Psyllid ID: psy3428

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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-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680--
Protein Sequence
MVTEVQIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHFYVLYVLSKGKIAGLFYL
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHcccccccccEEEEEEEccEEEEEEcccHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEccccccccccEEEccEEEccccccEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccccccccEEEcccHHHHHHHHHHHHHHHHHHHcccccccccccHHHHcccccHHHHHHHHHHHHHHHHcccccccccHHHccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccEEEEEccccccccEEEEEEEccEEEEccccccccccHHHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHcccccHHHHHHHHHHHHHHHHccccEEEEEEcccccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHcccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHcccccccccEEEEEEccccEEEEEccccHHHHHHHHHHHHHHHHHHHHHcccEEEcccccEEEEEEccccccccccEEEccEEEcccccEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccHHHHccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccEEEEEccccccccEEEEEEEEccccccccccccHHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccEEEccccccccccccccccccccccHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccHHHccccHHHccccccccccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEEEHHEHccccEEEEEEc
Coil and Loop (DISEMBL)
MVTEVQIHKVILMSLLFVGFAVTGvgmtcncdqdydlliIGRSKDLDLLLQRFQHTLDEihkwsdlngtifstdpgksvcidfnrlrnsrspalsyngiqLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYksftlpildygcfiygsaKDHVLNKLNTVHHAGIRIatgalrsspvvslyvdsgipplslRRSKLMLNYVSkvgaspfnpaqkilfdqdmsgftftinkpkplcvrykditafdnalesstfapymrftppwsnspppvdlslcdgkksdsapVVFQSLFREAINTkytshticytdgsktptttgcaysvgnvvrstllnpvnsiFSAELIAIFLCLEAildspsgkfliVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKkditfmwcpshcgikgneivdvaaknpttgttpfklctpedfKPFVTALMNSEWqnlwdnvpntnklktirpsikkditfmwcpshcgikgnelvdvaaknpttgttpfklctpedfKPFVTALMNSEWqslwdnvpntnklktirpsikvwktsdqdeigsprIENIIQLIRrgereeeeeeeeeeeeeeeeeeeeeeeeevqeeeeeeeeeeeeeeeeeeeeeeeeevrgggkeeiSLHFYVLYVLSkgkiaglfyl
Flexible Loop (DISEMBL)
MVTEVQIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSrspalsyngiqLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIAtgalrsspvVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHticytdgsktpttTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLaalsnvrfinpLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTgttpfklctpEDFKPFVTALMNSEWqnlwdnvpntnkLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAKNPTtgttpfklctpEDFKPFVTALMNSEWqslwdnvpntnklktirpsikvwktsdqdeigsprieNIIQLIrrgereeeeeeeeeeeeeeeeeeeeeeeeevqeeeeeeeeeeeeeeeeeeeeeeeeevrgggkeeiSLHFYVLYVLskgkiaglfyl
Low Complexity Region (SEG)
MVTEVQIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGereeeeeeeeeeeeeeeeeeeeeeeeevqeeeeeeeeeeeeeeeeeeeeeeeeeVRGGGKEEISLHFYVLYVLSKGKIAGLFYL
Disordered region (IsUnstruct)
****VQIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPW*******************APVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQSLWDNVPNTNKLKTIRPSIKVWKT**********IENIIQL****************************************************************************************
Disordered Region (DISOPRED)
*****QIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKN*T***TP*KLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCP**********************TPFKLCTPEDFKPFVTALMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGER**************************************************************LHFYVLYVLSKGKIAGLFYL
Disordered Region (DISEMBL)
MVTEVQIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIR*************************************************************KEEISLHFYVLYVLSKGKIAGLFYL
Disordered Region (DISPRO)
*VTEVQIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRG**********************************************************GKEEISLHFYVLYVLSKGKIAGLFYL
Transmembrane Helix (TMHMM)
iiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVTEVQIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGGGKEEISLHFYVLYVLSKGKIAGLFYL
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

No hits with e-value below 0.001 by BLAST

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	682
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.693	0.387	0.337	4e-65
427791807	1212	Putative tick transposon, partial [Rhipi	0.655	0.368	0.353	2e-59
427791321	1210	Putative tick transposon, partial [Rhipi	0.658	0.371	0.332	2e-55
427798889	1199	Putative tick transposon, partial [Rhipi	0.664	0.377	0.325	3e-55
427798887	1199	Putative tick transposon, partial [Rhipi	0.662	0.376	0.324	2e-53
427798885	1199	Putative tick transposon, partial [Rhipi	0.662	0.376	0.326	3e-53
427791063	1035	Putative tick transposon, partial [Rhipi	0.662	0.436	0.318	1e-51
427792011	1121	Putative tick transposon, partial [Rhipi	0.651	0.396	0.319	2e-51
427778603	1397	Putative tick transposon [Rhipicephalus	0.670	0.327	0.301	1e-48
427791981	1060	Putative tick transposon, partial [Rhipi	0.527	0.339	0.344	3e-44

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score =  255 bits (652), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 166/492 (33%), Positives = 255/492 (51%), Gaps = 19/492 (3%)

Query: 26   GMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNR 85
            G+ C+   D D +I+   K+++ L ++ Q  L++I  W++ NG  FS    K+V + F  
Sbjct: 656  GIECSLYVD-DFVILTYGKNMNTLERKLQLCLNKIQGWANYNGFKFSD--SKTVSMHFCN 712

Query: 86   LRNSR-SPALSYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCK 144
            LR     P L  +  ++  V +TKFLGLT D+K N+  HI+ LK +   SLN L+++S  
Sbjct: 713  LRGLHPDPELFIHKKKIPVVKTTKFLGLTLDSKFNFLPHIKELKKKCQKSLNILRVLSHT 772

Query: 145  KWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVV 204
             WG  R  LL  Y+S     LDYG  IYG+A+   L  L  + +A +R+  GA R+SP+ 
Sbjct: 773  DWGADRDTLLLLYRSLIRSKLDYGSIIYGAARKSYLKILEPIQNAALRLCLGAFRTSPIP 832

Query: 205  SLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFD-QDMSGFTFTINKPKPLCVR 263
            SL+V++G  P+ +R  KL + Y+ K+ ++P NPA   +F+  ++  +    N  +PL +R
Sbjct: 833  SLHVEAGELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVELYNRRPNVIQPLGLR 892

Query: 264  YKD-ITAFDNALE--SSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREA 320
             ++ I      ++  S    P     PPW  + P ++LSL + KK ++ P + Q  FRE 
Sbjct: 893  MREPIQNLTQPIDQISKIETPQ---NPPWLMNKPKLNLSLLNFKKENTDPSILQVHFRE- 948

Query: 321  INTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILD 380
            +   Y      YTDGSK      CA S  N   S  L    SIF+AEL AI L L A+  
Sbjct: 949  LQESYGDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKA 1008

Query: 381  SPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGN 440
            S   KF+I +DS+S+L AL  ++   PL+ K       +   ++D+TF+W PSH GI+GN
Sbjct: 1009 SERSKFIICSDSKSALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVGIEGN 1068

Query: 441  EIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKKD 500
            E  D  AK               D +  + +    EWQN W+     +KL+ I   ++  
Sbjct: 1069 EAADREAKRALNHAVSGTQIPYSDLRQSIASATYREWQNRWE-AETHSKLRQIVADVR-- 1125

Query: 501  ITFMWCPSHCGI 512
                W P+  G+
Sbjct: 1126 ----WRPTSKGL 1133

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|427791807|gb|JAA61355.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  237 bits (604), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 168/475 (35%), Positives = 248/475 (52%), Gaps = 28/475 (5%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNS-RSPAL 94
            DL I  R+  L    ++ Q T++++ KW+D NG  FST   K+  + F + R     PAL
Sbjct: 647  DLQIACRASSLSSCERQLQITINKLTKWADQNGFRFSTQ--KTTAVLFTQKRGLFPDPAL 704

Query: 95   SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLL 154
              N I L      KFLG+T+D K+N+  HI  LK +A  +LN LK++S K WG  R  LL
Sbjct: 705  KLNNIDLPVKREYKFLGVTFDQKLNFLSHINALKVKANKALNLLKVLSHKHWGSDRLCLL 764

Query: 155  RFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPP 214
            R Y+S    ILDYGC +YGSA++  + +L+ VH+ G+R+++GA R+SPV SLYVD   PP
Sbjct: 765  RIYRSIVRSILDYGCVVYGSARESYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNEPP 824

Query: 215  LSLRRSKLMLNYVSKVGASPFNPAQKILFD--QDMSGFTFTINKP---KPLCVRYKD--- 266
            LS RR+ L L+YV ++ +SP    Q I +D     S     +NK    KPL +R+++   
Sbjct: 825  LSHRRASLTLSYVLRIRSSP----QHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCR 880

Query: 267  -ITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKY 325
                 +  L+ +   P +   PPW +     D+SL    K  + P +    FR A+  KY
Sbjct: 881  TYVISEETLDVARKPPRI---PPWFDLAQLCDISLSHINKKVTPPELIIQEFR-ALQEKY 936

Query: 326  TSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGK 385
              +   YTDGSKT    G     G    S  +    SIF+AE+ A++     I+     K
Sbjct: 937  RDYAEFYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKK 996

Query: 386  FLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDIT--FMWCPSHCGIKGNEIV 443
             +I TDS S+L AL       PL+  + +    + +  K I+  F W PSH GI GNE  
Sbjct: 997  AIIYTDSLSALKALHIKSECEPLVGDILNM---VLINSKVISMRFCWVPSHVGIPGNEKA 1053

Query: 444  DVAAKNPTTGT-TPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSI 497
            D  A      T T  ++   +  +    AL+ ++WQ  WD+   +NKL  ++P++
Sbjct: 1054 DKCASLAAHKTLTKIRIPLKDSQRTIRLALL-AKWQQQWDSC-TSNKLHLVKPTL 1106

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791321|gb|JAA61112.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  223 bits (568), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 170/512 (33%), Positives = 251/512 (49%), Gaps = 63/512 (12%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFST----------------DPG--- 76
            DL I  R+  L    ++ Q T++++ KW+D NG  FST                DP    
Sbjct: 605  DLQIACRASSLSSCERQLQITINKLTKWADQNGFRFSTQKTTAVLFTQKRGLFPDPALKL 664

Query: 77   -----------KSVCIDFNRLRNSRS--------PALSYNGIQLKFVTSTKFLGLTWDAK 117
                       K + + F++  N           PAL  N I L      KFLG+T+D K
Sbjct: 665  NNIDLPVKREYKFLGVTFDQKLNFLXXXXXLFPDPALKLNNIGLPVKREYKFLGVTFDQK 724

Query: 118  MNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKD 177
            +N+  HI  LK +A  +LN LK++S K WG  R  LLR Y+S    ILDYGC +YGSA++
Sbjct: 725  LNFLSHINALKVKANKALNLLKVLSHKHWGSDRLCLLRIYRSIVRSILDYGCVVYGSARE 784

Query: 178  HVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNP 237
              + +L+ VH+ G+R+++GA R+SPV SLYVD   PPLS RR+ L L+YV ++ +SP   
Sbjct: 785  SYIRRLDPVHNLGLRLSSGAYRTSPVESLYVDCNEPPLSHRRASLTLSYVLRIRSSP--- 841

Query: 238  AQKILFD--QDMSGFTFTINKP---KPLCVRYKD----ITAFDNALESSTFAPYMRFTPP 288
             Q I +D     S     +NK    KPL +R+++        +  L+ +   P +   PP
Sbjct: 842  -QHICYDIATRCSSRLHYLNKSNLIKPLLLRFEEYCRTYVISEETLDVARKPPRI---PP 897

Query: 289  WSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSV 348
            W +     D+SL    K  + P +    FR A+  KY  +   YTDGSKT    G     
Sbjct: 898  WFDLAQLCDISLSHINKKVTPPELIIQEFR-ALQEKYRDYAEFYTDGSKTRDHVGIGIVT 956

Query: 349  GNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPL 408
            G    S  +    SIF+AE+ A++     I+     K +I TDS S+L AL       PL
Sbjct: 957  GESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIYTDSLSALKALHIKSECEPL 1016

Query: 409  ITKVYSTWSYLKLCKKDIT--FMWCPSHCGIKGNEIVDVAAKNPTTGT-TPFKLCTPEDF 465
            +  + +    + +  K I+  F W PSH GI GNE  D  A      T T  ++   +  
Sbjct: 1017 VGDILNM---VLINSKVISMRFCWVPSHVGIPGNEKADKCASLAAHKTLTKIRIPLKDSQ 1073

Query: 466  KPFVTALMNSEWQNLWDNVPNTNKLKTIRPSI 497
            +    AL+ ++WQ  WD+   +NKL  ++P++
Sbjct: 1074 RTIRLALL-AKWQQQWDSC-TSNKLHLVKPTL 1103

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798889|gb|JAA64896.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  223 bits (568), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 153/470 (32%), Positives = 234/470 (49%), Gaps = 17/470 (3%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSR-SPAL 94
            D+ +  +S +L +  ++ Q  L+++ KW+D NG  F  +P KS C+ F+R R     P +
Sbjct: 671  DVQLGSKSCNLAMCERQVQLALNKVSKWADENG--FKLNPQKSTCVLFSRKRGVHPDPDI 728

Query: 95   SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLL 154
              +G  L   T  KFLG+  D K+N+  HI+ +KN+ L ++N LK++S   WG  +  L+
Sbjct: 729  HLHGQHLSVKTEHKFLGIYLDTKLNFISHIKYIKNKCLKTMNILKVLSRTTWGSDKKCLM 788

Query: 155  RFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPP 214
              YKS     LDYG  IY SA    L  L+ VHH GIR++TGA R+SPV SLYV+S    
Sbjct: 789  NLYKSLIRTRLDYGAIIYQSASPTALKMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWS 848

Query: 215  LSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPK---PLCVRYKDITAFD 271
            L L+RS +   Y  KV A   +P+   +   D+S  T   N+P    P  +R +D+    
Sbjct: 849  LHLQRSYMSFLYYIKVNADKEHPSHSTI--NDLSCSTLFENRPSLKPPYSLRVRDLAEQT 906

Query: 272  N--ALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHT 329
                 E    AP   + PPW       D+S  +  K   AP+     +   +  KY    
Sbjct: 907  GLPLFEHRLMAP-AAYPPPWQWQLIDCDVSFMEVTK--HAPIAHIRTYFLELQHKYNCPA 963

Query: 330  ICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIV 389
              YTD SK+ T+   A    +   +  L+P  SIF+AE  AI   ++ I +    K +I 
Sbjct: 964  F-YTDASKSHTSVSYAAVGPSFSAAGALHPNTSIFTAEAYAILAAVKHIRELKLQKAVIY 1022

Query: 390  TDSRSSLAALSNV-RFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAK 448
            TDS S + AL  + +  NP++  +YS    +   K+ +   W P H  I+GN + D  A 
Sbjct: 1023 TDSLSVVKALKTLKKHRNPVLVSLYSLLCTIYTSKQHVVVCWVPGHREIQGNVMADQLAV 1082

Query: 449  NPTTGTTPFKLCTPE-DFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSI 497
            +    +    +  P  D KP++   + + WQ+ WD   + NKL  I+P +
Sbjct: 1083 SAHDSSANTSIAIPALDLKPYLKRKIRAYWQSTWDRQTH-NKLHVIKPQL 1131

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798887|gb|JAA64895.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  217 bits (552), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 153/471 (32%), Positives = 234/471 (49%), Gaps = 19/471 (4%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSR-SPAL 94
            D+ +  +S +L +  ++ Q  L+++ KW+D NG  F  +P KS C+ F+R R     P +
Sbjct: 671  DVQLGSKSCNLAMCERQVQLALNKVSKWADENG--FKLNPQKSTCVLFSRKRGVHPDPDI 728

Query: 95   SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLL 154
              +G  L   T  KFLG+  D K+N+  HI+ +KN+ L ++N LK++S   WG  +  L+
Sbjct: 729  HLHGQHLSVKTEHKFLGIYLDTKLNFISHIKYIKNKCLKTMNILKVLSRTTWGSDKKCLM 788

Query: 155  RFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPP 214
              YKS     LDYG  IY SA    L  L+ VHH GIR++TGA R+SPV SLYV+S    
Sbjct: 789  NLYKSLIRTRLDYGAIIYQSASPTALKMLDPVHHLGIRLSTGAFRTSPVESLYVESNEWS 848

Query: 215  LSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPK---PLCVRYKDITAFD 271
            L L+RS +   Y  KV A   +P+   +   D+S  T   N+P    P  +R + + A +
Sbjct: 849  LHLQRSYMSFLYYLKVNADKEHPSHSTI--NDLSSSTLFENRPSLRPPYSLRVRGL-AEE 905

Query: 272  NAL---ESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSH 328
              L   E    AP   + PPW       D+S  +  K   AP+     +   +  KY   
Sbjct: 906  TGLPLFEHRLMAP-AAYPPPWQWQLIDCDVSFMEVTK--HAPIAHIRTYFLELQHKYNCP 962

Query: 329  TICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLI 388
               YTD SK+ T+   A    +   +  L+P  SIF+AE  AI   ++ I +    K +I
Sbjct: 963  AF-YTDASKSHTSVSYAAVGPSFSAAGALHPNTSIFTAEAYAILAAVKHIRELKLQKAVI 1021

Query: 389  VTDSRSSLAALSNV-RFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAA 447
             TDS S + AL  + +  N ++  +YS    +   K+ +   W P H  I+GN + D  A
Sbjct: 1022 YTDSLSVVKALKTLKKHKNSILVSLYSLVCTVYTAKQHVVVCWVPGHREIQGNVMADHLA 1081

Query: 448  KNPTTGTTPFKLCTPE-DFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSI 497
             +    +    +  P  D KP +   + + WQ+ WD   + NKL  I+P +
Sbjct: 1082 ASTHDCSANTSIAIPALDLKPLLKRKLRAYWQSTWDQQTH-NKLHVIKPQL 1131

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427798885|gb|JAA64894.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  216 bits (550), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 154/471 (32%), Positives = 234/471 (49%), Gaps = 19/471 (4%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSR-SPAL 94
            D+ +  +S +L +  ++ Q  L++  KW+D NG  F  +P KS C+ F+R R     P +
Sbjct: 671  DVQLGSKSCNLAMCERQVQLGLNKFSKWADENG--FKLNPQKSTCVLFSRKRGVHPDPDI 728

Query: 95   SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLL 154
              +G +L   T  KFLGL  D K+N+  HIQ +KN+ L ++N LK++S   WG  +  L+
Sbjct: 729  HLHGQRLSVKTEHKFLGLYLDTKLNFISHIQYIKNKCLKTMNILKVLSRTTWGSDKKCLM 788

Query: 155  RFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPP 214
              YKS     LDYG  IY SA    L  L+ +HH GIR++TGA  +SPV SLYV+S    
Sbjct: 789  NLYKSLIRTCLDYGAIIYQSASPTALKMLDPIHHLGIRLSTGAFCTSPVESLYVESNEWS 848

Query: 215  LSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPK---PLCVRYKDITAFD 271
            L L+RS +   Y  KV A   +P+   +   D+S  T   N+P    P  +R + + A +
Sbjct: 849  LQLQRSYMSFLYYLKVNADKEHPSHSTI--NDLSSSTLFENRPSLRPPYSLRVRGL-AEE 905

Query: 272  NAL---ESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSH 328
              L   E    AP   + PPW       D+S  +  K   AP+     +   +  KY   
Sbjct: 906  TGLPLFEHRLMAP-AAYPPPWQWQLIDCDVSFMEVTK--HAPIAHIRTYFLELQHKYNCP 962

Query: 329  TICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLI 388
               YTD SK+ T+   A    +   + +L+P  SIF+AE  AI   ++ I +    K +I
Sbjct: 963  AF-YTDASKSHTSVSYAAVGPSFSDAGVLHPNTSIFTAEAYAILAAVKHIRELKLQKAVI 1021

Query: 389  VTDSRSSLAALSNV-RFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAA 447
             TDS S + AL  + +  N ++  +YS    L   K+ +   W P H  I+GN + D  A
Sbjct: 1022 YTDSLSVVKALKTLKKHKNSILVSLYSLVCTLYTAKQHVVVCWVPGHREIQGNVMADHLA 1081

Query: 448  KNPTTGTTPFKLCTPE-DFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSI 497
             +    +    +  P  D KP +   + + WQ+ WD   + NKL  I+P +
Sbjct: 1082 ASTHDCSANTSIAIPALDLKPLLKRKLRAYWQSTWDQQTH-NKLHVIKPQL 1131

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791063|gb|JAA60983.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  211 bits (536), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 150/471 (31%), Positives = 235/471 (49%), Gaps = 19/471 (4%)

Query: 36  DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRS-PAL 94
           D+ I  +S ++    ++ Q  L+++ KW++ NG  F  +P KS C+ FNR R   S P +
Sbjct: 505 DVQIGFKSCNISSCERQVQLALNKVSKWANENG--FKINPLKSSCVLFNRKRGLVSDPQV 562

Query: 95  SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLL 154
           + +G  ++     KFLG+  D+K+++  HI+ LK + L ++N LK++S   WG  R  L+
Sbjct: 563 NLDGQHIQINNEHKFLGVILDSKLSFIPHIKYLKTKCLKTMNILKILSHTTWGSDRKCLM 622

Query: 155 RFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPP 214
             YKS     LDYG  +Y SA    L  L+ +HH GIR+ATGA R+SPV SLYV+S    
Sbjct: 623 DIYKSLVRTRLDYGSVVYHSAAPSALKILDPIHHLGIRLATGAFRTSPVQSLYVESNQWS 682

Query: 215 LSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKP---KPLCVRYKDIT-AF 270
           L L+RS +   Y  KV A   +PA   +   D+S      N+P   +P  +R +D+    
Sbjct: 683 LHLQRSYMSFVYFLKVKAEKEHPAHSTV--NDLSSSVLYHNRPSVRQPYSLRVRDLAEEM 740

Query: 271 DNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTI 330
             +L   +      + PPW       D+S    + +  AP      +   +  KYT    
Sbjct: 741 GLSLHEHSLMARAAYLPPWQWQLIECDVSF--EQVTKHAPHAHIYTYFLELQHKYTFPEF 798

Query: 331 CYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAI--LDSPSGKFLI 388
            +TD SK  ++   A    +   + +L+   SIF+AE  AIF+ ++ I  L  PS   +I
Sbjct: 799 -FTDASKFNSSVSYAAVGPSFSDAGVLHQNTSIFTAEAYAIFVAVKHIEQLKLPSA--VI 855

Query: 389 VTDSRSSLAALSNV-RFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAA 447
            TDS S + AL  + +  NP++  +YS    +   K+ +   W P H  I+GN + D  A
Sbjct: 856 YTDSLSVVKALKTLKKHKNPVLASLYSLLCTVYALKQHVVVCWVPGHREIQGNVLADQLA 915

Query: 448 KNPTTGTTPFKLCTPE-DFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSI 497
            +         L  P  D KP +   + + WQ++WD     NKL  I+P +
Sbjct: 916 ASAHENAAHTFLAIPALDLKPLLKRKLRAYWQSIWD-TQTQNKLHAIKPQL 965

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427792011|gb|JAA61457.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  210 bits (534), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 149/467 (31%), Positives = 223/467 (47%), Gaps = 23/467 (4%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSR-SPAL 94
            D+ +  RS +L +  ++ Q  ++ + KW++ NG  F+ +  K+VC+ FN+ +  R +P +
Sbjct: 665  DVQVSFRSCNLSICERQIQLGVNRLSKWANENG--FAVNVDKTVCVLFNKCKGVRPAPCI 722

Query: 95   SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLL 154
              NG  +      KFLGL +D +M++  HI+ LK + L ++N LK++S   WG  +  L+
Sbjct: 723  KINGSPICVKNEHKFLGLIFDNRMSFIPHIKALKLKCLQTMNLLKLLSRPSWGTDKKCLM 782

Query: 155  RFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPP 214
              + S     L+YGC +Y SA    +  L+ V+H GIR+ATGA R+SPV SLYV++   P
Sbjct: 783  SLFNSLIKSRLNYGCIVYQSASKTAVKMLDPVYHLGIRLATGAFRTSPVSSLYVEANEWP 842

Query: 215  LSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKP---KPLCVRYKDITA-F 270
            + L R    L Y  KV + P +P  K++   D S   F   +P   KP  +      A  
Sbjct: 843  MQLEREYCTLMYTLKVTSIPTHPCAKLV--ADTSALRFFEKRPSLSKPFSLTCTATAAQA 900

Query: 271  DNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTI 330
            +  L+    AP M + PPW  +    D+S C   K        Q  F  ++  KY     
Sbjct: 901  EIPLQQVAKAPSMEWLPPWEKTRIKCDMSFCHIDKQRHPRAAIQQHFL-SLQYKYRGCHQ 959

Query: 331  CYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVT 390
             YTD SKT  +   A        S  LN   SIF+AE  AI + ++ IL+    K +I T
Sbjct: 960  FYTDASKTRDSVSAAAVGPEFTTSERLNVHTSIFTAEAYAILIAIKYILNHNITKSVIFT 1019

Query: 391  DSRSSLAALSNVR-FINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNE------IV 443
            DS S + AL   +   NP++  V    +       +IT  W P H GI GNE       V
Sbjct: 1020 DSLSVVRALHTGKPNKNPVLCDVEKQLTNAYRNTSEITVCWVPGHAGIDGNERADACAAV 1079

Query: 444  DVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNLWDNVPNTNKL 490
                 N    + P+     +D K  V   +   WQ  WD +   NKL
Sbjct: 1080 AAQKSNLDVNSVPY-----QDLKALVHRNLRERWQKEWD-LETNNKL 1120

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427778603|gb|JAA54753.1| Putative tick transposon [Rhipicephalus pulchellus]

 Score =  201 bits (511), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 158/524 (30%), Positives = 239/524 (45%), Gaps = 67/524 (12%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSR-SPAL 94
            D+ I  +S +L +  ++ Q  ++ + KW+D NG  F  +  K+ C+ F+R R     P +
Sbjct: 764  DIQISFKSCNLTICERQIQLGVNRLAKWADENG--FKINTEKTTCVLFSRRRGIHPDPCI 821

Query: 95   SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLL 154
              NG  L      KFLG+ +DAK+ +  HI+ LK + L ++N LK++S + WG  R  L+
Sbjct: 822  LMNGESLVIAKEQKFLGVIFDAKLTFIQHIKQLKLKCLKTMNLLKILSHQSWGTDRYCLI 881

Query: 155  RFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIPP 214
              ++S  L  +DYG  IY SA    L  L+ V+H GIR+A GA R+SPV SLY +S   P
Sbjct: 882  TLFRSLVLSRIDYGSIIYQSASKTALKLLDPVYHLGIRLALGAFRTSPVQSLYAESDQWP 941

Query: 215  LSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMSGFTFTINKPK-----PLCVR------ 263
            L  +R+ L + Y +++ +   +P + ++   D+S     IN+P      PL +R      
Sbjct: 942  LDYQRTYLGVTYATRIMSLKQHPCKSLM--NDVSTTQLYINRPSISPPFPLAIRPVVEKL 999

Query: 264  ---YKDITAFDN--------AL--ESSTFAPYMR-------------------------- 284
               ++D+   D         AL  + ST   Y+                           
Sbjct: 1000 KIHFEDLQEIDQVEXQHPCKALMNDVSTTQLYINRPSISPPFPLAIRPVVEKLKIHFEDL 1059

Query: 285  -------FTPPWSNSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSK 337
                     PPW   P   D S  D KK  +   + Q  F  A+  KY S    ++DGSK
Sbjct: 1060 QEIDQVEVIPPWKQCPIICDWSFKDLKKKTAPNALIQQHFL-ALEHKYRSAAF-FSDGSK 1117

Query: 338  TPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLA 397
            + T+  CA    +   +  L+   SIF+AE   I L +E I      + +I TDS S + 
Sbjct: 1118 SQTSVSCAAYGESFSDAKTLHAHTSIFTAEAYGILLIVEHIKQHMIRRSIIYTDSLSVVT 1177

Query: 398  ALSNVRFI-NPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTP 456
            ALS  +   NP+  K+ +           I   W P H GI GNE+VD  A+   +  T 
Sbjct: 1178 ALSCGKCSKNPVFNKLLNNMHEAYNQNLSIVLCWVPGHAGITGNEMVDKNAREAASRHTI 1237

Query: 457  FKLCTPE-DFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPSIKK 499
                 P  D  P V   + S WQ  WD   + NKL  ++P + K
Sbjct: 1238 DISSVPGVDLNPVVRRGLRSHWQVEWDKQVD-NKLHLVKPHLSK 1280

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427791981|gb|JAA61442.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  186 bits (473), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 137/398 (34%), Positives = 205/398 (51%), Gaps = 38/398 (9%)

Query: 36   DLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSR-SPAL 94
            DL I  RS ++    ++ Q  L+++ +W++ NG  FS +  K+V + F++ R  +  P L
Sbjct: 667  DLQIACRSSNMATCERQIQIALNKLTQWANKNGFRFSEE--KTVAVAFSQKRGLQPDPVL 724

Query: 95   SYNGIQLKFVTSTKFLGLTWDAKMNWSLHIQLLK---NRALN------------------ 133
              N   L      KFLG+ +D K+N+  HI  LK   N+ALN                  
Sbjct: 725  KLNETLLPIQHEQKFLGVIFDKKLNFLSHINKLKIKANKALNVLKVLSRKRWGSDXXKLK 784

Query: 134  -----SLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDHVLNKLNTVHH 188
                 +LN LK++S K+WG  R  LL  Y+S     LDYG  IYGSA+D  L +L+ VH+
Sbjct: 785  VKANKALNVLKVLSRKRWGSDRKCLLHIYRSLVRSKLDYGSIIYGSARDSYLKRLDPVHN 844

Query: 189  AGIRIATGALRSSPVVSLYVDSGIPPLSLRRSKLMLNYVSKVGASPFNPAQKILFDQDMS 248
             G+R+ATGA R+SP+ SLY +S  P L  RR++LM  YV KV +SP +    I+   D  
Sbjct: 845  KGLRLATGAYRTSPIPSLYAESNEPSLEYRRTQLMFTYVLKVRSSPDHICYSIVTRSDQR 904

Query: 249  GFTFTINKP---KPLCVRYKD-ITAFDNALESSTFAPYMRFTPPWSNSPPPVDLSLCDGK 304
                  NKP   KPL +R+++   A +   E+ + A   R   PWS+    +D SL   K
Sbjct: 905  --LHYANKPNAIKPLILRFEEKFHALNIPNEALSIAKRPRSLAPWSDFSMFLDFSLTHIK 962

Query: 305  KSDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNP-VNSI 363
            K  +        FR  +  KY +    YTDGSK     G +  VG +    +  P   S+
Sbjct: 963  KQGTPREHILQEFR-TLQEKYHTFNEFYTDGSKASAYVGSSV-VGEIYEEVVRLPQFVSV 1020

Query: 364  FSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSN 401
            ++AE  A+++ +  I++S   K +I +DS S+L ALS+
Sbjct: 1021 YTAECYALWIAVRNIINSNHKKAVIFSDSLSALRALSS 1058

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	682
ASPGD|ASPL0000055652	1054	AN0368 [Emericella nidulans (t	0.391	0.253	0.242	2.2e-10
ASPGD|ASPL0000077547	1581	AN8648 [Emericella nidulans (t	0.677	0.292	0.222	4e-08
ASPGD|ASPL0000033911	686	AN2796 [Emericella nidulans (t	0.412	0.409	0.208	4.5e-06
ASPGD|ASPL0000040226	1538	AN2661 [Emericella nidulans (t	0.302	0.133	0.217	2.5e-05
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.240	0.337	0.25	0.00039
ASPGD|ASPL0000037597	666	AN2711 [Emericella nidulans (t	0.542	0.555	0.217	0.0006

ASPGD|ASPL0000055652 AN0368 [Emericella nidulans (taxid:162425)]

 Score = 148 (57.2 bits), Expect = 2.2e-10, Sum P(2) = 2.2e-10
 Identities = 69/285 (24%), Positives = 122/285 (42%)

Query:    12 LMSLLFVGFAVTGV-GMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTI 70
             ++ LL+    V+ + G  C  D D  +L+ G +  L+   Q+      +I       G  
Sbjct:   562 ILFLLYAARIVSTLEGSFCYAD-DMGILLTGNT--LEESSQQLVEAYKQITALGTETGLP 618

Query:    71 FSTDPGKSVCIDFNRLRNSRSPALSYNGIQ-LKFVTSTKFLGLTWDAKMNWSLHIQLLKN 129
             FS +  K+    F+R +    P ++  GI  +     T++LG+  D K+ +  HI L+ +
Sbjct:   619 FSIE--KTEIQHFSRKQQQHLPTVTLPGIGGITPSLYTRWLGVLLDTKLTFKAHINLVFS 676

Query:   130 RALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIYGSAKDH--VLNKLNTVH 187
                     LK +S  + G   + +      + LP   YG  ++ + K    V+N L ++ 
Sbjct:   677 HGKRLAQHLKRLSNTQRGCPVAFMRAAVIQYVLPTALYGAEVFYTGKQQKGVVNSLLSLF 736

Query:   188 HAGIRIATGALRSSPVVSLYVDSGIP-PLSLRRSKLMLNYVSKVGASPFNPAQKILFDQD 246
                      A +++P  +L  ++ +P P +L  S L    VSK G  P  P  ++ +D +
Sbjct:   737 RTAALAIIPAYKTTPTAALLREADLPDPEALLNSILRRAAVSK-GHGPAGPRTEV-YDAE 794

Query:   247 MSGFTFTINKP--KPLCVRYKD--ITAFDNALESSTFAPYMRFTP 287
             + G    +     +P CV Y    +   DN   +S  A Y R TP
Sbjct:   795 IMGAVEGLRTALGQP-CVGYSTQLVILLDNLAAASLLASY-RPTP 837

GO:0005575 "cellular_component" evidence=ND

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

ASPGD|ASPL0000077547 AN8648 [Emericella nidulans (taxid:162425)]

 Score = 165 (63.1 bits), Expect = 4.0e-08, P = 4.0e-08
 Identities = 111/500 (22%), Positives = 195/500 (39%)

Query:    12 LMSLLFVGFAVTGV-GMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTI 70
             ++ LL+    V+ + G  C  D D  +L+ G +  L+   Q+      +I       G  
Sbjct:   995 ILFLLYAARIVSTLEGSFCYAD-DMGILLTGNT--LEESSQQLVEAYKQITALGTETGLP 1051

Query:    71 FSTDPGKSVCIDFNRLRNSRSPALSYNGI-QLKFVTSTKFLGLTWDAKMNWSLHIQLLKN 129
             FS +  K+    F+R +    P ++  GI ++     T++LG+  D K+ +  HI L+ +
Sbjct:  1052 FSIE--KTEIQHFSRKQQQHLPTVTLPGIGEITPSLYTRWLGVLLDTKLTFKAHINLVFS 1109

Query:   130 RALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIY--GSAKDHVLNKLNTVH 187
             R       LK +S  + G   + +        LP   YG  ++  G  +  V+N L ++ 
Sbjct:  1110 RGKRLAQHLKRLSNTQRGCPVASMRAAVIQCVLPTALYGAEVFYTGKRQKGVVNSLLSLF 1169

Query:   188 HAGIRIATGALRSSPVVSLYVDSGIP-PLSLRRSKLMLNYVSKVGASPFNPAQKILFDQD 246
                      A +++P  +L  ++ +P P +L  S L    V  +     +P  +I  +  
Sbjct:  1170 RTAALAIIPAYKTTPTAALLREADLPDPEALLNSILRRAAVRYMSLDTKHPIAQIAAET- 1228

Query:   247 MSGFTFTINKPKPLCVRYKDITAF---DNALESSTFAPY-MRFTPPWSNSPPPVDLSL-C 301
                   T  +PK    R   +      + A+      P  M  T     SP P+ +S+  
Sbjct:  1229 ------TAGRPKTRLKRILQLLLSPLPERAIIELPLPPLCMLPTDNKGYSPAPLQISVYS 1282

Query:   302 DGKK-SDSAPVVFQSLFREAINTKYTSHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPV 360
             DG + S  A   +   F   + +K   H      G +T             +R+ L  P 
Sbjct:  1283 DGSRTSQGAGYGYAIYFGPILVSK--GHGPA---GPRTEVYDAEIMGAVEGLRAALGQPC 1337

Query:   361 NSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLK 420
                +S +L+ +   L A     S +    T  R  L+        + L  +   + S L 
Sbjct:  1338 VG-YSTQLVILLDNLAAASLLASYR---PTPHRHGLSET-----FSQLAAQWMESPSILT 1388

Query:   421 LCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQNL 480
             + +K +   W P H GI GNE+ D  AK  ++  +P    +P   +      + +E    
Sbjct:  1389 MQRKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPDIPPSPAYLRREAKQWLRTETYTA 1448

Query:   481 WDN-VPNTNKLKTIRPSIKK 499
             + N  P T K   IRP  K+
Sbjct:  1449 YANKAPETYKALNIRPHTKE 1468

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000033911 AN2796 [Emericella nidulans (taxid:162425)]

 Score = 100 (40.3 bits), Expect = 4.5e-06, Sum P(3) = 4.5e-06
 Identities = 64/307 (20%), Positives = 126/307 (41%)

Query:    12 LMSLLFVGFAVTGVGMT-CNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTI 70
             ++ LL+    ++ +  + C  D D  +L+ G +  L+   Q+      +I       G  
Sbjct:   152 ILFLLYAARIISTLESSFCYAD-DMGILLTGNT--LEESSQQLVEAYKQITVLGTETGLP 208

Query:    71 FSTDPGKSVCIDFNRLRNSRSPALSYNGI-QLKFVTSTKFLGLTWDAKMNWSLHIQLLKN 129
             FS +  K+    F++ +    P ++  GI ++     T++LG+  D K+ +  HI  + +
Sbjct:   209 FSIE--KTEIQHFSKKQQQHFPIVTLPGIGEITPSLYTRWLGVLLDTKLTFKAHINWVFS 266

Query:   130 RALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIY--GSAKDHVLNKLNTVH 187
             R       LK +S  + G   + +        LP   YG  ++  G  +  V+N L ++ 
Sbjct:   267 RGKQLAQHLKRLSNTQRGCPVASMRAAVIQCVLPTALYGAEVFYTGKRQQWVVNSLLSLF 326

Query:   188 HAGIRIATGALRSSPVVSLYVDSGIP-PLSLRRSKLMLNYVSKVGASPFNPAQKILFDQD 246
                      A +++P  +L  ++ +P P +L  S L    V  +     +P  +I  +  
Sbjct:   327 RTAALAIIPAYKTTPTAALLREADLPDPEALFNSILRRAAVRYMSLDIKHPIAQIAAEA- 385

Query:   247 MSGFTFTINKPKPLCVRYKDITAFDNALESSTFA----PYMRFTPPWSN--SPPPVDLSL 300
                   T ++PK    R   +    + L   T      P +R  P  +   SP P+ +S+
Sbjct:   386 ------TTSRPKTRLKRILQLLL--SPLPERTIIGLPLPPLRMLPTDNKDYSPAPLQISV 437

Query:   301 -CDGKKS 306
               DG ++
Sbjct:   438 YSDGSRT 444

GO:0005575 "cellular_component" evidence=ND

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

ASPGD|ASPL0000040226 AN2661 [Emericella nidulans (taxid:162425)]

 Score = 98 (39.6 bits), Expect = 2.5e-05, Sum P(3) = 2.5e-05
 Identities = 47/216 (21%), Positives = 93/216 (43%)

Query:    12 LMSLLFVGFAVTGVGMT-CNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTI 70
             ++ LL+    V+ +  + C  D D  +L+ G +  L+   Q+      +I       G  
Sbjct:  1020 ILFLLYAARIVSTLESSFCYAD-DMGILLTGNT--LEESSQQLVEAYKQITVLGTETGLP 1076

Query:    71 FSTDPGKSVCIDFNRLRNSRSPALSYNGI-QLKFVTSTKFLGLTWDAKMNWSLHIQLLKN 129
             FS +  K+    F++ +    P ++  GI ++     T++LG+  D K+ +  HI  + +
Sbjct:  1077 FSIE--KTEIQHFSKKQQQHFPIVTLPGIGEITPSLYTRWLGVLLDTKLTFKAHINWVFS 1134

Query:   130 RALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGCFIY--GSAKDHVLNKLNTVH 187
             R       LK +S  + G   + +        LP   YG  ++  G  +  V+N L ++ 
Sbjct:  1135 RGKQLAQHLKRLSNTQRGCPVASMRAAVIQCVLPTALYGAEVFYTGKRQQWVVNSLLSLF 1194

Query:   188 HAGIRIATGALRSSPVVSLYVDSGIP-PLSLRRSKL 222
                      A +++P  +L  ++ +P P +L  S L
Sbjct:  1195 RTAALAIIPAYKTTPTAALLREADLPDPEALFNSIL 1230

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]

 Score = 122 (48.0 bits), Expect = 0.00039, P = 0.00039
 Identities = 44/176 (25%), Positives = 78/176 (44%)

Query:   332 YTDGSKTPTTTGCAYSVGN--VVRSTLLNPVN--SIFSAELIAIFLCLEAILDSPSGKFL 387
             YTDGS      G A       + RS+ +   +  +++ AEL  I L L  IL       +
Sbjct:   186 YTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILLALVIILQRQMQHAV 245

Query:   388 IVTDSRSSLAALSNVRFINP--LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDV 445
             I TD++++L AL N    +   ++  +    +  +    ++ F W P+H G++GNE  D 
Sbjct:   246 IFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADR 305

Query:   446 AAKNPTTGTTPFK-----LCTPEDFKPFVTALMNSEWQNLWDNVPNTNKLKTIRPS 496
              AK   TG    +     +      K     ++N+ W+N W +  +  +L  + P+
Sbjct:   306 RAKE-ATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHGRELYELTPT 360

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

ASPGD|ASPL0000037597 AN2711 [Emericella nidulans (taxid:162425)]

 Score = 122 (48.0 bits), Expect = 0.00060, P = 0.00060
 Identities = 88/405 (21%), Positives = 152/405 (37%)

Query:   110 LGLTWDAKMNWSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLPILDYGC 169
             +G+  D K+ +  HI  + +R       LK +S  + G   + +      + LP   YG 
Sbjct:   175 IGVLLDTKLTFKAHINWVFSRGKQLAQHLKRLSNTQRGCPVASMRAAVIQYVLPTALYGA 234

