cols=47  Identities=26%  Similarity=0.712  Sum_probs=39.5

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCC
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCS  324 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~  324 (446)
                      .+|.+|+...+.+ .||.|+.|...||..|++++.. ...+.|+|+.|.
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            3699999865544 5899999999999999999877 456799999986

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=97.95  E-value=3.2e-06  Score=76.00  Aligned_cols=50  Identities=24%  Similarity=0.504  Sum_probs=40.9

Q ss_pred             CcccccccccCCCCCCCeeecCCCCCcccccccccCCC--------CCCCcEEcCCCCCccc
Q psy128          275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVDE  328 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--------~~~~~w~Cp~C~~k~~  328 (446)
                      ...+|.+|+.   ++ .+|+||.|.+.||..|+.++..        .+.+.|+|+.|.....
T Consensus        62 ~~d~C~vC~~---GG-~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~pl  119 (142)
T 2lbm_A           62 MDEQCRWCAE---GG-NLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPL  119 (142)
T ss_dssp             CBCSCSSSCC---CS-SEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCCTT
T ss_pred             CCCeecccCC---CC-cEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCccH
Confidence            4568999993   44 4999999999999999997775        3678999999986543

>3rsn_A SET1/ASH2 histone methyltransferase complex subun; PHD domain, winged helix domain, binding, transcription; 2.10A {Homo sapiens} PDB: 3s32_A

Probab=97.78  E-value=1.5e-05  Score=73.92  Aligned_cols=51  Identities=12%  Similarity=0.240  Sum_probs=36.7

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-----CCCCcEEcCCCCCcc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKVD  327 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~~k~  327 (446)
                      ..+| .||.+.+-+..||+|+.|..|||..|+.....     .....|.|..|....
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 99998777779999999999999999986553     224478999998754

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=97.78  E-value=4.5e-06  Score=71.03  Aligned_cols=38  Identities=34%  Similarity=0.852  Sum_probs=30.8

Q ss_pred             CeeecCCCCCcccccccccCCC--------CCCCcEEcCCCCCccc
Q psy128          291 PMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVDE  328 (446)
Q Consensus       291 ~mIqCD~C~~WfH~~Cvg~~~~--------~~~~~w~Cp~C~~k~~  328 (446)
                      .||+||.|..|||..|++++..        +....|.|+.|.....
T Consensus         1 ~mi~c~~c~~w~H~~c~~~~~~~~~~l~~lp~~~~~~c~~C~~~~~   46 (140)
T 2ku7_A            1 SMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHV   46 (140)
T ss_dssp             CCCCCSCCSSCHHHHHCCCCHHHHHHHHSSCTTTTCCSSCCTTTSC
T ss_pred             CccccccCCCccCCcccccCHHHHHHHhhccccceeeCcccccccc
Confidence            3999999999999999999752        3344799999986543

>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=97.54  E-value=2.1e-05  Score=69.69  Aligned_cols=51  Identities=24%  Similarity=0.517  Sum_probs=40.3

Q ss_pred             CCcccccccccCCCCCCCeeecCCCCCcccccccccCCC--------CCCCcEEcCCCCCccc
Q psy128          274 KQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--------PETSDWFCPKCSKVDE  328 (446)
Q Consensus       274 ~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--------~~~~~w~Cp~C~~k~~  328 (446)
                      ....+|.+|+   +|+ .+|+||.|.+.||..|+.++..        .+.+.|+|..|.....
T Consensus        55 g~~~~C~vC~---dGG-~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~pl  113 (129)
T 3ql9_A           55 GMDEQCRWCA---EGG-NLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPL  113 (129)
T ss_dssp             SCBSSCTTTC---CCS-EEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCGGG
T ss_pred             CCCCcCeecC---CCC-eeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCHHH
Confidence            3456799999   344 4999999999999999987632        2578999999986544

>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=3.4e-05  Score=65.71  Aligned_cols=47  Identities=26%  Similarity=0.478  Sum_probs=33.0