Query:   170 FIY--GSAKDHVLNKLNTVHHAGIRIATGALRSSPVVSLYVDSGIP-PLSLRRSKLMLNY 226
              ++  G  +  V+N L ++          A +++P  +L  ++ +P P +L  S L    
Sbjct:   235 EVFYTGKRQQWVVNSLLSLFRTAALAIIPAYKTTPTAALLREADLPDPEALFNSILQRAV 294

Query:   227 VSKVGASPFNPAQKILFDQDMSGFTFTINKPKPLCVRYKDITAFDNALESSTFA----PY 282
             V  +     +P  +I  +        T ++PK    R   +    + L   T      P 
Sbjct:   295 VRYMSLDIKHPIAQIAAEA-------TTSRPKTRLKRILQLLL--SPLPERTIIGLPLPP 345

Query:   283 MRFTPPWSN--SPPPVDLSL-CDGKKS-DSAPVVFQSLFREAINTKYTSHTICYTDGSKT 338
             +R  P  +   SP P+ +S+  DG ++   A   +   F   + TK   H      G +T
Sbjct:   346 LRMLPTDNKDYSPAPLQISVYSDGSRTGQGAGYGYAIYFGPILVTK--GHGPA---GPRT 400

Query:   339 PTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAA 398
                          +R+ L  P    +S +L+ +   L A     S +    T  R  L+ 
Sbjct:   401 EVYDAEIMGAVEGLRAALGQPCVG-YSTQLVILLDNLAAASLLASYR---PTPHRHGLS- 455

Query:   399 LSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFK 458
                      L T+     S L   +K +   W P H GI GNE+ D  AK  ++  +P  
Sbjct:   456 ----ESFGQLATQWLEAPSILTRPRKPLQVRWIPGHSGIAGNELADKLAKLGSSIYSPNI 511

Query:   459 LCTPEDFKPFVTALMNSEWQNLW-DNVPNTNKLKTIRPSIKKDIT 502
               +P   +      + +E    +    P   K   IRP  K+  T
Sbjct:   512 PPSPAYLRREAKQWLRTEAYTAYASKAPQAYKTLDIRPHTKESRT 556


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.136   0.423    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      682       628   0.00091  120 3  11 22  0.37    34
                                                     36  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  626 (67 KB)
  Total size of DFA:  369 KB (2179 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:01
  No. of threads or processors used:  24
  Search cpu time:  51.07u 0.15s 51.22t   Elapsed:  00:00:03
  Total cpu time:  51.07u 0.15s 51.22t   Elapsed:  00:00:04
  Start:  Thu Aug 15 16:41:11 2013   End:  Thu Aug 15 16:41:15 2013

GO:0006278 "RNA-dependent DNA replication" evidence=IEA

GO:0003964 "RNA-directed DNA polymerase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!
3rd Layer	3.1.26	0.691

---

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	682
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	1e-30
pfam00075	126	pfam00075, RNase_H, RNase H	3e-17
pfam04147	809	pfam04147, Nop14, Nop14-like family	3e-12
pfam04147	809	pfam04147, Nop14, Nop14-like family	4e-12
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-12
pfam03344	715	pfam03344, Daxx, Daxx Family	5e-12
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	6e-12
pfam04147	809	pfam04147, Nop14, Nop14-like family	1e-11
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-11
pfam09756	189	pfam09756, DDRGK, DDRGK domain	2e-11
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-11
pfam03344	715	pfam03344, Daxx, Daxx Family	3e-11
pfam03344	715	pfam03344, Daxx, Daxx Family	6e-11
pfam03344	715	pfam03344, Daxx, Daxx Family	6e-11
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	6e-11
pfam03344	715	pfam03344, Daxx, Daxx Family	7e-11
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	8e-11
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	8e-11
pfam03344	715	pfam03344, Daxx, Daxx Family	9e-11
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	9e-11
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-10
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	2e-10
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	2e-10
pfam05285	317	pfam05285, SDA1, SDA1	2e-10
pfam05285	317	pfam05285, SDA1, SDA1	2e-10
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	2e-10
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	2e-10
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	3e-10
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	3e-10
pfam02029	431	pfam02029, Caldesmon, Caldesmon	3e-10
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	4e-10
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	4e-10
pfam05285	317	pfam05285, SDA1, SDA1	4e-10
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	4e-10
pfam04147	809	pfam04147, Nop14, Nop14-like family	5e-10
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	5e-10
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	5e-10
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	6e-10
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	6e-10
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	7e-10
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	7e-10
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	8e-10
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	8e-10
pfam04147	809	pfam04147, Nop14, Nop14-like family	9e-10
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-09
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	1e-09
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	1e-09
pfam05285	317	pfam05285, SDA1, SDA1	1e-09
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	1e-09
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	1e-09
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-09
pfam09756	189	pfam09756, DDRGK, DDRGK domain	3e-09
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	3e-09
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	3e-09
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	3e-09
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-09
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-09
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-09
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	3e-09
pfam03985	431	pfam03985, Paf1, Paf1	3e-09
pfam03985	431	pfam03985, Paf1, Paf1	3e-09
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-09
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	4e-09
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	4e-09
pfam05285	317	pfam05285, SDA1, SDA1	4e-09
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	4e-09
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	4e-09
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	4e-09
pfam03985	431	pfam03985, Paf1, Paf1	4e-09
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	5e-09
pfam05285	317	pfam05285, SDA1, SDA1	5e-09
pfam05285	317	pfam05285, SDA1, SDA1	5e-09
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	5e-09
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	5e-09
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	5e-09
pfam04147	809	pfam04147, Nop14, Nop14-like family	6e-09
pfam09756	189	pfam09756, DDRGK, DDRGK domain	6e-09
pfam09756	189	pfam09756, DDRGK, DDRGK domain	6e-09
pfam05285	317	pfam05285, SDA1, SDA1	7e-09
pfam02029	431	pfam02029, Caldesmon, Caldesmon	7e-09
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	8e-09
pfam03985	431	pfam03985, Paf1, Paf1	8e-09
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	8e-09
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	9e-09
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	9e-09
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	9e-09
pfam03985	431	pfam03985, Paf1, Paf1	9e-09
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	9e-09
pfam09756	189	pfam09756, DDRGK, DDRGK domain	1e-08
pfam09756	189	pfam09756, DDRGK, DDRGK domain	1e-08
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	1e-08
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	1e-08
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	1e-08
pfam00183	529	pfam00183, HSP90, Hsp90 protein	1e-08
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	1e-08
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	1e-08
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-08
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-08
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	2e-08
pfam05285	317	pfam05285, SDA1, SDA1	2e-08
pfam02029	431	pfam02029, Caldesmon, Caldesmon	2e-08
pfam02029	431	pfam02029, Caldesmon, Caldesmon	2e-08
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	2e-08
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	2e-08
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	2e-08
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	2e-08
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	2e-08
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	2e-08
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	2e-08
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	2e-08
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-08
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-08
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	3e-08
COG2811	108	COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase su	3e-08
pfam11705	221	pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym	4e-08
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	4e-08
pfam05285	317	pfam05285, SDA1, SDA1	4e-08
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	4e-08
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	4e-08
pfam03344	715	pfam03344, Daxx, Daxx Family	5e-08
pfam05285	317	pfam05285, SDA1, SDA1	5e-08
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	5e-08
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	5e-08
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	5e-08
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	5e-08
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	5e-08
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	5e-08
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	5e-08
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	5e-08
pfam09756	189	pfam09756, DDRGK, DDRGK domain	6e-08
pfam09756	189	pfam09756, DDRGK, DDRGK domain	6e-08
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-08
pfam05285	317	pfam05285, SDA1, SDA1	6e-08
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	6e-08
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-08
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-08
pfam09756	189	pfam09756, DDRGK, DDRGK domain	8e-08
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	8e-08
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	8e-08
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	8e-08
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	8e-08
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	8e-08
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	9e-08
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	9e-08
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	9e-08
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-08
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	9e-08
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	1e-07
pfam05285	317	pfam05285, SDA1, SDA1	1e-07
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	1e-07
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-07
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-07
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	1e-07
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	1e-07
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	1e-07
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	1e-07
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-07
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-07
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	1e-07
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-07
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-07
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	2e-07
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	2e-07
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	2e-07
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	2e-07
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	2e-07
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-07
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	2e-07
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	2e-07
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	2e-07
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	2e-07
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	2e-07
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	2e-07
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	2e-07
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-07
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	2e-07
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	2e-07
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	2e-07
pfam05285	317	pfam05285, SDA1, SDA1	3e-07
pfam05285	317	pfam05285, SDA1, SDA1	3e-07
pfam02029	431	pfam02029, Caldesmon, Caldesmon	3e-07
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	3e-07
pfam03985	431	pfam03985, Paf1, Paf1	3e-07
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	3e-07
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	3e-07
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	3e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-07
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	3e-07
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	3e-07
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	3e-07
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	3e-07
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	3e-07
pfam09756	189	pfam09756, DDRGK, DDRGK domain	4e-07
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	4e-07
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	4e-07
pfam00183	529	pfam00183, HSP90, Hsp90 protein	4e-07
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	4e-07
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	4e-07
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	4e-07
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	4e-07
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	4e-07
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	4e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-07
pfam02724	583	pfam02724, CDC45, CDC45-like protein	4e-07
pfam11942	92	pfam11942, Spt5_N, Spt5 transcription elongation f	4e-07
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	4e-07
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	5e-07
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	5e-07
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	5e-07
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	5e-07
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	5e-07
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	5e-07
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	5e-07
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	6e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	6e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	6e-07
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	6e-07
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	6e-07
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	6e-07
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	7e-07
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	7e-07
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	7e-07
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	7e-07
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	7e-07
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	7e-07
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	7e-07
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	7e-07
pfam11942	92	pfam11942, Spt5_N, Spt5 transcription elongation f	7e-07
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	7e-07
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	7e-07
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-07
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	7e-07
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	8e-07
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	8e-07
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	8e-07
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	9e-07
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	9e-07
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	9e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	9e-07
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	9e-07
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	9e-07
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	9e-07
pfam04147	809	pfam04147, Nop14, Nop14-like family	1e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-06
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	1e-06
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	1e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-06
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	1e-06
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	1e-06
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	1e-06
PRK04019	330	PRK04019, rplP0, acidic ribosomal protein P0; Vali	1e-06
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	1e-06
pfam11942	92	pfam11942, Spt5_N, Spt5 transcription elongation f	1e-06
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	1e-06
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	1e-06
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	1e-06
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	1e-06
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	1e-06
TIGR02926	85	TIGR02926, AhaH, ATP synthase archaeal, H subunit	1e-06
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	1e-06
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	1e-06
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-06
pfam03344	715	pfam03344, Daxx, Daxx Family	2e-06
pfam09756	189	pfam09756, DDRGK, DDRGK domain	2e-06
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	2e-06
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	2e-06
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	2e-06
pfam09747	178	pfam09747, DUF2052, Coiled-coil domain containing	2e-06
pfam03985	431	pfam03985, Paf1, Paf1	2e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-06
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	2e-06
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	2e-06
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	2e-06
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	2e-06
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	2e-06
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	2e-06
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	2e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-06
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	2e-06
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	2e-06
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	2e-06
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	2e-06
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	2e-06
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	2e-06
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	2e-06
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	2e-06
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	2e-06
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	2e-06
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	2e-06
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	2e-06
pfam11748	115	pfam11748, DUF3306, Protein of unknown function (D	2e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	2e-06
pfam00075	126	pfam00075, RNase_H, RNase H	3e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	3e-06
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	3e-06
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	3e-06
pfam03247	106	pfam03247, Prothymosin, Prothymosin/parathymosin f	3e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-06
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	3e-06
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	3e-06
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	3e-06
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	3e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-06
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	3e-06
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	3e-06
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	3e-06
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	3e-06
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	3e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-06
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	3e-06
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	3e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-06
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	3e-06
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-06
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	3e-06
COG5238	388	COG5238, RNA1, Ran GTPase-activating protein (RanG	3e-06
pfam09184	285	pfam09184, PPP4R2, PPP4R2	3e-06
pfam02029	431	pfam02029, Caldesmon, Caldesmon	4e-06
pfam02029	431	pfam02029, Caldesmon, Caldesmon	4e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	4e-06
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	4e-06
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-06
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	4e-06
pfam11942	92	pfam11942, Spt5_N, Spt5 transcription elongation f	4e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-06
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	4e-06
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	4e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	4e-06
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	4e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	5e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	5e-06
pfam02029	431	pfam02029, Caldesmon, Caldesmon	5e-06
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	5e-06
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	5e-06
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	5e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	5e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	5e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	5e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-06
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	5e-06
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	5e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	5e-06
pfam09184	285	pfam09184, PPP4R2, PPP4R2	5e-06
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	5e-06
COG5129	303	COG5129, MAK16, Nuclear protein with HMG-like acid	5e-06
pfam01271	585	pfam01271, Granin, Granin (chromogranin or secreto	5e-06
pfam09756	189	pfam09756, DDRGK, DDRGK domain	6e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-06
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	6e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	6e-06
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	6e-06
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	6e-06
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	6e-06
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	6e-06
pfam09184	285	pfam09184, PPP4R2, PPP4R2	6e-06
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	6e-06
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	6e-06
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	6e-06
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	7e-06
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	7e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	7e-06
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	7e-06
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	7e-06
PTZ00423	193	PTZ00423, PTZ00423, glideosome-associated protein	7e-06
pfam09736	141	pfam09736, Bud13, Pre-mRNA-splicing factor of RES	7e-06
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	8e-06
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	8e-06
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	8e-06
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	8e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	8e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	8e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	8e-06
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	8e-06
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	9e-06
PRK14891	131	PRK14891, PRK14891, 50S ribosomal protein L24e/unk	9e-06
pfam03985	431	pfam03985, Paf1, Paf1	9e-06
pfam03985	431	pfam03985, Paf1, Paf1	9e-06
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	9e-06
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	9e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-06
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	9e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	9e-06
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	9e-06
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	9e-06
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	9e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	9e-06
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	9e-06
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	9e-06
cd02988	192	cd02988, Phd_like_VIAF, Phosducin (Phd)-like famil	9e-06
pfam04147	809	pfam04147, Nop14, Nop14-like family	1e-05
pfam03344	715	pfam03344, Daxx, Daxx Family	1e-05
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	1e-05
pfam07133	164	pfam07133, Merozoite_SPAM, Merozoite surface prote	1e-05
pfam09756	189	pfam09756, DDRGK, DDRGK domain	1e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-05
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	1e-05
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	1e-05
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-05
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	1e-05
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	1e-05
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-05
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	1e-05
pfam11861	154	pfam11861, DUF3381, Domain of unknown function (DU	1e-05
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	1e-05
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	1e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	1e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	1e-05
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	1e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	1e-05
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	1e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	1e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	1e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	1e-05
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	1e-05
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	1e-05
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-05
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	1e-05
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	1e-05
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	1e-05
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	1e-05
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	1e-05
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	1e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	1e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	1e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	1e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	1e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-05
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	1e-05
pfam09073	424	pfam09073, BUD22, BUD22	1e-05
PRK06669	281	PRK06669, fliH, flagellar assembly protein H; Vali	1e-05
pfam04615	728	pfam04615, Utp14, Utp14 protein	1e-05
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	1e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-05
pfam07946	322	pfam07946, DUF1682, Protein of unknown function (D	1e-05
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	1e-05
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	1e-05
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	1e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	1e-05
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	1e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-05
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	2e-05
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	2e-05
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	2e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	2e-05
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	2e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	2e-05
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	2e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	2e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	2e-05
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	2e-05
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	2e-05
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	2e-05
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-05
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	2e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	2e-05
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	2e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	2e-05
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	2e-05
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	2e-05
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	2e-05
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	2e-05
cd02988	192	cd02988, Phd_like_VIAF, Phosducin (Phd)-like famil	2e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-05
PRK06007	542	PRK06007, fliF, flagellar MS-ring protein; Reviewe	2e-05
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	2e-05
PRK08404	103	PRK08404, PRK08404, V-type ATP synthase subunit H;	2e-05
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	2e-05
pfam11831	363	pfam11831, Myb_Cef, pre-mRNA splicing factor compo	2e-05
pfam11831	363	pfam11831, Myb_Cef, pre-mRNA splicing factor compo	2e-05
COG1579	239	COG1579, COG1579, Zn-ribbon protein, possibly nucl	2e-05
pfam05285	317	pfam05285, SDA1, SDA1	3e-05
pfam02029	431	pfam02029, Caldesmon, Caldesmon	3e-05
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-05
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	3e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-05
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	3e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	3e-05
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	3e-05
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	3e-05
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	3e-05
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	3e-05
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	3e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	3e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	3e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	3e-05
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	3e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-05
COG5238	388	COG5238, RNA1, Ran GTPase-activating protein (RanG	3e-05
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	3e-05
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	3e-05
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	3e-05
cd02988	192	cd02988, Phd_like_VIAF, Phosducin (Phd)-like famil	3e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-05
pfam11831	363	pfam11831, Myb_Cef, pre-mRNA splicing factor compo	3e-05
pfam11831	363	pfam11831, Myb_Cef, pre-mRNA splicing factor compo	3e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	3e-05
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	3e-05
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	3e-05
COG3351	214	COG3351, FlaD, Putative archaeal flagellar protein	3e-05
PRK12298	390	PRK12298, obgE, GTPase CgtA; Reviewed	3e-05
pfam00183	529	pfam00183, HSP90, Hsp90 protein	4e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-05
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-05
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	4e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	4e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-05
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	4e-05
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	4e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	4e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	4e-05
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	4e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	4e-05
COG4499	434	COG4499, COG4499, Predicted membrane protein [Func	4e-05
pfam09073	424	pfam09073, BUD22, BUD22	4e-05
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	4e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	4e-05
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	4e-05
COG3351	214	COG3351, FlaD, Putative archaeal flagellar protein	4e-05
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	4e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	4e-05
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	4e-05
pfam03343	603	pfam03343, SART-1, SART-1 family	4e-05
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	4e-05
PRK13108	460	PRK13108, PRK13108, prolipoprotein diacylglyceryl	4e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-05
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	5e-05
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	5e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-05
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-05
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	5e-05
TIGR02926	85	TIGR02926, AhaH, ATP synthase archaeal, H subunit	5e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	5e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	5e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	5e-05
pfam09184	285	pfam09184, PPP4R2, PPP4R2	5e-05
PTZ00423	193	PTZ00423, PTZ00423, glideosome-associated protein	5e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	5e-05
PRK12298	390	PRK12298, obgE, GTPase CgtA; Reviewed	5e-05
pfam06512	230	pfam06512, Na_trans_assoc, Sodium ion transport-as	5e-05
smart00784	106	smart00784, SPT2, SPT2 chromatin protein	5e-05
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	5e-05
pfam02029	431	pfam02029, Caldesmon, Caldesmon	6e-05
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-05
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	6e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	6e-05
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	6e-05
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	6e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	6e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	6e-05
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	6e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-05
smart00784	106	smart00784, SPT2, SPT2 chromatin protein	6e-05
pfam09745	128	pfam09745, DUF2040, Coiled-coil domain-containing	6e-05
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	6e-05
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	6e-05
COG1317	234	COG1317, FliH, Flagellar biosynthesis/type III sec	6e-05
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	6e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	7e-05
PRK12329	449	PRK12329, nusA, transcription elongation factor Nu	7e-05
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	7e-05
COG2811	108	COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase su	7e-05
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	7e-05
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	7e-05
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	7e-05
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	7e-05
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	7e-05
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	7e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	7e-05
pfam11748	115	pfam11748, DUF3306, Protein of unknown function (D	7e-05
pfam11748	115	pfam11748, DUF3306, Protein of unknown function (D	7e-05
pfam04615	728	pfam04615, Utp14, Utp14 protein	7e-05
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-05
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	7e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-05
PRK12298	390	PRK12298, obgE, GTPase CgtA; Reviewed	7e-05
COG3064	387	COG3064, TolA, Membrane protein involved in colici	7e-05
PRK02292	188	PRK02292, PRK02292, V-type ATP synthase subunit E;	7e-05
TIGR03825	255	TIGR03825, FliH_bacil, flagellar assembly protein	7e-05
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	8e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-05
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	8e-05
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	8e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	8e-05
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	8e-05
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	8e-05
pfam09073	424	pfam09073, BUD22, BUD22	8e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	8e-05
PRK12298	390	PRK12298, obgE, GTPase CgtA; Reviewed	8e-05
pfam03343	603	pfam03343, SART-1, SART-1 family	8e-05
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	8e-05
pfam05835	139	pfam05835, Synaphin, Synaphin protein	8e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	9e-05
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	9e-05
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	9e-05
pfam02459	548	pfam02459, Adeno_terminal, Adenoviral DNA terminal	9e-05
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	9e-05
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	9e-05
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	9e-05
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	9e-05
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	9e-05
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	9e-05
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	9e-05
COG5167	776	COG5167, VID27, Protein involved in vacuole import	9e-05
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	9e-05
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	1e-04
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	1e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	1e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	1e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-04
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	1e-04
PTZ00248	319	PTZ00248, PTZ00248, eukaryotic translation initiat	1e-04
pfam00183	529	pfam00183, HSP90, Hsp90 protein	1e-04
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	1e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	1e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	1e-04
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	1e-04
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	1e-04
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	1e-04
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	1e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	1e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	1e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	1e-04
pfam14265	125	pfam14265, DUF4355, Domain of unknown function (DU	1e-04
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	1e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	1e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	1e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	1e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	1e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	1e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	1e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	1e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	1e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	1e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	1e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	1e-04
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	1e-04
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	1e-04
pfam09073	424	pfam09073, BUD22, BUD22	1e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	1e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	1e-04
pfam11831	363	pfam11831, Myb_Cef, pre-mRNA splicing factor compo	1e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	1e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	1e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	1e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	1e-04
pfam03343	603	pfam03343, SART-1, SART-1 family	1e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	1e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	1e-04
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	1e-04
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	1e-04
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	1e-04
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	1e-04
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	1e-04
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	1e-04
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	1e-04
PRK05687	246	PRK05687, fliH, flagellar assembly protein H; Vali	1e-04
TIGR03779	410	TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative	1e-04
pfam12118	261	pfam12118, SprA-related, SprA-related family	1e-04
pfam09110	109	pfam09110, HAND, HAND	1e-04
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	1e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	2e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	2e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-04
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	2e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	2e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	2e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	2e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	2e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	2e-04
PRK12585	197	PRK12585, PRK12585, putative monovalent cation/H+	2e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	2e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	2e-04
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	2e-04
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	2e-04
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	2e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	2e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	2e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	2e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	2e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	2e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	2e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	2e-04
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	2e-04
pfam08597	242	pfam08597, eIF3_subunit, Translation initiation fa	2e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	2e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	2e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	2e-04
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	2e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	2e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	2e-04
pfam09507	427	pfam09507, CDC27, DNA polymerase subunit Cdc27	2e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	2e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	2e-04
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	2e-04
pfam09073	424	pfam09073, BUD22, BUD22	2e-04
PRK06669	281	PRK06669, fliH, flagellar assembly protein H; Vali	2e-04
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	2e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	2e-04
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	2e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	2e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	2e-04
pfam11831	363	pfam11831, Myb_Cef, pre-mRNA splicing factor compo	2e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	2e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	2e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-04
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	2e-04
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	2e-04
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	2e-04
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	2e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	2e-04
COG5167	776	COG5167, VID27, Protein involved in vacuole import	2e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	2e-04
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	2e-04
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	2e-04
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	2e-04
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	2e-04
pfam10156	454	pfam10156, Med17, Subunit 17 of Mediator complex	2e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	2e-04
pfam06246	253	pfam06246, Isy1, Isy1-like splicing family	2e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	2e-04
PRK14145	196	PRK14145, PRK14145, heat shock protein GrpE; Provi	2e-04
PRK14145	196	PRK14145, PRK14145, heat shock protein GrpE; Provi	2e-04
pfam12446	133	pfam12446, DUF3682, Protein of unknown function (D	2e-04
pfam07222	243	pfam07222, PBP_sp32, Proacrosin binding protein sp	2e-04
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	2e-04
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	2e-04
PRK12903	925	PRK12903, secA, preprotein translocase subunit Sec	2e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	2e-04
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	2e-04
pfam13476	204	pfam13476, AAA_23, AAA domain	2e-04
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	2e-04
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	2e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	3e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	3e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	3e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	3e-04
PRK14140	191	PRK14140, PRK14140, heat shock protein GrpE; Provi	3e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	3e-04
pfam04774	106	pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA bindi	3e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	3e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	3e-04
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	3e-04
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	3e-04
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	3e-04
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	3e-04
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	3e-04
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	3e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	3e-04
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	3e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-04
TIGR03685	105	TIGR03685, L12P_arch, 50S ribosomal protein L12P	3e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	3e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	3e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	3e-04
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	3e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	3e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	3e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	3e-04
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	3e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	3e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	3e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	3e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	3e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	3e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	3e-04
TIGR03825	255	TIGR03825, FliH_bacil, flagellar assembly protein	3e-04
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	3e-04
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	3e-04
pfam09110	109	pfam09110, HAND, HAND	3e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	3e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	3e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	3e-04
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	3e-04
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	3e-04
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	3e-04
pfam04111	356	pfam04111, APG6, Autophagy protein Apg6	3e-04
pfam05340	565	pfam05340, DUF740, Protein of unknown function (DU	3e-04
COG1390	194	COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase su	3e-04
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	3e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	4e-04
pfam02029	431	pfam02029, Caldesmon, Caldesmon	4e-04
COG3343	175	COG3343, RpoE, DNA-directed RNA polymerase, delta	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	4e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	4e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	4e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	4e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	4e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	4e-04
pfam06213	282	pfam06213, CobT, Cobalamin biosynthesis protein Co	4e-04
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	4e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	4e-04
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	4e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	4e-04
PTZ00423	193	PTZ00423, PTZ00423, glideosome-associated protein	4e-04
PTZ00423	193	PTZ00423, PTZ00423, glideosome-associated protein	4e-04
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	4e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	4e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	4e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	4e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	4e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	4e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	4e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	4e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	4e-04
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	4e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	4e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	4e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	4e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	4e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	4e-04
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	4e-04
COG3351	214	COG3351, FlaD, Putative archaeal flagellar protein	4e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	4e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	4e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	4e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	4e-04
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	4e-04
PRK14145	196	PRK14145, PRK14145, heat shock protein GrpE; Provi	4e-04
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	4e-04
pfam09731	493	pfam09731, Mitofilin, Mitochondrial inner membrane	4e-04
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	5e-04
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	5e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	5e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	5e-04
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	5e-04
PRK06402	106	PRK06402, rpl12p, 50S ribosomal protein L12P; Revi	5e-04
pfam09184	285	pfam09184, PPP4R2, PPP4R2	5e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	5e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	5e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	5e-04
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	5e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	5e-04
pfam04615	728	pfam04615, Utp14, Utp14 protein	5e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	5e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	5e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	5e-04
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	5e-04
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	5e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	5e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	5e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-04
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	5e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	5e-04
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	5e-04
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	5e-04
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	5e-04
PRK14145	196	PRK14145, PRK14145, heat shock protein GrpE; Provi	5e-04
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	5e-04
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	5e-04
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	5e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	5e-04
pfam03344	715	pfam03344, Daxx, Daxx Family	6e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	6e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	6e-04
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	6e-04
pfam05672	171	pfam05672, MAP7, MAP7 (E-MAP-115) family	6e-04
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	6e-04
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	6e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	6e-04
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	6e-04
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	6e-04
pfam05887	145	pfam05887, Trypan_PARP, Procyclic acidic repetitiv	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	6e-04
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	6e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	6e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	6e-04
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	6e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	6e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	6e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	6e-04
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	6e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	6e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	6e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	6e-04
PRK00409	782	PRK00409, PRK00409, recombination and DNA strand e	6e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	6e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	6e-04
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	6e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	6e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	6e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	6e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	6e-04
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	6e-04
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	6e-04
pfam08243	116	pfam08243, SPT2, SPT2 chromatin protein	6e-04
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	6e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	6e-04
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	7e-04
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	7e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	7e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	7e-04
pfam14153	185	pfam14153, Spore_coat_CotO, Spore coat protein Cot	7e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	7e-04
PHA00435	306	PHA00435, PHA00435, capsid assembly protein	7e-04
pfam08553	794	pfam08553, VID27, VID27 cytoplasmic protein	7e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	7e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	7e-04
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	7e-04
COG5406	1001	COG5406, COG5406, Nucleosome binding factor SPN, S	7e-04
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	7e-04
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	7e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	7e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	7e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	7e-04
pfam03343	603	pfam03343, SART-1, SART-1 family	7e-04
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	7e-04
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	7e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	7e-04
COG3064	387	COG3064, TolA, Membrane protein involved in colici	7e-04
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	7e-04
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	7e-04
pfam05758	832	pfam05758, Ycf1, Ycf1	7e-04
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	7e-04
pfam06658	142	pfam06658, DUF1168, Protein of unknown function (D	7e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	8e-04
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	8e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	8e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	8e-04
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	8e-04
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	8e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	8e-04
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	8e-04
pfam03896	281	pfam03896, TRAP_alpha, Translocon-associated prote	8e-04
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	8e-04
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	8e-04
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	8e-04
pfam09110	109	pfam09110, HAND, HAND	8e-04
pfam06246	253	pfam06246, Isy1, Isy1-like splicing family	8e-04
pfam05340	565	pfam05340, DUF740, Protein of unknown function (DU	8e-04
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	8e-04
pfam03962	188	pfam03962, Mnd1, Mnd1 family	8e-04
CHL00204	1832	CHL00204, ycf1, Ycf1; Provisional	8e-04
COG1667	254	COG1667, COG1667, Uncharacterized protein conserve	8e-04
pfam12757	126	pfam12757, DUF3812, Protein of unknown function (D	8e-04
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	8e-04
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	8e-04
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	9e-04
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	9e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	9e-04
PRK14145	196	PRK14145, PRK14145, heat shock protein GrpE; Provi	9e-04
pfam09731	493	pfam09731, Mitofilin, Mitochondrial inner membrane	9e-04
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	9e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.001
pfam02029	431	pfam02029, Caldesmon, Caldesmon	0.001
pfam02029	431	pfam02029, Caldesmon, Caldesmon	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.001
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	0.001
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	0.001
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.001
PHA03169	413	PHA03169, PHA03169, hypothetical protein; Provisio	0.001
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.001
pfam09538	104	pfam09538, FYDLN_acid, Protein of unknown function	0.001
TIGR02926	85	TIGR02926, AhaH, ATP synthase archaeal, H subunit	0.001
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.001
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.001
pfam14181	155	pfam14181, YqfQ, YqfQ-like protein	0.001
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.001
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.001
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.001
cd05832	106	cd05832, Ribosomal_L12p, Ribosomal protein L12p	0.001
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.001
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.001
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	0.001
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	0.001
pfam06991	277	pfam06991, Prp19_bind, Splicing factor, Prp19-bind	0.001
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	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
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	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
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	0.001
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.001
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.001
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.001
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.001
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.001
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.001
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
pfam03343	603	pfam03343, SART-1, SART-1 family	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.001
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.001
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.001
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.001
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.001
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.001
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.001
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.001
COG5167	776	COG5167, VID27, Protein involved in vacuole import	0.001
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.001
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	0.001
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	0.001
pfam12118	261	pfam12118, SprA-related, SprA-related family	0.001
pfam09110	109	pfam09110, HAND, HAND	0.001
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	0.001
pfam05758	832	pfam05758, Ycf1, Ycf1	0.001
PRK14145	196	PRK14145, PRK14145, heat shock protein GrpE; Provi	0.001
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	0.001
PRK13406	584	PRK13406, bchD, magnesium chelatase subunit D; Pro	0.001
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.001
pfam05340	565	pfam05340, DUF740, Protein of unknown function (DU	0.001
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.001
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.001
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.001
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.001
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.001
pfam03962	188	pfam03962, Mnd1, Mnd1 family	0.001
pfam12757	126	pfam12757, DUF3812, Protein of unknown function (D	0.001
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	0.001
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	0.001
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	0.001
COG5177	769	COG5177, COG5177, Uncharacterized conserved protei	0.001
COG5163	591	COG5163, NOP7, Protein required for biogenesis of	0.001
pfam11711	377	pfam11711, Tim54, Inner membrane protein import co	0.001
pfam11711	377	pfam11711, Tim54, Inner membrane protein import co	0.001
PRK04456	463	PRK04456, PRK04456, acetyl-CoA decarbonylase/synth	0.001
PRK04456	463	PRK04456, PRK04456, acetyl-CoA decarbonylase/synth	0.001
PRK14149	191	PRK14149, PRK14149, heat shock protein GrpE; Provi	0.001
pfam05395	170	pfam05395, DARPP-32, Protein phosphatase inhibitor	0.001
pfam05395	170	pfam05395, DARPP-32, Protein phosphatase inhibitor	0.001
pfam08703	181	pfam08703, PLC-beta_C, PLC-beta C terminal	0.001
cd01650	220	cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long term	0.001
COG5296	521	COG5296, COG5296, Transcription factor involved in	0.001
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	0.001
pfam04921	233	pfam04921, XAP5, XAP5, circadian clock regulator	0.001
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.002
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.002
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.002
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.002
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.002
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.002
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.002
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	0.002
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	0.002
COG5414	392	COG5414, COG5414, TATA-binding protein-associated	0.002
pfam05432	291	pfam05432, BSP_II, Bone sialoprotein II (BSP-II)	0.002
pfam04874	97	pfam04874, Mak16, Mak16 protein C-terminal region	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.002
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.002
pfam09805	134	pfam09805, Nop25, Nucleolar protein 12 (25kDa)	0.002
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	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
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.002
COG0576	193	COG0576, GrpE, Molecular chaperone GrpE (heat shoc	0.002
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	0.002
PRK02363	129	PRK02363, PRK02363, DNA-directed RNA polymerase su	0.002
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
pfam10243	506	pfam10243, MIP-T3, Microtubule-binding protein MIP	0.002
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	0.002
TIGR01651	600	TIGR01651, CobT, cobaltochelatase, CobT subunit	0.002
cd02988	192	cd02988, Phd_like_VIAF, Phosducin (Phd)-like famil	0.002
pfam09073	424	pfam09073, BUD22, BUD22	0.002
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.002
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	0.002
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	0.002
TIGR02907	338	TIGR02907, spore_VI_D, stage VI sporulation protei	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
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.002
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.002
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.002
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.002
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.002
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.002
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.002
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	0.002
COG3351	214	COG3351, FlaD, Putative archaeal flagellar protein	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
pfam03343	603	pfam03343, SART-1, SART-1 family	0.002
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.002
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.002
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.002
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.002
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.002
pfam14283	213	pfam14283, DUF4366, Domain of unknown function (DU	0.002
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.002
PRK02292	188	PRK02292, PRK02292, V-type ATP synthase subunit E;	0.002
TIGR03825	255	TIGR03825, FliH_bacil, flagellar assembly protein	0.002
pfam05835	139	pfam05835, Synaphin, Synaphin protein	0.002
COG5167	776	COG5167, VID27, Protein involved in vacuole import	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.002
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	0.002
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.002
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.002
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.002
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.002
pfam09110	109	pfam09110, HAND, HAND	0.002
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	0.002
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	0.002
PRK14156	177	PRK14156, PRK14156, heat shock protein GrpE; Provi	0.002
pfam05758	832	pfam05758, Ycf1, Ycf1	0.002
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.002
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.002
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.002
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.002
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.002
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.002
PRK09202	470	PRK09202, nusA, transcription elongation factor Nu	0.002
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.002
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.002
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.002
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.002
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.002
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.002
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.002
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	0.002
COG1667	254	COG1667, COG1667, Uncharacterized protein conserve	0.002
pfam12757	126	pfam12757, DUF3812, Protein of unknown function (D	0.002
pfam12757	126	pfam12757, DUF3812, Protein of unknown function (D	0.002
pfam12757	126	pfam12757, DUF3812, Protein of unknown function (D	0.002
PRK04456	463	PRK04456, PRK04456, acetyl-CoA decarbonylase/synth	0.002
PRK14149	191	PRK14149, PRK14149, heat shock protein GrpE; Provi	0.002
PRK14149	191	PRK14149, PRK14149, heat shock protein GrpE; Provi	0.002
pfam05395	170	pfam05395, DARPP-32, Protein phosphatase inhibitor	0.002
PHA02608	80	PHA02608, 67, prohead core protein; Provisional	0.002
PHA02608	80	PHA02608, 67, prohead core protein; Provisional	0.002
PHA02608	80	PHA02608, 67, prohead core protein; Provisional	0.002
PHA02608	80	PHA02608, 67, prohead core protein; Provisional	0.002
pfam05558	201	pfam05558, DREPP, DREPP plasma membrane polypeptid	0.002
pfam12720	169	pfam12720, DUF3807, Protein of unknown function (D	0.002
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.002
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.002
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.002
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.002
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.002
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.002
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.002
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.002
pfam12527	100	pfam12527, DUF3727, Protein of unknown function (D	0.002
PRK14520	155	PRK14520, rpsP, 30S ribosomal protein S16; Provisi	0.002
pfam05178	99	pfam05178, Kri1, KRI1-like family	0.002
pfam13300	88	pfam13300, DUF4078, Domain of unknown function (DU	0.002
pfam03286	198	pfam03286, Pox_Ag35, Pox virus Ag35 surface protei	0.002
cd09277	133	cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI	0.002
pfam14303	147	pfam14303, NAM-associated, No apical meristem-asso	0.002
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	0.002
pfam04712	481	pfam04712, Radial_spoke, Radial spokehead-like pro	0.003
COG5137	279	COG5137, COG5137, Histone chaperone involved in ge	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	0.003
pfam04006	613	pfam04006, Mpp10, Mpp10 protein	0.003
pfam05793	528	pfam05793, TFIIF_alpha, Transcription initiation f	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
pfam02463	1162	pfam02463, SMC_N, RecF/RecN/SMC N terminal domain	0.003
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.003
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.003
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.003
pfam01271	585	pfam01271, Granin, Granin (chromogranin or secreto	0.003
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.003
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	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
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
PRK14521	186	PRK14521, rpsP, 30S ribosomal protein S16; Provisi	0.003
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.003
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.003
COG2058	109	COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP	0.003
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	0.003
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.003
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.003
PRK14150	193	PRK14150, PRK14150, heat shock protein GrpE; Provi	0.003
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.003
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.003
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.003
COG1614	470	COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthas	0.003
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	0.003
pfam07222	243	pfam07222, PBP_sp32, Proacrosin binding protein sp	0.003
TIGR01554	384	TIGR01554, major_cap_HK97, phage major capsid prot	0.003
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.003
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.003
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.003
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.003
pfam00428	88	pfam00428, Ribosomal_60s, 60s Acidic ribosomal pro	0.003
PRK05306	746	PRK05306, infB, translation initiation factor IF-2	0.003
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	0.003
pfam12757	126	pfam12757, DUF3812, Protein of unknown function (D	0.003
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	0.003
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	0.003
PLN00152	130	PLN00152, PLN00152, DNA-directed RNA polymerase; P	0.003
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	0.003
COG5163	591	COG5163, NOP7, Protein required for biogenesis of	0.003
PRK04456	463	PRK04456, PRK04456, acetyl-CoA decarbonylase/synth	0.003
PRK14520	155	PRK14520, rpsP, 30S ribosomal protein S16; Provisi	0.003
pfam03286	198	pfam03286, Pox_Ag35, Pox virus Ag35 surface protei	0.003
pfam14303	147	pfam14303, NAM-associated, No apical meristem-asso	0.003
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	0.003
pfam04281	136	pfam04281, Tom22, Mitochondrial import receptor su	0.003
cd09280	150	cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase	0.003
COG2268	548	COG2268, COG2268, Uncharacterized protein conserve	0.003
pfam09845	121	pfam09845, DUF2072, Zn-ribbon containing protein (	0.003
COG0711	161	COG0711, AtpF, F0F1-type ATP synthase, subunit b [	0.003
pfam11719	397	pfam11719, Drc1-Sld2, DNA replication and checkpoi	0.003
PRK12766	232	PRK12766, PRK12766, 50S ribosomal protein L32e; Pr	0.003
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	0.004
pfam02029	431	pfam02029, Caldesmon, Caldesmon	0.004
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.004
PLN03142	1033	PLN03142, PLN03142, Probable chromatin-remodeling	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
PTZ00121	2084	PTZ00121, PTZ00121, MAEBL; Provisional	0.004
pfam11081	172	pfam11081, DUF2890, Protein of unknown function (D	0.004
pfam07423	214	pfam07423, DUF1510, Protein of unknown function (D	0.004
PTZ00341	1136	PTZ00341, PTZ00341, Ring-infected erythrocyte surf	0.004
PTZ00438	374	PTZ00438, PTZ00438, gamete antigen 27/25-like prot	0.004
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	0.004
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	0.004
PTZ00423	193	PTZ00423, PTZ00423, glideosome-associated protein	0.004
pfam04615	728	pfam04615, Utp14, Utp14 protein	0.004
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
pfam05279	240	pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylas	0.004
TIGR02794	346	TIGR02794, tolA_full, TolA protein	0.004
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	0.004
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	0.004
pfam12253	76	pfam12253, CAF1A, Chromatin assembly factor 1 subu	0.004
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
pfam04502	321	pfam04502, DUF572, Family of unknown function (DUF	0.004
pfam12619	145	pfam12619, MCM2_N, Mini-chromosome maintenance pro	0.004
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.004
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.004
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.004
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.004
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.004
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.004
COG5271	4600	COG5271, MDN1, AAA ATPase containing von Willebran	0.004
pfam00769	244	pfam00769, ERM, Ezrin/radixin/moesin family	0.004
TIGR03779	410	TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative	0.004
pfam12446	133	pfam12446, DUF3682, Protein of unknown function (D	0.004
pfam12446	133	pfam12446, DUF3682, Protein of unknown function (D	0.004
pfam05340	565	pfam05340, DUF740, Protein of unknown function (DU	0.004
COG1390	194	COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase su	0.004
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.004
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.004
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.004
PRK05299	258	PRK05299, rpsB, 30S ribosomal protein S2; Provisio	0.004
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.004
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.004
pfam13025	70	pfam13025, DUF3886, Protein of unknown function (D	0.004
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	0.004
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	0.004
pfam02841	297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	0.004
COG5163	591	COG5163, NOP7, Protein required for biogenesis of	0.004
COG5163	591	COG5163, NOP7, Protein required for biogenesis of	0.004
PRK04456	463	PRK04456, PRK04456, acetyl-CoA decarbonylase/synth	0.004
PHA02608	80	PHA02608, 67, prohead core protein; Provisional	0.004
pfam05558	201	pfam05558, DREPP, DREPP plasma membrane polypeptid	0.004
pfam03032	46	pfam03032, Brevenin, Brevenin/esculentin/gaegurin/	0.004
pfam08432	182	pfam08432, DUF1742, Fungal protein of unknown func	0.004
PRK14520	155	PRK14520, rpsP, 30S ribosomal protein S16; Provisi	0.004
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	0.004
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	0.004
pfam04281	136	pfam04281, Tom22, Mitochondrial import receptor su	0.004
COG2268	548	COG2268, COG2268, Uncharacterized protein conserve	0.004
pfam05327	554	pfam05327, RRN3, RNA polymerase I specific transcr	0.004
TIGR02031	589	TIGR02031, BchD-ChlD, magnesium chelatase ATPase s	0.004
COG5019	373	COG5019, CDC3, Septin family protein [Cell divisio	0.004
TIGR00600	1034	TIGR00600, rad2, DNA excision repair protein (rad2	0.004
pfam05470	593	pfam05470, eIF-3c_N, Eukaryotic translation initia	0.004
PHA03089	191	PHA03089, PHA03089, late transcription factor VLTF	0.004
pfam05914	379	pfam05914, RIB43A, RIB43A	0.004
PRK14715	1627	PRK14715, PRK14715, DNA polymerase II large subuni	0.004
smart00937	116	smart00937, PCRF, This domain is found in peptide	0.004

>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score =  116 bits (292), Expect = 1e-30
 Identities = 44/124 (35%), Positives = 63/124 (50%), Gaps = 5/124 (4%)

Query: 330 ICYTDGSKTPTTTGCAYSV---GNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSG-- 384
           + YTDGSK    TG  +++   G + RS  L P  S+F AEL+AI   L+  L       
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 385 KFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
           K  I +DS+++L AL + R  +PL+ ++      L      +   W P H GI+GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 445 VAAK 448
             AK
Sbjct: 121 RLAK 124

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 78.1 bits (193), Expect = 3e-17
 Identities = 38/125 (30%), Positives = 49/125 (39%), Gaps = 9/125 (7%)

Query: 328 HTICYTDGS--KTPTTTGCAYSV-GNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSG 384
               YTDGS    P   G  Y   G   RS  L P  +   AEL+A+   +EA+      
Sbjct: 3   AVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLAL---IEALEALSGQ 58

Query: 385 KFLIVTDSRSSL-AALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIV 443
           K  I TDS+  +    +     +         W  L   K  +   W P H GI GNE+ 
Sbjct: 59  KVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW-ELLQKKHKVYIQWVPGHSGIPGNELA 117

Query: 444 DVAAK 448
           D  AK
Sbjct: 118 DKLAK 122

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 69.3 bits (170), Expect = 3e-12
 Identities = 27/54 (50%), Positives = 46/54 (85%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + EEEE+  ++E+EE+++++ EEEEE+V   +EEE+EE+E+ ++E++EEEEEEE
Sbjct: 322 DEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEE 375

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 69.3 bits (170), Expect = 4e-12
 Identities = 32/84 (38%), Positives = 58/84 (69%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           D D+   P  ++   L +  E EEEEE+  ++E+EE+++++ EEEEE  +  +EEE+EE+
Sbjct: 301 DLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEED 360

Query: 639 EEEEEEEEEEEEEEVRGGGKEEIS 662
           E+ ++E++EEEEEE +   K++ +
Sbjct: 361 EDSDDEDDEEEEEEEKEKKKKKSA 384

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

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

 Score = 68.8 bits (169), Expect = 4e-12
 Identities = 33/78 (42%), Positives = 55/78 (70%), Gaps = 4/78 (5%)

Query: 579 DQDEI----GSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
            ++EI    GS +    I+ I     ++ EEE++E++++    +++EEEEE ++E++EEE
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEE 454

Query: 635 EEEEEEEEEEEEEEEEEE 652
           +EEEEEE EEE+EEEEE+
Sbjct: 455 KEEEEEEAEEEKEEEEEK 472

Length = 482

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 68.8 bits (168), Expect = 5e-12
 Identities = 36/53 (67%), Positives = 40/53 (75%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           +E EEEE  EEEEEEEEEEEEE QE EEEE E+EEEEEE E +   EEE+ G 
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGS 489

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 64.1 bits (156), Expect = 6e-12
 Identities = 29/69 (42%), Positives = 48/69 (69%), Gaps = 4/69 (5%)

Query: 589 ENII----QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           E+II     +    + ++EEEEEE+EEE EE E+ E+EEE V++EEEEEE+EE+  + ++
Sbjct: 34  EDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKD 93

Query: 645 EEEEEEEEV 653
            E++   ++
Sbjct: 94  IEKKNINDI 102

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 67.7 bits (166), Expect = 1e-11
 Identities = 26/68 (38%), Positives = 47/68 (69%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
                 E E+  ++E+EE+++++ EEEEE+ +   EEE+EE+E+ ++E++EEEEEEE+E+
Sbjct: 319 GEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEK 378

Query: 653 VRGGGKEE 660
            +    E 
Sbjct: 379 KKKKSAES 386

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 66.5 bits (162), Expect = 2e-11
 Identities = 35/51 (68%), Positives = 40/51 (78%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +E EEEE  EEEEEEEEEEEEEE+E +EEE E+EEEEEE E +   EEE E
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEME 487

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 63.2 bits (154), Expect = 2e-11
 Identities = 30/57 (52%), Positives = 42/57 (73%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           RR +RE EEEE EE ++ EE+ E E +EEE  EEE E+++EEEE +E EE+  +E+E
Sbjct: 17  RRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQE 73

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 67.3 bits (164), Expect = 2e-11
 Identities = 33/86 (38%), Positives = 44/86 (51%), Gaps = 11/86 (12%)

Query: 577 TSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE-----------EEEEE 625
           T   ++                + E  E+E   E + E +++E+           + EEE
Sbjct: 807 TEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEE 866

Query: 626 VQEEEEEEEEEEEEEEEEEEEEEEEE 651
            +EEEEEEEEEEEEEEEEEEEEE EE
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 66.1 bits (161), Expect = 3e-11
 Identities = 35/51 (68%), Positives = 39/51 (76%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +E EEEE  EEEEEEEEEEEEEE+  EEEE E+EEEEEE E +   EEE E
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEME 487

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 65.3 bits (159), Expect = 6e-11
 Identities = 34/55 (61%), Positives = 39/55 (70%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           +E EEEE  EEEEEEEEEEEE ++E EEEE E+EEEEEE E +   EE   G  E
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSE 491

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 65.3 bits (159), Expect = 6e-11
 Identities = 38/62 (61%), Positives = 43/62 (69%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E EEEE  EEEEEEEEEEEEEE+E EE + E+EEEEEE E +   EEE E   E  G G+
Sbjct: 438 ESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGE 497

Query: 659 EE 660
           E 
Sbjct: 498 EP 499

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 64.8 bits (158), Expect = 6e-11
 Identities = 31/83 (37%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 572 IKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEE 631
           IK     DQ+   +   E I Q   R E E  + E EE  E E+ E  EE+    +    
Sbjct: 370 IKDSAEYDQEAEDAKVAELISQ---REEEEALQREAEERLEAEQAERAEEDARLRELYPL 426

Query: 632 EEEEEEEEEEEEEEEEEEEEEVR 654
            E+E E+E+E EE + EEEEE R
Sbjct: 427 PEDEFEDEDELEEAQPEEEEEAR 449

Length = 449

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 64.9 bits (158), Expect = 7e-11
 Identities = 40/77 (51%), Positives = 45/77 (58%), Gaps = 11/77 (14%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE-----------EE 646
            E EE  EEEEEEEEEEEEEE+E EEEE ++EEEEEE E +   EEE           EE
Sbjct: 439 SEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEE 498

Query: 647 EEEEEEVRGGGKEEISL 663
            EE+ E R      IS 
Sbjct: 499 PEEDAERRNSEMAGISR 515

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 65.4 bits (159), Expect = 8e-11
 Identities = 31/59 (52%), Positives = 40/59 (67%), Gaps = 4/59 (6%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEE----EEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           GE+E   E + E +++E+  +        + E +EEEEEEEEEEEEEEEEEEEEEEE E
Sbjct: 833 GEQELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENE 891

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 62.1 bits (151), Expect = 8e-11
 Identities = 25/57 (43%), Positives = 43/57 (75%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + G   EEEE+ +E+    E++ +E E E+V EE+E++EEEEEEEEEE+E+ +++++
Sbjct: 138 KVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDD 194

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 64.5 bits (157), Expect = 9e-11
 Identities = 33/52 (63%), Positives = 38/52 (73%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            +  EEEE  EEEEEEEEEEEEEE+E E +E E+EEEEEE E +   EEE E
Sbjct: 436 SQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEME 487

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 59.6 bits (144), Expect = 9e-11
 Identities = 20/55 (36%), Positives = 33/55 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E E  + +E+ +E  E +  +E +EEE  +E  +E  +E + E EE +EEE+EE 
Sbjct: 75  EAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEA 129

Length = 131

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 63.9 bits (155), Expect = 2e-10
 Identities = 32/59 (54%), Positives = 38/59 (64%), Gaps = 2/59 (3%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++ E+  +     +  + EEEEEEEEEEEE  EEEEEEEEEEEEEE EE    E  E R
Sbjct: 846 KQDEKGVDGGGGSDGGDSEEEEEEEEEEEE--EEEEEEEEEEEEEENEEPLSLEWPETR 902

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 60.5 bits (147), Expect = 2e-10
 Identities = 22/55 (40%), Positives = 41/55 (74%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           EEEE+ +E+    E++ +E E E+  +E+E++EEEEEEEEEE+E+ ++++++   
Sbjct: 144 EEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDDD 198

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 60.5 bits (147), Expect = 2e-10
 Identities = 20/52 (38%), Positives = 38/52 (73%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            E  +E+    E++ +E E E+ +EE+E  EEEEEEEEEE+E+ ++++++++
Sbjct: 146 EEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDD 197

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 62.4 bits (152), Expect = 2e-10
 Identities = 22/66 (33%), Positives = 42/66 (63%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           ++ E E+  E +++++EEEE E EE+E+ + + E  + E ++E E  + E+EEE++E   
Sbjct: 84  KKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAK 143

Query: 656 GGKEEI 661
             KE+ 
Sbjct: 144 KAKEDS 149

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 62.4 bits (152), Expect = 2e-10
 Identities = 22/65 (33%), Positives = 40/65 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
            R ++E E+  E +++++EEEE E EE+E+  +E E  + E ++E E  + E+EEE+   
Sbjct: 82  ERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEA 141

Query: 656 GGKEE 660
             K +
Sbjct: 142 AKKAK 146

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

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

 Score = 60.5 bits (147), Expect = 2e-10
 Identities = 22/66 (33%), Positives = 36/66 (54%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
             +E ++ + E  EE+  +E E +EE+  +EE+ E EE E+EE  E+ EE  E      K
Sbjct: 1   MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELK 60

Query: 659 EEISLH 664
           +E +  
Sbjct: 61  DENNKL 66

Length = 211

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 63.2 bits (154), Expect = 2e-10
 Identities = 35/85 (41%), Positives = 41/85 (48%), Gaps = 29/85 (34%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEV-----------------------------QE 628
            E EEEEEEEE  E +E EE  + E  EV                             Q+
Sbjct: 288 EEEEEEEEEEEPAERDELEENPDFEGLEVRELADSLDNWVHHVQHILPQGRCTWVNPEQK 347

Query: 629 EEEEEEEEEEEEEEEEEEEEEEEEV 653
           +EEEE+E+EEEEEEEEE EE E E 
Sbjct: 348 DEEEEQEDEEEEEEEEEPEEPEPEE 372

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 60.2 bits (146), Expect = 3e-10
 Identities = 20/57 (35%), Positives = 42/57 (73%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +   E E+ +E+    E++ +E E E+ +EE +++EEEEEEEEEE+E+ ++++++++
Sbjct: 141 LFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDD 197

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 58.4 bits (141), Expect = 3e-10
 Identities = 18/55 (32%), Positives = 32/55 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E  E  + +E+ +E  E +  +E +EE + +E  +E  +E + E EE +EEE+E
Sbjct: 73  AEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDE 127

Length = 131

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 62.7 bits (152), Expect = 3e-10
 Identities = 29/70 (41%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE--EEEEEEEVRG 655
           G   E  EEEE+EE  EE EE EE E   + E++ +  + EE ++EE+  E EEEE+ + 
Sbjct: 105 GAENETVEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKR 164

Query: 656 GGKEEISLHF 665
           G  EE +  F
Sbjct: 165 GSLEENNGEF 174

Length = 431

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 63.1 bits (153), Expect = 4e-10
 Identities = 36/99 (36%), Positives = 49/99 (49%), Gaps = 27/99 (27%)

Query: 581 DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEE----------------- 623
           DE    ++E+  +     + E E + E + ++ E ++E  E+E                 
Sbjct: 794 DEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVD 853

Query: 624 ----------EEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
                     EE +EEEEEEEEEEEEEEEEEEEEEE EE
Sbjct: 854 GGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 58.0 bits (140), Expect = 4e-10
 Identities = 20/54 (37%), Positives = 33/54 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E  + +E+ +E  E +  +E +EEEE  +  +E  +E + E EE +EEE+EE E
Sbjct: 77  EAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEAE 130

Length = 131

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 61.6 bits (150), Expect = 4e-10
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 8/73 (10%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEE--------VQEEEEEEEEEEEEEEEEEEEE 647
           R+ +  E+  E +++++EEEE E EE+E+         V+ ++E E  + E+EEE++E  
Sbjct: 83  RKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAA 142

Query: 648 EEEEEVRGGGKEE 660
           ++ +E       E
Sbjct: 143 KKAKEDSDEELSE 155

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 57.3 bits (138), Expect = 4e-10
 Identities = 28/54 (51%), Positives = 36/54 (66%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E EE   +E ++E EEEEEV E++EEEE E EEEE EEEEE E    +   ++E
Sbjct: 38  ENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDE 91

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 62.3 bits (152), Expect = 5e-10
 Identities = 23/61 (37%), Positives = 48/61 (78%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           ++E+EE+++++ EEEEE+ +  +EE  EE+E+ ++E++EEEEEEE+E+++++     + E
Sbjct: 331 DDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRSE 390

Query: 661 I 661
           +
Sbjct: 391 L 391

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 57.7 bits (139), Expect = 5e-10
 Identities = 20/65 (30%), Positives = 30/65 (46%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
                  E  EE E  + +E+ +E  E +   E +EEEE +E  +E  +E + E EE   
Sbjct: 64  AAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADE 123

Query: 656 GGKEE 660
              EE
Sbjct: 124 EEDEE 128

Length = 131

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 58.5 bits (142), Expect = 5e-10
 Identities = 24/56 (42%), Positives = 38/56 (67%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            E E ++ EE+EE  EE+E++E  +EEEV   ++E++EE + EEE+     +EEEV
Sbjct: 3   SESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEV 58

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 59.4 bits (144), Expect = 6e-10
 Identities = 21/54 (38%), Positives = 41/54 (75%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E EE+ +E+    E++ +E E E+ +E  E++EEEEEEEEEE+E+ ++++++++
Sbjct: 144 EEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDD 197

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 59.4 bits (144), Expect = 6e-10
 Identities = 24/57 (42%), Positives = 41/57 (71%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R+     EEEE+ +E+    E++ +E E E  +EE+E++EEEEEEEEEE+E+ ++++
Sbjct: 137 RKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDD 193

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 57.3 bits (138), Expect = 7e-10
 Identities = 21/52 (40%), Positives = 33/52 (63%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           + +E+ +E  E +  +E +EEEE +E V E  +E + E EE +EEE+EE E 
Sbjct: 80  DADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEAEA 131

Length = 131

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 56.5 bits (136), Expect = 7e-10
 Identities = 28/55 (50%), Positives = 34/55 (61%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E EE   +E ++E EEEEE  +++EEEE E EEEE EEEEE E     R    EE
Sbjct: 38  ENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEE 92

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 61.9 bits (150), Expect = 8e-10
 Identities = 34/91 (37%), Positives = 45/91 (49%), Gaps = 17/91 (18%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEE--------- 629
           D+   G    E   +   + E E + E + ++ E ++E  E+E   E Q E         
Sbjct: 794 DEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVD 853

Query: 630 --------EEEEEEEEEEEEEEEEEEEEEEE 652
                   + EEEEEEEEEEEEEEEEEEEEE
Sbjct: 854 GGGGSDGGDSEEEEEEEEEEEEEEEEEEEEE 884

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 58.2 bits (141), Expect = 8e-10
 Identities = 22/55 (40%), Positives = 34/55 (61%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           GE +EE  EE+E++E  +EEE +  ++E  EE + EEE+     +EEE + E E 
Sbjct: 10  GEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEA 64

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 61.6 bits (150), Expect = 9e-10
 Identities = 24/67 (35%), Positives = 48/67 (71%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E   ++E+EE+++++ EEEEE+ +  + +E+EE+E+ ++E++EEEEEEE+E+++ +    
Sbjct: 327 EDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAES 386

Query: 659 EEISLHF 665
               L F
Sbjct: 387 TRSELPF 393

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 61.5 bits (149), Expect = 1e-09
 Identities = 35/102 (34%), Positives = 47/102 (46%), Gaps = 27/102 (26%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE------------------ 630
           E     +      E  E++E E + E + ++ E ++E  E+E                  
Sbjct: 795 EGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDG 854

Query: 631 ---------EEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
                    EEEEEEEEEEEEEEEEEEEEEE     +E +SL
Sbjct: 855 GGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSL 896

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 56.5 bits (136), Expect = 1e-09
 Identities = 20/53 (37%), Positives = 32/53 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
              +E+ +E  E +  +E +EEEE +E  +E  +E + E EE +EEE+EE E 
Sbjct: 79  ADADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEAEA 131

Length = 131

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 56.5 bits (136), Expect = 1e-09
 Identities = 19/52 (36%), Positives = 32/52 (61%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + +E+ +E  E +  +E +EEEE +   +E  +E + E EE +EEE+EE E 
Sbjct: 80  DADEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEAEA 131

Length = 131

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 60.1 bits (146), Expect = 1e-09
 Identities = 23/80 (28%), Positives = 49/80 (61%), Gaps = 5/80 (6%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE----EEEEEE 643
           I  + +L+ + + EE +++E E+  E +++++EEEE EV+E+E+ ++E E    E ++E 
Sbjct: 69  IPGL-ELLEKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEI 127

Query: 644 EEEEEEEEEVRGGGKEEISL 663
           E  + E+EE +    ++   
Sbjct: 128 ESSDSEDEEEKDEAAKKAKE 147

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

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

 Score = 58.2 bits (141), Expect = 1e-09
 Identities = 20/52 (38%), Positives = 34/52 (65%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
              EE+  +E E +EE++ +EE+ E EE+++EE  E+ EE  E + EE ++E
Sbjct: 11  ENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDE 62

Length = 211

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 60.8 bits (148), Expect = 1e-09
 Identities = 34/87 (39%), Positives = 43/87 (49%), Gaps = 29/87 (33%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQ-----------------------------EE 629
             EEEEEEEEEE  E +E EE  + E ++                             E+
Sbjct: 287 LEEEEEEEEEEEPAERDELEENPDFEGLEVRELADSLDNWVHHVQHILPQGRCTWVNPEQ 346

Query: 630 EEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           ++EEEE+E+EEEEEEEEE EE E   G
Sbjct: 347 KDEEEEQEDEEEEEEEEEPEEPEPEEG 373

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 60.3 bits (146), Expect = 2e-09
 Identities = 33/50 (66%), Positives = 39/50 (78%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           +E EEEE  EEEEE +EEEEEEE+E EEEE E+EEEEEE E   G +EE+
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEM 486

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 56.6 bits (137), Expect = 3e-09
 Identities = 27/60 (45%), Positives = 40/60 (66%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +L  +  R ++ E EEEE EE ++ EE+ E E  +EEE EEE E+++EEEE +E EE+  
Sbjct: 10  KLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQAR 69

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|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 59.0 bits (143), Expect = 3e-09
 Identities = 21/60 (35%), Positives = 30/60 (50%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E   + EEEE  + E EE  E E+  + EE+    E     E+E E+E+E E     +EE
Sbjct: 387 ELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEE 446

Length = 449

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

 Score = 57.1 bits (138), Expect = 3e-09
 Identities = 23/62 (37%), Positives = 36/62 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            + E  EE+  +E E +EE++ +EE+   EE E+EE  E+ EE  E + EE ++     K
Sbjct: 8   AKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLK 67

Query: 659 EE 660
           EE
Sbjct: 68  EE 69

Length = 211

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 56.2 bits (136), Expect = 3e-09
 Identities = 21/54 (38%), Positives = 34/54 (62%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E EE  EE+E++E  +EEE +  ++E+ +E + EEE+     +EEE + E E E
Sbjct: 12  EDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAE 65

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 56.9 bits (138), Expect = 3e-09
 Identities = 23/53 (43%), Positives = 32/53 (60%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            EE+ E+ EEE EE E EE  E+E  +E  EEE E E  +EE+ +  E E ++
Sbjct: 1   MEEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKL 53

Length = 191

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 56.9 bits (138), Expect = 3e-09
 Identities = 25/54 (46%), Positives = 33/54 (61%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EEE EE E EE  E+E EEE  EEE + E  +EE+ +  E E + +E EE  +R
Sbjct: 9   EEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEERYLR 62

Length = 191

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 56.5 bits (137), Expect = 3e-09
 Identities = 25/53 (47%), Positives = 34/53 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E+ E+ EEE EE E EE  E+E EEE V+EE E E  +EE+ +  E E + +E
Sbjct: 3   EKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDE 55

Length = 191

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 56.7 bits (137), Expect = 3e-09
 Identities = 26/62 (41%), Positives = 36/62 (58%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +   + R E   E  E++EEEE  EEEEE+ EEE  +EEEE +     EEEEE+ +  +E
Sbjct: 60  LESSLDREEARLELLEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDE 119

Query: 651 EE 652
             
Sbjct: 120 LP 121

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 59.4 bits (144), Expect = 3e-09
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 596 RRGERE---EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           RR   +    EE +E+E+EEEE+  +E EEEE    EEE  +  E+   E   +   + E
Sbjct: 358 RRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSE 417

Query: 653 VRG 655
            + 
Sbjct: 418 SKA 420

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 59.4 bits (144), Expect = 3e-09
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 592 IQLIRRGEREEEEE--EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
              +R   R   +    EE +E+E+EEEE+  +E E +E E+ EEE  +  E+   E   
Sbjct: 351 ESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSS 410

Query: 650 EEEVRGGGKEE 660
           +       K +
Sbjct: 411 DVGSDSESKAD 421

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 58.8 bits (143), Expect = 3e-09
 Identities = 29/70 (41%), Positives = 39/70 (55%), Gaps = 8/70 (11%)

Query: 593 QLIRRGEREEEEEEEEEE-------EEEEEEEEEEEEEEEVQEEEEEEEEE-EEEEEEEE 644
           + I R E E+E E EEE        E+ E EEE E E  E +EE+E E      ++EE E
Sbjct: 136 ERIERKEEEKEREREEELKILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAE 195

Query: 645 EEEEEEEEVR 654
           +E EE +E+R
Sbjct: 196 DEREELDELR 205

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|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 59.0 bits (143), Expect = 4e-09
 Identities = 20/59 (33%), Positives = 29/59 (49%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            + EEEE  + E EE  E E+ E  +E+    E     E+E E+E+E EE      +E 
Sbjct: 390 SQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEEEEA 448

Length = 449

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 59.0 bits (143), Expect = 4e-09
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            E   + EEEE  + E EE  E E+ +  EE+    E     E+E E+E+E      +EE
Sbjct: 386 AELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDELEEAQPEEE 445

Length = 449

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 58.1 bits (141), Expect = 4e-09
 Identities = 22/51 (43%), Positives = 34/51 (66%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E ++E E  + E+EEE++E  ++ +   +EE  EE+EEE  EEEE E E+E
Sbjct: 122 ESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKE 172

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 54.2 bits (130), Expect = 4e-09
 Identities = 26/55 (47%), Positives = 37/55 (67%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E   +E ++E EEEEE +E++EEEE E +EEE EEEEE E    +   E+EE++ 
Sbjct: 41  ENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDDA 95

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 54.2 bits (130), Expect = 4e-09
 Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 4/68 (5%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE----EEEEEEEEVR 654
             E   +E ++E EEEEE +E++EEEE + EEEE EEEEE E        E+EE++ E +
Sbjct: 39  NEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDDAETK 98

Query: 655 GGGKEEIS 662
               +E  
Sbjct: 99  KQKTDEDD 106

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 56.3 bits (136), Expect = 4e-09
 Identities = 30/56 (53%), Positives = 38/56 (67%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E++EEEE  EEEEE+ EEE EEEEEE  +    EEEEE+ +  +E    EE EE+R
Sbjct: 75  EQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTPEEREELR 130

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 59.0 bits (143), Expect = 4e-09
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 10/72 (13%)

Query: 581 DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           D I    ++           +E+EEEE+  +E EEEE E+ EEE  Q  E+   E   + 
Sbjct: 363 DPIDFEEVD----------EDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDV 412

Query: 641 EEEEEEEEEEEE 652
             + E + ++E 
Sbjct: 413 GSDSESKADKES 424

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 55.2 bits (133), Expect = 5e-09
 Identities = 28/56 (50%), Positives = 46/56 (82%), Gaps = 2/56 (3%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE--EEEEEEEEEEEE 652
           ++E+  +E E+ ++E++E++EEEEEE+ +E EE E+ E+EEE  E+EEEEEE+EE+
Sbjct: 32  DKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEED 87

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 58.1 bits (141), Expect = 5e-09
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            GE  + E ++E E  + E+EEE++E  +  +E+ +EE  EE+EEE  EEEE E E
Sbjct: 115 EGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAE 170

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 57.7 bits (140), Expect = 5e-09
 Identities = 23/51 (45%), Positives = 35/51 (68%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           E ++E E  + E+EEE++E  ++ +E+  EE  EE+EEE  EEEE E E+E
Sbjct: 122 ESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKE 172

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

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

 Score = 56.7 bits (137), Expect = 5e-09
 Identities = 20/54 (37%), Positives = 36/54 (66%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +E E +EE++ +EE+ E EE E+EE +++ EE  E + EE ++E  + +EE +
Sbjct: 18  CKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENK 71

Length = 211

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 55.9 bits (134), Expect = 5e-09
 Identities = 27/68 (39%), Positives = 37/68 (54%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           RR  RE+ E+EE+E  E+EE++  E EE + +  EE    EEE   +EEE   E+EE   
Sbjct: 32  RRQAREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKAK 91

Query: 656 GGKEEISL 663
              EE   
Sbjct: 92  RKAEEEEK 99

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

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

 Score = 57.0 bits (138), Expect = 5e-09
 Identities = 25/52 (48%), Positives = 37/52 (71%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EEEE++EE E EEEEEEEE + +  + E++E E ++EEE E+E + EE   +
Sbjct: 35  EEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKK 86

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

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 59.2 bits (144), Expect = 6e-09
 Identities = 24/57 (42%), Positives = 45/57 (78%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            E EE+++++ EEEEE+ +  +EEE+EE ++ ++E++EEEEEEE+E+++++  E  R
Sbjct: 332 DEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTR 388

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 55.9 bits (135), Expect = 6e-09
 Identities = 26/56 (46%), Positives = 39/56 (69%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +   ++ E EEEE EE ++ EE+ E E +EEEE EEE E+++EEEE +E EE+  +
Sbjct: 15  QARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARK 70

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 55.9 bits (135), Expect = 6e-09
 Identities = 28/76 (36%), Positives = 47/76 (61%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R +   +   R ER++ EE+ E E +EEEE EEE E+++ +EE +E EE+  +E+EE E+
Sbjct: 18  RQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQEEYEK 77

Query: 647 EEEEEEVRGGGKEEIS 662
            +    V   G +++S
Sbjct: 78  LKSSFVVEEEGTDKLS 93

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|218538 pfam05285, SDA1, SDA1

 Score = 57.7 bits (140), Expect = 7e-09
 Identities = 22/51 (43%), Positives = 35/51 (68%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E ++E E  + E+EEE++E  ++  ++ +EE  EE+EEE  EEEE E E+E
Sbjct: 122 ESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKE 172

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 58.1 bits (140), Expect = 7e-09
 Identities = 28/63 (44%), Positives = 38/63 (60%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
             E  EEEE+EE  EE EE EE E   +  Q+ +  + EE ++EE+E E EEEE+  RG 
Sbjct: 107 ENETVEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGS 166

Query: 657 GKE 659
            +E
Sbjct: 167 LEE 169

Length = 431

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 55.1 bits (133), Expect = 8e-09
 Identities = 20/52 (38%), Positives = 33/52 (63%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           EE+E++E  +EEE +  ++E++EE   EEE+     +EEE + E E E + E
Sbjct: 18  EEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDRE 69

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 58.2 bits (141), Expect = 8e-09
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EE +E+E+EEEE+  +E EEEE E+ +EE  +  E+   E   +   + E +       +
Sbjct: 368 EEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKESASD 427

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 57.4 bits (139), Expect = 8e-09
 Identities = 27/68 (39%), Positives = 45/68 (66%), Gaps = 8/68 (11%)

Query: 588 IENII-----QLIRRGERE---EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           I+ +I         +GE E    +EE+ EE  E+ EEEEEE++  E ++E+EE+E+EEEE
Sbjct: 252 IKEVIKKKGGDFKVKGEPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEE 311

Query: 640 EEEEEEEE 647
           E+++E ++
Sbjct: 312 EDDDEGDK 319

Length = 319

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

 Score = 58.0 bits (141), Expect = 9e-09
 Identities = 33/92 (35%), Positives = 54/92 (58%), Gaps = 8/92 (8%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E I  L    +  ++ ++  E+ E++ EEE++E++++    +++EEEEEEE+E++EEE+E
Sbjct: 397 EEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKE 456

Query: 649 EEEEVRGGGKEEISLHFYVLYVLSKGKIAGLF 680
           EEEE     KEE            K K A LF
Sbjct: 457 EEEEEAEEEKEEEE--------EKKKKQATLF 480

Length = 482

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 53.0 bits (127), Expect = 9e-09
 Identities = 29/63 (46%), Positives = 39/63 (61%), Gaps = 9/63 (14%)

Query: 599 EREEEEEEEEE---------EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           E++E  EE+E          E EE   +E ++E EE +E +E++EEEE E EEEE EEEE
Sbjct: 18  EKKEVVEEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEE 77

Query: 650 EEE 652
           E E
Sbjct: 78  ETE 80

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 55.1 bits (133), Expect = 9e-09
 Identities = 20/55 (36%), Positives = 33/55 (60%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E  EE+E++E  +EEE +  ++E++EE   EEE+     +EEE + E E E + 
Sbjct: 14  EELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDR 68

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 57.8 bits (140), Expect = 9e-09
 Identities = 18/65 (27%), Positives = 32/65 (49%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
              E +E+E+EEEE+  +E EEEE E+  +E  +  E+   E   +   + E +  +   
Sbjct: 366 DFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKADKESA 425

Query: 658 KEEIS 662
            +  S
Sbjct: 426 SDSDS 430

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 58.7 bits (142), Expect = 9e-09
 Identities = 22/58 (37%), Positives = 35/58 (60%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
           EEE+   +  EEE+EEE E   +    + +++E   E+E+E+EE++EE     K EIS
Sbjct: 1   EEEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEIS 58

Length = 1033

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 55.1 bits (133), Expect = 1e-08
 Identities = 26/67 (38%), Positives = 40/67 (59%), Gaps = 8/67 (11%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE--------EEEEEEEE 647
           +  E+ E E +EEEE EEE E+++EEEE + +EE+  +E+EE E        EEE  ++ 
Sbjct: 33  KLEEKREGERKEEEELEEEREKKKEEEERKEREEQARKEQEEYEKLKSSFVVEEEGTDKL 92

Query: 648 EEEEEVR 654
             +EE  
Sbjct: 93  SADEESN 99

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 55.1 bits (133), Expect = 1e-08
 Identities = 26/66 (39%), Positives = 41/66 (62%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            + G ++  + EE++   ++ E EEEE EE  + EE+ E E +EEEE EEE E+++EE  
Sbjct: 1   KKIGAKKRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEE 60

Query: 655 GGGKEE 660
              +EE
Sbjct: 61  RKEREE 66

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|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 54.7 bits (132), Expect = 1e-08
 Identities = 20/57 (35%), Positives = 35/57 (61%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
              E E ++ EE+EE  EE+E++   +EEE +  ++E++EE + EEE+  V    +E
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEE 57

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 55.0 bits (133), Expect = 1e-08
 Identities = 25/54 (46%), Positives = 33/54 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E + E+ EEE EE E EE  E+E EEE  EEE E E  +EE+ +  E E + +E
Sbjct: 2   EEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDE 55

Length = 191

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 53.2 bits (128), Expect = 1e-08
 Identities = 25/49 (51%), Positives = 32/49 (65%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            ++E  E  EE+ EEEE+ E EE Q  EEE  +E   EEEE EEEE++E
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKE 78

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 57.9 bits (140), Expect = 1e-08
 Identities = 28/65 (43%), Positives = 44/65 (67%), Gaps = 3/65 (4%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE---EEEEE 648
           I L    E E+E  +EEEEEE+EE++EEEE+  + +EE +EEEE+EE++++    +E   
Sbjct: 23  IYLWVEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTT 82

Query: 649 EEEEV 653
           E E +
Sbjct: 83  EWELL 87

Length = 529

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 54.2 bits (131), Expect = 1e-08
 Identities = 21/54 (38%), Positives = 37/54 (68%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             +++E+EEEEEEE E EE +EEE++ E  E+E  + + E+  E E +++E ++
Sbjct: 95  GLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEILK 148

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 55.9 bits (135), Expect = 1e-08
 Identities = 21/98 (21%), Positives = 44/98 (44%), Gaps = 11/98 (11%)

Query: 567 TIRPSIKVWKTSDQDEIGSPRI------ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE 620
               ++      D+D+     I      E+             + +  +++ ++++ E+E
Sbjct: 84  DKSTNLDASNEGDEDDDEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDE 143

Query: 621 EEE-----EEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
                   E++++E  EE+E EEEE+  EEE+  EEE+
Sbjct: 144 TAALLRELEKIKKERAEEKEREEEEKAAEEEKAREEEI 181

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score = 52.6 bits (127), Expect = 2e-08
 Identities = 11/25 (44%), Positives = 13/25 (52%)

Query: 499 KDITFMWCPSHCGIKGNELVDVAAK 523
             +   W P H GI+GNE  D  AK
Sbjct: 100 VKVRLHWVPGHSGIEGNERADRLAK 124

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 57.7 bits (140), Expect = 2e-08
 Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 20/84 (23%)

Query: 597 RGEREEEEEEEEE--------------------EEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           RGE E++EEEE+                       + EE+EEEEE+  + ++EE+++++ 
Sbjct: 283 RGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDL 342

Query: 637 EEEEEEEEEEEEEEEEVRGGGKEE 660
           EEEEE+ +  +EEE+E      +E
Sbjct: 343 EEEEEDVDLSDEEEDEEDEDSDDE 366

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 54.1 bits (130), Expect = 2e-08
 Identities = 29/64 (45%), Positives = 48/64 (75%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           EN+++ ++    ++E+  +E E+ ++E++E++EEEEE  EEE EE E+ E+EEE  E+EE
Sbjct: 20  ENLLEHVKITSWDKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEIVEDEE 79

Query: 649 EEEE 652
           EEEE
Sbjct: 80  EEEE 83

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 55.8 bits (135), Expect = 2e-08
 Identities = 23/56 (41%), Positives = 36/56 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E E  + E ++E E  + E+EEE++E  ++ +E+ +EE  EE+EEE  EEEE E  
Sbjct: 115 EGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAE 170

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 57.0 bits (137), Expect = 2e-08
 Identities = 23/59 (38%), Positives = 35/59 (59%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E+   E E  EEEE+EE  EE EEV+E E   + E++ +  + EE ++EE+     +EE
Sbjct: 102 EDSGAENETVEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEE 160

Length = 431

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 57.0 bits (137), Expect = 2e-08
 Identities = 25/66 (37%), Positives = 35/66 (53%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E EE+EE  EE EE EE E   + E++    + EE ++EE+E E EEEE+ +        
Sbjct: 112 EEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENN 171

Query: 659 EEISLH 664
            E   H
Sbjct: 172 GEFMTH 177

Length = 431

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 54.0 bits (130), Expect = 2e-08
 Identities = 29/60 (48%), Positives = 37/60 (61%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            +L    ++EEEE  EEEEE+ EEE EEEEEE +     EEEEE+ +  +E    EE EE
Sbjct: 69  ARLELLEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTPEEREE 128

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

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

 Score = 55.1 bits (133), Expect = 2e-08
 Identities = 28/64 (43%), Positives = 39/64 (60%), Gaps = 4/64 (6%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE----EEEEEEEEEEEEEEEVRGG 656
           EEE EE+E        EEEE++EE   EEEEEEEE +    + E++E E ++EEE  +  
Sbjct: 19  EEELEEDEFFWTYLLFEEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKEL 78

Query: 657 GKEE 660
            +EE
Sbjct: 79  QREE 82

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

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 57.0 bits (137), Expect = 2e-08
 Identities = 32/116 (27%), Positives = 55/116 (47%), Gaps = 3/116 (2%)

Query: 547 LMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEE 606
           L   E  S W+N          RP++K  K   ++E      E  + +   G  E E +E
Sbjct: 232 LARQERVSSWENFKEEPGEPLSRPALKKEKQGAEEEGEEGMSEEDLDV---GAAEIENKE 288

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
             E ++E+++EE E  E   +E + +  +E  EE+EE++E EE E       +E++
Sbjct: 289 VSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERHTELLADELN 344

Length = 392

>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 55.9 bits (134), Expect = 2e-08
 Identities = 30/97 (30%), Positives = 39/97 (40%), Gaps = 13/97 (13%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE-------------EEEEE 642
           ++  +E+E +E+EEEEEEEEEEE E EE E           E             EE EE
Sbjct: 127 KKATKEDESDEDEEEEEEEEEEEAEVEENEQGTNGTSTNSTEVDHGNGSSGGDNGEEGEE 186

Query: 643 EEEEEEEEEEVRGGGKEEISLHFYVLYVLSKGKIAGL 679
           E   E E E     G    S +          ++ G 
Sbjct: 187 ESVTEAEAEGTTVAGPTTTSPNGGFQPTTPPQEVYGT 223

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 55.8 bits (134), Expect = 2e-08
 Identities = 29/92 (31%), Positives = 44/92 (47%), Gaps = 11/92 (11%)

Query: 574 VWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE-----EEEEEVQE 628
           VW   + ++   P   ++         EEE  EE +  EEEE+EE       E   E+ E
Sbjct: 157 VWDNDEDNDEAPPAQPDV------DNEEEERLEESDGREEEEDEEVGSDSYGEGNRELNE 210

Query: 629 EEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EEEEE E  ++ E+  + E E  + + G +EE
Sbjct: 211 EEEEEAEGSDDGEDVVDYEGERIDKKQGEEEE 242

Length = 279

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 51.8 bits (124), Expect = 2e-08
 Identities = 28/52 (53%), Positives = 34/52 (65%)

Query: 590 NIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           NI Q   +   E EE EE +EEEEEEEEEE+E E E   ++EE EEE E+ E
Sbjct: 45  NISQSAFKKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 53.0 bits (128), Expect = 2e-08
 Identities = 33/134 (24%), Positives = 49/134 (36%), Gaps = 19/134 (14%)

Query: 331 CYTDGSKTPTTTGCA-YSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIV 389
            +TDGS      G A  +  +V+    L    S   AELIA+   + A+  +      I 
Sbjct: 2   VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58

Query: 390 TDSR---SSLAALSNVRFINPLIT----KVYSTWSYLK---LCKKDITFMWCPSHCG--- 436
           TDS      L AL  +      +T     + S    L+      K +  +   +H G   
Sbjct: 59  TDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRAHSGLPG 118

Query: 437 --IKGNEIVDVAAK 448
               GN   D AA+
Sbjct: 119 PLALGNARADQAAR 132

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 52.4 bits (126), Expect = 2e-08
 Identities = 33/128 (25%), Positives = 47/128 (36%), Gaps = 15/128 (11%)

Query: 332 YTDGSKTPTTTGCAYSVGNVVR---------STLLNPVNSIFSAELIAIFLCLEAILDSP 382
            TDGS            G V+R          +L  P  +   AEL+A+   LE  LD  
Sbjct: 1   NTDGSCKGN--PGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLG 58

Query: 383 SGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEI 442
             K +I TDS+  +  +++          +      L     DI F   P     +GNE+
Sbjct: 59  LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR----EGNEV 114

Query: 443 VDVAAKNP 450
            D  AK  
Sbjct: 115 ADRLAKEA 122

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 53.8 bits (130), Expect = 3e-08
 Identities = 25/55 (45%), Positives = 33/55 (60%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           + E+ EEE EE E EE  E+E EEE  EE  E E  +EE+ +  E E + +E EE
Sbjct: 4   KNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEE 58

Length = 191

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 55.7 bits (135), Expect = 3e-08
 Identities = 25/63 (39%), Positives = 35/63 (55%), Gaps = 7/63 (11%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE-------EEEEEEEEEEEEE 651
           EREEE E E  E +EE+E E      + +E E+E EE +E       EE E +E ++E+E
Sbjct: 164 EREEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKE 223

Query: 652 EVR 654
           E  
Sbjct: 224 EAE 226

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|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 51.6 bits (124), Expect = 3e-08
 Identities = 25/51 (49%), Positives = 35/51 (68%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           G  ++E  E  EE+ EEEE+ E EE++ V+EE  +E   EEEE EEEE++E
Sbjct: 28  GSVKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKE 78

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|225368 COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]

 Score = 51.6 bits (124), Expect = 3e-08
 Identities = 28/75 (37%), Positives = 39/75 (52%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +  I +     + E EE +EE E+  +E  EE  E  E  EEE E+  +E  EE  EE E
Sbjct: 9   LREIKKAEISADEEIEEAKEEAEQIIKEAREEAREIIEEAEEEAEKLAQEILEEAREEAE 68