Q ss_pred             ccccCCCCCCCeeecCCCCCcccccccccCCC-----CCCCcEEcCCCCCcc
Q psy128          281 ACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKVD  327 (446)
Q Consensus       281 VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~~k~  327 (446)
                      .|....+.+..||+|+.|+.|||..|+++...     ..++.|+|+.|.+..
T Consensus        64 ~c~~~~~~~~~m~~C~~C~~~~H~~C~~~~~~~~~~~~~~~~~~C~~C~~~~  115 (117)
T 4bbq_A           64 QNEETQDFEKKLMECCICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQED  115 (117)
T ss_dssp             CHHHHCCGGGSCEEETTTCCEECGGGCCSCCCCEECSSSSSEEECTTTC---
T ss_pred             ccccccccCcceEEeeecCCeEECCCCCCCccccccccCCCCeECCCCcCCC
Confidence            34333333337999999999999999998765     234569999998653

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=97.45  E-value=2.4e-05  Score=66.88  Aligned_cols=47  Identities=26%  Similarity=0.582  Sum_probs=36.6

Q ss_pred             ccccccccCC------CCCCCeeecCCCCCcccccccccCCC----CCCCcEEcCCCC
Q psy128          277 WICPACGVQD------DGSLPMIGCDGCDAWYHWVCVGLVAE----PETSDWFCPKCS  324 (446)
Q Consensus       277 ~~C~VCg~pd------d~~~~mIqCD~C~~WfH~~Cvg~~~~----~~~~~w~Cp~C~  324 (446)
                      .+|.+|...+      +++ .||.|+.|+.+||.+|+++...    ...+.|+|+.|.
T Consensus         6 ~~C~~C~~~~~~~~~g~~~-~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            6 PICSFCLGTKEQNREKKPE-ELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             SSBTTTCCCTTCCTTSCCC-CCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             ccccccCCchhhCcCCCch-hceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            4688997642      233 6999999999999999987432    345689999997

>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=97.21  E-value=4.8e-05  Score=65.23  Aligned_cols=46  Identities=22%  Similarity=0.573  Sum_probs=36.0

Q ss_pred             cccccccCC-------CCCCCeeecCCCCCcccccccccCCC----CCCCcEEcCCCC
Q psy128          278 ICPACGVQD-------DGSLPMIGCDGCDAWYHWVCVGLVAE----PETSDWFCPKCS  324 (446)
Q Consensus       278 ~C~VCg~pd-------d~~~~mIqCD~C~~WfH~~Cvg~~~~----~~~~~w~Cp~C~  324 (446)
                      +|.+|...+       +++ .||.|+.|...||.+|+++...    .+.+.|+|+.|.
T Consensus         3 ~C~~C~~~~~~n~k~g~~~-~Li~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   59 (114)
T 2kwj_A            3 YCDFCLGGSNMNKKSGRPE-ELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECK   59 (114)
T ss_dssp             CCSSSCCBTTBCTTTCCCC-CCEECSSSCCEECTTTTTCCHHHHHHHHHTTCCCGGGC
T ss_pred             cCccCCCCccccccCCCCC-CCeEeCCCCCccchhhCCChhhhhhccCCCccCccccC
Confidence            688897543       233 7999999999999999998743    345689999885

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=95.87  E-value=0.0045  Score=51.18  Aligned_cols=47  Identities=23%  Similarity=0.604  Sum_probs=36.6

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccC------------CC-CCCCcEEcCCCCC
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV------------AE-PETSDWFCPKCSK  325 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~------------~~-~~~~~w~Cp~C~~  325 (446)
                      ..|.||..-..++  ++.|..|.+.||..|+...            +. ....-|.|+.|..
T Consensus        16 ~~C~VC~~~t~~~--l~pCRvC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T~~GWSC~~Cen   75 (89)
T 1wil_A           16 EMCDVCEVWTAES--LFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDN   75 (89)
T ss_dssp             CCCTTTCCCCSSC--CSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCC
T ss_pred             cccCccccccccc--eeccccccccccHhhcccccccccHHHHHHHHccCCCCCccccccch
Confidence            3699999765555  9999999999999998653            11 2456899999974

>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger, histone binding, chromosomal protein, DNA damag repair, DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens} PDB: 3a1a_A*

Probab=92.19  E-value=0.048  Score=49.80  Aligned_cols=51  Identities=22%  Similarity=0.510  Sum_probs=39.7