Query: 648 EEEEEVRGGGKEEIS 662
           EE EE+    ++E S
Sbjct: 69  EEAEEILAEAEKEAS 83

Length = 108

>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31

 Score = 54.0 bits (130), Expect = 4e-08
 Identities = 22/48 (45%), Positives = 35/48 (72%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
             EEEE+ +E+    E++ +  E E+ +EE+E++EEEEEEEEEE+E+ 
Sbjct: 142 FTEEEEDIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDF 189

RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. Length = 221

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 51.9 bits (124), Expect = 4e-08
 Identities = 20/50 (40%), Positives = 30/50 (60%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            E  +E  E +  +E +EEEE +E  +E  +E + E EE +EEE+EE E 
Sbjct: 82  DEDADEAAEADAADEADEEEETDEAVDETADEADAEAEEADEEEDEEAEA 131

Length = 131

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 55.0 bits (133), Expect = 4e-08
 Identities = 21/54 (38%), Positives = 35/54 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +  E  + E ++E E  + E+EEE++E  ++ +E+ +EE  EE+EEE  EEEE 
Sbjct: 114 DEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEA 167

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 53.2 bits (128), Expect = 4e-08
 Identities = 29/76 (38%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEE--------EEEEEEEVQEEEEEEEEEEEEEEEEE 644
           Q I +   EEE E     +   E            EE   E+ E++EEEE  EEEEE+ E
Sbjct: 32  QYIGQFLTEEEREARGRAKRWSEGLSGVLESSLDREEARLELLEQQEEEESAEEEEEDPE 91

Query: 645 EEEEEEEEVRGGGKEE 660
           EE EEEEE    G   
Sbjct: 92  EENEEEEEEYQRGPFG 107

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

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

 Score = 55.6 bits (134), Expect = 4e-08
 Identities = 15/78 (19%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 575 WKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
           +    Q +  + R E      R+ + +++ EE ++++  E+E  ++ E+E +  +E++++
Sbjct: 64  YNRQQQQQKSAKRAEEQ----RKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQ 119

Query: 635 EEEEEEEEEEEEEEEEEE 652
            EE  ++   ++++ EE 
Sbjct: 120 AEEAAKQAALKQKQAEEA 137

Length = 387

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 56.1 bits (135), Expect = 5e-08
 Identities = 32/50 (64%), Positives = 37/50 (74%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           +E EEEE  EEEEEE +EEEEEE+E EEEE E+EEEEEE E   G  +E 
Sbjct: 437 QESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEM 486

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 54.7 bits (132), Expect = 5e-08
 Identities = 23/62 (37%), Positives = 38/62 (61%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           +E E  + E ++E E  + E+EEE+ +  ++ +E+ +EE  EE+EEE  EEE     KE+
Sbjct: 114 DEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKEK 173

Query: 661 IS 662
            S
Sbjct: 174 AS 175

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 51.1 bits (122), Expect = 5e-08
 Identities = 25/54 (46%), Positives = 37/54 (68%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           G+ E EEEEE +E++EEEE E EEEE E +EE E    +   E+EE++ E +++
Sbjct: 47  GDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDDAETKKQ 100

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 51.1 bits (122), Expect = 5e-08
 Identities = 28/69 (40%), Positives = 41/69 (59%)

Query: 584 GSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           G+   EN  Q       EEEE +E++EEEE E EEEE EEEE  E    +   E+EE++ 
Sbjct: 36  GNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEEEETEGATGKRAAEDEEDDA 95

Query: 644 EEEEEEEEE 652
           E ++++ +E
Sbjct: 96  ETKKQKTDE 104

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

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

 Score = 53.9 bits (130), Expect = 5e-08
 Identities = 25/51 (49%), Positives = 37/51 (72%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           EEEE++EE E EEEEEEEE + + +  E++E E ++EEE E+E + EE  +
Sbjct: 35  EEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLK 85

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

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 50.9 bits (122), Expect = 5e-08
 Identities = 24/49 (48%), Positives = 32/49 (65%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            ++E  E  EE+ EEEE+ E EE+   EEE  +E   EEEE EEEE++E
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKE 78

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 53.3 bits (128), Expect = 5e-08
 Identities = 25/55 (45%), Positives = 42/55 (76%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           + +EEE++ E EE E+E+E  E E E++ E++E+EE  +EEE+EEE E+ +++EV
Sbjct: 51  KSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEEAEDVKQQEV 105

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

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

 Score = 55.1 bits (133), Expect = 5e-08
 Identities = 19/63 (30%), Positives = 34/63 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E+E + E++ +E E  EE++ E+   E    +E  E   EE +++ EEE ++E    G 
Sbjct: 203 YEKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDDESAWEGF 262

Query: 658 KEE 660
           + E
Sbjct: 263 ESE 265

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|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 53.3 bits (129), Expect = 5e-08
 Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 10/77 (12%)

Query: 588 IENIIQLIRRGEREEE----------EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           I  +++   R E  E           +             E E +EE+++++++++E+E+
Sbjct: 5   IAYLLEQYDRVEAGEGRLSDLISGFIDPNAAAAAATAAAIESELDEEDLEDDDDDDEDED 64

Query: 638 EEEEEEEEEEEEEEEVR 654
           E++EEE +   + EE R
Sbjct: 65  EDDEEEADLGPDPEEAR 81

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 52.8 bits (127), Expect = 5e-08
 Identities = 19/53 (35%), Positives = 44/53 (83%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           ++EEEE++E +  ++E ++E+E+++E V+   E++E +E+E+++E+EE+EE++
Sbjct: 123 DKEEEEDDEVDSLDDENDDEDEDDDEIVEILIEDDEVDEDEDDDEDEEDEEDK 175

Length = 175

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 53.2 bits (128), Expect = 6e-08
 Identities = 25/63 (39%), Positives = 43/63 (68%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           +R + EE++   ++ E EEEE EE ++++E+ E E +EEEE EEE E+++EEEE +   +
Sbjct: 7   KRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREE 66

Query: 659 EEI 661
           +  
Sbjct: 67  QAR 69

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 52.8 bits (127), Expect = 6e-08
 Identities = 26/60 (43%), Positives = 41/60 (68%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +  +  E++   ++ E EEEE EE ++ EE+ E + +EEEE EEE E+++EEEE +E EE
Sbjct: 7   KRAKLEEKQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREE 66

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 55.8 bits (134), Expect = 6e-08
 Identities = 26/39 (66%), Positives = 30/39 (76%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           E EEEEEEEEEEEEEEEEEEEEE EE +  E  E  +++
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETRQKQ 905

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 54.7 bits (132), Expect = 6e-08
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            E E  + E+EEE++E  ++ +E+ +EE+ EE+EEE  EEEE E E+E
Sbjct: 125 KEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEAEAEKE 172

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 52.4 bits (126), Expect = 6e-08
 Identities = 21/56 (37%), Positives = 35/56 (62%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
              E E ++ EE+EE  EE+E  E  +EEE +  ++E++EE + EEE++    +EE
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEE 56

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 54.9 bits (133), Expect = 6e-08
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 10/74 (13%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEE----EEEEEEVQEEEEEEEE------EEEEE 640
           I++  R     EEE E E  E +EE+E E      ++EE ++E EE +E      +EE E
Sbjct: 155 ILEYQREKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYE 214

Query: 641 EEEEEEEEEEEEVR 654
            +E ++E+EE E R
Sbjct: 215 RKERQKEKEEAEKR 228

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

 Score = 55.5 bits (134), Expect = 7e-08
 Identities = 32/76 (42%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 587 RIENIIQLIR-RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            +E  I L+R R E  E E EE EE  EE +E+ E  +EE++E E   EE E+   E EE
Sbjct: 299 ELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEE 358

Query: 646 EEEEEEEVRGGGKEEI 661
            +EE EE      EE+
Sbjct: 359 AKEELEEKLSALLEEL 374

Length = 1163

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

 Score = 55.9 bits (134), Expect = 7e-08
 Identities = 20/63 (31%), Positives = 41/63 (65%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            ++ EEE + +  EE ++ EE++++ EE ++ EE+E++  E  ++E EE ++ EE++    
Sbjct: 1653 KKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEA 1712

Query: 659  EEI 661
            EE 
Sbjct: 1713 EEK 1715

Length = 2084

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 52.4 bits (126), Expect = 8e-08
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
                 EE E+++EEEE +E EE+  +E+EE ++ +     EEE  ++   +EE  E
Sbjct: 44  EEEELEEEREKKKEEEERKEREEQARKEQEEYEKLKSSFVVEEEGTDKLSADEESNE 100

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|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 54.5 bits (132), Expect = 8e-08
 Identities = 21/68 (30%), Positives = 37/68 (54%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R E      R  + E+E E      ++EE E+E EE +E++ +  +EE E +E ++E+EE
Sbjct: 165 REEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEE 224

Query: 647 EEEEEEVR 654
            E+    +
Sbjct: 225 AEKRRRQK 232

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|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 53.5 bits (129), Expect = 8e-08
 Identities = 25/54 (46%), Positives = 37/54 (68%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           EEEE++EE E EEEEEEEE + +    E++E E ++EEE E+E + EE  + + 
Sbjct: 35  EEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKKKK 88

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

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

 Score = 53.5 bits (129), Expect = 8e-08
 Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 5/61 (8%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE-----EEEEEEEEEEEEEEEEEEV 653
           E E EE+E        EEEE++EE E  +EEEEEE      + E++E E ++EEE E+E+
Sbjct: 19  EEELEEDEFFWTYLLFEEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKEL 78

Query: 654 R 654
           +
Sbjct: 79  Q 79

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

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 50.3 bits (120), Expect = 8e-08
 Identities = 24/45 (53%), Positives = 33/45 (73%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           ++  E EE EE +EEEEEEEEEE+E E++   ++EE EEE E+ E
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 52.2 bits (125), Expect = 8e-08
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           ++EEE+ + + EE EE+EEE E+ E   +EE+EE EE EEE     +      +   +E 
Sbjct: 18  KDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKAPSSSSKSSSQET 77

Query: 661 IS 662
           IS
Sbjct: 78  IS 79

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 52.0 bits (124), Expect = 9e-08
 Identities = 27/60 (45%), Positives = 39/60 (65%), Gaps = 2/60 (3%)

Query: 597 RGEREEE--EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           R  REEE   +EEE   E+EE+ + + EEEE QE+EE+E  ++++EE E    EE E +R
Sbjct: 68  RLRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMR 127

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 50.5 bits (121), Expect = 9e-08
 Identities = 24/49 (48%), Positives = 33/49 (67%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            ++E  E  EE+ EEEE+ E EE++  EEE  +E   EEEE EEEE++E
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKE 78

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 49.9 bits (119), Expect = 9e-08
 Identities = 24/48 (50%), Positives = 31/48 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
              ++  E EE EE +EEEEEEEEEE+  E E   ++EE EEE E+ E
Sbjct: 49  SAFKKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 55.1 bits (133), Expect = 9e-08
 Identities = 27/74 (36%), Positives = 37/74 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            I  + + +   E E EE EE  EE +E+ E  +EE EE +   EE E+   E EE +EE
Sbjct: 303 EISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEE 362

Query: 647 EEEEEEVRGGGKEE 660
            EE+        EE
Sbjct: 363 LEEKLSALLEELEE 376

Length = 1163

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 55.0 bits (132), Expect = 9e-08
 Identities = 30/109 (27%), Positives = 52/109 (47%), Gaps = 2/109 (1%)

Query: 553 QSLWDNVPNTNKLKTIRPS-IKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEE 611
           + + D++        I    I+V     QD        +   +      ++EEEEEE+E 
Sbjct: 68  KPILDDLNQKYVEFLINKEHIRVLAKL-QDSESHEDGSDGSDMDSEDSADDEEEEEEDES 126

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            E+E  ++E+E +   E E   E+  ++E E++EE++ EEE  G  KE 
Sbjct: 127 LEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEEAGEEKES 175

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 54.4 bits (131), Expect = 1e-07
 Identities = 18/64 (28%), Positives = 30/64 (46%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           ++E E+ +  E   + EEEE  + E E + E E+ E  EE+    E     E+E     +
Sbjct: 377 DQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLPEDEFEDEDE 436

Query: 659 EEIS 662
            E +
Sbjct: 437 LEEA 440

Length = 449

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 53.9 bits (130), Expect = 1e-07
 Identities = 19/62 (30%), Positives = 37/62 (59%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E+E+ ++E E  + E ++E E  +   EEE++E  ++ +E+ +EE  EE+EE     +E 
Sbjct: 108 EDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAEEEEA 167

Query: 661 IS 662
            +
Sbjct: 168 EA 169

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

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

 Score = 52.4 bits (126), Expect = 1e-07
 Identities = 20/61 (32%), Positives = 37/61 (60%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           EN+ +   +    +EE++ +EE+ E EE E+EE  E+ +E  E + EE ++E  + +EE 
Sbjct: 11  ENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEEN 70

Query: 649 E 649
           +
Sbjct: 71  K 71

Length = 211

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 54.3 bits (130), Expect = 1e-07
 Identities = 25/82 (30%), Positives = 40/82 (48%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
             E +EE  EE EE EE E   + E++ + ++ EE ++EE+E E EEEE+ +        
Sbjct: 112 EEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENN 171

Query: 657 GKEEISLHFYVLYVLSKGKIAG 678
           G+       +     S+G   G
Sbjct: 172 GEFMTHKLKHTENTFSRGGAEG 193

Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 53.8 bits (130), Expect = 1e-07
 Identities = 30/86 (34%), Positives = 44/86 (51%), Gaps = 21/86 (24%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEE-------------------EEEEEEEEEEEEEEVQE- 628
           E + ++I R + E+E E +E+ E                   +EEE+E E EEE ++ E 
Sbjct: 99  EQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEY 158

Query: 629 -EEEEEEEEEEEEEEEEEEEEEEEEV 653
             E+ E EEE E E  E +EE+E EV
Sbjct: 159 QREKAEREEEREAERRERKEEKEREV 184

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|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 52.0 bits (124), Expect = 1e-07
 Identities = 25/62 (40%), Positives = 39/62 (62%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +L RR   E    EEE   +EEE   E+EE+ + + EEEE++E+EE+E  ++++EE E  
Sbjct: 59  ELKRRAAEERLRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEAR 118

Query: 653 VR 654
            R
Sbjct: 119 AR 120

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 51.5 bits (124), Expect = 1e-07
 Identities = 22/52 (42%), Positives = 36/52 (69%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           G  ++E+EEEEEEE E EE +EEE+ +E+ E+E  + + E+  E E +++E 
Sbjct: 95  GLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEI 146

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 52.1 bits (125), Expect = 1e-07
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           I++ + +EEE+E  +E  + +EEE++ E EE ++E+E  E E E+  E++E+EE  +E  
Sbjct: 33  IKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEE 92

Query: 655 GGGKEE 660
              + E
Sbjct: 93  KEEEAE 98

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 51.7 bits (124), Expect = 1e-07
 Identities = 23/87 (26%), Positives = 53/87 (60%)

Query: 566 KTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEE 625
           + I+   +      +D+      E     +   E +EEEE++E +  ++E ++E+E+++E
Sbjct: 89  EEIQAMTEKKDIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDEDDDE 148

Query: 626 VQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + E   E++E +E+E+++E+EE+EE++
Sbjct: 149 IVEILIEDDEVDEDEDDDEDEEDEEDK 175

Length = 175

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

 Score = 52.8 bits (127), Expect = 1e-07
 Identities = 25/59 (42%), Positives = 38/59 (64%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
            ++E  E EE +EEE+E    E++E++   E+E+EE EEE EEE+EE  +E E+E    
Sbjct: 55  DDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEK 113

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 = 52.8 bits (127), Expect = 1e-07
 Identities = 25/64 (39%), Positives = 39/64 (60%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           + + +E  E EE +EEE+E    E++E++   E+E+EE EEE EEE+EE  +E E+    
Sbjct: 53  KSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEE 112

Query: 657 GKEE 660
             E 
Sbjct: 113 KTES 116

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|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 54.2 bits (130), Expect = 1e-07
 Identities = 10/62 (16%), Positives = 13/62 (20%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                          E    E        Q     +   E+  EE E    E E    G 
Sbjct: 133 SHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGP 192

Query: 658 KE 659
            +
Sbjct: 193 PQ 194

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 54.2 bits (130), Expect = 1e-07
 Identities = 12/70 (17%), Positives = 14/70 (20%), Gaps = 5/70 (7%)

Query: 596 RRGEREEEEE-----EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           R GE+EE  +        E             EE       E       E          
Sbjct: 80  RHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSPENTSGSSPESPASHSPPPS 139

Query: 651 EEVRGGGKEE 660
                G  E 
Sbjct: 140 PPSHPGPHEP 149

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 53.3 bits (128), Expect = 1e-07
 Identities = 15/56 (26%), Positives = 32/56 (57%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           +E E  + E+ E+E++ +E+E++++ +EEE    +   E+ +   EE E  E+   
Sbjct: 214 DEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAA 269

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 53.9 bits (130), Expect = 2e-07
 Identities = 22/55 (40%), Positives = 41/55 (74%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E ++++ EEEEE+ +  +EEE+EE+E+  +E++EEEEEEE+E+++++  E    
Sbjct: 335 EEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRS 389

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 54.1 bits (130), Expect = 2e-07
 Identities = 29/57 (50%), Positives = 35/57 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R  +  +      E      +E EEEE  E +EEEEEEEEEEE+E EEEE E+EEEE
Sbjct: 417 RSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEE 473

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 50.3 bits (120), Expect = 2e-07
 Identities = 17/63 (26%), Positives = 26/63 (41%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           G  E+          E  EE E  + +E  +E  E +  +E +EEEE +E  +E      
Sbjct: 56  GRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDETADEAD 115

Query: 658 KEE 660
            E 
Sbjct: 116 AEA 118

Length = 131

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

 Score = 52.1 bits (125), Expect = 2e-07
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +  E +EE++ +EE+ E EE E+EE     EE  E + EE ++E  + +EE +++ 
Sbjct: 19  KENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENKKLE 74

Length = 211

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

 Score = 51.7 bits (124), Expect = 2e-07
 Identities = 20/55 (36%), Positives = 35/55 (63%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            +EE++ +EE+ E EE E+EE  E+ E   E + EE ++E  + +EE ++ E E+
Sbjct: 23  NKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENKKLENEL 77

Length = 211

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 51.2 bits (123), Expect = 2e-07
 Identities = 18/51 (35%), Positives = 31/51 (60%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            + E  +EEE +  ++E++EE + EEE++    +EEE + E E E + E E
Sbjct: 21  EDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDREFE 71

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 51.7 bits (124), Expect = 2e-07
 Identities = 29/61 (47%), Positives = 38/61 (62%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           ++L+ + E EE  EEEEE+ EEE EEEEEE +     EEEEE+ +  +E    EE EE  
Sbjct: 71  LELLEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTPEEREELR 130

Query: 652 E 652
           E
Sbjct: 131 E 131

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 53.4 bits (129), Expect = 2e-07
 Identities = 22/51 (43%), Positives = 35/51 (68%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +EE E +E ++E+EE E+   +++E+Q   EE+ EE+EE  +EE  EEE E
Sbjct: 210 QEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAE 260

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|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 51.2 bits (122), Expect = 2e-07
 Identities = 22/57 (38%), Positives = 33/57 (57%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +R +  E+ E+EE+E  E+EE++  E EE  +   EE    EEE   +EEE   E+E
Sbjct: 31  KRRQAREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREKE 87

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 51.2 bits (122), Expect = 2e-07
 Identities = 27/84 (32%), Positives = 43/84 (51%)

Query: 577 TSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           T+D +E      E   Q   + E+EE+E  E+EE++  E EE +    E +   EEE   
Sbjct: 18  TTDAEEATRLLAEKRRQAREQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARR 77

Query: 637 EEEEEEEEEEEEEEEEVRGGGKEE 660
           +EEE   E+EE+ + +     K+E
Sbjct: 78  QEEERAREKEEKAKRKAEEEEKQE 101

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 49.3 bits (118), Expect = 2e-07
 Identities = 22/46 (47%), Positives = 29/46 (63%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            ++E  E  EE+ EEEE+   EE++  EEE  +E   EEEE EEEE
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEE 75

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 24/45 (53%), Positives = 31/45 (68%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           ++  E EE EE +EEEEEEEEEE + E E   ++EE EEE E+ E
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 51.8 bits (124), Expect = 2e-07
 Identities = 24/56 (42%), Positives = 37/56 (66%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E E++ E EE E+E+E  E E E+  E QE+EE  +EEE+EEE E+ +++E    +
Sbjct: 54  EEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEEAEDVKQQEVFSFK 109

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 51.4 bits (123), Expect = 2e-07
 Identities = 23/54 (42%), Positives = 38/54 (70%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E  + +EEE++ E EE E+E+E  E E ++  E++E+EE  +EEE+EEE E+ +
Sbjct: 48  EHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEEAEDVK 101

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

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

 Score = 53.6 bits (129), Expect = 2e-07
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 599 EREEEEEEEEEEEEEEEEEEE-----EEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E E+E + E++ +E E  EE+       E   + E  E   EE +++ EEE ++E   E 
Sbjct: 202 EYEKEVKAEKKRQELERVEEKKLEKMAPEASRLDEMSEGLLEESDDDGEEESDDESAWEG 261

Query: 654 RGGGKEE 660
                E 
Sbjct: 262 FESEYEP 268

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

 Score = 51.7 bits (124), Expect = 2e-07
 Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 10/94 (10%)

Query: 559 VPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEE 618
            P++   +      +  K+ DQ+             I   + EE+E    E++E++ + E
Sbjct: 36  FPSSPSDQAAADEQEAKKSDDQET----------AEIEEVKEEEKEAANSEDKEDKGDAE 85

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +E+EE E + EEE+EE  +E E+E EE+ E   E
Sbjct: 86  KEDEESEEENEEEDEESSDENEKETEEKTESNVE 119

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|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 52.9 bits (127), Expect = 2e-07
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E  + E+ E+E++ +E+E++++ EEEE    +   E+ +   EE E  E E  E 
Sbjct: 217 ESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEA 271

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 52.9 bits (127), Expect = 2e-07
 Identities = 15/55 (27%), Positives = 31/55 (56%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           G+  E  + E+ E+E++ +E+E++++ E +E    +   E+ +   EE E  E E
Sbjct: 213 GDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEME 267

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 50.0 bits (120), Expect = 2e-07
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 8/65 (12%)

Query: 596 RRGEREEEEEEE--------EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            R ER++E E++        +  EEE ++EE+ E E+    E++E E   E    + EEE
Sbjct: 57  IREERKQELEKQLKERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEE 116

Query: 648 EEEEE 652
             +E+
Sbjct: 117 YIDED 121

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 52.7 bits (127), Expect = 3e-07
 Identities = 18/63 (28%), Positives = 35/63 (55%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E E E EE+E+ ++E E  + E ++E    + E+EEE++E  ++ +E+ +EE       
Sbjct: 100 EEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEE 159

Query: 658 KEE 660
           +  
Sbjct: 160 EAA 162

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 52.4 bits (126), Expect = 3e-07
 Identities = 19/54 (35%), Positives = 34/54 (62%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E  ++E E  + E ++E E  + E+EE ++E  ++ +E+ +EE  EE+EEE  E
Sbjct: 110 EDSDDEGEWIDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEEAAE 163

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 53.1 bits (127), Expect = 3e-07
 Identities = 23/62 (37%), Positives = 34/62 (54%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +   E+EE  EE EE EE E   + E++ +    EE ++EE+E E EEEE+ +    E  
Sbjct: 111 VEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEEN 170

Query: 655 GG 656
            G
Sbjct: 171 NG 172

Length = 431

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 48.8 bits (116), Expect = 3e-07
 Identities = 23/54 (42%), Positives = 32/54 (59%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           +E  EE+E  +       E EE   +  ++E EEEEE +E++EEEE E EEEE 
Sbjct: 20  KEVVEEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEG 73

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 53.2 bits (128), Expect = 3e-07
 Identities = 21/58 (36%), Positives = 31/58 (53%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
           +  + EE +E+E+EEEE+   E EEEE E+ EEE  +  E+   E     G +  S  
Sbjct: 363 DPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSESSSDVGSDSESKA 420

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 50.9 bits (121), Expect = 3e-07
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R EREE +    EE    EEE   +EEE  +E+EE+ + + EEEE++E+EE+E  +
Sbjct: 54  RLEREELKRRAAEERLRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQ 109

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 48.6 bits (116), Expect = 3e-07
 Identities = 23/47 (48%), Positives = 32/47 (68%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            ++E  E  EE+ EEEE+ EV+E++  EEE  +E   EEEE EEEE+
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEED 76

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 50.6 bits (121), Expect = 3e-07
 Identities = 25/69 (36%), Positives = 41/69 (59%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
             E+E  +E  + +EEE++ E EE E+E+   E E E+  E++E+EE  +EEE+EE    
Sbjct: 40  EEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEEAED 99

Query: 657 GKEEISLHF 665
            K++    F
Sbjct: 100 VKQQEVFSF 108

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 53.1 bits (127), Expect = 3e-07
 Identities = 10/62 (16%), Positives = 14/62 (22%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
                          E    E       Q+     +   E+  EE E    E E    G 
Sbjct: 133 SHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGP 192

Query: 659 EE 660
            +
Sbjct: 193 PQ 194

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 53.1 bits (127), Expect = 3e-07
 Identities = 10/62 (16%), Positives = 15/62 (24%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
                        E    E       +      +   E+  EE E    E E +  G  +
Sbjct: 135 SPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQ 194

Query: 659 EE 660
            E
Sbjct: 195 SE 196

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 52.1 bits (125), Expect = 3e-07
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E  +E E  + E+ E+E++ +E+E+++  EEEE    +   E+ +   EE E 
Sbjct: 211 ELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMES 263

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 49.6 bits (119), Expect = 3e-07
 Identities = 16/58 (27%), Positives = 31/58 (53%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
            +E  ++  +   +  EEE ++EE+ E E+ E+ E++E     E    + EEE  +E+
Sbjct: 64  ELEKQLKERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDED 121

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 52.6 bits (127), Expect = 3e-07
 Identities = 22/45 (48%), Positives = 28/45 (62%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           +++  +EE +E    Q +    EEEEEEEEEEEEEE  EEE   G
Sbjct: 280 DKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSEEEAAAG 324

Length = 330

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 53.3 bits (128), Expect = 3e-07
 Identities = 19/56 (33%), Positives = 28/56 (50%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
              E  E   EE E  +E EE+E E  + E +E E +  E  E+ E +E +E+ E 
Sbjct: 242 DNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTET 297

Length = 620

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

 Score = 53.0 bits (127), Expect = 3e-07
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           +E  EE+   +      + EE E+++  E   + E E++E+ EE EEE+ EE  G  K+ 
Sbjct: 279 DEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKG 338

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|220383 pfam09756, DDRGK, DDRGK domain

 Score = 50.5 bits (121), Expect = 4e-07
 Identities = 21/54 (38%), Positives = 33/54 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E EEE E+++EEEE +E EE+  +E+E  E+ +     EEE  ++   +EE  E
Sbjct: 47  ELEEEREKKKEEEERKEREEQARKEQEEYEKLKSSFVVEEEGTDKLSADEESNE 100

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|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 50.1 bits (120), Expect = 4e-07
 Identities = 18/53 (33%), Positives = 31/53 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            + ++E  +EEE +  ++E++EE + EE Q     +EEE + E E E + E E
Sbjct: 19  EDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDREFE 71

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 50.5 bits (121), Expect = 4e-07
 Identities = 26/53 (49%), Positives = 32/53 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E   EEEEE+ EEE EEEEEE +     +EEEE+ +  +E    EE EE  EE
Sbjct: 80  EESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTPEEREELREE 132

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 52.8 bits (127), Expect = 4e-07
 Identities = 24/51 (47%), Positives = 43/51 (84%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E+E E+E  +EEEEEE+EE++E +E+  ++EEE +EEEE+EE++++ ++V+
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVK 78

Length = 529

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 49.6 bits (119), Expect = 4e-07
 Identities = 21/56 (37%), Positives = 41/56 (73%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +++E+EEEEEEE E EE +EEE+ +E +++E  + + E+  E E +++E  +E+++
Sbjct: 97  DKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEILKEQMK 152

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 49.6 bits (119), Expect = 4e-07
 Identities = 20/49 (40%), Positives = 32/49 (65%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +    +++E+EEEEEEE E EE+ EEE+ +E  E+E  + + E+  E E
Sbjct: 92  KLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENE 140

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 48.3 bits (115), Expect = 4e-07
 Identities = 24/45 (53%), Positives = 30/45 (66%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           ++  E EE EE +EEEEEEEEE  E E E   ++EE EEE E+ E
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 50.2 bits (120), Expect = 4e-07
 Identities = 21/56 (37%), Positives = 37/56 (66%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E++ E EE E+E+E  E E E+  E++ +EE  +EEE+EEE E+ +++E    + +
Sbjct: 56  EQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEEAEDVKQQEVFSFKRK 111

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 50.3 bits (120), Expect = 4e-07
 Identities = 21/42 (50%), Positives = 30/42 (71%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           + EEE+ + + EE EE+EEE E+ E+ + EE+EE EE EEE 
Sbjct: 18  KDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEET 59

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 52.7 bits (126), Expect = 4e-07
 Identities = 23/65 (35%), Positives = 39/65 (60%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E   ++EEEEEE+E  E+E  ++E+E     E E   E+  ++E E++EE++ E    G
Sbjct: 111 SEDSADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEEAG 170

Query: 658 KEEIS 662
           +E+ S
Sbjct: 171 EEKES 175

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 52.7 bits (126), Expect = 4e-07
 Identities = 6/63 (9%), Positives = 9/63 (14%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
               EE       E       E                  E    E       ++     
Sbjct: 108 SGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFL 167

Query: 658 KEE 660
           +  
Sbjct: 168 QPS 170

Length = 413

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 53.1 bits (128), Expect = 4e-07
 Identities = 15/74 (20%), Positives = 44/74 (59%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
              + + +   G+ EEE ++E   ++   + EE+++++E  +EE+EE  + E++E+++++
Sbjct: 93  FGSDQVVIFDDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDD 152

Query: 647 EEEEEEVRGGGKEE 660
           +++++        E
Sbjct: 153 DDDDDIATRERSLE 166

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic N-terminal

 Score = 47.8 bits (114), Expect = 4e-07
 Identities = 26/62 (41%), Positives = 38/62 (61%), Gaps = 6/62 (9%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE------EEEEEEEEEEEEEEEEEEEE 652
           E E ++EEEEEEEEE++ E+  +E+E + E E E        +   E+EEEE+ EE  E 
Sbjct: 5   EAEVDDEEEEEEEEEDDLEDLSDEDEFIDEAEAEDDRRHRRLDRRREKEEEEDAEELAEY 64

Query: 653 VR 654
           +R
Sbjct: 65  LR 66

This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. Length = 92

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

 Score = 50.5 bits (120), Expect = 4e-07
 Identities = 25/56 (44%), Positives = 37/56 (66%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R EREE EE  E E  EE+ +E E++EE+ +E EE+  EE+ ++ E E  E++E E
Sbjct: 132 RQEREELEERMEWERREEKIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQDESE 187

Length = 197

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 50.1 bits (120), Expect = 5e-07
 Identities = 28/57 (49%), Positives = 35/57 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++ E E  EEEEE+ EEE EEEEEE +     EEEEE+ +  +E    EE EE  EE
Sbjct: 76  QQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTPEEREELREE 132

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 49.6 bits (119), Expect = 5e-07
 Identities = 19/55 (34%), Positives = 34/55 (61%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           R+    +++E+EEEEEEE E EE +E ++ +E  E+E  + + E+  E E ++  
Sbjct: 91  RKLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKE 145

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 51.5 bits (123), Expect = 5e-07
 Identities = 25/55 (45%), Positives = 33/55 (60%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           G RE  EEEEEE E  ++ E+  + E E  ++++ EEEE EEE     E E EEE
Sbjct: 204 GNRELNEEEEEEAEGSDDGEDVVDYEGERIDKKQGEEEEMEEEVINLFEIEWEEE 258

Length = 279

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 50.2 bits (120), Expect = 5e-07
 Identities = 22/56 (39%), Positives = 36/56 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E ++ E EE E+E+E  E E E+  E+ ++EE  +EEE+EEE E+ +++E     R
Sbjct: 55  EEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEEEKEEEAEDVKQQEVFSFKR 110

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 48.9 bits (117), Expect = 5e-07
 Identities = 22/67 (32%), Positives = 36/67 (53%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           R    EE ++E E++ +E +E  +  EEE  +EE+ E E+ E+ E++E E   E  V   
Sbjct: 54  RKRIREERKQELEKQLKERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDY 113

Query: 657 GKEEISL 663
            +E I  
Sbjct: 114 EEEYIDE 120

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 49.6 bits (117), Expect = 5e-07
 Identities = 31/53 (58%), Positives = 35/53 (66%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           + ++E EEEEE E EEE EEE E EEE +EE E EE  EEE E E E E E E
Sbjct: 59  DPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPE 111

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 53.1 bits (127), Expect = 5e-07
 Identities = 21/50 (42%), Positives = 41/50 (82%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           ++E+E+E++++EE++EEEEEEEEE++  ++E+EE+E  E+   E+ E ++
Sbjct: 156 DDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFTYEKSEVDK 205

Length = 2849

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 52.7 bits (126), Expect = 6e-07
 Identities = 33/86 (38%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEE---EEEEEEEEEEEEEVQEEEEEEEE 635
           + +  G    E  I   R+GE+E E E E +E +   E E EE E E E   E  E+E E
Sbjct: 672 ETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGE 731

Query: 636 EEEEEEEEEEEEEEEEEVRGGGKEEI 661
            E  EE EE E+E E E  G  + E 
Sbjct: 732 IETGEEGEEVEDEGEGEAEGKHEVET 757

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.9 bits (124), Expect = 6e-07
 Identities = 11/68 (16%), Positives = 20/68 (29%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           +     + E        +   +E  E      ++      ++  E E+E  E E  G   
Sbjct: 188 DSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPPF 247

Query: 659 EEISLHFY 666
                H Y
Sbjct: 248 PGHRSHSY 255

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.9 bits (124), Expect = 6e-07
 Identities = 6/62 (9%), Positives = 10/62 (16%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
                 E                  E    E       ++     +   E+  E      
Sbjct: 123 TSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPT 182

Query: 659 EE 660
            E
Sbjct: 183 SE 184

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.9 bits (124), Expect = 6e-07
 Identities = 6/65 (9%), Positives = 7/65 (10%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
                          EE       E       E                  E    E   
Sbjct: 97  SESVGSPTPSPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHN 156

Query: 656 GGKEE 660
               +
Sbjct: 157 PSPNQ 161

Length = 413

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

 Score = 50.1 bits (119), Expect = 6e-07
 Identities = 28/77 (36%), Positives = 49/77 (63%), Gaps = 3/77 (3%)

Query: 580 QDEIGSPRIENIIQ---LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           +D++ S + ++I +   LI R E+ E+  +E EE EE  E E  EE+ + +E++EE+E E
Sbjct: 104 RDQLRSVKKDDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQERE 163

Query: 637 EEEEEEEEEEEEEEEEV 653
            EE+  EE+ ++ E E+
Sbjct: 164 REEQTIEEQSDDSEHEI 180

Length = 197

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 52.7 bits (126), Expect = 6e-07
 Identities = 18/47 (38%), Positives = 35/47 (74%)

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            EE+    +   + +++E+E+E++++EE++EEEEEEEEE++G   E+
Sbjct: 141 AEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDED 187

Length = 2849

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 51.4 bits (123), Expect = 6e-07
 Identities = 22/54 (40%), Positives = 30/54 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
              E  ++     +   E++E   E  + E+ EEEE EE EE+EEEE EEE EE
Sbjct: 48  AEPETSDDPYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEE 101

Length = 306

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 48.8 bits (116), Expect = 7e-07
 Identities = 15/52 (28%), Positives = 23/52 (44%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E    E+          E  EE E    +E+ +E  E +  +E +EEEE +E
Sbjct: 54  EAGRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDE 105

Length = 131

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 50.0 bits (120), Expect = 7e-07
 Identities = 23/45 (51%), Positives = 30/45 (66%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            EE+ E+ EEE EE EV+E  E+E EEE  EEE E E  +EE+ +
Sbjct: 1   MEEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAK 45

Length = 191

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 47.6 bits (113), Expect = 7e-07
 Identities = 23/45 (51%), Positives = 31/45 (68%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           ++  E EE EE +EEEEEEE +E+E E E   ++EE EEE E+ E
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 47.6 bits (113), Expect = 7e-07
 Identities = 23/50 (46%), Positives = 32/50 (64%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            +   ++  E EE EE +EEEEEEEE ++E E E   ++EE EEE E+ E
Sbjct: 47  SQSAFKKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 52.8 bits (126), Expect = 7e-07
 Identities = 20/61 (32%), Positives = 44/61 (72%), Gaps = 3/61 (4%)

Query: 600  REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
            ++ EE++++ EE ++ EE+E++  E +++E EE ++ EE +++E EE+++ EE++   K 
Sbjct: 1668 KKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELK---KA 1724

Query: 660  E 660
            E
Sbjct: 1725 E 1725

Length = 2084

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 49.5 bits (118), Expect = 7e-07
 Identities = 22/51 (43%), Positives = 32/51 (62%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           +L  R    ++EEE+ + + EE EE+EEE E+     +EE+EE EE EEE 
Sbjct: 9   KLKVRPPPTKDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEET 59

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 49.5 bits (118), Expect = 7e-07
 Identities = 20/56 (35%), Positives = 34/56 (60%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +   ++ +      ++EEE+ + + EE EE +EE E+ E+  +EE+EE EE EEE 
Sbjct: 4   KGNAKKLKVRPPPTKDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEEET 59

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 52.2 bits (125), Expect = 7e-07
 Identities = 19/55 (34%), Positives = 29/55 (52%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            + +  E+ E   EE E  +E EE+E E  + E EE E +  E  E+ E +E +E
Sbjct: 239 DQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDE 293

Length = 620

>gnl|CDD|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic N-terminal

 Score = 47.4 bits (113), Expect = 7e-07
 Identities = 21/56 (37%), Positives = 34/56 (60%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            + EEEEEEEE++ E+  +E+E  +E E +++      +   E+EEEE+ EE  E 
Sbjct: 9   DDEEEEEEEEEDDLEDLSDEDEFIDEAEAEDDRRHRRLDRRREKEEEEDAEELAEY 64

This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. Length = 92

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 51.4 bits (123), Expect = 7e-07
 Identities = 28/68 (41%), Positives = 36/68 (52%), Gaps = 4/68 (5%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEV----QEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E  E E  ++     +   E++E   EV      EEEE EE EE+EEEE EEE EE E  
Sbjct: 46  ELAEPETSDDPYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPL 105

Query: 655 GGGKEEIS 662
           G   EE++
Sbjct: 106 GDTPEELT 113

Length = 306

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 52.0 bits (125), Expect = 7e-07
 Identities = 28/46 (60%), Positives = 28/46 (60%), Gaps = 2/46 (4%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           L RR  R       E EEEEEEEEE  EEEEE  EEEEEE   EEE
Sbjct: 290 LRRRRRRRPPPSPPEPEEEEEEEEEVPEEEEE--EEEEEERTFEEE 333

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

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

 Score = 52.3 bits (125), Expect = 7e-07
 Identities = 26/89 (29%), Positives = 43/89 (48%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
             + ++E+ +   E   +     E +   E+EE+ +EEE EE   E +EE + E+  EEE
Sbjct: 797 LKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELKEEQKLEKLAEEE 856

Query: 636 EEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
            E  EEE  +EE  +E +    + E    
Sbjct: 857 LERLEEEITKEELLQELLLKEEELEEQKL 885

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|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 48.4 bits (116), Expect = 7e-07
 Identities = 18/56 (32%), Positives = 33/56 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E+ + E+++EE++ E E+  +   EE+ + E E+ E+E EE E E    E + E +
Sbjct: 20  EKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAELARRELKAEAK 75

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 49.3 bits (118), Expect = 8e-07
 Identities = 25/59 (42%), Positives = 33/59 (55%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
           + EE   E  E++EEEE  EEE ++ EEE EEEEEE +     EEEEE+     +    
Sbjct: 65  DREEARLELLEQQEEEESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTP 123

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.5 bits (123), Expect = 8e-07
 Identities = 6/63 (9%), Positives = 9/63 (14%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E        E       E                  E    E       ++        
Sbjct: 111 AEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPS 170

Query: 658 KEE 660
            E+
Sbjct: 171 HED 173

Length = 413

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

 Score = 51.9 bits (124), Expect = 8e-07
 Identities = 18/60 (30%), Positives = 31/60 (51%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           ++E  EE+   +      + EE E+    E   + E E++E+ EE EEE+ E  GG  ++
Sbjct: 278 DDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKK 337

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|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 51.1 bits (123), Expect = 9e-07
 Identities = 29/85 (34%), Positives = 36/85 (42%), Gaps = 25/85 (29%)

Query: 593 QLIRRGEREEEEEEEEEEE--------EEEEEEEEEEEE-----------------EEVQ 627
           Q+  + ER +EE  EEE E         E+EE E+E  E                 EE +
Sbjct: 242 QIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQIEEKE 301

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEEE 652
           E    E EEE EE E   EEE E +
Sbjct: 302 ERRAAEREEELEEGERLREEEAERQ 326

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|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 47.2 bits (112), Expect = 9e-07
 Identities = 23/45 (51%), Positives = 31/45 (68%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           ++  E EE EE +EEEEEE +EE+E E E   ++EE EEE E+ E
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 49.4 bits (118), Expect = 9e-07
 Identities = 25/69 (36%), Positives = 44/69 (63%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +Q     ++ +E+EEE+E  +E  + +EEE++ E +E E+E+E  E E E+  E++E+EE
Sbjct: 27  MQKTFIIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEE 86

Query: 652 EVRGGGKEE 660
             +   KEE
Sbjct: 87  IAQEEEKEE 95

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

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

 Score = 52.0 bits (125), Expect = 9e-07
 Identities = 26/74 (35%), Positives = 33/74 (44%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E + +L  + E  +EE EE E   EE E+   E EE  +E EE+     EE EE  E   
Sbjct: 323 ERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALR 382

Query: 649 EEEEVRGGGKEEIS 662
           EE         EI 
Sbjct: 383 EELAELEAELAEIR 396

Length = 1163

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 50.6 bits (121), Expect = 9e-07
 Identities = 17/66 (25%), Positives = 35/66 (53%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           ++   +  EE  +E E  + E+ E+E++ +E+  +++ EEEE    +   E+ +   EE+
Sbjct: 202 MLSSMDMAEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEM 261

Query: 654 RGGGKE 659
             G  E
Sbjct: 262 ESGEME 267

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

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

 Score = 51.5 bits (123), Expect = 9e-07
 Identities = 19/55 (34%), Positives = 30/55 (54%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           G+ E  EE+   +      + EE E++   E   + E E++E+ EE EEE+ EEE
Sbjct: 277 GDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEE 331

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|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 49.6 bits (119), Expect = 9e-07
 Identities = 26/54 (48%), Positives = 36/54 (66%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            EE + EE EE E+ EEEE EEEE  +E E EEE++E  E E + EE +++ +R
Sbjct: 8   TEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKDKYLR 61

Length = 193

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 51.5 bits (124), Expect = 1e-06
 Identities = 22/58 (37%), Positives = 39/58 (67%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +RR   EEE++EEEE+ +E  ++ ++E E +  +     + EE+EEEEE+  ++E+EE
Sbjct: 279 LRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEE 336

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 51.1 bits (123), Expect = 1e-06
 Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 21/80 (26%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEE------------EEVQEEEEEEEEEEEEEEE- 642
           RR +   EEE  +   EEEE E + +EE            EE ++  +EE EE  +E E 
Sbjct: 41  RRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQEREQ 100

Query: 643 --------EEEEEEEEEEVR 654
                   +EE+E E +E R
Sbjct: 101 MDEIIERIQEEDEAEAQEKR 120

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|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 48.6 bits (115), Expect = 1e-06
 Identities = 24/62 (38%), Positives = 36/62 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           +R E EE +    EE    EEE   +E +   E+EE+ + + EEEE++E+EE+E     K
Sbjct: 53  DRLEREELKRRAAEERLRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQK 112

Query: 659 EE 660
           EE
Sbjct: 113 EE 114

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 46.8 bits (111), Expect = 1e-06
 Identities = 23/45 (51%), Positives = 31/45 (68%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++  E EE EE +EEEEE +EEE+E E E   ++EE EEE E+ E
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 52.1 bits (124), Expect = 1e-06
 Identities = 18/55 (32%), Positives = 37/55 (67%)

Query: 600  REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            +  EE ++ EE++++ EE ++ EE+E +  E  ++E EE ++ EE +++E EE +
Sbjct: 1662 KAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKK 1716

Length = 2084

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

 Score = 51.7 bits (123), Expect = 1e-06
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 5/78 (6%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE-----EEEEEE 643
            EN I+     ++ EE++++ EE ++ EE+E++  E   +E EE ++ EE      EE+++
Sbjct: 1658 ENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKK 1717

Query: 644  EEEEEEEEEVRGGGKEEI 661
             EE ++ EE      EE 
Sbjct: 1718 AEELKKAEEENKIKAEEA 1735

Length = 2084

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.1 bits (122), Expect = 1e-06
 Identities = 6/63 (9%), Positives = 7/63 (11%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                     EE       E       E                  E    E        
Sbjct: 102 SPTPSPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQ 161

Query: 658 KEE 660
           +  
Sbjct: 162 QPS 164

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.1 bits (122), Expect = 1e-06
 Identities = 9/63 (14%), Positives = 15/63 (23%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                 E    E       ++     +   E+  EE E    E E +     + E     
Sbjct: 142 SHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSS 201

Query: 658 KEE 660
              
Sbjct: 202 PPP 204

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.1 bits (122), Expect = 1e-06
 Identities = 5/62 (8%), Positives = 11/62 (17%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E       E       E                  E    E       ++    ++   +
Sbjct: 113 ELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHE 172

Query: 659 EE 660
           + 
Sbjct: 173 DS 174

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 51.1 bits (122), Expect = 1e-06
 Identities = 6/63 (9%), Positives = 6/63 (9%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                    EE       E       E                  E    E         
Sbjct: 103 PTPSPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQ 162

Query: 658 KEE 660
              
Sbjct: 163 PSS 165

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.7 bits (121), Expect = 1e-06
 Identities = 7/67 (10%), Positives = 9/67 (13%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                 EE       E       E                  E    E        +   
Sbjct: 106 SPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSS 165

Query: 658 KEEISLH 664
             + S  
Sbjct: 166 FLQPSHE 172

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.7 bits (121), Expect = 1e-06
 Identities = 14/70 (20%), Positives = 18/70 (25%), Gaps = 7/70 (10%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEE-------EEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           G R+ E + E  EE    E+EE  +        E V           EE       E   
Sbjct: 65  GHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSPENTS 124

Query: 651 EEVRGGGKEE 660
                     
Sbjct: 125 GSSPESPASH 134

Length = 413

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 48.1 bits (115), Expect = 1e-06
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
              EEE ++EE+ E E+ E+ E++E E   E    + EEE  +E++ +     EE+
Sbjct: 77  KLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKTTVTVEEL 132

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 48.1 bits (115), Expect = 1e-06
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 10/75 (13%)

Query: 596 RRGEREEEEEEEEEEEEEEE-----EEEEEEEEEEVQE-----EEEEEEEEEEEEEEEEE 645
           RR + +EE +E+E EE  EE     EE ++E E++++E     +  EEE ++EE+ E E+
Sbjct: 34  RRKKAQEEAKEKEREERIEERKRIREERKQELEKQLKERKEALKLLEEENDDEEDAETED 93

Query: 646 EEEEEEEVRGGGKEE 660
            E+ E++   G  E 
Sbjct: 94  TEDVEDDEWEGFPEP 108

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 47.7 bits (114), Expect = 1e-06
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           R+  REE ++E E++ +E +E  +  EEE   EE+ E E+ E+ E++E E   E    
Sbjct: 54  RKRIREERKQELEKQLKERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVT 111

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated

 Score = 50.6 bits (122), Expect = 1e-06
 Identities = 23/69 (33%), Positives = 33/69 (47%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E    ++ +   +         +++  +EE +E      +    EEEEEEEEEEEEEE  
Sbjct: 258 ETADDILSKAVAQALALAAALADKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPS 317

Query: 649 EEEEVRGGG 657
           EEE   G G
Sbjct: 318 EEEAAAGLG 326

Length = 330

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

 Score = 51.5 bits (123), Expect = 1e-06
 Identities = 15/65 (23%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV-----RG 655
           +      + EE E++   E   + E++++E+ EE EEE+ EEE    ++ +++     + 
Sbjct: 289 DSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKK 348

Query: 656 GGKEE 660
            G ++
Sbjct: 349 NGLDK 353

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|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic N-terminal

 Score = 46.7 bits (111), Expect = 1e-06
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
           + E E ++EEEEEEEEE++ E+   E+E  +E E E++      +   E+      EE++
Sbjct: 3   DTEAEVDDEEEEEEEEEDDLEDLSDEDEFIDEAEAEDDRRHRRLDRRREKEEEEDAEELA 62

This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. Length = 92

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 51.6 bits (123), Expect = 1e-06
 Identities = 27/73 (36%), Positives = 47/73 (64%), Gaps = 2/73 (2%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           + EIG   ++ II   RR     EE+    +    ++++E+E+E++  EE++EEEEEEEE
Sbjct: 121 KAEIGD--LDMIIIKRRRARHLAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEE 178

Query: 640 EEEEEEEEEEEEE 652
           E +  ++E+EE+E
Sbjct: 179 EIKGFDDEDEEDE 191

Length = 2849

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 49.3 bits (118), Expect = 1e-06
 Identities = 26/54 (48%), Positives = 36/54 (66%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + ++ EE + EE EE E+ EEEE EEE  EEE E EEE++E  E E + EE ++
Sbjct: 4   KEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKD 57

Length = 193

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 48.9 bits (117), Expect = 1e-06
 Identities = 26/55 (47%), Positives = 37/55 (67%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            ++E++ EE + EE EE E+ EEEE EE + EEE E EEE++E  E E + EE +
Sbjct: 2   SDKEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELK 56

Length = 193

>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 47.3 bits (113), Expect = 1e-06
 Identities = 6/56 (10%), Positives = 40/56 (71%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
              +  +++E+EE+E++   ++++++++++   + ++++ + ++++++  E++++E
Sbjct: 49  DAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDDDDFLEDDDDE 104

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 51.4 bits (123), Expect = 1e-06
 Identities = 21/55 (38%), Positives = 37/55 (67%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           ++  E EEE+E++ EE +++E+E E  E+ E E E + E+ EE+E+E++ E   G
Sbjct: 642 QQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEG 696

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|131972 TIGR02926, AhaH, ATP synthase archaeal, H subunit

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 29/74 (39%), Positives = 40/74 (54%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +E I +     E   EE EEE ++   E  EE  E  E  EEE  +  EE  +E EEE E
Sbjct: 1   LEEIKKAEEDAEELIEEAEEERKQRIAEAREEARELLEEAEEEASKLGEEIIKEAEEEIE 60

Query: 648 EEEEEVRGGGKEEI 661
           +E E++R  G++EI
Sbjct: 61  KEAEKIREEGEKEI 74

he A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The hydrophilic A1 "stalk" complex (AhaABCDEFG) is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. It is unclear precisely where AhaH fits into these complexes. Length = 85

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 47.7 bits (114), Expect = 1e-06
 Identities = 12/52 (23%), Positives = 37/52 (71%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +EE    EE+ ++++++  + +++ + ++   +++ +EE+ +EE++E+EE+E
Sbjct: 77  DEEIIPLEEKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDEEDE 128

Length = 129

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 51.3 bits (123), Expect = 1e-06
 Identities = 22/48 (45%), Positives = 34/48 (70%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           E    E ++EEEE+EEEEEEE+E+E   +E  ++EE EE++ E + E+
Sbjct: 382 EDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYED 429

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 51.1 bits (122), Expect = 2e-06
 Identities = 31/66 (46%), Positives = 37/66 (56%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R E   Q       +  +      E      +E EEEE V+EEEEEEEEEEEEE+E EEE
Sbjct: 406 RQERERQGTSSRSSDPSKASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEE 465

Query: 647 EEEEEE 652
           E E+EE
Sbjct: 466 EGEDEE 471

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 51.1 bits (122), Expect = 2e-06
 Identities = 24/64 (37%), Positives = 31/64 (48%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
             EEE E+EEEEEE E +   EEE E   E + + EE EE+ E    E      +  G +
Sbjct: 462 SEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRNSEMAGISRMSEGQQ 521

Query: 659 EEIS 662
              S
Sbjct: 522 PRGS 525

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 48.5 bits (116), Expect = 2e-06
 Identities = 21/57 (36%), Positives = 35/57 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
              ERE+++EEEE +E EE+  +E+EE E+++     EEE  ++   +EE  E  E+
Sbjct: 48  LEEEREKKKEEEERKEREEQARKEQEEYEKLKSSFVVEEEGTDKLSADEESNELLED 104

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|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 47.6 bits (113), Expect = 2e-06
 Identities = 16/55 (29%), Positives = 24/55 (43%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           R  E  E    E+          E  EE E  + +E+ +E  E +  +E +EEEE
Sbjct: 48  RDLEWTEAGRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEE 102

Length = 131

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

 Score = 48.6 bits (116), Expect = 2e-06
 Identities = 21/53 (39%), Positives = 34/53 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           ++ +EE+ E EE E+EE  E+ EE  EV+ EE ++E  + +EE ++ E E E 
Sbjct: 27  DKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENKKLENELEA 79

Length = 211

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 48.1 bits (115), Expect = 2e-06
 Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E E++E  +EEE +  ++E++EE + E  EE+     +EEE + E E E + E
Sbjct: 19  EDEDDESSDEEEVDLPDDEQDEESDSE--EEQIFVTRQEEEVDPEAEAEFDRE 69

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein (DUF2052)

 Score = 48.2 bits (115), Expect = 2e-06
 Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE---- 652
               EEEE+ EEE EEEEEE +     EE +E+ +  +E    EE EE  EE   E    
Sbjct: 81  ESAEEEEEDPEEENEEEEEEYQRGPFGEEEEEDGDSYDELPTPEEREELREEFISEMHQR 140

Query: 653 -VRGGGKE 659
            + G  K+
Sbjct: 141 FLSGEDKD 148

This entry is of sequences of two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. Length = 178

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 50.5 bits (121), Expect = 2e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
            +E +  ++     +  + EE +E ++EEEE+  +E EEEE E+ EEE  + R  G  E 
Sbjct: 349 TKESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSSES 408

Query: 662 S 662
           S
Sbjct: 409 S 409

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 50.3 bits (121), Expect = 2e-06
 Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 16/78 (20%)

Query: 593 QLIRRGEREEEEEEEEEE-----EEEEEEEEEEEEEEEVQEEEEE-----------EEEE 636
           Q+  +   + EE+EEE       EEE  +   EEEE E + +EE            EE E
Sbjct: 25  QIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEERE 84

Query: 637 EEEEEEEEEEEEEEEEVR 654
           +  +EE EE  +E E++ 
Sbjct: 85  KRRQEEYEERLQEREQMD 102

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|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 49.3 bits (118), Expect = 2e-06
 Identities = 23/51 (45%), Positives = 35/51 (68%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           E EE++EE E EEEEEEEE + + ++   +E E ++EEE E+E + EE  +
Sbjct: 35  EEEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLK 85

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

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 46.6 bits (111), Expect = 2e-06
 Identities = 21/45 (46%), Positives = 27/45 (60%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            ++E  E  EE+ EEEE  E EE++  EEE  +E   EEEE EE 
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEE 74

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            ++E  E  EE+ EEEE+ E  +++  EEE  +E   EEEE EEEE++
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDK 77

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 47.7 bits (114), Expect = 2e-06
 Identities = 20/57 (35%), Positives = 37/57 (64%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           +  ++ L ++ + EEEEEE E EE +EEE+ +E  E+E+ + + E+  E E +++E 
Sbjct: 90  VRKLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEI 146

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 48.7 bits (116), Expect = 2e-06
 Identities = 23/67 (34%), Positives = 39/67 (58%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            I +   E+EEE+E  +E  + +EEE++ E E  E+E+E  E E E+  E++E+EE  + 
Sbjct: 31  FIIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQE 90

Query: 654 RGGGKEE 660
               +E 
Sbjct: 91  EEKEEEA 97

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 48.2 bits (115), Expect = 2e-06
 Identities = 19/56 (33%), Positives = 42/56 (75%), Gaps = 1/56 (1%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE-EEEEEEEEEEEEEEEEEEEEV 653
             E++EEEE++E +  ++E ++E+E++ +  E   E++E +E+E+++E+EE+EE+ 
Sbjct: 120 YDEDKEEEEDDEVDSLDDENDDEDEDDDEIVEILIEDDEVDEDEDDDEDEEDEEDK 175

Length = 175

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 50.8 bits (121), Expect = 2e-06
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEE------EEEEEEEEEEEEEEEEVQEE 629
             S +D      +++        E EE+E  E+E      E +   E E   E+    E 
Sbjct: 97  SESHEDGSDGSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDET 156

Query: 630 EEEEEEEEEEEEEEEEEEEEEEEVRG 655
           E++EE++ EEEE  EE+E  E+  R 
Sbjct: 157 EDDEEKKMEEEEAGEEKESVEQATRE 182

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 16/94 (17%), Positives = 25/94 (26%), Gaps = 2/94 (2%)

Query: 566 KTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEE 625
            T   + K    +       P++  + +   R    + E  EE    E+EE  +      
Sbjct: 38  GTAARAAKPAPPAPTTS--GPQVRAVAEQGHRQTESDTETAEESRHGEKEERGQGGPSGS 95

Query: 626 VQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
             E             EE       E   G   E
Sbjct: 96  GSESVGSPTPSPSGSAEELASGLSPENTSGSSPE 129

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 9/63 (14%), Positives = 14/63 (22%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                        E    E       ++     +   E+  EE E    E E +      
Sbjct: 135 SPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQ 194

Query: 658 KEE 660
            E 
Sbjct: 195 SET 197

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.7 bits (121), Expect = 2e-06
 Identities = 9/55 (16%), Positives = 18/55 (32%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
               + E        +   +E  E +    ++      ++  E E+E  E E E 
Sbjct: 190 PGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREG 244

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.4 bits (120), Expect = 2e-06
 Identities = 7/62 (11%), Positives = 15/62 (24%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
              E       ++     +   E+  EE +    E E +     + E             
Sbjct: 150 APPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPD 209

Query: 658 KE 659
           + 
Sbjct: 210 EP 211

Length = 413

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 47.6 bits (112), Expect = 2e-06
 Identities = 33/56 (58%), Positives = 34/56 (60%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
              E EEEEE E EEE EEE E EEE EEE + EE  EEE E E E E E E E E
Sbjct: 60  PDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPEPEPE 115

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 51.6 bits (123), Expect = 2e-06
 Identities = 26/70 (37%), Positives = 46/70 (65%), Gaps = 4/70 (5%)

Query: 581 DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           +E  SPR   +I      + E+E+E++++EE++EEEEEEEEE +   +E+EE+E  E+  
Sbjct: 142 EEDMSPRDNFVID----DDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFT 197

Query: 641 EEEEEEEEEE 650
            E+ E ++ +
Sbjct: 198 YEKSEVDKTD 207

Length = 2849

>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 46.5 bits (111), Expect = 2e-06
 Identities = 8/61 (13%), Positives = 40/61 (65%), Gaps = 4/61 (6%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE----EEEEEEEEEEEEE 651
           R    + E+  +++E+EE+E++   +++++  ++++  + +++    ++++++  E++++
Sbjct: 44  RAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDDDDFLEDDDD 103

Query: 652 E 652
           E
Sbjct: 104 E 104

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 51.0 bits (122), Expect = 2e-06
 Identities = 23/58 (39%), Positives = 36/58 (62%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           E EEE+E++ EE +++E+E E  E  E E E + E+ EE+E+E++ E  E V    K 
Sbjct: 646 EGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDKA 703

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 51.3 bits (123), Expect = 2e-06
 Identities = 22/50 (44%), Positives = 35/50 (70%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           E E+   E ++EEEE+EEEEEEE+E +   +E  ++EE EE++ E + E+
Sbjct: 380 EIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYED 429

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 50.9 bits (122), Expect = 2e-06
 Identities = 23/50 (46%), Positives = 36/50 (72%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E E+   E ++EEEE+EEEEEEE+E+E   +E  ++EE EE++ E + E+
Sbjct: 380 EIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYED 429

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 50.9 bits (122), Expect = 2e-06
 Identities = 29/110 (26%), Positives = 49/110 (44%), Gaps = 23/110 (20%)

Query: 538 EDFKPFVTALMNSEWQSL----WDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQ 593
           + F  F      + W++L    W     T +   I  +    +  D +            
Sbjct: 339 DAFTHFQEGFTQALWETLNKQKWTKAKETEQ-DYILDAFSALEIEDANT----------- 386

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
                  E ++EEEE+EEEEEEE+E+E   +E  ++EE EE++ E + E+
Sbjct: 387 -------ERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYED 429

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 47.0 bits (112), Expect = 2e-06
 Identities = 19/29 (65%), Positives = 19/29 (65%)

Query: 629 EEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                EEEEEEEEEEEEEEEE EE    G
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEEAMAG 99

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 47.0 bits (112), Expect = 2e-06
 Identities = 20/29 (68%), Positives = 20/29 (68%)

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
                EEEEEEEEEEEEEEEE EEE   G
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEEAMAG 99

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 46.6 bits (111), Expect = 2e-06
 Identities = 20/30 (66%), Positives = 21/30 (70%)

Query: 626 VQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
                 EEEEEEEEEEEEEEEE EEE + G
Sbjct: 70  AAAAAAEEEEEEEEEEEEEEEESEEEAMAG 99

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 51.3 bits (122), Expect = 2e-06
 Identities = 33/76 (43%), Positives = 36/76 (47%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            ENI + I   + E  EE EE  EE  EE  EE  EE V+E EE  EE  EE  EE  EE 
Sbjct: 1055 ENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAEENAEEN 1114

Query: 649  EEEEVRGGGKEEISLH 664
             EE       E    H
Sbjct: 1115 AEENAEEYDDENPEEH 1130

Length = 1136

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 49.7 bits (119), Expect = 2e-06
 Identities = 20/67 (29%), Positives = 39/67 (58%), Gaps = 12/67 (17%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEE------------VQEEEEEEEEEEEEEEEEEE 645
            E E+++ ++  +EEE+EE+EEE+ +              ++E+E+ + E+EE+   E E
Sbjct: 26  DEDEDDDVKDSWDEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELE 85

Query: 646 EEEEEEE 652
           E+  E+E
Sbjct: 86  EDTPEDE 92

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|221203 pfam11748, DUF3306, Protein of unknown function (DUF3306)

 Score = 46.5 bits (111), Expect = 2e-06
 Identities = 19/61 (31%), Positives = 24/61 (39%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           RR      EE  E  E  EEE          +EEEE E E+EE  EE +  + +      
Sbjct: 8   RRKLAVRAEEPAEPAETAEEEAAAAAPAPAPEEEEEAELEDEELLEELDLPDPDTLTPGS 67

Query: 656 G 656
            
Sbjct: 68  D 68

This family of proteobacterial species proteins has no known function. Length = 115

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

 Score = 50.3 bits (120), Expect = 2e-06
 Identities = 18/62 (29%), Positives = 42/62 (67%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
               +EEE+E+E+ +EE+++++E+ +E  ++ + +EE +E+   +E+E+E+E++V     
Sbjct: 100 NESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRD 159

Query: 659 EE 660
            E
Sbjct: 160 RE 161

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 47.3 bits (113), Expect = 2e-06
 Identities = 16/32 (50%), Positives = 27/32 (84%)

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            EE+  +++EE+EEEE++EE+++E+E EEEE 
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 46.5 bits (111), Expect = 3e-06
 Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 6/47 (12%)

Query: 483 NVPNTNKLKTIRPSI------KKDITFMWCPSHCGIKGNELVDVAAK 523
             P  ++ K I+  I      K  +   W P H GI GNEL D  AK
Sbjct: 76  GWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAK 122

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 50.0 bits (120), Expect = 3e-06
 Identities = 22/52 (42%), Positives = 37/52 (71%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            +  EEEEE+ +  +EEE+EE+E+ ++E  EEEEEEE+E+++++  E    E
Sbjct: 339 DDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKEKKKKKSAESTRSE 390

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 46.9 bits (111), Expect = 3e-06
 Identities = 13/59 (22%), Positives = 23/59 (38%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           R  R+ E  E    E+          E   + E  + +E+ +E  E +  +E +EE   
Sbjct: 45  REARDLEWTEAGRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEET 103

Length = 131

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 46.5 bits (110), Expect = 3e-06
 Identities = 15/63 (23%), Positives = 24/63 (38%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E  E    E+          E  EE +  + +E+ +E  E +  +E +EEEE      E 
Sbjct: 51  EWTEAGRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADAADEADEEEETDEAVDET 110

Query: 661 ISL 663
              
Sbjct: 111 ADE 113

Length = 131

>gnl|CDD|217450 pfam03247, Prothymosin, Prothymosin/parathymosin family

 Score = 46.1 bits (109), Expect = 3e-06
 Identities = 25/61 (40%), Positives = 37/61 (60%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           +E++E  EE+E  +       E EE   +E ++E EEEEE +E++EEEE E E   G +E
Sbjct: 17  KEKKEVVEEKENGKNAPANGNENEENGAQEGDDEMEEEEEVDEDDEEEEGEGEEEEGEEE 76

Query: 660 E 660
           E
Sbjct: 77  E 77

Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. Length = 106

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 49.9 bits (120), Expect = 3e-06
 Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 15/77 (19%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE--------- 642
           +   R  + EE++  + EE+EEE   +E  EEE ++   EEEE E + +EE         
Sbjct: 18  VNKERDAQIEEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQ 77

Query: 643 ------EEEEEEEEEEV 653
                 E+  +EE EE 
Sbjct: 78  EQIEEREKRRQEEYEER 94

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|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 49.5 bits (119), Expect = 3e-06
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 16/80 (20%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEE-------EEEEEEEEEEEEEEVQEEEEEEEE------ 635
           E  +  +R  + E E+E EE +E       EE E +E ++E+EE ++   +++E      
Sbjct: 181 EREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQKEKEEAEKRRRQKQELQRARE 240

Query: 636 ---EEEEEEEEEEEEEEEEE 652
              EE+EE  +EE  EEE E
Sbjct: 241 EQIEEKEERLQEERAEEEAE 260

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|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 49.3 bits (118), Expect = 3e-06
 Identities = 19/53 (35%), Positives = 34/53 (64%)

Query: 584 GSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           G P +    +       E+ EEEEEE++  E E+E+EE+E+E +EE+++E ++
Sbjct: 267 GEPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319

Length = 319

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 49.2 bits (117), Expect = 3e-06
 Identities = 25/57 (43%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 598 GEREEEEEEEEEEEEEEEEEEE---EEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           GE   E  EEEEEE E  ++ E   + E E + +++ EEEE EEE     E E EEE
Sbjct: 202 GEGNRELNEEEEEEAEGSDDGEDVVDYEGERIDKKQGEEEEMEEEVINLFEIEWEEE 258

Length = 279

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 48.3 bits (116), Expect = 3e-06
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 11/78 (14%)

Query: 602 EEEEEEEEEE-----------EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           E+ +  E  E           +               E +EE+ E++++++E+E+E++EE
Sbjct: 10  EQYDRVEAGEGRLSDLISGFIDPNAAAAAATAAAIESELDEEDLEDDDDDDEDEDEDDEE 69

Query: 651 EEVRGGGKEEISLHFYVL 668
           E   G   EE    F  L
Sbjct: 70  EADLGPDPEEARERFAEL 87

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

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

 Score = 48.6 bits (116), Expect = 3e-06
 Identities = 21/51 (41%), Positives = 33/51 (64%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E++E++ + E+E+EE EEE EEE+E   +E E+E EE+ E   E+E     
Sbjct: 76  EDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITNPS 126

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|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.0 bits (119), Expect = 3e-06
 Identities = 6/54 (11%), Positives = 10/54 (18%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
                                E    E       ++     +   E+  EE E 
Sbjct: 127 SPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEP 180

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 50.0 bits (119), Expect = 3e-06
 Identities = 14/60 (23%), Positives = 18/60 (30%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E+   + E + E  EE    E+EE  Q        E             EE   G   E 
Sbjct: 63  EQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSPEN 122

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.6 bits (118), Expect = 3e-06
 Identities = 10/63 (15%), Positives = 16/63 (25%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           G  E    E       ++     +   E   EE E    E E +     + E        
Sbjct: 145 GPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPP 204

Query: 658 KEE 660
           +  
Sbjct: 205 QSP 207

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.6 bits (118), Expect = 3e-06
 Identities = 5/61 (8%), Positives = 9/61 (14%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
               E       E                  E    E       ++     +       +
Sbjct: 117 GLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPE 176

Query: 659 E 659
           E
Sbjct: 177 E 177

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.6 bits (118), Expect = 3e-06
 Identities = 7/63 (11%), Positives = 13/63 (20%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
              E                  E    E       ++     +   E+  EE E      
Sbjct: 126 SSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEP 185

Query: 658 KEE 660
           + +
Sbjct: 186 EPD 188

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 49.4 bits (118), Expect = 3e-06
 Identities = 16/74 (21%), Positives = 36/74 (48%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
               +++ +       EE  +E E  + E+ E+E++ +E +++++ EEEE    +   E+
Sbjct: 194 AFARVVRDMLSSMDMAEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSED 253

Query: 647 EEEEEEVRGGGKEE 660
            +   E    G+ E
Sbjct: 254 SDASSEEMESGEME 267

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 46.6 bits (111), Expect = 3e-06
 Identities = 19/54 (35%), Positives = 30/54 (55%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           QL  R E  +  EEE ++EE+ E E+ E+ E++  E   E    + EEE  +E+
Sbjct: 68  QLKERKEALKLLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDED 121

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 50.2 bits (120), Expect = 3e-06
 Identities = 20/60 (33%), Positives = 30/60 (50%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
             E+ E   EE E  +E EE+E E  + + EE E +  E  E+ E +E +E+ E  G   
Sbjct: 243 NNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTETPGEDA 302

Length = 620

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 47.3 bits (111), Expect = 3e-06
 Identities = 32/55 (58%), Positives = 34/55 (61%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           G   ++E EEEEE E EEE EEE E EE  EEE E EE  EEE E E E E E E
Sbjct: 57  GTDPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPE 111

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 46.9 bits (110), Expect = 3e-06
 Identities = 34/69 (49%), Positives = 38/69 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E  E EEE EEE E EEE EEE E EE  EEE E E E E E E E E E E E      
Sbjct: 68  EEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPEPEPEPEPEPEPGAATL 127

Query: 659 EEISLHFYV 667
           + ++L F +
Sbjct: 128 KSVALPFAI 136

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

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

 Score = 50.4 bits (120), Expect = 3e-06
 Identities = 24/81 (29%), Positives = 38/81 (46%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             +     +   + E+ + +EEE    EEE +EE E  E ++   E+EE+ +EEE EE  
Sbjct: 781 EEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELA 840

Query: 647 EEEEEEVRGGGKEEISLHFYV 667
            E +EE +     E  L    
Sbjct: 841 LELKEEQKLEKLAEEELERLE 861

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 = 50.4 bits (120), Expect = 3e-06
 Identities = 26/75 (34%), Positives = 44/75 (58%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           EN++ L      EE  +  +E   +E+EE E  ++E  +EEE   +  +E +EEE+E++ 
Sbjct: 225 ENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKL 284

Query: 649 EEEEVRGGGKEEISL 663
           +EEE++   KEE  L
Sbjct: 285 QEEELKLLAKEEEEL 299

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 50.3 bits (120), Expect = 3e-06
 Identities = 20/56 (35%), Positives = 36/56 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E EEE+E++ EE +++E+E E  E+ E + E + E+ EE+E+E++ E  E    + 
Sbjct: 646 EGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPID 701

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 50.2 bits (119), Expect = 3e-06
 Identities = 29/72 (40%), Positives = 35/72 (48%)

Query: 581  DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
            +E     +E I + I     E  EE  EE  EE EE  EE  EE  +E  EE  EE  EE
Sbjct: 1062 EEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAEENAEENAEENAEE 1121

Query: 641  EEEEEEEEEEEE 652
             ++E  EE  EE
Sbjct: 1122 YDDENPEEHNEE 1133

Length = 1136

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 46.9 bits (112), Expect = 3e-06
 Identities = 17/31 (54%), Positives = 27/31 (87%)

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            EE+E  ++EE+EEEE++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 49.7 bits (118), Expect = 3e-06
 Identities = 26/65 (40%), Positives = 45/65 (69%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            + +I + E E   ++EEEE+E+ EE EE EE E V+EE +++E+ E+++E+E + E +E
Sbjct: 92  GLNIIVKNEEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAEGDE 151

Query: 651 EEVRG 655
            E+ G
Sbjct: 152 NELAG 156

Length = 374

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 46.1 bits (110), Expect = 3e-06
 Identities = 16/29 (55%), Positives = 19/29 (65%)

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
                 EE++EEEEEEEE+EE EEE   G
Sbjct: 72  AAAAAAEEKKEEEEEEEEKEESEEEAAAG 100

Length = 106

>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 47.1 bits (112), Expect = 3e-06
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 5/73 (6%)

Query: 586 PRIEN---IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           P + N   + ++ R  E    ++EEEE EEE  +E E+E+  E + E +E+++ E  + +
Sbjct: 76  PLVRNLPAMWKIFR--ELSSSDDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPK 133

Query: 643 EEEEEEEEEEVRG 655
            E+E+ + E  + 
Sbjct: 134 TEKEKPKTEPKKP 146

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

 Score = 49.5 bits (118), Expect = 3e-06
 Identities = 19/74 (25%), Positives = 35/74 (47%)

Query: 577 TSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
              +        E+I +++   E++E +   EE  +EE E+E E +E  ++E  E E  E
Sbjct: 314 RIKELADFGDYYEDIFEVVEVVEKQEGDVVTEESTDEESEDEVEIDESVIEEVAEMELLE 373

Query: 637 EEEEEEEEEEEEEE 650
            + ++  E   E E
Sbjct: 374 VQVDDLAERLAETE 387

Length = 388

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 49.1 bits (117), Expect = 3e-06
 Identities = 20/42 (47%), Positives = 36/42 (85%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            ++ ++EE+++++ +  EE+E++E+EEEEE EEEEEEE+E+E
Sbjct: 244 NKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 49.3 bits (117), Expect = 4e-06
 Identities = 21/58 (36%), Positives = 30/58 (51%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
                 E EE EE E   + E++ +  + EE Q+EE+E E EEEE+ +    EE   E
Sbjct: 116 KEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGE 173

Length = 431

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 49.3 bits (117), Expect = 4e-06
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E EE +++ EE  +  EEEE+  ++EE   +  EEEE+   +EE E    E  E R
Sbjct: 215 ELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAEAAEKR 270

Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 49.1 bits (118), Expect = 4e-06
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 17/78 (21%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEE---------EEVQEEEEEEEEEEEEE---- 640
                + E E +E ++E+EE E+   +++E         EE +E  +EE  EEE E    
Sbjct: 205 RADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERM 264

Query: 641 ----EEEEEEEEEEEEVR 654
                E+EE E+E  E R
Sbjct: 265 LEKQAEDEELEQENAEKR 282

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|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 49.3 bits (118), Expect = 4e-06
 Identities = 25/80 (31%), Positives = 51/80 (63%), Gaps = 2/80 (2%)

Query: 565 LKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEE 624
           ++ I  +++  K   + + G  +++   +++   E + EE  E+ EEEEEE++  E E+E
Sbjct: 242 MEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDE 301

Query: 625 EVQEEEEEEEEEEEEEEEEE 644
           +  EE+E+EEEEE+++E ++
Sbjct: 302 D--EEDEDEEEEEDDDEGDK 319

Length = 319

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

 Score = 50.1 bits (120), Expect = 4e-06
 Identities = 25/75 (33%), Positives = 36/75 (48%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           +  ++ E    +IE + + +   E   EE E+   E EE +EE EE+   + EE EE  E
Sbjct: 320 ELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFE 379

Query: 636 EEEEEEEEEEEEEEE 650
              EE  E E E  E
Sbjct: 380 ALREELAELEAELAE 394

Length = 1163

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.6 bits (118), Expect = 4e-06
 Identities = 9/54 (16%), Positives = 17/54 (31%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            + E        +   +E  E +    +       ++  E E+E  E E E   
Sbjct: 193 PQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPP 246

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.6 bits (118), Expect = 4e-06
 Identities = 6/63 (9%), Positives = 8/63 (12%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           G          EE       E                          E    E       
Sbjct: 101 GSPTPSPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPN 160

Query: 658 KEE 660
           ++ 
Sbjct: 161 QQP 163

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.6 bits (118), Expect = 4e-06
 Identities = 4/62 (6%), Positives = 8/62 (12%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
                  E                  E    E       ++     +   E+        
Sbjct: 122 NTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPP 181

Query: 659 EE 660
             
Sbjct: 182 TS 183

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.6 bits (118), Expect = 4e-06
 Identities = 10/55 (18%), Positives = 17/55 (30%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             + E        +   +E  E +     Q      ++  E E+E  E E E   
Sbjct: 192 PPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPP 246

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.2 bits (117), Expect = 4e-06
 Identities = 6/63 (9%), Positives = 9/63 (14%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                 E       E                  E    E       ++     +      
Sbjct: 115 ASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDS 174

Query: 658 KEE 660
            EE
Sbjct: 175 PEE 177

Length = 413

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

 Score = 49.6 bits (118), Expect = 4e-06
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            REE+   +      + EE E++   E+  + E E++E+ EE EEE+ EEE    + G K
Sbjct: 281 GREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKK 340

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|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic N-terminal

 Score = 45.1 bits (107), Expect = 4e-06
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           + E E ++EEEEEEEEE++ E+   ++E  +E E E++      +   E+E    
Sbjct: 3   DTEAEVDDEEEEEEEEEDDLEDLSDEDEFIDEAEAEDDRRHRRLDRRREKEEEED 57

This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. Length = 92

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

 Score = 50.0 bits (119), Expect = 4e-06
 Identities = 30/102 (29%), Positives = 53/102 (51%)

Query: 563 NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
           +K+      ++      ++E    R++   +   + E   +E+E  EEEE+ E+ + EEE
Sbjct: 733 DKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEE 792

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
           +EE  + +EEE    EEE +EE E  EEE++    +E+I   
Sbjct: 793 KEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEE 834

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 49.9 bits (119), Expect = 4e-06
 Identities = 20/53 (37%), Positives = 35/53 (66%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
              E EEE+E++ EE +++E+E E  E+ + E E + E+ EE+E+E++ E  E
Sbjct: 643 QLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANE 695

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 49.8 bits (119), Expect = 4e-06
 Identities = 22/62 (35%), Positives = 36/62 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E++   +     E E+   E ++EEEE +EEEEEE+E+E   +E  ++EE EE+      
Sbjct: 368 EQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKY 427

Query: 659 EE 660
           E+
Sbjct: 428 ED 429

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

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

 Score = 49.5 bits (118), Expect = 4e-06
 Identities = 17/58 (29%), Positives = 42/58 (72%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           + + + +EE+++++E+ +EE ++ + +EE +E+   +E+E+E+E++ EE  + EEE +
Sbjct: 108 KEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKK 165

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|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 45.7 bits (109), Expect = 4e-06
 Identities = 15/32 (46%), Positives = 18/32 (56%)

Query: 626 VQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                    EE++EEEEEEEE+EE EE    G
Sbjct: 69  AAAAAAAAAEEKKEEEEEEEEKEESEEEAAAG 100

Length = 106

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 49.6 bits (119), Expect = 5e-06
 Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 31/94 (32%)

Query: 601 EEEEEEEEEE-----EEE-------EEEEEEEEEEEEVQEE------------------- 629
           EEE  +EE E     E E       EEE++EEEE+ +   +                   
Sbjct: 260 EEELAKEEAERLKKLEAERLRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQG 319

Query: 630 EEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
           EE+EEEEE+  ++E+EE+++++        ++S 
Sbjct: 320 EEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSD 353

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 49.6 bits (118), Expect = 5e-06
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE---EEEEEEEEEEEE 645
           E   +     E E + +E E E E E E +E+E+E E+Q  E+ E   +E  E + E E 
Sbjct: 746 EGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEG 805

Query: 646 EEEEEEEVRGGGKEE 660
           E E  E+    G+ E
Sbjct: 806 ETEAGEKDEHEGQSE 820

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 48.9 bits (116), Expect = 5e-06
 Identities = 20/62 (32%), Positives = 35/62 (56%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            +++ EE  +  EEEE+  ++EE + + +EEEE+   +EE E    E  E+ ++V   G 
Sbjct: 219 LKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAEAAEKRQKVPEDGL 278

Query: 659 EE 660
            E
Sbjct: 279 SE 280

Length = 431

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 47.0 bits (111), Expect = 5e-06
 Identities = 21/54 (38%), Positives = 32/54 (59%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E++  E EE +    EE    EEE    +EE   E+EE+ + + EEEE++E+EE
Sbjct: 51  EQDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEE 104

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 45.5 bits (108), Expect = 5e-06
 Identities = 26/54 (48%), Positives = 35/54 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             EE+ EEEE+ E EE++  EEE  +E   EEEE EEEE++E   EE E+  +E
Sbjct: 37  LTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKEMTLEEYEKALQE 90

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 48.5 bits (115), Expect = 5e-06
 Identities = 32/105 (30%), Positives = 40/105 (38%), Gaps = 45/105 (42%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEE-------------------------------- 625
           G+  EEE EEE   EEE  E+ +  E+E                                
Sbjct: 57  GDSSEEEGEEETSNEEENNEDSDGNEDEEAEAENTTLSTVTLGYGGDATPGTGNIGLAAL 116

Query: 626 -------------VQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                         +E+E +E+EEEEEEEEEEE E EE E    G
Sbjct: 117 QLPKKAGNAGKKATKEDESDEDEEEEEEEEEEEAEVEENEQGTNG 161

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

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

 Score = 49.8 bits (118), Expect = 5e-06
 Identities = 21/65 (32%), Positives = 47/65 (72%)

Query: 596  RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
            ++ E  +++E EE+++ EE ++ EEE + + +E ++E EE++++ EE +++EEE++++  
Sbjct: 1702 KKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAH 1761

Query: 656  GGKEE 660
              KEE
Sbjct: 1762 LKKEE 1766

Length = 2084

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.2 bits (117), Expect = 5e-06
 Identities = 9/62 (14%), Positives = 18/62 (29%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            ++     +   E+  EE E    E E       + E        +   +E  E      
Sbjct: 160 NQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTP 219

Query: 658 KE 659
           ++
Sbjct: 220 QQ 221

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 49.2 bits (117), Expect = 5e-06
 Identities = 6/62 (9%), Positives = 7/62 (11%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                  EE       E       E                  E    E       +   
Sbjct: 105 PSPSGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPS 164

Query: 658 KE 659
             
Sbjct: 165 SF 166

Length = 413

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

 Score = 49.6 bits (118), Expect = 5e-06
 Identities = 27/77 (35%), Positives = 40/77 (51%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E   +  +    EE+EE+ + +EEE    EEE +EE    EEE+   E+EE+ +EEE 
Sbjct: 777 LAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEEL 836

Query: 647 EEEEEEVRGGGKEEISL 663
           EE   E++   K E   
Sbjct: 837 EELALELKEEQKLEKLA 853

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 49.5 bits (118), Expect = 5e-06
 Identities = 20/65 (30%), Positives = 42/65 (64%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           ++ I+ +++  E +   ++  E EEE+E++ EE +++E + E  E+ E E E + E+ EE
Sbjct: 625 LQLILDVLKADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEE 684

Query: 648 EEEEE 652
           +E+E+
Sbjct: 685 DEQED 689

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 45.4 bits (108), Expect = 5e-06
 Identities = 19/25 (76%), Positives = 19/25 (76%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
                EEEEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 46.5 bits (111), Expect = 5e-06
 Identities = 17/31 (54%), Positives = 26/31 (83%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
            EE+E +++EE+EEEE++EE  +E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 48.7 bits (116), Expect = 5e-06
 Identities = 22/77 (28%), Positives = 47/77 (61%)

Query: 575 WKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
             + D+++      E         + +  +  + + ++ ++EE+++++ + V+E+E +E+
Sbjct: 209 DSSQDKNKSLEEYYEKESSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKED 268

Query: 635 EEEEEEEEEEEEEEEEE 651
           EEEEE EEEEEEE+E+E
Sbjct: 269 EEEEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