Q ss_pred             CcccccccccCCCCCCCeeecC--CCCCcccccccccCCC-------CCCCcEEcCCCCCcccC
Q psy128          275 QVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVDEG  329 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD--~C~~WfH~~Cvg~~~~-------~~~~~w~Cp~C~~k~~~  329 (446)
                      -..||.+|+.   |+ .+|.||  .|.+.|-..|+.....       ...+.|.|..|.+....
T Consensus        78 ~~~yC~wC~~---Gg-~l~~Cdn~~C~r~FC~~CI~~nvG~~~~~~i~~~d~W~Cy~C~P~~l~  137 (159)
T 3a1b_A           78 YQSYCTICCG---GR-EVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTY  137 (159)
T ss_dssp             SBSSCTTTSC---CS-EEEECSSTTTCCEEEHHHHHHHTCTTHHHHHHTSSSCCCTTTCSSCEE
T ss_pred             CcceeeEecC---CC-eEEeeCCCCCCCchhHHHHHHhcCHhHHHHHhccCCCEEEecCCccHH
Confidence            3668999994   44 599999  7999999999765444       34578999999987643

>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*

Probab=91.11  E-value=0.072  Score=54.73  Aligned_cols=53  Identities=23%  Similarity=0.604  Sum_probs=41.1

Q ss_pred             CCCcccccccccCCCCCCCeeecC--CCCCcccccccccCCC-------CCCCcEEcCCCCCcccC
Q psy128          273 SKQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE-------PETSDWFCPKCSKVDEG  329 (446)
Q Consensus       273 ~~~~~~C~VCg~pdd~~~~mIqCD--~C~~WfH~~Cvg~~~~-------~~~~~w~Cp~C~~k~~~  329 (446)
                      +....||.+|+.   |+ .+|.||  .|.+.|-..|+.....       ...+.|.|..|.+....
T Consensus        90 DG~~~yCr~C~~---Gg-~l~~Cdn~~C~r~FC~~Ci~~n~g~~~~~~i~~~d~W~Cf~C~p~p~~  151 (386)
T 2pv0_B           90 DGYQSYCSICCS---GE-TLLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSSRS  151 (386)
T ss_dssp             SSSBCSCTTTCC---CS-SCEECCSTTCCCEECHHHHHHHTCTTHHHHHHHCSSCCCTTTSSCCEE
T ss_pred             CCCcccceEcCC---CC-eEEEeCCCCCCcchHHHHHHHhcChhHHHHhhccCCceEEEcCCcchH
Confidence            445679999994   44 599999  8999999999876654       23468999999987643

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

Probab=85.60  E-value=0.75  Score=34.61  Aligned_cols=47  Identities=21%  Similarity=0.457  Sum_probs=32.1

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      ...|.||.....+-  .+.  .|+-.||..|+..-.........||.|+..
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            45799999754432  222  799889999986544322346789999854

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

Probab=83.65  E-value=0.78  Score=32.66  Aligned_cols=46  Identities=20%  Similarity=0.342  Sum_probs=31.5

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCC
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      ..|.||......+...+....|+-.||..|+..-...   ...||.|+.
T Consensus         6 ~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~---~~~CP~Cr~   51 (55)
T 1iym_A            6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS---HSTCPLCRL   51 (55)
T ss_dssp             CCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT---CCSCSSSCC
T ss_pred             CcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc---CCcCcCCCC
Confidence            3599998765443244555579999999998654332   357999984

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

Probab=82.95  E-value=0.38  Score=36.07  Aligned_cols=47  Identities=21%  Similarity=0.290  Sum_probs=30.4

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      ...|.||......+ ..+..-.|+-.||..|+..-...   ...||.|+..
T Consensus        14 ~~~C~IC~~~~~~~-~~~~~~~C~H~fc~~Ci~~~~~~---~~~CP~Cr~~   60 (69)
T 2kiz_A           14 EEKCTICLSILEEG-EDVRRLPCMHLFHQVCVDQWLIT---NKKCPICRVD   60 (69)
T ss_dssp             CCSBTTTTBCCCSS-SCEEECTTSCEEEHHHHHHHHHH---CSBCTTTCSB
T ss_pred             CCCCeeCCccccCC-CcEEEeCCCCHHHHHHHHHHHHc---CCCCcCcCcc
Confidence            44699998655433 23344469999999998643221   2359999854

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

Probab=82.61  E-value=1  Score=34.47  Aligned_cols=48  Identities=23%  Similarity=0.365  Sum_probs=30.8