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

 Score = 49.1 bits (117), Expect = 5e-06
 Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 4/64 (6%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEV----QEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             E+E+E+ +  ++  E+E+E+EE E V     EEEE EE E     ++EEE+EE     
Sbjct: 287 TEEKEKEKRKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEKEEVTVSP 346

Query: 655 GGGK 658
            GG+
Sbjct: 347 DGGR 350

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|227458 COG5129, MAK16, Nuclear protein with HMG-like acidic region [General function prediction only]

 Score = 48.5 bits (115), Expect = 5e-06
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQ---------EEEEEEEEEEEEEEEEE 644
                ER  EEEEE + E E   ++ E+E+ + +         +  E  E EEEE  E E
Sbjct: 196 RQDEKERYVEEEEESDTELEAVTDDSEKEKTKKKDLEKWLGSDQSMETSESEEEESSESE 255

Query: 645 EEEEEEEEVRGGGKE 659
            +E+E+E+ +G  ++
Sbjct: 256 SDEDEDEDNKGKIRK 270

Length = 303

>gnl|CDD|216403 pfam01271, Granin, Granin (chromogranin or secretogranin)

 Score = 49.2 bits (117), Expect = 5e-06
 Identities = 27/99 (27%), Positives = 43/99 (43%), Gaps = 4/99 (4%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           K+   DE  + R  NI      G  +    EE EE++ +EE +  +E         +E +
Sbjct: 199 KSYQDDEDDTYRQNNIPYEDVVGGEDWNPIEEGEEDQTQEEVKRSKERTHKGRSLPDESK 258

Query: 636 EE----EEEEEEEEEEEEEEEVRGGGKEEISLHFYVLYV 670
                  E+E EEE+EE+ +E RG    +  L  +V   
Sbjct: 259 RSGQLGLEDEAEEEKEEKGQESRGLSAVQTYLLRWVNAR 297

Length = 585

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 47.0 bits (112), Expect = 6e-06
 Identities = 20/63 (31%), Positives = 32/63 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R     +     E  E+++EEEE +E EE+  +E+EE E  +     EEE  ++   +EE
Sbjct: 38  REGERKEEEELEEEREKKKEEEERKEREEQARKEQEEYEKLKSSFVVEEEGTDKLSADEE 97

Query: 647 EEE 649
             E
Sbjct: 98  SNE 100

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|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 48.4 bits (116), Expect = 6e-06
 Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 16/78 (20%)

Query: 591 IIQLI--RRGEREEEEEEEEEEEE---------EEEEEEEEEEEEEVQEEEEEE-----E 634
           + + I  R   R+EE EE  +E E         +EE+E E +E+ E Q++  EE     E
Sbjct: 76  LQEQIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNE 135

Query: 635 EEEEEEEEEEEEEEEEEE 652
           E  E +EEE+E E EEE 
Sbjct: 136 ERIERKEEEKEREREEEL 153

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|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 48.5 bits (116), Expect = 6e-06
 Identities = 20/41 (48%), Positives = 32/41 (78%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +EE+ EE  E+ E +EEE++  E E+E+EE+E+EEEEE++
Sbjct: 274 GDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDD 314

Length = 319

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 48.8 bits (116), Expect = 6e-06
 Identities = 8/60 (13%), Positives = 15/60 (25%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            E       ++     +   E+  E  E    E E +     + E        +    E 
Sbjct: 152 PESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEP 211

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 48.3 bits (115), Expect = 6e-06
 Identities = 14/60 (23%), Positives = 33/60 (55%), Gaps = 6/60 (10%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE------EEEEEEEEE 652
           + E+E++ +E+E++++ EEEE    + + E+ +   EE E  E E      ++  + ++ 
Sbjct: 223 DNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSDDA 282

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

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

 Score = 47.4 bits (112), Expect = 6e-06
 Identities = 24/58 (41%), Positives = 36/58 (62%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           I +  +E EE EE  E E  EE+ +E E++E QE E EE+  EE+ ++ E E  E++E
Sbjct: 128 IEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQDE 185

Length = 197

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 49.7 bits (118), Expect = 6e-06
 Identities = 23/77 (29%), Positives = 46/77 (59%)

Query: 583 IGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
            G   I ++  +I +  R     EE+    +    ++++E+E+  +++EE++EEEEEEEE
Sbjct: 119 HGKAEIGDLDMIIIKRRRARHLAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEE 178

Query: 643 EEEEEEEEEEVRGGGKE 659
           E +  ++E+E   GG++
Sbjct: 179 EIKGFDDEDEEDEGGED 195

Length = 2849

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 48.9 bits (117), Expect = 6e-06
 Identities = 24/36 (66%), Positives = 25/36 (69%), Gaps = 1/36 (2%)

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEEEEE-EEEVR 654
               E  +EEEEEEE  EEEEEEEEEEE   EEEVR
Sbjct: 300 PSPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEEVR 335

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 48.3 bits (115), Expect = 6e-06
 Identities = 20/42 (47%), Positives = 35/42 (83%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            ++ ++EE+++++ +  EE+E +E+EEEEE EEEEEEE+E+E
Sbjct: 244 NKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDEDE 285

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 45.2 bits (107), Expect = 6e-06
 Identities = 17/30 (56%), Positives = 23/30 (76%)

Query: 627 QEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
              EE+ EE+EEE+++EEE+EEEEEE   G
Sbjct: 72  AAAEEKAEEKEEEKKKEEEKEEEEEEALAG 101

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

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

 Score = 49.0 bits (117), Expect = 6e-06
 Identities = 15/70 (21%), Positives = 44/70 (62%), Gaps = 2/70 (2%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE--EEEEEEEEEEEEEEEE 646
           +   +L++   ++ ++  ++  E ++E +  EE E + +EE+  +EE E++++E+ +E++
Sbjct: 365 DKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDK 424

Query: 647 EEEEEEVRGG 656
           E+ +++ R  
Sbjct: 425 EKRQKDERKK 434

Length = 434

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 48.8 bits (116), Expect = 6e-06
 Identities = 17/61 (27%), Positives = 45/61 (73%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           IR+  +E EEE  EEE+++EE+++++++E+E  ++++++E++E+E++++    ++     
Sbjct: 38  IRKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADD 97

Query: 655 G 655
           G
Sbjct: 98  G 98

This is a family of uncharacterized proteins. Length = 449

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

 Score = 47.1 bits (112), Expect = 7e-06
 Identities = 20/56 (35%), Positives = 34/56 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E + +EE+ E EE E+EE  E+ EE    + EE ++E  + +EE ++ E E E ++
Sbjct: 26  EDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENKKLENELEALK 81

Length = 211

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

 Score = 48.7 bits (116), Expect = 7e-06
 Identities = 19/56 (33%), Positives = 43/56 (76%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
              +EEE+E+E+ +EE+++++E+ +EE + ++ +EE +E+   +E+E+E+E++ EE
Sbjct: 101 ESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEE 156

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 46.2 bits (110), Expect = 7e-06
 Identities = 16/31 (51%), Positives = 27/31 (87%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEE 631
            EE+E +++EE+EEEE++EE+++E+  EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 46.2 bits (110), Expect = 7e-06
 Identities = 16/31 (51%), Positives = 27/31 (87%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
            EE+E +++EE+EEEE++EE+++E + EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 44.9 bits (107), Expect = 7e-06
 Identities = 15/28 (53%), Positives = 18/28 (64%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQE 628
                 EE++EEEEEEEE+EE EEE   
Sbjct: 72  AAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 49.2 bits (117), Expect = 7e-06
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E E+EE+ ++++  E E+EE+ E E E QE    +E E  + E E  EEE  +  +    
Sbjct: 208 ESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLP 267

Query: 659 EE 660
           +E
Sbjct: 268 DE 269

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional

 Score = 47.0 bits (111), Expect = 7e-06
 Identities = 22/54 (40%), Positives = 38/54 (70%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           R+ +E  E E+ ++E EE  E++ E++ EE E++ EE  E+EEE EE++ +EE+
Sbjct: 16  RDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENEEQKPKEEI 69

Length = 193

>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex

 Score = 45.8 bits (109), Expect = 7e-06
 Identities = 22/52 (42%), Positives = 35/52 (67%), Gaps = 3/52 (5%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEE---EEVQEEEEEEEEEEEEEEEEE 644
           R  + EE+ EE+E E+EE+E +EE+E+E     VQ+EE E+  EE E+ + +
Sbjct: 10  RIIDIEEKREEKEREKEEKERKEEKEKEWGKGLVQKEEREKRLEELEKAKNK 61

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|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 46.2 bits (109), Expect = 8e-06
 Identities = 21/58 (36%), Positives = 35/58 (60%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +   E EE +    EE    EEE   +EE +  E+EE+ + + EEEE++E+EE+E ++
Sbjct: 52  QDRLEREELKRRAAEERLRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQ 109

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 46.7 bits (111), Expect = 8e-06
 Identities = 23/76 (30%), Positives = 43/76 (56%)

Query: 574 VWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
           + K +D+ E      +  ++     ++ E EE E+E+E  E E E+  E++E +E  +EE
Sbjct: 32  IIKKADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEIAQEE 91

Query: 634 EEEEEEEEEEEEEEEE 649
           E+EEE E+ +++E   
Sbjct: 92  EKEEEAEDVKQQEVFS 107

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 48.7 bits (116), Expect = 8e-06
 Identities = 18/56 (32%), Positives = 27/56 (48%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
               + E   EE E  +E EE+E E  +   EE E +  E  E+ E +E +E+ E 
Sbjct: 242 DNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTET 297

Length = 620

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

 Score = 48.8 bits (116), Expect = 8e-06
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 10/75 (13%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEE----------EEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           +RG  ++ +E + ++ ++E  EE           + EE E +   E   + E E++E+ E
Sbjct: 262 KRGGDDDADEYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDSE 321

Query: 646 EEEEEEEVRGGGKEE 660
           E EEE+    GG  +
Sbjct: 322 ESEEEKNEEEGGLSK 336

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

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

 Score = 48.8 bits (116), Expect = 8e-06
 Identities = 24/66 (36%), Positives = 38/66 (57%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
                 +L    E+ E+ + EEE+EE+ + +EEE    E + +EE E  EEE+   E+EE
Sbjct: 770 LSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEE 829

Query: 647 EEEEEE 652
           + +EEE
Sbjct: 830 KIKEEE 835

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.8 bits (109), Expect = 8e-06
 Identities = 15/31 (48%), Positives = 27/31 (87%)

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
            EE+E +++EE+ +EE++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.8 bits (109), Expect = 8e-06
 Identities = 16/31 (51%), Positives = 27/31 (87%)

Query: 615 EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            EE+E +++EE +EEE++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.8 bits (109), Expect = 8e-06
 Identities = 17/31 (54%), Positives = 26/31 (83%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            EE+E +  EE+EEEE++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 48.8 bits (116), Expect = 9e-06
 Identities = 27/68 (39%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE-----EEEEEEEE 652
           GE  EE   E E+E E E + E E E E+  E + E+E E E E +E     E E EE E
Sbjct: 657 GENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVE 716

Query: 653 VRGGGKEE 660
             G  + E
Sbjct: 717 HEGETEAE 724

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain fusion protein; Provisional

 Score = 45.3 bits (107), Expect = 9e-06
 Identities = 16/68 (23%), Positives = 25/68 (36%)

Query: 585 SPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
             + E    L R     E  E    E+          E  E  E  + +E+ +E  E + 
Sbjct: 34  DSKCEKNYDLGREARDLEWTEAGRAEKGPAAAATAAAEAAEEAEAADADEDADEAAEADA 93

Query: 645 EEEEEEEE 652
            +E +EEE
Sbjct: 94  ADEADEEE 101

Length = 131

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 48.2 bits (115), Expect = 9e-06
 Identities = 17/52 (32%), Positives = 30/52 (57%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +E +  ++     +  + EE +E+E +EEE+  +E EEEE E+ EEE  +  
Sbjct: 350 KESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSR 401

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 48.2 bits (115), Expect = 9e-06
 Identities = 21/71 (29%), Positives = 35/71 (49%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           + +  R    +E +  ++     +  + EE +E+  EEEE+  +E EEEE E+ EEE  +
Sbjct: 340 LNVKLRNPSTKESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQ 399

Query: 652 EVRGGGKEEIS 662
               G  E  S
Sbjct: 400 SREDGSSESSS 410

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 48.0 bits (115), Expect = 9e-06
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 2/52 (3%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           EE++  + EE+EEE  + E  EEE  +   EEEE E + +EE     G+  +
Sbjct: 27  EEKKRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERRE--GRAVL 76

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|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 46.3 bits (110), Expect = 9e-06
 Identities = 17/66 (25%), Positives = 44/66 (66%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           I+  IQ +   +  + +++E +  EE +E+E + +E++ +EE++E +  ++E ++E+E++
Sbjct: 87  IDEEIQAMTEKKDIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDEDD 146

Query: 648 EEEEEV 653
           +E  E+
Sbjct: 147 DEIVEI 152

Length = 175

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

 Score = 49.0 bits (116), Expect = 9e-06
 Identities = 18/56 (32%), Positives = 41/56 (73%)

Query: 597  RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            + + E+ +++E EE+++ EE ++ EEE +++  EE ++ EE++++ EE ++ EE+E
Sbjct: 1632 KKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDE 1687

Length = 2084

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

 Score = 49.0 bits (116), Expect = 9e-06
 Identities = 21/68 (30%), Positives = 44/68 (64%), Gaps = 5/68 (7%)

Query: 592  IQLIRRGEREEEEEEEEEEEEEEE-----EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            ++ +++ E EE+++ EE ++ EEE      EE ++ EE+ ++ EE ++ EE+E++  E  
Sbjct: 1635 VEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEAL 1694

Query: 647  EEEEEEVR 654
            ++E EE +
Sbjct: 1695 KKEAEEAK 1702

Length = 2084

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 48.4 bits (115), Expect = 9e-06
 Identities = 9/50 (18%), Positives = 16/50 (32%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
                 +   +E  E +    ++      Q+  E E+E  E E E     
Sbjct: 199 TSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPPFP 248

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 48.4 bits (115), Expect = 9e-06
 Identities = 13/75 (17%), Positives = 16/75 (21%), Gaps = 10/75 (13%)

Query: 596 RRGEREEEEEEEEEEEEEEEE----------EEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           R+ E + E  EE    E+EE           E             EE       E     
Sbjct: 67  RQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSPENTSGS 126

Query: 646 EEEEEEEVRGGGKEE 660
             E            
Sbjct: 127 SPESPASHSPPPSPP 141

Length = 413

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 48.7 bits (116), Expect = 9e-06
 Identities = 18/55 (32%), Positives = 33/55 (60%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           +  EE+ +EE+ ++++ +  E+ E  +EE E  +E EE+E E  + E EE E+  
Sbjct: 225 DGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDA 279

Length = 620

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 48.7 bits (116), Expect = 9e-06
 Identities = 18/55 (32%), Positives = 29/55 (52%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           G+ ++ +  E+ E   EE E  +E EE+  E  + E EE E +  E  E+ E +E
Sbjct: 236 GDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDE 290

Length = 620

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

 Score = 48.8 bits (116), Expect = 9e-06
 Identities = 24/65 (36%), Positives = 38/65 (58%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            E   +  +  + + EEE+EE+ + +EEE    EEE + + E  EEE+   E+EE+ +EE
Sbjct: 775 KELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEE 834

Query: 648 EEEEE 652
           E EE 
Sbjct: 835 ELEEL 839

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 = 48.8 bits (116), Expect = 9e-06
 Identities = 28/107 (26%), Positives = 43/107 (40%), Gaps = 7/107 (6%)

Query: 564  KLKTIRPSIKVWKTSDQDEI-----GSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEE 618
            K K  +  ++     D            RI     ++ + E E EE   EE +E+E+EE+
Sbjct: 895  KEKEEKKELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEED 954

Query: 619  --EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
              EEEEE   +    +EE          E EE+EE       ++  L
Sbjct: 955  NKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERL 1001

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|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 48.9 bits (116), Expect = 9e-06
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 7/62 (11%)

Query: 598 GEREEEEEEEEEEEEEE-------EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           G  +E +E EEE  E E       +E +E+EE +E  E+  E+E E +  +EE+ E+ +E
Sbjct: 926 GSDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDGEDWDE 985

Query: 651 EE 652
            E
Sbjct: 986 LE 987

Length = 1001

>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis

 Score = 46.5 bits (111), Expect = 9e-06
 Identities = 19/58 (32%), Positives = 31/58 (53%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            L ++G    +    +EEEEE  E   +E  E   E++  +E +EE +EEE++   EE
Sbjct: 6   ILRKKGILPPKPPSPKEEEEEALELAIQEAHENALEKKLLDELDEELDEEEDDRFLEE 63

It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 48.1 bits (115), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 36/56 (64%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R  R   EEE++EEEE+ +E  ++ ++E   ++++     + EE+EEEEE+  ++E
Sbjct: 278 RLRRMRGEEEDDEEEEDSKESADDLDDEFEPDDDDNFGLGQGEEDEEEEEDGVDDE 333

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 48.4 bits (115), Expect = 1e-05
 Identities = 25/88 (28%), Positives = 36/88 (40%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           +  +  E      E   +  +  E EE E+EEEEEE E +   EEE E   + + + EE 
Sbjct: 440 EEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEP 499

Query: 636 EEEEEEEEEEEEEEEEEVRGGGKEEISL 663
           EE+ E    E         G      S+
Sbjct: 500 EEDAERRNSEMAGISRMSEGQQPRGSSV 527

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 22/43 (51%), Positives = 35/43 (81%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           ++E+  +E E+ ++E QE++EEEEEE+EEE EE E+ E+EEE+
Sbjct: 32  DKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDEEEI 74

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM)

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 8/99 (8%)

Query: 560 PNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEE-- 617
               K + +   +K+  TS   E      E++    +  + EEEEE+EEE EE E+ E  
Sbjct: 14  EEEKKDENLLEHVKI--TSWDKEDIIKENEDVKDEKQEDDEEEEEEDEEEIEEPEDIEDE 71

Query: 618 ----EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
               E+EEEEEE +E+  + ++ E++   +     +++ 
Sbjct: 72  EEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFNSTQDDN 110

This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteristic of a well-defined structural element. Length = 164

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 45.8 bits (109), Expect = 1e-05
 Identities = 20/57 (35%), Positives = 33/57 (57%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           L    E+++EEEE +E EE+  +E+EE E+ +     EEE  ++   +EE  E  E+
Sbjct: 48  LEEEREKKKEEEERKEREEQARKEQEEYEKLKSSFVVEEEGTDKLSADEESNELLED 104

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|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 48.5 bits (115), Expect = 1e-05
 Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 8/71 (11%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE------ 651
           GE E + E E E E   E + E+E E E++ +E + + E E EE E E E E E      
Sbjct: 671 GETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEG 730

Query: 652 --EVRGGGKEE 660
             E    G+E 
Sbjct: 731 EIETGEEGEEV 741

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 48.1 bits (114), Expect = 1e-05
 Identities = 25/63 (39%), Positives = 32/63 (50%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           GER  E E E  EE   E E+E E E + + E E E   E + E+E E E E +E    G
Sbjct: 649 GERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKG 708

Query: 658 KEE 660
           + E
Sbjct: 709 ETE 711

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 46.7 bits (111), Expect = 1e-05
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHF 665
            E+E ++ + E  EE+   + E +EE++ +EE+ E EE E+EE         E+ +  
Sbjct: 1   MEKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEE 58

Length = 211

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

 Score = 46.7 bits (111), Expect = 1e-05
 Identities = 23/71 (32%), Positives = 37/71 (52%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           K  + +E      EN  +   + E  E EE E+EE  E+ EE  E + EE+++E  + +E
Sbjct: 9   KHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKE 68

Query: 636 EEEEEEEEEEE 646
           E ++ E E E 
Sbjct: 69  ENKKLENELEA 79

Length = 211

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 48.1 bits (114), Expect = 1e-05
 Identities = 20/55 (36%), Positives = 29/55 (52%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E   E EE +++ EE  +  EEEE+   QEE + +  EEEE+   +EE E     
Sbjct: 211 EAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAE 265

Length = 431

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 45.8 bits (109), Expect = 1e-05
 Identities = 17/49 (34%), Positives = 29/49 (59%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
               +EEE +  ++E++EE + EEE+    ++EEE + E E E + E E
Sbjct: 23  DESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDPEAEAEFDREFE 71

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 46.1 bits (110), Expect = 1e-05
 Identities = 21/46 (45%), Positives = 27/46 (58%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
            EE+ E+ EE  EE E EE  E+E EEE  EEE E E+    + +I
Sbjct: 1   MEEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKI 46

Length = 191

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 47.6 bits (114), Expect = 1e-05
 Identities = 29/75 (38%), Positives = 41/75 (54%), Gaps = 13/75 (17%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE------- 645
           Q+    ER +EE+E E +E+ E++++  EE +E  EE  E +EEE+E E EEE       
Sbjct: 100 QMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEEKEREREEELKILEYQ 159

Query: 646 ------EEEEEEEVR 654
                 EEE E E R
Sbjct: 160 REKAEREEEREAERR 174

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|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 19/52 (36%), Positives = 33/52 (63%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           R++  +    +++E+EEEEEEE E E  +EEE+ +E  E+E  + + E+  E
Sbjct: 87  RKKVRKLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRE 138

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381)

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 33/56 (58%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           +    +++E+EEEEEEE E  + +EEE+ +E  E+E  + + E+  E     KE +
Sbjct: 92  KLLGLDKKEKEEEEEEEVEVEELDEEEQIDELLEKELAKLKREKRRENERKQKEIL 147

This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. Length = 154

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 47.8 bits (113), Expect = 1e-05
 Identities = 29/108 (26%), Positives = 49/108 (45%), Gaps = 6/108 (5%)

Query: 563 NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEE------EEEEE 616
           ++ +  R        + ++E G P     ++  ++G  EE EE   EE+      E E +
Sbjct: 228 DEKELARQERVSSWENFKEEPGEPLSRPALKKEKQGAEEEGEEGMSEEDLDVGAAEIENK 287

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
           E  E ++E+ QEE E  E  +EE + +  +E  EE+      EE   H
Sbjct: 288 EVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERH 335

Length = 392

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 47.3 bits (112), Expect = 1e-05
 Identities = 24/57 (42%), Positives = 30/57 (52%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R    EEEEE E  ++ E+  + E E  ++ Q EEEE EEE     E E EEE   E
Sbjct: 206 RELNEEEEEEAEGSDDGEDVVDYEGERIDKKQGEEEEMEEEVINLFEIEWEEESPSE 262

Length = 279

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

 Score = 47.9 bits (114), Expect = 1e-05
 Identities = 11/51 (21%), Positives = 33/51 (64%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EE+ +++E+++ EE ++++  E +  ++ E+E    +E++++ EE  ++  
Sbjct: 78  EEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAA 128

Length = 387

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

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 12/62 (19%), Positives = 32/62 (51%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E ++++  E+E  ++ E+E    +E++ Q EE  ++   ++++ EE   +     +   +
Sbjct: 91  ELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAE 150

Query: 659 EE 660
            E
Sbjct: 151 AE 152

Length = 387

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 45.9 bits (109), Expect = 1e-05
 Identities = 26/81 (32%), Positives = 50/81 (61%), Gaps = 4/81 (4%)

Query: 575 WKTSDQ-DEIGSPRIENIIQLIRRGEREEEEEEEEEEEE-EEEEEEEEEEEEEVQEEEEE 632
           W   D+ DE      E   + I+  ++E +  EE +E+E + +E++EEEE++EV   ++E
Sbjct: 81  WYPLDEIDEEIQAMTEK--KDIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDE 138

Query: 633 EEEEEEEEEEEEEEEEEEEEV 653
            ++E+E+++E  E   E++EV
Sbjct: 139 NDDEDEDDDEIVEILIEDDEV 159

Length = 175

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

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 25/66 (37%), Positives = 34/66 (51%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R+E + + I   + E EE E   EE E+   E EE +EE++E+     EE EE  E   E
Sbjct: 324 RLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALRE 383

Query: 647 EEEEEE 652
           E  E E
Sbjct: 384 ELAELE 389

Length = 1163

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

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 33/75 (44%), Positives = 46/75 (61%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
               + E     IE + + I   E + +E EEE EE E+E EE +EE EE++ E+EE E+
Sbjct: 818 SLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELED 877

Query: 636 EEEEEEEEEEEEEEE 650
           E +E EEE+EE EEE
Sbjct: 878 ELKELEEEKEELEEE 892

Length = 1163

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

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 21/66 (31%), Positives = 33/66 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E + + +   + + E  +EE EE E   EE E+   E++E +EE EE+     EE EE
Sbjct: 317 ELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEE 376

Query: 647 EEEEEE 652
             E   
Sbjct: 377 LFEALR 382

Length = 1163

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

 Score = 48.2 bits (115), Expect = 1e-05
 Identities = 23/67 (34%), Positives = 30/67 (44%)

Query: 586 PRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
             ++  I+ ++    E E   EE E+   E EE +EE EE      EE EE  E   EE 
Sbjct: 326 EELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREEL 385

Query: 646 EEEEEEE 652
            E E E 
Sbjct: 386 AELEAEL 392

Length = 1163

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

 Score = 48.6 bits (115), Expect = 1e-05
 Identities = 20/72 (27%), Positives = 44/72 (61%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            E   + + + +++E EE+++ EE ++ EEE + +  E  ++ EE++++ EE ++ EE+E+
Sbjct: 1629 EEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEK 1688

Query: 649  EEEEVRGGGKEE 660
            +  E      EE
Sbjct: 1689 KAAEALKKEAEE 1700

Length = 2084

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

 Score = 48.2 bits (114), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 45/62 (72%), Gaps = 1/62 (1%)

Query: 600  REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE-EEEEEEEEEEEEEEEEEEVRGGGK 658
            ++ EEE+++ E+ +++E EE+++ EE+++ EEE + +  EE ++ EE++++ EE +   +
Sbjct: 1626 KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEE 1685

Query: 659  EE 660
            +E
Sbjct: 1686 DE 1687

Length = 2084

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 48.0 bits (114), Expect = 1e-05
 Identities = 8/62 (12%), Positives = 13/62 (20%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
                  E    E       ++         E+  EE E    E E +     +      
Sbjct: 141 PSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTS 200

Query: 659 EE 660
             
Sbjct: 201 SP 202

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 47.7 bits (113), Expect = 1e-05
 Identities = 10/63 (15%), Positives = 17/63 (26%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
              +   E+  EE E    E E +     Q E        +   +E  E +     +   
Sbjct: 165 SFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPS 224

Query: 658 KEE 660
              
Sbjct: 225 PNT 227

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 47.7 bits (113), Expect = 1e-05
 Identities = 13/61 (21%), Positives = 19/61 (31%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
             E+   + E + E  EE    E+EE  +        E             EE+  G   
Sbjct: 61  VAEQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSP 120

Query: 660 E 660
           E
Sbjct: 121 E 121

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 47.7 bits (113), Expect = 1e-05
 Identities = 10/57 (17%), Positives = 18/57 (31%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            E        +   +E  E +    ++      ++  E E+E  E E E       R
Sbjct: 195 SETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGPPFPGHR 251

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 14/56 (25%), Positives = 27/56 (48%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             E + +E+E++++ EEEE    +   E+     EE E  E E  E   ++  + +
Sbjct: 225 EDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSD 280

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 18/55 (32%), Positives = 32/55 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           G+   EE+ +EE+ ++++ +  E+ E   +E E  +E EE+E E  + E EE E 
Sbjct: 223 GDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEM 277

Length = 620

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E  +EE+ ++++ +  E+ E   EE E  +E EE+E E  + E EE E +  E
Sbjct: 229 EDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAE 281

Length = 620

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 47.9 bits (114), Expect = 1e-05
 Identities = 17/53 (32%), Positives = 31/53 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           G  E+ +EE+ ++++ +  E+ E   EE +  +E EE+E E  + E EE E +
Sbjct: 226 GIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMD 278

Length = 620

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

 Score = 46.6 bits (110), Expect = 1e-05
 Identities = 21/53 (39%), Positives = 36/53 (67%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           ER EE+ +E E++EE+E E EE+  EE  ++ E E  E++E E E ++++ E+
Sbjct: 145 ERREEKIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQDESETESDDDKTEK 197

Length = 197

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 45.3 bits (106), Expect = 1e-05
 Identities = 32/55 (58%), Positives = 32/55 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
              EEEE E EEE EEE E EEE EEE   EE  EEE E E E E E E E E E
Sbjct: 63  EPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPEPEPEPE 117

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 47.5 bits (113), Expect = 1e-05
 Identities = 23/60 (38%), Positives = 32/60 (53%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           I+L      ++     +   E++E   E    E+ +EEE EE EE+EEEE EEE EE E 
Sbjct: 45  IELAEPETSDDPYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEP 104

Length = 306

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

 Score = 48.8 bits (116), Expect = 1e-05
 Identities = 28/89 (31%), Positives = 46/89 (51%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
            ++++    + E   +      +E+E  EEEE+ E+ + EEE+EE+ + QEEE    EEE
Sbjct: 751 EEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEE 810

Query: 638 EEEEEEEEEEEEEEEVRGGGKEEISLHFY 666
            +EE E  EEE+    +    +E  L   
Sbjct: 811 LKEEAELLEEEQLLIEQEEKIKEEELEEL 839

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 = 48.4 bits (115), Expect = 1e-05
 Identities = 28/93 (30%), Positives = 44/93 (47%)

Query: 561 NTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE 620
              K +  +   +  K+    +      E       + E E+EE+ + +EEE    EEE 
Sbjct: 752 EEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEEL 811

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           +EE E+ EEE+   E+EE+ +EEE EE   E  
Sbjct: 812 KEEAELLEEEQLLIEQEEKIKEEELEELALELK 844

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 = 48.0 bits (114), Expect = 1e-05
 Identities = 25/76 (32%), Positives = 39/76 (51%)

Query: 577 TSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
               +E        + +      + +EEE    EEE +EE E  EEE+ + E+EE+ +EE
Sbjct: 775 KELAEEEEKTEKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEE 834

Query: 637 EEEEEEEEEEEEEEEE 652
           E EE   E +EE++ E
Sbjct: 835 ELEELALELKEEQKLE 850

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|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 44.6 bits (106), Expect = 1e-05
 Identities = 17/49 (34%), Positives = 31/49 (63%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            +E+ + E+++EE++ E E+  ++  EE+ E E E+ E+E EE E E  
Sbjct: 18  AKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAELA 66

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 21/66 (31%), Positives = 41/66 (62%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            I ++++      R ++  E EEE+E++ EE +++E+E    E+ E E E + E+ EE+E
Sbjct: 627 LILDVLKADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDE 686

Query: 647 EEEEEE 652
           +E++ E
Sbjct: 687 QEDDAE 692

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 20/63 (31%), Positives = 37/63 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           ++  E EEE+E++ EE +++E+E E     E E E + E+ EE+E+E++ E  E      
Sbjct: 642 QQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPID 701

Query: 659 EEI 661
           + +
Sbjct: 702 KAV 704

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 11/48 (22%), Positives = 36/48 (75%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
             EE+ ++++++  + +++  ++++  +++ +EE+ +EE++E+EE+EE
Sbjct: 82  PLEEKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDEEDEE 129

Length = 129

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 23/54 (42%), Positives = 36/54 (66%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
            E E+   E ++EEEE+EEEEEEE ++E   +E  ++EE EE++ E + E+  G
Sbjct: 379 LEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDG 432

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 43.9 bits (104), Expect = 1e-05
 Identities = 19/25 (76%), Positives = 19/25 (76%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEE 622
                EEEEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 48.6 bits (115), Expect = 1e-05
 Identities = 32/73 (43%), Positives = 35/73 (47%)

Query: 588  IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            IE  I+       EE EE  EE  EE  EE  EE  EE++E  EE  EE  EE  EE  E
Sbjct: 1057 IEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAEENAEENAE 1116

Query: 648  EEEEEVRGGGKEE 660
            E  EE      EE
Sbjct: 1117 ENAEEYDDENPEE 1129

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 48.6 bits (115), Expect = 1e-05
 Identities = 33/95 (34%), Positives = 47/95 (49%)

Query: 565  LKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEE 624
            ++ +  +++ +   + +EI     EN+ + I     E +EE  EE EE  EE  EE  EE
Sbjct: 1027 VEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEE 1086

Query: 625  EVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
             V+E  EE EE  EE  EE  EE  EE      +E
Sbjct: 1087 NVEENVEEIEENVEENVEENAEENAEENAEENAEE 1121

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 48.2 bits (114), Expect = 1e-05
 Identities = 28/63 (44%), Positives = 33/63 (52%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            ENI + I     E  EE  EE EE  EE  EE  EE  +E  EE  EE ++E  EE  EE
Sbjct: 1074 ENIEENIEENVEENVEENVEEIEENVEENVEENAEENAEENAEENAEEYDDENPEEHNEE 1133

Query: 649  EEE 651
             +E
Sbjct: 1134 YDE 1136

Length = 1136

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

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 19/59 (32%), Positives = 43/59 (72%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             G+ EE+E+E+ +EE+++++E+ +EE ++ + +EE +E+   +E+E+E+E++ EE   
Sbjct: 101 ESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRD 159

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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 48.0 bits (114), Expect = 1e-05
 Identities = 19/64 (29%), Positives = 43/64 (67%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E +++++E+ +EE ++ + +EE +E+   +E+E+E+E++ EE  + EEE++ E VR   +
Sbjct: 115 EEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSR 174

Query: 659 EEIS 662
            +  
Sbjct: 175 PKKP 178

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 15/31 (48%), Positives = 27/31 (87%)

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            EE+E +++ ++EEEE++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 17/31 (54%), Positives = 26/31 (83%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
            EE+E +++EE+EEEE  EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 15/30 (50%), Positives = 25/30 (83%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQ 627
            E +++EE+EEEE++EE+++E+E EEEE  
Sbjct: 112 DESDDDEEDEEEEDDEEDDDEDESEEEESP 141

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.4 bits (108), Expect = 1e-05
 Identities = 16/31 (51%), Positives = 26/31 (83%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
            EE+E +++EE+EEEE++EE+++  E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 16/31 (51%), Positives = 26/31 (83%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
            EE+E +++EE+EEE  +EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 15/32 (46%), Positives = 26/32 (81%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEE 625
           L+   E E +++EE+EEEE++EE+++E+E EE
Sbjct: 106 LVASEEDESDDDEEDEEEEDDEEDDDEDESEE 137

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 48.0 bits (114), Expect = 1e-05
 Identities = 17/62 (27%), Positives = 30/62 (48%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
              E+EE+ ++++  E E+EE+ E E   +E    +E E  + E E  EEE  +      
Sbjct: 207 TESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDL 266

Query: 659 EE 660
            +
Sbjct: 267 PD 268

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 48.3 bits (115), Expect = 1e-05
 Identities = 16/60 (26%), Positives = 42/60 (70%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            ++G+ +++ ++ +++E +E  ++++EEE E ++E + EE  E++ ++EEEE+ + E+  
Sbjct: 146 AKKGKAKKKTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDYS 205

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

>gnl|CDD|235850 PRK06669, fliH, flagellar assembly protein H; Validated

 Score = 47.3 bits (113), Expect = 1e-05
 Identities = 40/125 (32%), Positives = 54/125 (43%), Gaps = 22/125 (17%)

Query: 558 NVPNTNKLKTI---RPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEE 614
           NV N  KLKT    +   KV    +++ +     E + QL      E +E  EE EE+  
Sbjct: 10  NVINKEKLKTHEIQKYRFKVLSIKEKERLREEEEEQVEQLREEANDEAKEIIEEAEEDAF 69

Query: 615 EEEEEEEEE----------------EEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG-- 656
           E  E  EEE                E++Q + E E+EE EEE E   EE + E    G  
Sbjct: 70  EIVEAAEEEAKEELLKKTDEASSIIEKLQMQIEREQEEWEEELERLIEEAKAEGYEEGYE 129

Query: 657 -GKEE 660
            G+EE
Sbjct: 130 KGREE 134

Length = 281

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

 Score = 48.5 bits (116), Expect = 1e-05
 Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 11/94 (11%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEE-----------EEEEEEEEEEEEEEV 626
            + D+      EN   L ++  + +E E++EE             E  ++EE + E EE+
Sbjct: 338 DEDDDEDDDDGENPWMLRKKLGKLKEGEDDEENSGLLSMKFMQRAEARKKEENDAEIEEL 397

Query: 627 QEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           + E E EEE +EEE EE  ++       G    E
Sbjct: 398 RRELEGEEESDEEENEEPSKKNVGRRKFGPENGE 431

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|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 48.3 bits (116), Expect = 1e-05
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 588 IENIIQLIRR---GE---REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           I+ I++   R   GE   RE  +   +   EE+      E EE   +E+EEEEE+E ++ 
Sbjct: 149 IDAILEWYDRLENGERRLRELIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDS 208

Query: 642 EEEEEEEEEEEVR 654
              +E E  E+V 
Sbjct: 209 LAADESELPEKVL 221

Length = 619

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 44.4 bits (104), Expect = 1e-05
 Identities = 13/35 (37%), Positives = 30/35 (85%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E EE+ +   +EEE++++E+EE+++E+++E+++EV
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEV 41

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

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

 Score = 48.1 bits (115), Expect = 1e-05
 Identities = 8/55 (14%), Positives = 44/55 (80%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           + ++++++++ ++++ ++++++E+++E  ++++ ++E+EE++E +E E+  +++ 
Sbjct: 132 DDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDD 186

Length = 509

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

 Score = 48.1 bits (115), Expect = 1e-05
 Identities = 13/100 (13%), Positives = 57/100 (57%)

Query: 561 NTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE 620
                  +  S K  K +  D+         I ++ + + +++++++++ ++++ +++++
Sbjct: 93  KKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDD 152

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           +E+++  +++++ ++E+EE++E +E E+  ++      E+
Sbjct: 153 DEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDED 192

Length = 509

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

 Score = 47.6 bits (114), Expect = 1e-05
 Identities = 29/110 (26%), Positives = 54/110 (49%), Gaps = 17/110 (15%)

Query: 562 TNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIR---------------RGEREEEEEE 606
           T   K +  S  + K+ +  E   P +  ++ L+                   REEEEE+
Sbjct: 212 TKPKKRLIISFNLPKSKEDLEDLLPLLNLVLYLVDKLANLKLSPEVLRKVDKTREEEEEK 271

Query: 607 --EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             +  EEE +EE +E++EE++ +E E +  +   EE+ + EE+E +++ R
Sbjct: 272 ILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKERKKQAR 321

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|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 47.2 bits (112), Expect = 1e-05
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 9/74 (12%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEE---------VQEEEEEEEEEEEEEEEEEEEEEE 649
           E EEE+E  EEEEEE EEEEE + E++          ++++    +E E E  +E+  EE
Sbjct: 6   ELEEEDESGEEEEEESEEEEETDSEDDMEPRLKPVFTRKKDRITIQEREREAAKEKALEE 65

Query: 650 EEEVRGGGKEEISL 663
           E + +   ++  +L
Sbjct: 66  EAKRKAEERKRETL 79

This family represents the C-terminus (approximately 300 residues) of proteins that are involved as binding partners for Prp19 as part of the nuclear pore complex. The family in Drosophila is necessary for pre-mRNA splicing, and the human protein has been found in purifications of the spliceosome. In the past this family was thought, erroneously, to be associated with microfibrillin. Length = 277

>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 46.8 bits (111), Expect = 1e-05
 Identities = 28/74 (37%), Positives = 36/74 (48%), Gaps = 18/74 (24%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE------------------EEEEEEEEEE 640
           E E  E EEE+E  EEEEEE EEEEE   E++                  +E E E  +E
Sbjct: 1   ETEVLELEEEDESGEEEEEESEEEEETDSEDDMEPRLKPVFTRKKDRITIQEREREAAKE 60

Query: 641 EEEEEEEEEEEEVR 654
           +  EEE + + E R
Sbjct: 61  KALEEEAKRKAEER 74

This family represents the C-terminus (approximately 300 residues) of proteins that are involved as binding partners for Prp19 as part of the nuclear pore complex. The family in Drosophila is necessary for pre-mRNA splicing, and the human protein has been found in purifications of the spliceosome. In the past this family was thought, erroneously, to be associated with microfibrillin. Length = 277

>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 46.8 bits (111), Expect = 1e-05
 Identities = 29/84 (34%), Positives = 42/84 (50%), Gaps = 20/84 (23%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEE-----------EEEEVQEEEEEEEEEEEE 639
           +++L    E  EEEEEE EEEEE + E++ E           +   +QE E E  +E+  
Sbjct: 4   VLELEEEDESGEEEEEESEEEEETDSEDDMEPRLKPVFTRKKDRITIQEREREAAKEKAL 63

Query: 640 EEEEEEEEEE---------EEEVR 654
           EEE + + EE         EEEV+
Sbjct: 64  EEEAKRKAEERKRETLKIVEEEVK 87

This family represents the C-terminus (approximately 300 residues) of proteins that are involved as binding partners for Prp19 as part of the nuclear pore complex. The family in Drosophila is necessary for pre-mRNA splicing, and the human protein has been found in purifications of the spliceosome. In the past this family was thought, erroneously, to be associated with microfibrillin. Length = 277

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

 Score = 48.1 bits (115), Expect = 1e-05
 Identities = 35/100 (35%), Positives = 50/100 (50%), Gaps = 2/100 (2%)

Query: 563 NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
             L  +   IK      +  I   R ENI +LI+  E+E EE   E  E   E  E  EE
Sbjct: 165 KNLGEVIKEIKRRIERLEKFIK--RTENIEELIKEKEKELEEVLREINEISSELPELREE 222

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
            E++++E +E EE +EE EE E+E E  E  +   +E+I 
Sbjct: 223 LEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIR 262

Length = 880

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 47.2 bits (112), Expect = 1e-05
 Identities = 22/59 (37%), Positives = 34/59 (57%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           QL    E   EEE  EE E+E E E E+EE+   ++ E+ ++E+    + ++  EEEEE
Sbjct: 209 QLESEVEASPEEENYEEYEDETELEVEDEEKALDEQTEDPQQEDALAGDAKKALEEEEE 267

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 47.7 bits (113), Expect = 2e-05
 Identities = 24/57 (42%), Positives = 32/57 (56%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +  + + E E EE E E E E E  E+E E++  EE EE E+E E E E + E E E
Sbjct: 702 KEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETE 758

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 21/39 (53%), Positives = 29/39 (74%)