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCcc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKVD  327 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k~  327 (446)
                      ...|.||....... ..+.--.|.-.||..|+..-..   ....||.|+...
T Consensus        15 ~~~C~IC~~~~~~~-~~~~~~~C~H~fc~~Ci~~~~~---~~~~CP~Cr~~~   62 (78)
T 2ect_A           15 GLECPVCKEDYALG-ESVRQLPCNHLFHDSCIVPWLE---QHDSCPVCRKSL   62 (78)
T ss_dssp             SCCCTTTTSCCCTT-SCEEECTTSCEEETTTTHHHHT---TTCSCTTTCCCC
T ss_pred             CCCCeeCCccccCC-CCEEEeCCCCeecHHHHHHHHH---cCCcCcCcCCcc
Confidence            34699998755443 2222235888999999864332   135799998654

---

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	446
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	6e-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	4e-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-	1e-07
d2pnxa1	51	g.50.1.2 (A:195-245) Inhibitor of growth protein 4	2e-07
d1weva_	88	g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu	3e-07
d1wesa_	71	g.50.1.2 (A:) PHD Inhibitor of growth protein 2, I	2e-06
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	8e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	0.001
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	0.001
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	0.002
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	0.003
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	0.004

>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 = 63.5 bits (154), Expect = 1e-13
 Identities = 18/57 (31%), Positives = 22/57 (38%), Gaps = 2/57 (3%)

Query: 271 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSK 325
           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 = 57.8 bits (139), Expect = 2e-11
 Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 3/69 (4%)

Query: 276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVDEGSRKE 333
           V +   C    + +  MI C  C  W+H  CVG+  E   +   + CP C +   G    
Sbjct: 11  VPVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDC-EAVFGPSIM 69

Query: 334 KKKRGRKKK 342
           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 = 55.8 bits (134), Expect = 6e-11
 Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 282 CGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP-ETSDWFCPKCSK 325
           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: 282 CGVQDDGSLPMIGCDGCDAWYHWVCVGL------VAEPETSDWFCPKCS 324
           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 = 48.8 bits (116), Expect = 1e-08
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 2/46 (4%)

Query: 279 CPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKC 323
           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 = 47.6 bits (113), Expect = 4e-08
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 5/55 (9%)

Query: 271 GDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCS 324
           G    +  C  C    +    ++ CD C + YH  C+   + E    +W CP+C+
Sbjct: 4   GSDHHMEFCRVCKDGGE----LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCT 54

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 78

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 47.0 bits (111), Expect = 1e-07
 Identities = 12/62 (19%), Positives = 18/62 (29%), Gaps = 6/62 (9%)

Query: 269 DTGDSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEP------ETSDWFCPK 322
           D    +    C      +  S+       C  W H  CV L  +P          ++C  
Sbjct: 9   DPFQPEIKVRCVCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEI 68

Query: 323 CS 324
           C 
Sbjct: 69  CR 70

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (109), Expect = 1e-07
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGL-VAEPETSDWFCPKCSKVDEGSRKEKKK 336
           IC  C    D    ++ C+ C+  +H  C    + +    +W C  C  + +   ++   
Sbjct: 9   ICRVCQKPGD----LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDVDL 64

Query: 337 RGRK 340
           +  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 = 44.9 bits (106), Expect = 2e-07
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 282 CGVQDDGSLPMI-GCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK 325
           C     G +      D    W+H+ CVGL  +P    WFCP+CS+
Sbjct: 7   CHQVSYGEMIGCDNPDCSIEWFHFACVGLTTKPR-GKWFCPRCSQ 50

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]} Length = 88

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.0 bits (108), Expect = 3e-07
 Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 279 CPACG-VQDDGSLPMIGCDGCDAWYHWVCVG-----LVAEPETSDWFCPKCSKVDEGSRK 332
           C  C  +       ++ C  C   YH  C                W+C +C++  +   +
Sbjct: 19  CVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRMAQ 78

Query: 333 EKKKRG 338
           + +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 = 43.4 bits (102), Expect = 2e-06
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

Query: 282 CGVQDDGSLPMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKC 323
           C     G +     + C   W+H+ CV L  +P+   W+CPKC
Sbjct: 21  CNQVSYGEMIGCDNEQCPIEWFHFSCVSLTYKPK-GKWYCPKC 62

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 8e-04
 Identities = 18/122 (14%), Positives = 54/122 (44%)

Query: 103 EIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEE 162
           E  +     ++      K KE +     + D+   + +++ + ++ K +  +   +   E
Sbjct: 166 EEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHE 225

Query: 163 KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSHE 222
            ++K E+  + KE   +   K   E+ ++++ +  K++++ L  +  ++++  KE    E
Sbjct: 226 MQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKE 285

Query: 223 KE 224
             
Sbjct: 286 SR 287

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 0.001
 Identities = 15/116 (12%), Positives = 52/116 (44%)

Query: 97  SSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEE 156
           S E + +          +K  + + +    +      K   + + K+++  E+++   +E
Sbjct: 184 SKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQE 243

Query: 157 KEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKK 212
             K+  ++ + ++   +KE +     K++++E+  ++  + + +  K + + L+ K
Sbjct: 244 HLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTK 299

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 0.001
 Identities = 22/128 (17%), Positives = 59/128 (46%), Gaps = 1/128 (0%)

Query: 102 GEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKE 161
             I+ ++ ++   K+ +      ++  +   +K+K    E+ K +  +   K   + +++
Sbjct: 170 KGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRK 229

Query: 162 EKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKEKERSSH 221
            ++  E+KE   +E  ++  EK+  +     KE++ +    KL++++   K+  ++ S  
Sbjct: 230 NEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQE-RTLALKLQEQEQLLKEGFQKESRI 288

Query: 222 EKEVIPKL 229
            K  I  L
Sbjct: 289 MKNEIQDL 296

>d1sa0e_ a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 138

class: All alpha proteins
fold: Non-globular all-alpha subunits of globular proteins
superfamily: Stathmin
family: Stathmin
domain: Stathmin 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 20/108 (18%), Positives = 52/108 (48%), Gaps = 3/108 (2%)

Query: 108 KSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEKKEEKEKKE 167
            S+ + +    ++ ++K++  ++++   + +  +   EK+E E+   E  +K  E+    
Sbjct: 34  ASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHER---EVIQKAIEENNNF 90

Query: 168 EKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKLKKEKLKKKKKE 215
            K  K K  ++    K  +E   +   ++ ++KDK  ++ +  K+ KE
Sbjct: 91  IKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKE 138

>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 = 37.5 bits (86), Expect = 0.003
 Identities = 31/193 (16%), Positives = 63/193 (32%), Gaps = 6/193 (3%)

Query: 22   PPMLQHPLIPQPLVHPPGTPPPSKMKDKVSPKDKTSPKEKMSSKEKTSPKEKEYSKVKDV 81
             P L   L P                +  + K  T   E     +  S    E  ++  +
Sbjct: 1112 TPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQL 1171

Query: 82   ELGVTPMVPNIVKVTSSEDLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKE 141
               +            S  L  ++ D++   DK     +  E+I K+  K D   I +++
Sbjct: 1172 HFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERI-KQTFKNDLFVIWSED 1230

Query: 142  KDKEK-----KEKEKGKKEEKEKKEEKEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKK 196
             D++        + K    E E +E+   K+ +   ++    + VE I +        K 
Sbjct: 1231 NDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKV 1290

Query: 197  SKDKDKKLKKEKL 209
                 + +K+ + 
Sbjct: 1291 PSPTGEYVKEPEW 1303

>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 = 37.1 bits (85), Expect = 0.004
 Identities = 14/106 (13%), Positives = 32/106 (30%), Gaps = 1/106 (0%)

Query: 100 DLGEIKKDKSIKKDKKTHKKKEKEKIKKKKDKKDKDKIKNKEKDKEKKEKEKGKKEEKEK 159
           D       +++       +      + K K   + D     +  +       G  +   +
Sbjct: 115 DEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIR 174

Query: 160 KEE-KEKKEEKEFKMKEDKEKPVEKIRKEEKDSEKEKKSKDKDKKL 204
           K+  K     K+ +   D ++P  ++   E+     K    KD   
Sbjct: 175 KDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTS 220

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	446
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	99.23
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	99.22
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	99.09
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	99.09
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	99.09
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	99.06
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	99.03
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	99.02
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	98.99
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	98.95
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	98.72
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	87.81
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	86.91
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	86.72
d1weqa_	85	PHD finger protein 7 (NYD-SP6) {Mouse (Mus musculu	81.67