Query: 615 EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            +EE+ EE  E  EEEEEE++  E E+E+EE+E+EEEE 
Sbjct: 274 GDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEE 312

Length = 319

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 46.5 bits (110), Expect = 2e-05
 Identities = 24/55 (43%), Positives = 31/55 (56%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E EEEE E  ++ E+  + E E  +++  EEEE EEE     E E EEE   EEV
Sbjct: 210 EEEEEEAEGSDDGEDVVDYEGERIDKKQGEEEEMEEEVINLFEIEWEEESPSEEV 264

Length = 279

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 43.7 bits (103), Expect = 2e-05
 Identities = 21/41 (51%), Positives = 29/41 (70%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           ++  E EE EE + +EEEEEEEE+E E E   ++EE EEE+
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEI 92

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 12/53 (22%), Positives = 32/53 (60%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EE+ +++E+++ EE +++   E+E  ++ E+E    +E++++ EE       +
Sbjct: 78  EEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALK 130

Length = 387

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 45.1 bits (107), Expect = 2e-05
 Identities = 17/58 (29%), Positives = 41/58 (70%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           E+++ + +++E +  EE +E+E + +E +EEEE++E +  ++E ++E+E+++E V   
Sbjct: 96  EKKDIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDEDDDEIVEIL 153

Length = 175

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

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 33/64 (51%), Positives = 45/64 (70%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E++ Q   R E+E EE EEE EE EE+ +E EEE EE+++E EE +EE EE E E+EE
Sbjct: 815 ELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEE 874

Query: 647 EEEE 650
            E+E
Sbjct: 875 LEDE 878

Length = 1163

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

 Score = 47.4 bits (113), Expect = 2e-05
 Identities = 30/70 (42%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R+E + + +   E E EE +E  EE EEE E  EE   +++EE EE EE+ +  +EE EE
Sbjct: 738 RLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEE 797

Query: 647 -EEEEEEVRG 655
            EEE EE   
Sbjct: 798 LEEELEEAER 807

Length = 1163

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

 Score = 47.4 bits (113), Expect = 2e-05
 Identities = 24/59 (40%), Positives = 29/59 (49%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            I   E E     E  EE E E EE EE  EE++E+ E  +EE EE E   EE E+   
Sbjct: 296 EIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLA 354

Length = 1163

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

 Score = 47.8 bits (113), Expect = 2e-05
 Identities = 20/56 (35%), Positives = 40/56 (71%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            ++E EE ++ EE +++E EE+++ EE  + EEE + + EE ++E EE++++ EE +
Sbjct: 1695 KKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAK 1750

Length = 2084

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

 Score = 45.9 bits (109), Expect = 2e-05
 Identities = 23/61 (37%), Positives = 40/61 (65%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           E ++ +++E  E EE +EEE+E    E++E++ + E+E+EE EEE EEE+E      E+ 
Sbjct: 50  EAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSDENEKE 109

Query: 662 S 662
           +
Sbjct: 110 T 110

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|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 7/62 (11%), Positives = 16/62 (25%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
               ++     +   E+  EE E    E + +     + E        +   +E      
Sbjct: 157 PSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQS 216

Query: 658 KE 659
             
Sbjct: 217 PT 218

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 8/63 (12%), Positives = 14/63 (22%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                  E    E       ++     +   E+  EE E    E E +     +      
Sbjct: 141 PSHPGPHEPAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTS 200

Query: 658 KEE 660
              
Sbjct: 201 SPP 203

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 46.9 bits (111), Expect = 2e-05
 Identities = 8/62 (12%), Positives = 20/62 (32%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           +   E+  EE E    E E +     + +        +   +E  E +    ++      
Sbjct: 168 QPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNT 227

Query: 659 EE 660
           ++
Sbjct: 228 QQ 229

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 46.9 bits (111), Expect = 2e-05
 Identities = 9/63 (14%), Positives = 19/63 (30%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
             ++     +   E+  EE E    E E       + E        +   +E  E +   
Sbjct: 159 PNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPT 218

Query: 658 KEE 660
            ++
Sbjct: 219 PQQ 221

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 46.9 bits (111), Expect = 2e-05
 Identities = 9/62 (14%), Positives = 16/62 (25%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                +   E+  EE E    E E +     + E        +   +E  E +       
Sbjct: 163 PSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQA 222

Query: 658 KE 659
             
Sbjct: 223 PS 224

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 46.3 bits (110), Expect = 2e-05
 Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 6/60 (10%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE------EEEEEEEE 652
           E  E+E++ +E+E++++ EEEE    +   E+ +   EE E  E E      ++  + ++
Sbjct: 222 EDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSDD 281

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +  EE+ +EE+ ++++ +  E+ E    + E  +E EE+E E  + E EE E +
Sbjct: 224 DDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMD 278

Length = 620

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E + +EE+ ++++ +  E+ E   EE    +E EE+E E  + E EE E +  E
Sbjct: 228 EEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAE 281

Length = 620

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 45.0 bits (105), Expect = 2e-05
 Identities = 34/73 (46%), Positives = 38/73 (52%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           + E G+    +        +  EEEEE E EEE EEE E EEE EE  E EE  EEE E 
Sbjct: 43  KGEKGTKVGADDTNGTDPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEEPEP 102

Query: 640 EEEEEEEEEEEEE 652
           E E E E E E E
Sbjct: 103 EPEPEPEPEPEPE 115

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 44.6 bits (104), Expect = 2e-05
 Identities = 31/68 (45%), Positives = 38/68 (55%)

Query: 584 GSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           G  + E   ++        + ++E EEEEE E EEE EEE E +EE EEE E EE  EEE
Sbjct: 40  GKGKGEKGTKVGADDTNGTDPDDEPEEEEEPEPEEEGEEEPEPEEEGEEEPEPEETGEEE 99

Query: 644 EEEEEEEE 651
            E E E E
Sbjct: 100 PEPEPEPE 107

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 48.1 bits (114), Expect = 2e-05
 Identities = 20/52 (38%), Positives = 41/52 (78%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++++E+E+E++++EE++EEEEEEEE  +  ++E+EE+E  E+   E+ E ++
Sbjct: 154 DDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFTYEKSEVDK 205

Length = 2849

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 46.4 bits (110), Expect = 2e-05
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 589 ENIIQL---IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           +N++ L    R G+   E  E E  ++     +   E++E + E    E+ EEEE EE E
Sbjct: 29  QNMLALDVAARDGDDAIELAEPETSDDPYGNPDPFGEDDEGRIEVRISEDGEEEEVEEGE 88

Query: 646 EEEEEEEVRGGGKEEI 661
           E+EEEE      + E 
Sbjct: 89  EDEEEEGEEESEEFEP 104

Length = 306

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

 Score = 47.7 bits (113), Expect = 2e-05
 Identities = 14/56 (25%), Positives = 29/56 (51%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           R+ +   ++  EE E   E   + EE + +  + +E+ ++  E  + +E+ E EEE
Sbjct: 170 RKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEE 225

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

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

 Score = 47.7 bits (113), Expect = 2e-05
 Identities = 24/66 (36%), Positives = 41/66 (62%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E  I L++   R+E+EE E  ++E E+EEE   +  +  +EEE+E++ +EEE +   +
Sbjct: 235 LNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAK 294

Query: 647 EEEEEE 652
           EEEE +
Sbjct: 295 EEEELK 300

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

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

 Score = 47.7 bits (113), Expect = 2e-05
 Identities = 16/58 (27%), Positives = 32/58 (55%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            ++ ER ++  EE E   E   + EE + +E++ +E+ ++  E  + +E+ E EEE  
Sbjct: 170 RKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEENL 227

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

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

 Score = 47.7 bits (113), Expect = 2e-05
 Identities = 25/77 (32%), Positives = 47/77 (61%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           +  +   +     E   +L++   R+ ++EE+ +E E+E ++ E+E ++E +E EE E+E
Sbjct: 285 QEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKE 344

Query: 636 EEEEEEEEEEEEEEEEE 652
            +E E + E EEEEEE+
Sbjct: 345 LKELEIKREAEEEEEEQ 361

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

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

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 25/64 (39%), Positives = 42/64 (65%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           ++ E+E ++E+EE EE E+E +E E + + EEEEEE+ E+ +E+ E+ EEE    +    
Sbjct: 325 KKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLES 384

Query: 659 EEIS 662
           E +S
Sbjct: 385 ERLS 388

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 47.6 bits (113), Expect = 2e-05
 Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 2/59 (3%)

Query: 598 GEREEEE--EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           GE E+E+  EE +++E+E E  E+ E E E   E+ EE+E+E++ E  E     ++ VR
Sbjct: 647 GEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDKAVR 705

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 17/31 (54%), Positives = 26/31 (83%)

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            EE+E   +EE+EEEE++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 16/30 (53%), Positives = 22/30 (73%)

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
              EE+ EE+EEE+++EEE+EEEEE    G
Sbjct: 72  AAAEEKAEEKEEEKKKEEEKEEEEEEALAG 101

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

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

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 20/92 (21%), Positives = 50/92 (54%), Gaps = 8/92 (8%)

Query: 561 NTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE 620
            T   + ++        S+ D  G  R E + +  ++ +   ++  E ++E +  EE E 
Sbjct: 349 LTKLYEEVK--------SNTDLSGDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEA 400

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + +EE  ++EE E++++E+ +E++E+ +++E 
Sbjct: 401 KAKEEKLKQEENEKKQKEQADEDKEKRQKDER 432

Length = 434

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 14/58 (24%), Positives = 43/58 (74%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           +E EEE  EEE+++EE+++++++E+  +++++++E++E+E++++    ++     G +
Sbjct: 43  KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGNE 100

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 47.2 bits (112), Expect = 2e-05
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E E+EE+ E E E +E    +E E  + + E  EEE  + ++++  +E +++ E  G G 
Sbjct: 222 ENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDESDDDSETPGEGA 281

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 47.2 bits (112), Expect = 2e-05
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           E  ++ E E+EE+ ++++  E E+EE+ + E E +E    +E E  + E E  E   
Sbjct: 202 EMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEM 258

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 47.7 bits (113), Expect = 2e-05
 Identities = 19/62 (30%), Positives = 33/62 (53%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E EEE  E E   ++E +E +E+EE +   E+  E+E E +  +EE+ E+ +E       
Sbjct: 933 ESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDGEDWDELESKAAY 992

Query: 659 EE 660
           + 
Sbjct: 993 DS 994

Length = 1001

>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis

 Score = 45.3 bits (108), Expect = 2e-05
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            +    +EEEEE  E   +   E   E++  +E +EE +EEE++  +
Sbjct: 15  PKPPSPKEEEEEALELAIQEAHENALEKKLLDELDEELDEEEDDRFL 61

It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192

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

 Score = 47.7 bits (114), Expect = 2e-05
 Identities = 9/53 (16%), Positives = 41/53 (77%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +++ ++++++E+++E++++++ ++E +E++E +E E+  ++++   +E++ E
Sbjct: 143 DDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSE 195

Length = 509

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

 Score = 47.3 bits (113), Expect = 2e-05
 Identities = 10/50 (20%), Positives = 38/50 (76%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            ++++++E+++E++++++ ++E+EE +E +E E+  ++++   +E++ E 
Sbjct: 147 IDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEA 196

Length = 509

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

 Score = 46.9 bits (112), Expect = 2e-05
 Identities = 8/52 (15%), Positives = 41/52 (78%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           ++++ ++++++E+++E++++++ + ++EE++E +E E+  ++++   +E++ 
Sbjct: 143 DDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDS 194

Length = 509

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

 Score = 47.8 bits (114), Expect = 2e-05
 Identities = 28/74 (37%), Positives = 42/74 (56%)

Query: 582 EIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E+    +E + + + R + E E  EE EE E+E  E EEE  E ++ EE  +EE EE+ E
Sbjct: 477 ELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLE 536

Query: 642 EEEEEEEEEEEVRG 655
           + E   EE EE++ 
Sbjct: 537 KLENLLEELEELKE 550

Length = 908

>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed

 Score = 47.6 bits (114), Expect = 2e-05
 Identities = 24/60 (40%), Positives = 32/60 (53%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             R    EEE  EEE   EE   EE+EE     E  ++EE EEE+ EEE + E+  + +R
Sbjct: 461 RLRPLLPEEELAEEEAAAEEAALEEDEEAALEVELSDDEELEEEKAEEELKYEDLLKRLR 520

Length = 542

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 45.5 bits (108), Expect = 2e-05
 Identities = 18/51 (35%), Positives = 22/51 (43%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           E++  E   E   E++  E      EE    EEEE EE   EE   EE  E
Sbjct: 136 EKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAEEAPAEEAPAEESAE 186

Length = 186

>gnl|CDD|169428 PRK08404, PRK08404, V-type ATP synthase subunit H; Validated

 Score = 43.6 bits (103), Expect = 2e-05
 Identities = 26/77 (33%), Positives = 50/77 (64%), Gaps = 5/77 (6%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEE-----EEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           +E++I+ I + E+E EE  E+ +EE      + +EE ++ EEE+ ++ EEE ++  E+++
Sbjct: 1   MEDVIKEIVKAEKEAEERIEKAKEEAKKIIRKAKEEAKKIEEEIIKKAEEEAQKLIEKKK 60

Query: 643 EEEEEEEEEEVRGGGKE 659
           +E EEE ++ +  G KE
Sbjct: 61  KEGEEEAKKILEEGEKE 77

Length = 103

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

 Score = 46.1 bits (109), Expect = 2e-05
 Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           R+ +++ EEE +E+ +   E+    ++EE+   +E + +E++    E+ ++ +E  E  G
Sbjct: 95  RKTKQKVEEEVKEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEA-G 153

Query: 656 GGKEEI 661
              EE 
Sbjct: 154 KVHEET 159

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|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 20/47 (42%), Positives = 28/47 (59%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           + + E E E  EEEEEE EE EE  EE+  + +  +   EE +E+EE
Sbjct: 140 KPKNEFELELPEEEEEEPEEMEEELEEDAADRDARKRAAEEAKEQEE 186

This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. Length = 363

>gnl|CDD|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 20/51 (39%), Positives = 29/51 (56%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           + + E E E  EEEEEE EE E + EE+  + +  +   EE +E+EE   R
Sbjct: 140 KPKNEFELELPEEEEEEPEEMEEELEEDAADRDARKRAAEEAKEQEELRRR 190

This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. Length = 363

>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 28/110 (25%), Positives = 45/110 (40%), Gaps = 7/110 (6%)

Query: 564 KLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGERE----EEEEEEEEEEEEEEEEEE 619
           ++K     +   K   +    +  I+   + I   E E     EE E+ E+E E+ +E  
Sbjct: 74  RIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERL 133

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHFYVLY 669
           E  E+ + E E   EEE  E  EE +E   + E     KE++       Y
Sbjct: 134 ERLEKNLAEAEARLEEEVAEIREEGQELSSKREEL---KEKLDPELLSEY 180

Length = 239

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 46.2 bits (110), Expect = 3e-05
 Identities = 21/66 (31%), Positives = 39/66 (59%), Gaps = 4/66 (6%)

Query: 595 IRRGEREE--EEEEEEEEEEEE--EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +  GE++   EEE  +     E  E+ +EEE +++  E+  E +++++EEEE E EE+E+
Sbjct: 52  LEAGEKKGYGEEEVVDGIPGLELLEKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDED 111

Query: 651 EEVRGG 656
            +  G 
Sbjct: 112 SDDEGE 117

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 46.6 bits (110), Expect = 3e-05
 Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 14/86 (16%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEE--------------EEEEVQEEEEEEE 634
           +    L R   REE  +E   E  E ++E +                E+   + E  EEE
Sbjct: 55  DEAALLERLARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQEDSGAENETVEEE 114

Query: 635 EEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E+EE  EE EE EE E   +   K +
Sbjct: 115 EKEESREEREEVEETEGVTKSEQKND 140

Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 46.4 bits (111), Expect = 3e-05
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 18/86 (20%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEE-------------EEEEEEEEEEEEEVQEEEEE- 632
           RI+ +++  R     EEEE E + +E             EE E+  +EE EE  +E E+ 
Sbjct: 42  RIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQEREQM 101

Query: 633 ----EEEEEEEEEEEEEEEEEEEEVR 654
               E  +EE+E E +E+ E+++++R
Sbjct: 102 DEIIERIQEEDEAEAQEKREKQKKLR 127

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|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 44.7 bits (105), Expect = 3e-05
 Identities = 22/55 (40%), Positives = 36/55 (65%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +  ER  E+EE+ + + EEEE++E+EE+E +Q+++EE E    EE E    E E+
Sbjct: 78  QEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRLEREK 132

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

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

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 25/66 (37%), Positives = 29/66 (43%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E I  L    E  E   EE E+   E EE +EE EE++    EE EE  E   EE  E
Sbjct: 328 LKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAE 387

Query: 647 EEEEEE 652
            E E  
Sbjct: 388 LEAELA 393

Length = 1163

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

 Score = 47.4 bits (112), Expect = 3e-05
 Identities = 20/62 (32%), Positives = 41/62 (66%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            ++ EE+E++  E  ++E EE ++ EE  ++E EE+++ EE ++ EEE + + EE +   +
Sbjct: 1681 KKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAE 1740

Query: 659  EE 660
            E+
Sbjct: 1741 ED 1742

Length = 2084

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

 Score = 47.4 bits (112), Expect = 3e-05
 Identities = 24/79 (30%), Positives = 49/79 (62%)

Query: 582  EIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
            +    RIE +++L    ++ + EE ++ EE + + EE ++ EEE ++ E+ +++E EE++
Sbjct: 1588 KAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKK 1647

Query: 642  EEEEEEEEEEEVRGGGKEE 660
            + EE ++ EEE +    EE
Sbjct: 1648 KAEELKKAEEENKIKAAEE 1666

Length = 2084

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

 Score = 47.1 bits (111), Expect = 3e-05
 Identities = 22/66 (33%), Positives = 46/66 (69%), Gaps = 3/66 (4%)

Query: 600  REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE---EEEEEEEEEEEEEEEEEEVRGG 656
            ++E EE ++ EE +++E EE+++ EE+++ EEE +   EE ++E EE++++ EE +    
Sbjct: 1695 KKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEE 1754

Query: 657  GKEEIS 662
             K++I+
Sbjct: 1755 EKKKIA 1760

Length = 2084

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 46.9 bits (111), Expect = 3e-05
 Identities = 7/62 (11%), Positives = 15/62 (24%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
               E       ++     +   E+   + E    E E +     + E            
Sbjct: 149 PAPPESHNPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPP 208

Query: 659 EE 660
           +E
Sbjct: 209 DE 210

Length = 413

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 46.5 bits (110), Expect = 3e-05
 Identities = 9/63 (14%), Positives = 16/63 (25%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
                 +   E+  EE E    E E +     + E        +   +E  E +      
Sbjct: 162 QPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQ 221

Query: 658 KEE 660
              
Sbjct: 222 APS 224

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 46.0 bits (109), Expect = 3e-05
 Identities = 15/54 (27%), Positives = 28/54 (51%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             + E+E++ +E+E++++ EEEE        E+ +   EE E  E E  E   +
Sbjct: 221 SEDNEDEDDPKEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASAD 274

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 47.1 bits (112), Expect = 3e-05
 Identities = 19/55 (34%), Positives = 32/55 (58%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           EE  ++  EE+ +EE+ ++++    E+ E   EE E  +E EE+E E   G G+E
Sbjct: 220 EETGDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEE 274

Length = 620

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

 Score = 45.1 bits (106), Expect = 3e-05
 Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           Q++I   R E   +L  R E E  EE+ +E E++EE+E E EE+   ++ ++ E E  E+
Sbjct: 125 QEQIEKARQERE-ELEERMEWERREEKIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQ 183

Query: 640 EEEEEEEEEEEEE 652
           +E E E ++++ E
Sbjct: 184 DESETESDDDKTE 196

Length = 197

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 28/56 (50%), Positives = 33/56 (58%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +R  E  EEEE EE EE+EEEE EEE EE E   +  EE  E  E+ EE EE  + 
Sbjct: 73  VRISEDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEELTEASEQLEEHEEGFQA 128

Length = 306

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 46.6 bits (111), Expect = 3e-05
 Identities = 21/37 (56%), Positives = 23/37 (62%)

Query: 625 EVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
                 E EEEEEEEEE  EEEEEEEEE     +EE+
Sbjct: 298 PPPSPPEPEEEEEEEEEVPEEEEEEEEEEERTFEEEV 334

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 43.8 bits (104), Expect = 3e-05
 Identities = 17/49 (34%), Positives = 32/49 (65%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            +E+ + E+++EE++ E E++ +   EE+ E E E+ E+E EE E E+ 
Sbjct: 18  AKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAELA 66

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 45.0 bits (107), Expect = 3e-05
 Identities = 29/66 (43%), Positives = 37/66 (56%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E   +     E EE E+ EEEE EEEE EEE E EEE QE  E E + EE +++    + 
Sbjct: 5   EQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKDKYLRAQA 64

Query: 649 EEEEVR 654
           E E +R
Sbjct: 65  EFENLR 70

Length = 193

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 47.1 bits (111), Expect = 3e-05
 Identities = 30/73 (41%), Positives = 35/73 (47%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EN  + +     E  EE +EE  EE EE  EE  EE V+E  EE  EE EE  EE  EE 
Sbjct: 1047 ENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEEN 1106

Query: 649  EEEEVRGGGKEEI 661
             EE      +E  
Sbjct: 1107 AEENAEENAEENA 1119

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 47.1 bits (111), Expect = 3e-05
 Identities = 32/83 (38%), Positives = 40/83 (48%)

Query: 579  DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
            + DE     +E  ++       EE EE  EE  EE  EE  EE +EE  EE EE  EE  
Sbjct: 1021 EYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENI 1080

Query: 639  EEEEEEEEEEEEEEVRGGGKEEI 661
            EE  EE  EE  EE+    +E +
Sbjct: 1081 EENVEENVEENVEEIEENVEENV 1103

Length = 1136

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

 Score = 46.8 bits (111), Expect = 3e-05
 Identities = 18/63 (28%), Positives = 42/63 (66%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
             +E + E  +EEE+E+E+ +EE+++++ + +EE ++ + +EE +E+   +E+E+ +   
Sbjct: 94  PAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKK 153

Query: 658 KEE 660
            EE
Sbjct: 154 VEE 156

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 44.2 bits (105), Expect = 3e-05
 Identities = 16/31 (51%), Positives = 27/31 (87%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EE+E ++ +E+EEEE++EE+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 44.2 bits (105), Expect = 3e-05
 Identities = 17/33 (51%), Positives = 28/33 (84%), Gaps = 2/33 (6%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
            EE+E +++EE+EEEE++EE+  ++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDEED--DDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 44.2 bits (105), Expect = 3e-05
 Identities = 17/33 (51%), Positives = 28/33 (84%), Gaps = 2/33 (6%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
            EE+E +++EE+EEEE++E  E+++E+E EEEE
Sbjct: 109 SEEDESDDDEEDEEEEDDE--EDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 46.6 bits (110), Expect = 3e-05
 Identities = 23/59 (38%), Positives = 41/59 (69%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           ++ +    + EEE   ++EEEE+E+ EE EE EEV+  EEE +++E+ E+++E+E + E
Sbjct: 90  LEGLNIIVKNEEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAE 148

Length = 374

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 43.4 bits (103), Expect = 3e-05
 Identities = 14/25 (56%), Positives = 17/25 (68%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
                  EE++EEEEEEEE+EE EE
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEE 95

Length = 106

>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

 Score = 46.5 bits (110), Expect = 3e-05
 Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 14/101 (13%)

Query: 561 NTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEE-------EEEEEEEEE 613
           N  +   I          +QD      +  ++ L R G R +E        E+  E  E 
Sbjct: 282 NERRGGIILDIS--LNEFEQD-----AVPLLVDLERNGNRIKELADFGDYYEDIFEVVEV 334

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            E++E +   EE  +EE E+E E +E   EE  E E  EV+
Sbjct: 335 VEKQEGDVVTEESTDEESEDEVEIDESVIEEVAEMELLEVQ 375

Length = 388

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

 Score = 46.8 bits (111), Expect = 3e-05
 Identities = 24/62 (38%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEE-EEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
             E+E+E+ +  ++  E+E+E+EE E   E   EEEE EE E     ++EEE+EE  V  
Sbjct: 287 TEEKEKEKRKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEKEEVTVSP 346

Query: 656 GG 657
            G
Sbjct: 347 DG 348

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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 43.3 bits (102), Expect = 3e-05
 Identities = 16/25 (64%), Positives = 22/25 (88%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
             EE+ EE+EEE+++EEE+EEEEEE
Sbjct: 73  AAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 46.9 bits (111), Expect = 3e-05
 Identities = 15/65 (23%), Positives = 47/65 (72%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           + EN I+ + +   EE  EEE+++EE+++++++E+E+++  +++E++E+E++++    ++
Sbjct: 33  KKENAIRKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDD 92

Query: 647 EEEEE 651
              ++
Sbjct: 93  SSADD 97

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis

 Score = 45.3 bits (108), Expect = 3e-05
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            +    +EEEEE  E   +E  E   E++  +E +EE +EEE++  
Sbjct: 15  PKPPSPKEEEEEALELAIQEAHENALEKKLLDELDEELDEEEDDRF 60

It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192

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

 Score = 46.9 bits (112), Expect = 3e-05
 Identities = 9/54 (16%), Positives = 42/54 (77%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++ ++++++E+++E++++++ ++E+ +++E +E E+  ++++   +E++ E +R
Sbjct: 145 DDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALR 198

Length = 509

>gnl|CDD|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component

 Score = 46.2 bits (110), Expect = 3e-05
 Identities = 20/47 (42%), Positives = 30/47 (63%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           + + E E E  EEEEEE EE EEE++E+  + +  +   EE +E+EE
Sbjct: 140 KPKNEFELELPEEEEEEPEEMEEELEEDAADRDARKRAAEEAKEQEE 186

This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. Length = 363

>gnl|CDD|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component

 Score = 46.2 bits (110), Expect = 3e-05
 Identities = 20/41 (48%), Positives = 25/41 (60%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E E  EEEEEE EE EEE EE+  +    +   EE +E+EE
Sbjct: 146 ELELPEEEEEEPEEMEEELEEDAADRDARKRAAEEAKEQEE 186

This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. Length = 363

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

 Score = 46.4 bits (110), Expect = 3e-05
 Identities = 14/56 (25%), Positives = 34/56 (60%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R ++ E++ EE E++   E+  ++E E+    E+  ++ E+  ++ EE++++ EE 
Sbjct: 69  RQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEA 124

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 43.2 bits (102), Expect = 3e-05
 Identities = 14/30 (46%), Positives = 18/30 (60%)

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E   E +E EEEE+EEE EEE ++    G
Sbjct: 77  AEAAAEADEAEEEEKEEEAEEESDDDMLFG 106

Length = 109

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 13/30 (43%), Positives = 25/30 (83%)

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           + E EEEEE E+++ E+EE+EEE+++++ +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|225887 COG3351, FlaD, Putative archaeal flagellar protein D/E [Cell motility and secretion]

 Score = 45.2 bits (107), Expect = 3e-05
 Identities = 15/54 (27%), Positives = 29/54 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            E +E+ EE   + ++ ++E  EE  E  ++ +E    E+ +  EEE  E+E+ 
Sbjct: 21  EELKEKIEELPIQAKKSDDELVEELPERYEQTKENSLIEKVDSIEEEISEKEKV 74

Length = 214

>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed

 Score = 46.4 bits (111), Expect = 3e-05
 Identities = 18/53 (33%), Positives = 34/53 (64%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EE   EE EE E  E+ E   ++  +E+ EE EEE++++ +++ +E+++E V 
Sbjct: 333 EENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDDWDEDDDEGVE 385

Length = 390

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 46.3 bits (110), Expect = 4e-05
 Identities = 23/42 (54%), Positives = 32/42 (76%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E+E E+EV +EEEEEE+EE++EEEE+  ++EEE      KEE
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEE 69

Length = 529

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

 Score = 46.6 bits (111), Expect = 4e-05
 Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 587 RIENIIQLIRRGEREEEEEEEE-EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            +E++++ +RR   E E + EE + E    EEE E+ +  ++E EEE EE EEE EE +E
Sbjct: 699 SLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQE 758

Query: 646 EEEEEEEVRGGGKEEIS 662
             EE EE     +E ++
Sbjct: 759 RLEELEEELESLEEALA 775

Length = 1163

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

 Score = 46.7 bits (110), Expect = 4e-05
 Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 10/74 (13%)

Query: 596  RRGEREEEEEEEEEEEEEEEEEEEEE----------EEEEVQEEEEEEEEEEEEEEEEEE 645
            ++ E  ++ EE+E++  E  ++E EE          E EE ++ EE ++ EEE + + EE
Sbjct: 1675 KKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734

Query: 646  EEEEEEEVRGGGKE 659
             ++E EE +   +E
Sbjct: 1735 AKKEAEEDKKKAEE 1748

Length = 2084

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 46.5 bits (110), Expect = 4e-05
 Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 6/93 (6%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE------EEEEEEEEE 642
           E+I  L +  + E  E+  +  + + E+  ++EEEEE  E  E+E      E +   E E
Sbjct: 86  EHIRVLAKLQDSESHEDGSDGSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESE 145

Query: 643 EEEEEEEEEEVRGGGKEEISLHFYVLYVLSKGK 675
              E+  ++E     ++++          S  +
Sbjct: 146 SSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQ 178

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 46.1 bits (109), Expect = 4e-05
 Identities = 8/55 (14%), Positives = 18/55 (32%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E E +     + E        +   +E  E +    ++      ++  E E+E 
Sbjct: 183 SEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEP 237

Length = 413

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

 Score = 46.9 bits (111), Expect = 4e-05
 Identities = 24/68 (35%), Positives = 38/68 (55%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E I  L      E+EE E  ++E E+EEE   +  +E +EEE+E++ +EEE +   +E
Sbjct: 236 NEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKE 295

Query: 647 EEEEEEVR 654
           EEE +   
Sbjct: 296 EEELKSEL 303

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 = 46.9 bits (111), Expect = 4e-05
 Identities = 15/56 (26%), Positives = 31/56 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +++E  ++  EE E   E   + EE ++QE + +E+ ++  E  + +E+ E EE  
Sbjct: 171 KKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEN 226

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|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 46.3 bits (110), Expect = 4e-05
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           E   +++  + +E E++   +     E E+   E ++EEEE+EEEEEEE+E  G  KE  
Sbjct: 354 ETLNKQKWTKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHS 413

Query: 662 S 662
            
Sbjct: 414 D 414

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 42.7 bits (101), Expect = 4e-05
 Identities = 19/25 (76%), Positives = 19/25 (76%)

Query: 624 EEVQEEEEEEEEEEEEEEEEEEEEE 648
                EEEEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 47.1 bits (111), Expect = 4e-05
 Identities = 31/73 (42%), Positives = 39/73 (53%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EN+ + I     E  EE  EE  EE +EE  EE EE V+E +EE  EE EE  EE  EE 
Sbjct: 997  ENVEENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEEN 1056

Query: 649  EEEEVRGGGKEEI 661
             EE +    +E +
Sbjct: 1057 IEENIEEYDEENV 1069

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 46.7 bits (110), Expect = 4e-05
 Identities = 30/73 (41%), Positives = 36/73 (49%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            E  ++ I     E  EE  EE  EE +EE  EE EE ++E  EE  EE  EE  EE EE 
Sbjct: 1039 EENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEEN 1098

Query: 649  EEEEVRGGGKEEI 661
             EE V    +E  
Sbjct: 1099 VEENVEENAEENA 1111

Length = 1136

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

 Score = 46.4 bits (110), Expect = 4e-05
 Identities = 15/56 (26%), Positives = 36/56 (64%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            + +++E+ +EE ++ + +EE +E+   +E ++E+E++ EE  + EEE++ E    
Sbjct: 116 EKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRA 171

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|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 43.0 bits (102), Expect = 4e-05
 Identities = 15/29 (51%), Positives = 18/29 (62%)

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
                  EE++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

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

 Score = 46.3 bits (110), Expect = 4e-05
 Identities = 16/62 (25%), Positives = 37/62 (59%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           G++ +E  +E  ++ ++  ++  E ++E    EE E + +EE+ ++EE E++++E     
Sbjct: 364 GDKRQELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADED 423

Query: 658 KE 659
           KE
Sbjct: 424 KE 425

Length = 434

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 46.4 bits (110), Expect = 4e-05
 Identities = 14/56 (25%), Positives = 39/56 (69%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + ++ + +++ ++ +++E +E  ++++EE  E E+E + EE  E++ ++EEEE+ +
Sbjct: 145 KAKKGKAKKKTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSD 200

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 46.0 bits (109), Expect = 4e-05
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
             E E   EEE  EE E+E E E E+EE+  +E+ E+ ++E+    + ++  EEEE +G 
Sbjct: 211 ESEVEASPEEENYEEYEDETELEVEDEEKALDEQTEDPQQEDALAGDAKKALEEEEEKGE 270

Query: 657 GKE 659
             E
Sbjct: 271 RPE 273

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

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

 Score = 46.7 bits (111), Expect = 4e-05
 Identities = 25/77 (32%), Positives = 44/77 (57%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           + E + +L++   +E + + EE E +  E  E+ E+  E  EEE +E ++ EE +EE+EE
Sbjct: 168 KYEKLSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEE 227

Query: 647 EEEEEEVRGGGKEEISL 663
           EE E+E+    +    L
Sbjct: 228 EELEQEIEALEERLAEL 244

Length = 908

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 43.2 bits (102), Expect = 4e-05
 Identities = 13/31 (41%), Positives = 16/31 (51%)

Query: 627 QEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
              E   E +E EEEE+EEE EEE +     
Sbjct: 75  AGAEAAAEADEAEEEEKEEEAEEESDDDMLF 105

Length = 109

>gnl|CDD|225887 COG3351, FlaD, Putative archaeal flagellar protein D/E [Cell motility and secretion]

 Score = 44.8 bits (106), Expect = 4e-05
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 4/79 (5%)

Query: 586 PRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEE--EEVQEEEEEEEEEEEEEEEE 643
           P +E  I+   +      EE +E+ EE   + ++ ++E  EE+ E  E+ +E    E+ +
Sbjct: 3   PYLEEKIEKAEKVTAFALEELKEKIEELPIQAKKSDDELVEELPERYEQTKENSLIEKVD 62

Query: 644 E--EEEEEEEEVRGGGKEE 660
              EE  E+E+V     +E
Sbjct: 63  SIEEEISEKEKVMSEKLKE 81

Length = 214

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

 Score = 46.7 bits (112), Expect = 4e-05
 Identities = 23/62 (37%), Positives = 41/62 (66%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E + +LI   E  E E E++ EE E   +E E+ +EE++E++E+ +EEE++  EE E+E 
Sbjct: 516 EKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEA 575

Query: 649 EE 650
           ++
Sbjct: 576 QQ 577

Length = 782

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

 Score = 46.6 bits (111), Expect = 4e-05
 Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 9/91 (9%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           S  +E  S RIE  ++ I   E++      E+E  E+E +E +E+  +++E+ +  E+E 
Sbjct: 801 SKLEEEVS-RIEARLREI---EQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEI 856

Query: 638 EE-----EEEEEEEEEEEEEVRGGGKEEISL 663
           E      EE EEE EE E  +R        L
Sbjct: 857 ENLNGKKEELEEELEELEAALRDLESRLGDL 887

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|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 46.3 bits (111), Expect = 4e-05
 Identities = 27/76 (35%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R   + +L +R  ++EE  + + E  E+ EEE E++E+E++++++E E++EEE EE  EE
Sbjct: 80  RRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEE 139

Query: 647 EEEE-EEVRGGGKEEI 661
           + +E E + G   EE 
Sbjct: 140 QLQELERISGLTAEEA 155

Length = 520

>gnl|CDD|217502 pfam03343, SART-1, SART-1 family

 Score = 46.3 bits (110), Expect = 4e-05
 Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 2/64 (3%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE--EEEEV 653
           +   ++E  EE  + EE++E+EE+E+ + +V+    + +EE+EEE++E       EEE  
Sbjct: 411 KPENKDESVEEISDAEEDDEDEEDEDGDGDVEMSAVDNDEEKEEEDKEAIPSTILEEEPT 470

Query: 654 RGGG 657
            GGG
Sbjct: 471 VGGG 474

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 45.5 bits (108), Expect = 4e-05
 Identities = 19/49 (38%), Positives = 31/49 (63%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
            +      ++  E+EE E++  +E+EE+E  V+E+E E  EEEE+EE E
Sbjct: 24  GKGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase; Reviewed

 Score = 46.1 bits (109), Expect = 4e-05
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 4/87 (4%)

Query: 574 VWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
           V + +D+D   +P +E         + E E+  +   +     + + E      EE    
Sbjct: 349 VVQVADRDGESTPAVEET----SEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAAL 404

Query: 634 EEEEEEEEEEEEEEEEEEEVRGGGKEE 660
             E  +E E E  E+          +E
Sbjct: 405 ASEAHDETEPEVPEKAAPIPDPAKPDE 431

Length = 460

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 46.6 bits (111), Expect = 4e-05
 Identities = 27/64 (42%), Positives = 33/64 (51%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            R E E E+ EE   +  +E  E E E++E EE  EE EEE  E E E EE E      K
Sbjct: 736 ARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLK 795

Query: 659 EEIS 662
           EE+ 
Sbjct: 796 EELK 799

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|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 44.3 bits (104), Expect = 5e-05
 Identities = 22/57 (38%), Positives = 36/57 (63%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           RR E E   E+EE+ + + EEEE++E+EE+ + ++++EE E    EE E    E E+
Sbjct: 76  RRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRLEREK 132

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 46.3 bits (110), Expect = 5e-05
 Identities = 18/62 (29%), Positives = 34/62 (54%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + +     EEE+EEE E        + +++E   ++E+E+EE++EE E   + E  + E+
Sbjct: 3   EQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEISKREK 62

Query: 653 VR 654
            R
Sbjct: 63  AR 64

Length = 1033

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

 Score = 46.6 bits (111), Expect = 5e-05
 Identities = 29/66 (43%), Positives = 39/66 (59%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           ++E + + +   E E E+ +   EE EEE EE EEE EE+QE  EE EEE E  EE   +
Sbjct: 717 QLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAK 776

Query: 647 EEEEEE 652
            +EE E
Sbjct: 777 LKEEIE 782

Length = 1163

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

 Score = 46.2 bits (110), Expect = 5e-05
 Identities = 36/74 (48%), Positives = 45/74 (60%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E I +L  + +  EEE EE E+E EE +EE EE E E +E E+E +E EEE+EE EEE  
Sbjct: 835 EEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELR 894

Query: 649 EEEEVRGGGKEEIS 662
           E E      KEEI 
Sbjct: 895 ELESELAELKEEIE 908

Length = 1163

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 45.7 bits (108), Expect = 5e-05
 Identities = 9/62 (14%), Positives = 19/62 (30%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           +  EE E    E E +     + E        +   +E  E +    ++      +   +
Sbjct: 173 DSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQSPTPQQAPSPNTQQAVE 232

Query: 659 EE 660
            E
Sbjct: 233 HE 234

Length = 413

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

 Score = 46.5 bits (110), Expect = 5e-05
 Identities = 25/62 (40%), Positives = 37/62 (59%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E E EE   E +EE++ E+  EEE E ++EE  +EE  +E   +EEE EE++ +     K
Sbjct: 833 EEELEELALELKEEQKLEKLAEEELERLEEEITKEELLQELLLKEEELEEQKLKDELESK 892

Query: 659 EE 660
           EE
Sbjct: 893 EE 894

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 = 46.5 bits (110), Expect = 5e-05
 Identities = 24/54 (44%), Positives = 41/54 (75%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E+E ++ E+E ++E+EE EE E+E +E++ + E EEEEEE+ E+ +E+ E+ EE
Sbjct: 321 EKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEE 374

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 = 46.5 bits (110), Expect = 5e-05
 Identities = 24/68 (35%), Positives = 37/68 (54%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E     I+R   EEEEE+ E+ +E+ E+ EEE   ++  E E      + +EEE E +
Sbjct: 342 EKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELELK 401

Query: 647 EEEEEEVR 654
            EEE+E +
Sbjct: 402 NEEEKEAK 409

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 = 46.1 bits (109), Expect = 5e-05
 Identities = 23/61 (37%), Positives = 42/61 (68%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
              + +  E+E ++ E+E ++E+EE EE E+E++E E + E EEEEEE+ E+ +E+ E++
Sbjct: 313 DEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQL 372

Query: 654 R 654
            
Sbjct: 373 E 373

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 46.4 bits (110), Expect = 5e-05
 Identities = 20/64 (31%), Positives = 37/64 (57%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E +  ++   + +E +   ++  E EEE+E++ EE +  E+E E  E+ E E E + E+ 
Sbjct: 623 EGLQLILDVLKADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDG 682

Query: 649 EEEE 652
           EE+E
Sbjct: 683 EEDE 686

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|131972 TIGR02926, AhaH, ATP synthase archaeal, H subunit

 Score = 41.8 bits (98), Expect = 5e-05
 Identities = 25/56 (44%), Positives = 32/56 (57%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            R +R  E  EE  E  EE EEE  +  EE+ +E EEE E+E E+  EE E+E E 
Sbjct: 21  ERKQRIAEAREEARELLEEAEEEASKLGEEIIKEAEEEIEKEAEKIREEGEKEIEA 76

he A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The hydrophilic A1 "stalk" complex (AhaABCDEFG) is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. It is unclear precisely where AhaH fits into these complexes. Length = 85

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 46.3 bits (109), Expect = 5e-05
 Identities = 31/74 (41%), Positives = 39/74 (52%)

Query: 588  IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            IE  ++       EE EE  EE +EE  EE EE  EE V+E  EE  EE +EE  EE EE
Sbjct: 1015 IEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEE 1074

Query: 648  EEEEEVRGGGKEEI 661
              EE +    +E +
Sbjct: 1075 NIEENIEENVEENV 1088

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 46.3 bits (109), Expect = 5e-05
 Identities = 30/85 (35%), Positives = 42/85 (49%)

Query: 563  NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
            N  + I  +I+ +   + +EI     ENI + +     E  EE EE  EE  EE  EE  
Sbjct: 1052 NVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAEENA 1111

Query: 623  EEEVQEEEEEEEEEEEEEEEEEEEE 647
            EE  +E  EE ++E  EE  EE +E
Sbjct: 1112 EENAEENAEEYDDENPEEHNEEYDE 1136

Length = 1136

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 42.6 bits (101), Expect = 5e-05
 Identities = 15/29 (51%), Positives = 18/29 (62%)