>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=99.23  E-value=1.3e-12  Score=101.91  Aligned_cols=54  Identities=31%  Similarity=0.800  Sum_probs=45.2

Q ss_pred             CCCCcccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCc
Q psy128          272 DSKQVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKV  326 (446)
Q Consensus       272 d~~~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k  326 (446)
                      .+++.++| +|+.+++++..||+||.|+.|||+.|++++.. .+.+.|+|+.|...
T Consensus        12 ~~~~~~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~   66 (72)
T d1weea_          12 VDNWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             SCSSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             CCCCeEEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCc
Confidence            34567789 99988766658999999999999999999877 55679999999854

>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=99.22  E-value=2.3e-12  Score=102.58  Aligned_cols=51  Identities=31%  Similarity=0.714  Sum_probs=42.9

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCCCCcc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKVD  327 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C~~k~  327 (446)
                      .++| +|+++++.+.+||+||.|+.|||+.|++++..  ...+.|+|+.|....
T Consensus        12 pv~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          12 PVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             CeEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            5689 99998765558999999999999999999876  455689999998643

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=1.8e-11  Score=89.42  Aligned_cols=47  Identities=26%  Similarity=0.767  Sum_probs=42.0

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~  325 (446)
                      .|.+|+..++++ .||.||.|+.|||+.|++++.. .+.+.|+|+.|+.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588999988777 8999999999999999999877 6677999999985

>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=99.09  E-value=3.5e-11  Score=94.37  Aligned_cols=52  Identities=37%  Similarity=1.027  Sum_probs=39.3

Q ss_pred             CCCCcccccccccCCCCCCCeeec--CCCC-CcccccccccCCCCCCCcEEcCCCCCcc
Q psy128          272 DSKQVWICPACGVQDDGSLPMIGC--DGCD-AWYHWVCVGLVAEPETSDWFCPKCSKVD  327 (446)
Q Consensus       272 d~~~~~~C~VCg~pdd~~~~mIqC--D~C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~k~  327 (446)
                      ++++..+| ||+.+++++  ||.|  +.|. .|||+.||+++.. +.++|||+.|....
T Consensus        12 d~~e~~~C-iC~~~~~~~--~i~c~~~~C~~~wfH~~Cvgl~~~-p~~~w~C~~C~~~~   66 (71)
T d1wesa_          12 DPNEPTYC-LCNQVSYGE--MIGCDNEQCPIEWFHFSCVSLTYK-PKGKWYCPKCRGDS   66 (71)
T ss_dssp             CSSSCCCS-TTCCCCCSS--EECCSCTTCSCCCEETTTTTCSSC-CSSCCCCTTTSSCC
T ss_pred             CCCCCCEE-EeCCCCCCC--EEEEECCCCCCcCccCccCCCCcC-CCCcEECcCCcccc
Confidence            33445789 999987776  5555  5674 7999999998755 45689999998543

>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=99.09  E-value=1.3e-11  Score=93.96  Aligned_cols=50  Identities=32%  Similarity=0.733  Sum_probs=42.7

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccCCC--CCCCcEEcCCCCCc
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE--PETSDWFCPKCSKV  326 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~--~~~~~w~Cp~C~~k  326 (446)
                      ..|.+|+.+++++.+||+||.|+.|||+.|++++..  .....|+|+.|...
T Consensus         7 ~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           7 GQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             CCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            469999998766658999999999999999999877  34578999999854

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.06  E-value=8.4e-12  Score=97.70  Aligned_cols=50  Identities=32%  Similarity=0.911  Sum_probs=41.3

Q ss_pred             CcccccccccCCCCCCCeeecCCCCCcccccccccCCC------CCCCcEEcCCCCCc
Q psy128          275 QVWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE------PETSDWFCPKCSKV  326 (446)
Q Consensus       275 ~~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~------~~~~~w~Cp~C~~k  326 (446)
                      +..+| +|+++++++ .||+||.|..|||+.|++++..      .....|+|+.|...
T Consensus        15 ~~~~C-iC~~~~~~~-~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          15 NALYC-ICRQPHNNR-FMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TCCCS-TTCCCCCSS-CEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CcCEE-ECCCccCCC-eEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            45679 999988776 8999999999999999998753      23457999999743

>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=99.03  E-value=3.2e-11  Score=95.47  Aligned_cols=53  Identities=28%  Similarity=0.699  Sum_probs=41.9

Q ss_pred             CCCCcccccccccCCCCCCCeeecC--CCCCcccccccccCCC------CCCCcEEcCCCCCc
Q psy128          272 DSKQVWICPACGVQDDGSLPMIGCD--GCDAWYHWVCVGLVAE------PETSDWFCPKCSKV  326 (446)
Q Consensus       272 d~~~~~~C~VCg~pdd~~~~mIqCD--~C~~WfH~~Cvg~~~~------~~~~~w~Cp~C~~k  326 (446)
                      ++++..+| +|+.+++++ .||+|+  .|..|||+.|||++..      .....|+|+.|...
T Consensus        12 ~~~~~~~C-~C~~~~~~~-~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T d1wewa_          12 QPEIKVRC-VCGNSLETD-SMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             SCCCCCCC-SSCCCCCCS-CEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCCCccEe-ECCCccCCC-cEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCc
Confidence            34456789 999987766 799988  6999999999999764      23347999999743

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.02  E-value=9.7e-11  Score=88.67  Aligned_cols=48  Identities=27%  Similarity=0.767  Sum_probs=39.6

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCccc
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  328 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~~  328 (446)
                      .+|.+|+.   ++ .||+||.|+.|||+.|++++.. .+.+.|+|+.|.....
T Consensus        10 ~~C~~C~~---~g-~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~~   58 (61)
T d1mm2a_          10 EFCRVCKD---GG-ELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             SSCTTTCC---CS-SCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             CCCcCCCC---CC-eEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCccc
Confidence            37999984   33 5999999999999999998877 5567999999986543

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=98.99  E-value=2.7e-11  Score=89.19  Aligned_cols=46  Identities=43%  Similarity=1.146  Sum_probs=38.6

Q ss_pred             cccccccccCCCCCCCeeecCC---CCCcccccccccCCCCCCCcEEcCCCCC
Q psy128          276 VWICPACGVQDDGSLPMIGCDG---CDAWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~---C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      ..|| +|+.+++++  ||.||.   |..|||+.|||++.. +.++|||+.|..
T Consensus         2 ~~yC-~C~~~~~~~--mi~Cd~~~C~~~WfH~~Cvgl~~~-p~~~w~C~~C~~   50 (51)
T d2pnxa1           2 PTYC-LCHQVSYGE--MIGCDNPDCSIEWFHFACVGLTTK-PRGKWFCPRCSQ   50 (51)
T ss_dssp             CEET-TTTEECCSE--EEECSCTTCSSCEEEGGGGTCSSC-CSSCCCCHHHHC
T ss_pred             CcEE-EcCCCCCCC--EEEEecCCCCCCCEeCCccCCCcC-CCCcEECcCCCC
Confidence            3589 999988776  999997   578999999998765 456899999974

>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=98.95  E-value=4.3e-11  Score=96.26  Aligned_cols=51  Identities=20%  Similarity=0.588  Sum_probs=40.5

Q ss_pred             cccccccccCCCC-CCCeeecCCCCCcccccccccCCC-----CCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDG-SLPMIGCDGCDAWYHWVCVGLVAE-----PETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~-~~~mIqCD~C~~WfH~~Cvg~~~~-----~~~~~w~Cp~C~~k  326 (446)
                      ..+|.+|+....+ ...||+||.|..|||..|++++..     .+.+.|||+.|...
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            4568899976432 237999999999999999998765     45668999999743

>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=98.72  E-value=4e-09  Score=81.70  Aligned_cols=49  Identities=20%  Similarity=0.607  Sum_probs=39.7

Q ss_pred             cccccccccCCCCCCCeeecCCCCCcccccccccCCC-CCCCcEEcCCCCCccc
Q psy128          276 VWICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAE-PETSDWFCPKCSKVDE  328 (446)
Q Consensus       276 ~~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~-~~~~~w~Cp~C~~k~~  328 (446)
                      ..+|.+|+.   ++ .||.||.|..|||..|++++.. .+.+.|+|+.|.....
T Consensus         7 c~~C~~C~~---~~-~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           7 ATICRVCQK---PG-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSCCSSSCS---SS-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCC---cC-EEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            346888874   33 4999999999999999999876 6677999999985543

>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=87.81  E-value=0.027  Score=40.62  Aligned_cols=50  Identities=22%  Similarity=0.385  Sum_probs=32.5

Q ss_pred             cccccccccCCCCC-CCeeecCCCCCcccccccccCCCCCCCcEEcCCCCCc
Q psy128          276 VWICPACGVQDDGS-LPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSKV  326 (446)
Q Consensus       276 ~~~C~VCg~pdd~~-~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~k  326 (446)
                      ...|.||...+++. .....|.+|..+||..|+.-=.. ..+.+.||.|+..
T Consensus         6 ~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~-~~~~~~CP~Cr~~   56 (60)
T d1vyxa_           6 VPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLT-ISRNTACQICGVV   56 (60)
T ss_dssp             CCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHH-HHTCSBCTTTCCB
T ss_pred             CCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHh-hCCCCCCcccCCe
Confidence            34699998655444 12235678889999999864222 1124679999854

>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=86.91  E-value=0.2  Score=35.55  Aligned_cols=45  Identities=20%  Similarity=0.369  Sum_probs=33.2

Q ss_pred             cccccccCCCCCCCeeecCCCCCcccccccccCCCCCCCcEEcCCCCC
Q psy128          278 ICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLVAEPETSDWFCPKCSK  325 (446)
Q Consensus       278 ~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~~~~~~~~w~Cp~C~~  325 (446)
                      .|.||.....++...+.+..|+..||..|+..-...   .-.||.|+.
T Consensus         7 ~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~---~~~CP~CR~   51 (55)
T d1iyma_           7 ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS---HSTCPLCRL   51 (55)
T ss_dssp             CCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT---CCSCSSSCC
T ss_pred             CCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHh---CCcCCCCCC
Confidence            499998766544356677789999999998765542   236999985

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.72  E-value=0.23  Score=38.99  Aligned_cols=48  Identities=23%  Similarity=0.649  Sum_probs=34.7

Q ss_pred             ccccccccCCCCCCCeeecCCCCCcccccccccC----CC---------CCCCcEEcCCCCCc
Q psy128          277 WICPACGVQDDGSLPMIGCDGCDAWYHWVCVGLV----AE---------PETSDWFCPKCSKV  326 (446)
Q Consensus       277 ~~C~VCg~pdd~~~~mIqCD~C~~WfH~~Cvg~~----~~---------~~~~~w~Cp~C~~k  326 (446)
                      ..|.||.-...+.  .+.|-.|.+-||..|+.--    ..         ....-|.|..|..-
T Consensus        16 ~mC~vC~v~t~~~--l~pCRvCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~nl   76 (89)
T d1wila_          16 EMCDVCEVWTAES--LFPCRVCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNI   76 (89)
T ss_dssp             CCCTTTCCCCSSC--CSSCSSSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCC
T ss_pred             ccccccCcccccc--eecceeecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcch
Confidence            3699997654444  7799999999999996321    11         23447999999853

>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=81.67  E-value=1.6  Score=33.86  Aligned_cols=50  Identities=24%  Similarity=0.480  Sum_probs=34.3

Q ss_pred             cccccccccCCCCC-----CCeeecCCCC-CcccccccccCCCCCCCcEEcCCCCCccc
Q psy128          276 VWICPACGVQDDGS-----LPMIGCDGCD-AWYHWVCVGLVAEPETSDWFCPKCSKVDE  328 (446)
Q Consensus       276 ~~~C~VCg~pdd~~-----~~mIqCD~C~-~WfH~~Cvg~~~~~~~~~w~Cp~C~~k~~  328 (446)
                      ...| +|...-+..     -.+|.|..|+ ..-|..|..+...  ...|.|..|.....
T Consensus        26 a~~C-lc~~GR~~~~~~~~W~ii~C~~CGS~gtH~~C~~l~~~--~~~y~C~~C~~v~~   81 (85)
T d1weqa_          26 APIC-LYEQGRDSFEDEGRWRLILCATCGSHGTHRDCSSLRPN--SKKWECNECLPASG   81 (85)
T ss_dssp             CSCC-CSTTCSSCCBSSSTTBCEECSSSCCCEECSGGGTCCTT--CSCCCCTTTSCCSS
T ss_pred             cccc-cCCCCccccCCCCcEEEEeecccCCccchhhhcCCcCC--CCCEECCcCcchhC
Confidence            4457 775422211     1489999999 8899999766433  34799999986543