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
                  EE++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 45.2 bits (107), Expect = 5e-05
 Identities = 19/52 (36%), Positives = 38/52 (73%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +++  +  + + ++ ++EE+++++    EE+E +E+EEEEE EEEEEEE+E
Sbjct: 232 SQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDE 283

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional

 Score = 44.3 bits (104), Expect = 5e-05
 Identities = 23/71 (32%), Positives = 44/71 (61%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           +++   P+  +I +L  R + ++E EE  E++ E+  EE E++ EE  E+EEE EE++ +
Sbjct: 7   KNKAKEPKRRDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENEEQKPK 66

Query: 640 EEEEEEEEEEE 650
           EE +   +E +
Sbjct: 67  EEIDYPIQENK 77

Length = 193

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 42.4 bits (99), Expect = 5e-05
 Identities = 14/42 (33%), Positives = 32/42 (76%)

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E EE+ + +  EEE++++E+EE+++E+++E+++E  V   G+
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPSFGE 48

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed

 Score = 46.0 bits (110), Expect = 5e-05
 Identities = 18/58 (31%), Positives = 33/58 (56%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           L+   E    EE EE E  E+ E   ++   E  EE EEE++++ +++ +E+++E  E
Sbjct: 328 LMTFIEENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDDWDEDDDEGVE 385

Length = 390

>gnl|CDD|219069 pfam06512, Na_trans_assoc, Sodium ion transport-associated

 Score = 45.1 bits (107), Expect = 5e-05
 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 11/70 (15%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE-----------EEEEEEE 643
           I  GE + E   +E+   E     +EE ++   E  + EE++           E  EEEE
Sbjct: 107 IASGESDLENLNDEDTSSESSYGFKEESKKGSAETLKLEEKDSSSSEGSTVDLEPPEEEE 166

Query: 644 EEEEEEEEEV 653
           EE  EEEEEV
Sbjct: 167 EEIAEEEEEV 176

Members of this family contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of pfam00520 and, less often, one copy of pfam00612. Length = 230

>gnl|CDD|214818 smart00784, SPT2, SPT2 chromatin protein

 Score = 42.7 bits (101), Expect = 5e-05
 Identities = 14/53 (26%), Positives = 28/53 (52%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +R    ++++++++ E    + +EEE         E+ EEE  E+EEE E+  
Sbjct: 50  KRYAYRDDDDDDDDMEAGGADIQEEERRSARLARLEDREEERLEKEEEREKRA 102

This entry includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation. Length = 106

>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 45.5 bits (108), Expect = 5e-05
 Identities = 28/101 (27%), Positives = 39/101 (38%), Gaps = 36/101 (35%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEE---------------EEEVQEEEEE-------- 632
            R    ++ +EE+EE  E+E EEE                  E EV E  EE        
Sbjct: 105 TRNYEADKLDEEQEERVEKEREEELAGDAMKKLENRTADSKREMEVLERLEELKELQSRR 164

Query: 633 -------------EEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
                          E++EEEEEEEE+E   + +  G + E
Sbjct: 165 ADVDVNSMLEALFRREKKEEEEEEEEDEALIKSLSFGPETE 205

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 45.8 bits (108), Expect = 6e-05
 Identities = 17/58 (29%), Positives = 29/58 (50%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            +  R    E EE E   + E++ +  + EE ++ ++E E EEEE+ +    EE   E
Sbjct: 116 KEESREEREEVEETEGVTKSEQKNDWRDAEECQKEEKEPEPEEEEKPKRGSLEENNGE 173

Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 45.7 bits (109), Expect = 6e-05
 Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 26/91 (28%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEE------------EE-----EEEEEEVQEEEE 631
           E  I  +   ER +   EEEE E + +EE            EE     +EE EE  +E E
Sbjct: 40  ERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQERE 99

Query: 632 ---------EEEEEEEEEEEEEEEEEEEEEV 653
                    +EE+E E +E+ E++++  EE+
Sbjct: 100 QMDEIIERIQEEDEAEAQEKREKQKKLREEI 130

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|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 45.8 bits (108), Expect = 6e-05
 Identities = 16/53 (30%), Positives = 34/53 (64%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++E + + EEE+EE++E+E++++EEE  E   ++ + +E   E  + E  +E 
Sbjct: 286 KKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKEL 338

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 46.0 bits (109), Expect = 6e-05
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R E E  +E EE+E E  + E EE E +  +  E+ E +E +E+ E   E
Sbjct: 251 REESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTETPGE 300

Length = 620

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 42.6 bits (101), Expect = 6e-05
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +E+ + E+++EE++ E E+  +   +E+ E E E+ E+E EE E E    E
Sbjct: 18  AKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAELARRE 69

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 16/68 (23%)

Query: 601 EEEEEEEEEEEEEEEE-------------EEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +EEE+EE+EEE+ +               EE+E+ + E +E+   E EE+  E+E  E+ 
Sbjct: 38  DEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTPEDELAEKL 97

Query: 648 ---EEEEE 652
              + +EE
Sbjct: 98  RLRKLQEE 105

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 42.2 bits (100), Expect = 6e-05
 Identities = 14/29 (48%), Positives = 17/29 (58%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
                  EE++EEEEEEEE+E  EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

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

 Score = 46.2 bits (110), Expect = 6e-05
 Identities = 31/90 (34%), Positives = 53/90 (58%), Gaps = 1/90 (1%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +E + + ++  E  +EE EE E+E E  E  + + EE+++E EE  EE ++E EE EE+ 
Sbjct: 223 LEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKV 282

Query: 648 EEEEEVRGGGKEEISL-HFYVLYVLSKGKI 676
           +E +E++   +E I L  FY  Y+    +I
Sbjct: 283 KELKELKEKAEEYIKLSEFYEEYLDELREI 312

Length = 880

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 45.1 bits (107), Expect = 6e-05
 Identities = 20/55 (36%), Positives = 34/55 (61%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHF 665
            ++  E+EE E++   ++EE+E   EE+E E  EEEE+EE EV+     + ++ F
Sbjct: 31  AQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGEVKASPDADTTILF 85

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 46.2 bits (110), Expect = 6e-05
 Identities = 31/78 (39%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 587 RIENIIQLIR----RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           R+E   Q++R      ER+ EE E + EE E + +E  EE  E++E+ EE +EE E  E 
Sbjct: 299 RLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEA 358

Query: 643 EEEEEEEEEEVRGGGKEE 660
           E EE E E E      EE
Sbjct: 359 ELEELEAELEELESRLEE 376

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|214818 smart00784, SPT2, SPT2 chromatin protein

 Score = 42.4 bits (100), Expect = 6e-05
 Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 34/93 (36%)

Query: 596 RRGEREEEEEEEEE---EEEEEEEEEEEEE---------------------------EEE 625
            R + +EEE+E+ +   E+++EE++ + +E                             +
Sbjct: 11  SRDDYDEEEDEDMDDFIEDDDEEDDYDRDEIWAMFNKGRKRYAYRDDDDDDDDMEAGGAD 70

Query: 626 VQEEEEEEE----EEEEEEEEEEEEEEEEEEVR 654
           +QEEE         E+ EEE  E+EEE E+  R
Sbjct: 71  IQEEERRSARLARLEDREEERLEKEEEREKRAR 103

This entry includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation. Length = 106

>gnl|CDD|220376 pfam09745, DUF2040, Coiled-coil domain-containing protein 55 (DUF2040)

 Score = 42.8 bits (101), Expect = 6e-05
 Identities = 32/101 (31%), Positives = 55/101 (54%), Gaps = 6/101 (5%)

Query: 564 KLKTIRPSIKVWKTSDQDEIGSPR-IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
            +K  +   K  K S++ E   P+ I ++++   R +RE E  EE + ++E E+E +E  
Sbjct: 26  SIKAAKEEKKQAKLSERKENRKPKYIGSLLEAAERRKREREIAEERKLQKEREKEGDEFA 85

Query: 623 EEEV-----QEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           ++E       +++ EE  + EEEE+E EE EEE +V  G  
Sbjct: 86  DKEKFVTSAYKKQLEENRKLEEEEKEREELEEENDVTKGKD 126

This entry is a conserved domain of approximately 130 residues of proteins conserved from fungi to humans. The proteins do contain a coiled-coil domain, but the function is unknown. Length = 128

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 44.6 bits (106), Expect = 6e-05
 Identities = 13/40 (32%), Positives = 15/40 (37%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           EEE+          V      E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 43.5 bits (103), Expect = 6e-05
 Identities = 13/29 (44%), Positives = 24/29 (82%)

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           E+E +EEEE++++ ++ +EE EEEE+ E+
Sbjct: 1   EDEPDEEEELEDDIDDLDEEAEEEEDGED 29

This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. Length = 145

>gnl|CDD|224236 COG1317, FliH, Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]

 Score = 44.7 bits (106), Expect = 6e-05
 Identities = 28/97 (28%), Positives = 42/97 (43%), Gaps = 7/97 (7%)

Query: 558 NVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEE 617
           N+ N ++   +    +V +  D    G         L      EEE E+  E +EEE E 
Sbjct: 3   NIINEDRDDALPF--QVIEFKDLANAGPKVAPEKAVL-----EEEELEQALEAKEEELES 55

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             +E +E ++E   E  EE  +   EE  EE +EE R
Sbjct: 56  AAQELQEGIEEGAREGYEEGFQLGYEEGFEEGQEEGR 92

Length = 234

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 45.8 bits (109), Expect = 6e-05
 Identities = 28/75 (37%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R E++ +LI       E  EE+ E  EE  E   E E E +E+ E   E EEE EE  EE
Sbjct: 517 RREDLEELI---AERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREE 573

Query: 647 EEEEEEVRGGGKEEI 661
             E        KE I
Sbjct: 574 VAELNSKLAELKERI 588

Length = 880

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 46.1 bits (109), Expect = 7e-05
 Identities = 26/63 (41%), Positives = 36/63 (57%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E E E  EE EE E+E E E E + E   E + +E E E E E E +E+E+E E++ G  
Sbjct: 729 EGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGED 788

Query: 659 EEI 661
            E+
Sbjct: 789 GEM 791

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|237063 PRK12329, nusA, transcription elongation factor NusA; Provisional

 Score = 45.5 bits (108), Expect = 7e-05
 Identities = 17/54 (31%), Positives = 26/54 (48%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
            E ++E E+ +  E    +EEEE  + E EE  E E+ E  EE+ R      + 
Sbjct: 374 AEYDQEAEDAKVAELISQREEEEALQREAEERLEAEQAERAEEDARLRELYPLP 427

Length = 449

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 45.0 bits (106), Expect = 7e-05
 Identities = 18/61 (29%), Positives = 29/61 (47%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E+          + +E+ +E    + +V  EEEE  EE +  EEEE+EE   +    G +
Sbjct: 147 EKPRVTRFNIVWDNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSYGEGNR 206

Query: 659 E 659
           E
Sbjct: 207 E 207

Length = 279

>gnl|CDD|225368 COG2811, NtpF, Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 25/64 (39%), Positives = 31/64 (48%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E I +     E+  +E  EE  E  EE EEE E+  +   EE  EE EEE EE   E E+
Sbjct: 21  EEIEEAKEEAEQIIKEAREEAREIIEEAEEEAEKLAQEILEEAREEAEEEAEEILAEAEK 80

Query: 649 EEEE 652
           E   
Sbjct: 81  EASA 84

Length = 108

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

 Score = 44.3 bits (105), Expect = 7e-05
 Identities = 20/50 (40%), Positives = 32/50 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           ++E++ + E+E+EE EEE EEE+EE   + E+E EE+ E   E+E     
Sbjct: 77  DKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITNPS 126

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|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 42.7 bits (101), Expect = 7e-05
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           L+     +EE+ E E+ E+ E++E E   E  V + EEE  +E++ +     EE +
Sbjct: 78  LLEEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKTTVTVEELD 133

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

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

 Score = 46.1 bits (109), Expect = 7e-05
 Identities = 20/75 (26%), Positives = 40/75 (53%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E  +  +   +  EE  +  +E   +E+EE E  ++E+++EEE   +  +E +EEE+E
Sbjct: 222 LEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKE 281

Query: 647 EEEEEEVRGGGKEEI 661
           ++ +EE      +E 
Sbjct: 282 KKLQEEELKLLAKEE 296

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|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 43.9 bits (104), Expect = 7e-05
 Identities = 23/43 (53%), Positives = 32/43 (74%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           ++E++ EE + EE E  E+ EEEE EEEE EEE E EEE++E+
Sbjct: 3   DKEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEI 45

Length = 193

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 45.9 bits (109), Expect = 7e-05
 Identities = 22/60 (36%), Positives = 34/60 (56%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
              E E+   E ++EEEE+EEE +EE+E+E   +E  ++EE EE++ E          SL
Sbjct: 377 SALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYEDSDGNSSL 436

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 42.0 bits (99), Expect = 7e-05
 Identities = 18/25 (72%), Positives = 19/25 (76%)

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEE 646
                +EEEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 45.9 bits (108), Expect = 7e-05
 Identities = 32/73 (43%), Positives = 38/73 (52%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EN+ + +     E  EE  EE  EE  EE  EE +EE  EE EE  EE +EE  EE EE 
Sbjct: 989  ENVEENVEENVEENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEEN 1048

Query: 649  EEEEVRGGGKEEI 661
             EE V    +E I
Sbjct: 1049 AEENVEENIEENI 1061

Length = 1136

>gnl|CDD|221203 pfam11748, DUF3306, Protein of unknown function (DUF3306)

 Score = 42.3 bits (100), Expect = 7e-05
 Identities = 15/54 (27%), Positives = 21/54 (38%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E  E  E  EEE          EEE + E E+EE  EE +  + +      +  
Sbjct: 17  EPAEPAETAEEEAAAAAPAPAPEEEEEAELEDEELLEELDLPDPDTLTPGSDFS 70

This family of proteobacterial species proteins has no known function. Length = 115

>gnl|CDD|221203 pfam11748, DUF3306, Protein of unknown function (DUF3306)

 Score = 42.3 bits (100), Expect = 7e-05
 Identities = 20/54 (37%), Positives = 23/54 (42%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           R  R +     EE  E  E  EEE          EEEEE E E+EE  EE +  
Sbjct: 5   RWSRRKLAVRAEEPAEPAETAEEEAAAAAPAPAPEEEEEAELEDEELLEELDLP 58

This family of proteobacterial species proteins has no known function. Length = 115

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

 Score = 45.8 bits (109), Expect = 7e-05
 Identities = 26/101 (25%), Positives = 42/101 (41%), Gaps = 31/101 (30%)

Query: 593 QLIRR--GEREEEEEEEEEEEEEEEEEEEEE------------------EEEEVQEEEE- 631
           +L R+  G+   EE+E+E+ + EEE+E+++E                  +E E  EE   
Sbjct: 313 ELRRKIEGKSVSEEDEDEDSDSEEEDEDDDEDDDDGENPWMLRKKLGKLKEGEDDEENSG 372

Query: 632 ----------EEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
                     E  ++EE + E EE   E E      +EE  
Sbjct: 373 LLSMKFMQRAEARKKEENDAEIEELRRELEGEEESDEEENE 413

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

 Score = 45.8 bits (109), Expect = 7e-05
 Identities = 10/54 (18%), Positives = 40/54 (74%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++++++E+++E++++++ ++E+EE+ + +E E+  ++++   +E++ E   + R
Sbjct: 148 DDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQAR 201

Length = 509

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

 Score = 45.8 bits (109), Expect = 7e-05
 Identities = 23/66 (34%), Positives = 36/66 (54%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E  +  +R  E+     EEE    EE  +E EE+EE ++E +++ +E E+  EE EE  E
Sbjct: 303 EEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHE 362

Query: 649 EEEEVR 654
             EE +
Sbjct: 363 LYEEAK 368

Length = 880

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

 Score = 45.9 bits (109), Expect = 7e-05
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            IE + + +R  E EEE  E  E EE  +EE EE+ E+     EE EE +E+ + ++ +E
Sbjct: 502 EIEELEKELR--ELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKE 559

Query: 647 EEEEEEVR 654
           E  + E R
Sbjct: 560 ELRQLEDR 567

Length = 908

>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed

 Score = 45.2 bits (108), Expect = 7e-05
 Identities = 18/53 (33%), Positives = 32/53 (60%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E   EE EE E  E+ E   ++    Q EE EEE++++ +++ +E+++E  EV
Sbjct: 334 ENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDDWDEDDDEGVEV 386

Length = 390

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

 Score = 45.3 bits (107), Expect = 7e-05
 Identities = 19/71 (26%), Positives = 47/71 (66%), Gaps = 5/71 (7%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE-----EEEVQEEEEEEEEEEEEEE 641
           RI++     ++GE++ +++EE+  EE + ++  E+E     E+E  + +E++++ EE E+
Sbjct: 66  RIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEK 125

Query: 642 EEEEEEEEEEE 652
           + + E++++EE
Sbjct: 126 QAQLEQKQQEE 136

Length = 387

>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional

 Score = 43.8 bits (104), Expect = 7e-05
 Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEE--EEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           +E +++ IR   R    E   E +EE EE   E E + EE+ E+ E E E E E+  E+E
Sbjct: 3   LETVVEDIRDEARARASEIRAEADEEAEEIIAEAEADAEEILEDREAEAEREIEQLREQE 62

Length = 188

>gnl|CDD|234366 TIGR03825, FliH_bacil, flagellar assembly protein FliH

 Score = 44.8 bits (106), Expect = 7e-05
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           Q+    E E+E  +EE+E E+  E+ E E  + +++ E +     E+ E+E  + EEE E
Sbjct: 24  QVTDVPETEQELADEEQEFEQILEKAEAEAAQIIEQAEAQAAAIREQIEQERAQWEEERE 83

This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes. Length = 255

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 41.8 bits (98), Expect = 8e-05
 Identities = 19/47 (40%), Positives = 28/47 (59%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
             +  ++     E +EEEEEEEEEE+E E E   ++EE  +E E+ E
Sbjct: 50  AFKKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDLE 96

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 45.9 bits (109), Expect = 8e-05
 Identities = 33/62 (53%), Positives = 44/62 (70%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +  L +R ER E+E EE EEE EE EE+ +E EEE++E E+E EE +EE EE E E+EE 
Sbjct: 816 LESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEEL 875

Query: 651 EE 652
           E+
Sbjct: 876 ED 877

Length = 1163

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 45.4 bits (107), Expect = 8e-05
 Identities = 15/76 (19%), Positives = 36/76 (47%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           + + I+  + +   E    +E      + ++ E  E+     + + E+  ++EEEEEE+E
Sbjct: 66  QNKPILDDLNQKYVEFLINKEHIRVLAKLQDSESHEDGSDGSDMDSEDSADDEEEEEEDE 125

Query: 647 EEEEEEVRGGGKEEIS 662
             E+E +    + ++ 
Sbjct: 126 SLEDEMIDDEDEADLF 141

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 42.0 bits (99), Expect = 8e-05
 Identities = 18/25 (72%), Positives = 18/25 (72%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEE 630
                EEEEEEEEEEEEEEE  EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 45.5 bits (107), Expect = 8e-05
 Identities = 30/81 (37%), Positives = 37/81 (45%)

Query: 581  DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
            +E     +E I +       E  EE  EE +EE  EE EE  EE ++E  EE  EE  EE
Sbjct: 1035 EEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEE 1094

Query: 641  EEEEEEEEEEEEVRGGGKEEI 661
             EE  EE  EE      +E  
Sbjct: 1095 IEENVEENVEENAEENAEENA 1115

Length = 1136

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 41.9 bits (99), Expect = 8e-05
 Identities = 14/29 (48%), Positives = 18/29 (62%)

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
                  +E++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 41.7 bits (98), Expect = 8e-05
 Identities = 16/25 (64%), Positives = 22/25 (88%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEE 623
             EE+ EE+EEE+++EEE+EEEEEE
Sbjct: 73  AAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 45.2 bits (107), Expect = 8e-05
 Identities = 16/64 (25%), Positives = 38/64 (59%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           +  ++ +++E +E  ++++EEE E E+E   EE  E++ ++EEEE+ + E+  + +    
Sbjct: 153 KKTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGMLV 212

Query: 657 GKEE 660
              +
Sbjct: 213 DSSD 216

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 42.1 bits (98), Expect = 8e-05
 Identities = 12/34 (35%), Positives = 28/34 (82%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           E EE+ + + +EEE++++E+EE  +E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed

 Score = 45.2 bits (108), Expect = 8e-05
 Identities = 17/60 (28%), Positives = 35/60 (58%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            +++  I    REE EE E  E+ E   ++   E+ E  EEE++++ +++ +E+++E  E
Sbjct: 326 WDLMTFIEENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDDWDEDDDEGVE 385

Length = 390

>gnl|CDD|217502 pfam03343, SART-1, SART-1 family

 Score = 45.5 bits (108), Expect = 8e-05
 Identities = 20/63 (31%), Positives = 39/63 (61%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EE+ E ++E  EE  + EE++E+EE ++ + + E    + +EE+EEE++E       +EE
Sbjct: 409 EEKPENKDESVEEISDAEEDDEDEEDEDGDGDVEMSAVDNDEEKEEEDKEAIPSTILEEE 468

Query: 661 ISL 663
            ++
Sbjct: 469 PTV 471

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 44.8 bits (106), Expect = 8e-05
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            G+      ++  E+EE E++  +E+EE+    EE+E E  EEEE+EE E
Sbjct: 23  NGKGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|218771 pfam05835, Synaphin, Synaphin protein

 Score = 42.6 bits (100), Expect = 8e-05
 Identities = 30/80 (37%), Positives = 43/80 (53%), Gaps = 17/80 (21%)

Query: 598 GEREEEEEEEEEEEEEEEEEE---EEEEEEEVQEEEEEEEEEE--------------EEE 640
           G +E+E +E + EEE+EE +E   E EEE + +  + EEE E               EE+
Sbjct: 21  GGKEDEGDESDAEEEDEEIQEALREAEEERKAKHRKMEEEREVMRQGIRDKYGIKKKEED 80

Query: 641 EEEEEEEEEEEEVRGGGKEE 660
           EEE +   EEEE R G K++
Sbjct: 81  EEEPQAAAEEEEGRLGRKKK 100

This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerisation of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles. Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin transmembrane regions that reside in opposing membranes prior to fusion. Length = 139

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 45.8 bits (108), Expect = 9e-05
 Identities = 25/61 (40%), Positives = 34/61 (55%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           GE E  EE EE E+E E E E + E E   + +E E E E E E +E+E+E E +    G
Sbjct: 730 GEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDG 789

Query: 658 K 658
           +
Sbjct: 790 E 790

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 41.6 bits (98), Expect = 9e-05
 Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 584 GSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           GS + E I +L      EEE+ E EE++  EEE  +E   EE + EEEE++E   EE E+
Sbjct: 28  GSVKDE-IAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKEMTLEEYEK 86

Query: 644 EEEE 647
             +E
Sbjct: 87  ALQE 90

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 45.2 bits (107), Expect = 9e-05
 Identities = 18/50 (36%), Positives = 26/50 (52%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            E  E  +E EE+E E  + E EE E +  E  E+ E +E +E+ E   E
Sbjct: 251 REESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTETPGE 300

Length = 620

>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein

 Score = 45.0 bits (107), Expect = 9e-05
 Identities = 37/102 (36%), Positives = 41/102 (40%), Gaps = 23/102 (22%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEV----QEEEEEEEEEEEEEEEEEE--------- 645
           E EEEEEE  EEEEEEEEEEE   EEEV     E     EEE        E         
Sbjct: 307 EEEEEEEEVPEEEEEEEEEEERTFEEEVRATVAEAIRLLEEELTVSARRHEFFNFAVDFY 366

Query: 646 ----EEEEEEEVRGGGKEEISLHFYVLYVLSKGKIAG-LFYL 682
                 E+   +      E  L  +V+Y      IA  L YL
Sbjct: 367 ELLQRLEDLGRI-----TESFLRRWVMYFFIAEHIASTLNYL 403

This protein is covalently attached to the terminii of replicating DNA in vivo. Length = 548

>gnl|CDD|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 42.2 bits (100), Expect = 9e-05
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            +E+ + E+++EE++ E E+  +   EE+ E E E+ E+E EE E E  R
Sbjct: 18  AKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEELEAELAR 67

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 42.0 bits (99), Expect = 9e-05
 Identities = 19/25 (76%), Positives = 19/25 (76%)

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEE 647
                EEEEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 45.5 bits (107), Expect = 9e-05
 Identities = 32/73 (43%), Positives = 36/73 (49%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EN+ + +     E  EE  EE  EE  EE  EE  EE  EE  EE  EE +EE  EE EE
Sbjct: 973  ENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENVEEVEE 1032

Query: 649  EEEEVRGGGKEEI 661
              EE      EEI
Sbjct: 1033 NVEEYDEENVEEI 1045

Length = 1136

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 41.7 bits (98), Expect = 9e-05
 Identities = 15/27 (55%), Positives = 22/27 (81%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEE 645
               EE+ +E+EEE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 41.7 bits (97), Expect = 9e-05
 Identities = 11/34 (32%), Positives = 28/34 (82%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           E EE+ + + +EEE++++E+E  ++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

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

 Score = 45.5 bits (108), Expect = 9e-05
 Identities = 23/68 (33%), Positives = 36/68 (52%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +  + +L+   E + E  EE E E EE EEE E     ++E EE  E+ +  EE  E+ 
Sbjct: 275 ELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKL 334

Query: 647 EEEEEEVR 654
           EE+ E++ 
Sbjct: 335 EEKLEKLE 342

Length = 908

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

 Score = 44.2 bits (104), Expect = 9e-05
 Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 598 GEREEEEEEEEE----EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            E E +    +     EEE +E+ +   E+  V ++EE+   +E + +E++    E+ + 
Sbjct: 86  AEEEGQLAVRKTKQKVEEEVKEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDD 145

Query: 654 R 654
           R
Sbjct: 146 R 146

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|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]

 Score = 45.4 bits (107), Expect = 9e-05
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 596 RRGEREEEEEE---EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + G  E E ++   +      E++ ++    E+++ E    EE E EEE E+ E+E +  
Sbjct: 340 KWGNEEAERKDYILDSSSVPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDENDHS 399

Query: 653 VRGGGKEEISLHF 665
            R    +E+  HF
Sbjct: 400 KRICDDDELENHF 412

Length = 776

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

 Score = 45.8 bits (108), Expect = 9e-05
 Identities = 16/54 (29%), Positives = 33/54 (61%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            + + ++++  +  E++E+  E+  EE VQE EE  E+  + +EE E+ E  E++
Sbjct: 4044 DEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQ 4097

Length = 4600

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 45.4 bits (107), Expect = 1e-04
 Identities = 24/63 (38%), Positives = 36/63 (57%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E EE E+E E E E + E E E + +E + E E E E +E+E+E E +  E+ E++G  
Sbjct: 736 EEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDE 795

Query: 658 KEE 660
             E
Sbjct: 796 GAE 798

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 45.0 bits (106), Expect = 1e-04
 Identities = 26/62 (41%), Positives = 33/62 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           GE E E  E+E E E  EE EE E+E E + E + E E E + +E E E E E E +   
Sbjct: 719 GETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDE 778

Query: 658 KE 659
            E
Sbjct: 779 DE 780

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

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

 Score = 43.6 bits (103), Expect = 1e-04
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E + E EE E+EE  E+ EE  E + E  ++E  + +EE ++ E E E  ++  +R
Sbjct: 31  EEDLEFEEIEKEEIIEDSEESNEVKIEELKDENNKLKEENKKLENELEALKDRLLR 86

Length = 211

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEE---EVQEEEEEEEE 635
           R   +    +  E E+E+EEEEEEEEE EE E EE       + E+     +
Sbjct: 338 RCTWVNPEQKDEEEEQEDEEEEEEEEEPEEPEPEEGPPLLTPISEDAPLPND 389

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 44.6 bits (105), Expect = 1e-04
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +R ER +  EEEE+  ++EE + +  EEEE +  +EE E    E  E+ ++  E+  
Sbjct: 222 KREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAEAAEKRQKVPEDGL 278

Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 44.9 bits (107), Expect = 1e-04
 Identities = 31/84 (36%), Positives = 37/84 (44%), Gaps = 22/84 (26%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEE--EVQEEEEEEEEEEEE----------------- 639
            REE+ EE+EE  +EE  EEE E E   E Q E+EE E+E  E                 
Sbjct: 238 AREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQI 297

Query: 640 ---EEEEEEEEEEEEEVRGGGKEE 660
              EE    E EEE E     +EE
Sbjct: 298 EEKEERRAAEREEELEEGERLREE 321

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|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 44.5 bits (106), Expect = 1e-04
 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 16/83 (19%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEE-------------EEEEEEEEEEEEVQEEEEEEE 634
           ++ +   + + E E +E ++E+EE E             EE+ EE+EE  + +  EEE E
Sbjct: 201 LDELRADLYQEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAE 260

Query: 635 EE---EEEEEEEEEEEEEEEEVR 654
            E   E++ E+EE E+E  E+ R
Sbjct: 261 RERMLEKQAEDEELEQENAEKRR 283

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|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 19/47 (40%), Positives = 31/47 (65%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
            + E E EEEEEEEE + + ++ E++E   ++EEE E+E + EE  +
Sbjct: 39  DDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLK 85

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

>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2 subunit 1; Provisional

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 19/43 (44%), Positives = 30/43 (69%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            +EE+ EE+ E+ EEEEEE++  E E+E+EE+E+E      +E
Sbjct: 274 GDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDE 316

Length = 319

>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 20/42 (47%), Positives = 30/42 (71%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           E+E E+E   EEEEEE+EE++EEEE+  ++EEE +     +E
Sbjct: 28  EKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEE 69

Length = 529

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 44.2 bits (104), Expect = 1e-04
 Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 12/82 (14%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE---- 644
             I+    R  R     + +E+ +E    + + + EE +  EE +  EEEE+EE      
Sbjct: 142 REILAEKPRVTRFNIVWDNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDSY 201

Query: 645 --------EEEEEEEEVRGGGK 658
                   EEEEEE E    G+
Sbjct: 202 GEGNRELNEEEEEEAEGSDDGE 223

Length = 279

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

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 23/66 (34%), Positives = 36/66 (54%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R+E + + +   E    + +EE EE EE+ +  +EE EE++EE EE E   +  E E E 
Sbjct: 759 RLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELES 818

Query: 647 EEEEEE 652
            E+  E
Sbjct: 819 LEQRRE 824

Length = 1163

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

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 31/64 (48%), Positives = 42/64 (65%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            IE + + +   E E EE E+E EE +EE EE E E+EE+++E +E EEE+EE EEE  E
Sbjct: 836 EIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRE 895

Query: 647 EEEE 650
            E E
Sbjct: 896 LESE 899

Length = 1163

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 45.0 bits (106), Expect = 1e-04
 Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 15/81 (18%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE---------------EEEEEE 642
            E   E+  ++E E++EE++ EEEE  E +E  E+   E               +E  E 
Sbjct: 144 SESSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQATREKKFDKSGVDDKFFKLDEMNEF 203

Query: 643 EEEEEEEEEEVRGGGKEEISL 663
            E  E EEE   G   +    
Sbjct: 204 LEATEAEEEAALGDEDDFEDY 224

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 45.0 bits (106), Expect = 1e-04
 Identities = 20/77 (25%), Positives = 47/77 (61%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           +  + DE G+   E+      + ++++  ++ E E++E ++E  ++E +   EEE+EE++
Sbjct: 242 EDEEDDEEGNIEYEDFFDPKEKDKKKDAGDDAELEDDEPDKEAVKKEADSKPEEEDEEDD 301

Query: 636 EEEEEEEEEEEEEEEEE 652
           E+E++++EEE  E   +
Sbjct: 302 EQEDDQDEEEPPEAAMD 318

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

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

 Score = 43.2 bits (102), Expect = 1e-04
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E +E++ + E+E+EE EEE EEE+EE   E E+E EE+ E   E+E      + V
Sbjct: 76  EDKEDKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITNPSWKPV 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|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 16/54 (29%), Positives = 29/54 (53%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E E ++EE+ E E+ E+ E++E E        + EEE  +E++ +     EE +
Sbjct: 80  EEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKTTVTVEELD 133

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 19/51 (37%), Positives = 26/51 (50%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           G  E E  +E EE+E E  + E EE E    E  E+ E +E +E+ E   E
Sbjct: 250 GREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDTETPGE 300

Length = 620

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           EE  ++  EE+ +EE+ ++++ +     E   EE E  +E EE+E E  + E   G
Sbjct: 220 EETGDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEG 275

Length = 620

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 19/84 (22%), Positives = 43/84 (51%)

Query: 583 IGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
                IE  +Q   R +    + EE+++++EE +EE+EE  +   +E++++++++++   
Sbjct: 101 FDDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIAT 160

Query: 643 EEEEEEEEEEVRGGGKEEISLHFY 666
            E   E     R   ++   L FY
Sbjct: 161 RERSLERRRRRREWEEKRAELEFY 184

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 2/84 (2%)

Query: 571 SIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE 630
            + ++   D D     + E       R   E+++++EE +EE+EE  + E++E++  +++
Sbjct: 97  QVVIF--DDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDD 154

Query: 631 EEEEEEEEEEEEEEEEEEEEEEVR 654
           +++    E   E      E EE R
Sbjct: 155 DDDIATRERSLERRRRRREWEEKR 178

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 44.4 bits (105), Expect = 1e-04
 Identities = 23/48 (47%), Positives = 28/48 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           GE +E   E    E+ EEEE EE EE+E +E EEE EE E   +  EE
Sbjct: 64  GEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEE 111

Length = 306

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

 Score = 45.3 bits (107), Expect = 1e-04
 Identities = 27/92 (29%), Positives = 53/92 (57%)

Query: 563 NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
            +L   +      K +++ ++   +I+   +   +   ++EEEEEE+ E   +E+E  EE
Sbjct: 721 EELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEE 780

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EE+ ++ + EEE+EE+ + +EEE    EEE++
Sbjct: 781 EEKTEKLKVEEEKEEKLKAQEEELRALEEELK 812

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 = 45.3 bits (107), Expect = 1e-04
 Identities = 27/75 (36%), Positives = 46/75 (61%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             ++ I    +   ++ +E+EEEEE+   ++EEEEEE+     +E+E  EEEE+ E+ + 
Sbjct: 730 EAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEKTEKLKV 789

Query: 647 EEEEEEVRGGGKEEI 661
           EEE+EE     +EE+
Sbjct: 790 EEEKEEKLKAQEEEL 804

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 = 45.3 bits (107), Expect = 1e-04
 Identities = 22/90 (24%), Positives = 36/90 (40%)

Query: 563  NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
             K   I   I             P    + +   + + E+ +EEEEE  +     +EE  
Sbjct: 915  EKENEIEERIAEEAIILLKYESEPEELLLEEADEKEKEEDNKEEEEERNKRLLLAKEELG 974

Query: 623  EEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
               +    E EE+EE   ++E ++E  EEE
Sbjct: 975  NVNLMAIAEFEEKEERYNKDELKKERLEEE 1004

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 = 45.0 bits (106), Expect = 1e-04
 Identities = 12/55 (21%), Positives = 32/55 (58%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           RE+ +++E  ++  EE E   E   +++E + +E + +E+ ++  E  + +E++ 
Sbjct: 167 REKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLE 221

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 = 45.0 bits (106), Expect = 1e-04
 Identities = 26/82 (31%), Positives = 46/82 (56%), Gaps = 4/82 (4%)

Query: 587 RIENIIQLIRRGEREEE----EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           RI+ + +L+R  + E E    E E+EEE   +  +E +EEE+E + +EEE +   +EEEE
Sbjct: 239 RIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEE 298

Query: 643 EEEEEEEEEEVRGGGKEEISLH 664
            + E  + E  +   +E++   
Sbjct: 299 LKSELLKLERRKVDDEEKLKES 320

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|222636 pfam14265, DUF4355, Domain of unknown function (DUF4355)

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           KT    E+        I   +    +++EE++ E E+  +   EE+ E E+++ E+E EE
Sbjct: 6   KTFTDKEVDK-----AIAKEKAKWEKKQEEKKSEAEKLAKMSAEEKAEYELEKLEKELEE 60

Query: 636 EEEEEEEEEEEEE 648
            E E    E + E
Sbjct: 61  LEAELARRELKAE 73

This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. Length = 125

>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 26/64 (40%), Positives = 34/64 (53%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +         E  EE E+ EEEE EEEE EEE E EE Q+E  E E + EE +++    +
Sbjct: 4   KEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAELEAQLEELKDKYLRAQ 63

Query: 649 EEEE 652
            E E
Sbjct: 64  AEFE 67

Length = 193

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEE 643
                EE +EEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEE 644
                E +EEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEE 642
                EEE +EEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEE 645
                 +EEEEEEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 45.5 bits (107), Expect = 1e-04
 Identities = 31/61 (50%), Positives = 32/61 (52%)

Query: 601  EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            EE  EE  EE +EE  EE EE  EE  EE  EE EE  EE  EE  EE  EE      EE
Sbjct: 1012 EENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEE 1071

Query: 661  I 661
            I
Sbjct: 1072 I 1072

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 45.2 bits (106), Expect = 1e-04
 Identities = 29/63 (46%), Positives = 31/63 (49%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            E   EE  EE  EE  EE  EE  EE V+E  EE  EE  EE  EE  EE  EE      
Sbjct: 968  EENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENV 1027

Query: 659  EEI 661
            EE+
Sbjct: 1028 EEV 1030

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 45.2 bits (106), Expect = 1e-04
 Identities = 30/73 (41%), Positives = 38/73 (52%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EN+ + +     E  EE  EE  EE  EE  EE  EE  EE +EE  EE EE  EE +EE
Sbjct: 981  ENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEE 1040

Query: 649  EEEEVRGGGKEEI 661
              EE+    +E +
Sbjct: 1041 NVEEIEENAEENV 1053

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 45.2 bits (106), Expect = 1e-04
 Identities = 31/73 (42%), Positives = 36/73 (49%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EN+ + +     E  EE  EE  EE  EE  EE  EE  EE  EE EE  EE +EE  EE
Sbjct: 985  ENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENVEEVEENVEEYDEENVEE 1044

Query: 649  EEEEVRGGGKEEI 661
             EE      +E I
Sbjct: 1045 IEENAEENVEENI 1057

Length = 1136

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

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 34/70 (48%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           +R   ++  E+E+E+EE E   E   EEEE +E E     ++EEE+EE     +    RG
Sbjct: 294 KRKRLKKMMEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEEEKEEVTVSPDGGRRRG 353

Query: 656 GGKEEISLHF 665
             +      F
Sbjct: 354 RRRVMKKKTF 363

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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 16/27 (59%), Positives = 21/27 (77%)

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEE 646
               EE  EE+EEE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 15/26 (57%), Positives = 21/26 (80%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEV 626
              EE+ EE+EEE+++EEE+EEEEE 
Sbjct: 72  AAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 44.9 bits (106), Expect = 1e-04
 Identities = 15/56 (26%), Positives = 30/56 (53%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
              E+EE+ E E E +E    +E E  + E +  EEE  + ++++  +E +++ E 
Sbjct: 221 TENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDESDDDSET 276

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 44.9 bits (106), Expect = 1e-04
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           EE  ++ E E+EE+ ++++  E  QEE+ E E E +E    +E E  + E   G +E
Sbjct: 201 EEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEE 257

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 44.4 bits (105), Expect = 1e-04
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 2/93 (2%)

Query: 573 KVWKTSDQDEIGSP--RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE 630
           K  K+  ++   S     E   +     + EE  E++ ++EEEE+ + E+  + +    +
Sbjct: 154 KTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGMLVD 213

Query: 631 EEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
             +EEE EE       E+  E        EIS 
Sbjct: 214 SSDEEEGEEAPSINYNEDTSESESDESDSEISE 246

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

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

 Score = 44.7 bits (106), Expect = 1e-04
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE-----EEEEEEEEEEEEEEEEV 653
            R++EE + E EE   E E EEE +EE  EE  ++         E  E+E E ++ ++E 
Sbjct: 384 ARKKEENDAEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKEN 443

Query: 654 RGGGKEEIS 662
           +   KE+  
Sbjct: 444 KNEFKEKKE 452

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

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 29/68 (42%), Positives = 40/68 (58%)

Query: 585 SPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           S  +E+I  L+   E E +E ++ EE +EE+EEEE E+E E  EE   E EEE+E  EE 
Sbjct: 195 SELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEEL 254

Query: 645 EEEEEEEE 652
           +    E E
Sbjct: 255 KARLLEIE 262

Length = 908

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

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           ++     +++ + + +R+ E   +E  +E  EE       +EE EE++E  +E +++ +E
Sbjct: 546 EELKEKLQLQQLKEELRQLEDRLQE-LKELLEELRLLRTRKEELEELRERLKELKKKLKE 604

Query: 640 EEEEEEEEEEEEEVRGGGKEEISLH 664
            EE   + EE  +     + E  L 
Sbjct: 605 LEERLSQLEELLQSLELSEAENELE 629

Length = 908

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

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 23/65 (35%), Positives = 34/65 (52%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R+E + + I   E E E      EE EE  E+ +  EE +++ EE+ E+ E E EE  EE
Sbjct: 292 RLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEE 351

Query: 647 EEEEE 651
           + E  
Sbjct: 352 KNELA 356

Length = 908

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

 Score = 43.8 bits (103), Expect = 1e-04
 Identities = 18/56 (32%), Positives = 33/56 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E+  E+E E+ +E  E+ E  + E ++V EE+ +EE+   E+ +  +EE  +E V 
Sbjct: 179 EKASEQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIKEELAKEPVE 234

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|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 6/54 (11%)

Query: 586 PRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           P+ +N  +L      E  EEEEEE EE EEE EE+  + + ++   EE +E+EE
Sbjct: 139 PKPKNEFEL------ELPEEEEEEPEEMEEELEEDAADRDARKRAAEEAKEQEE 186

This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. Length = 363

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

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 16/75 (21%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 580 QDEIGSPR--IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           Q +  + +   E   +L ++ E  E++   E+  ++E E+    E+   Q E+  ++ EE
Sbjct: 57  QQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEE 116

Query: 638 EEEEEEEEEEEEEEE 652
           ++++ EE + ++  E
Sbjct: 117 KQKQAEEAKAKQAAE 131

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 14/30 (46%), Positives = 20/30 (66%)

Query: 627 QEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
            E   E +E EEEE+EEE EEE ++++  G
Sbjct: 77  AEAAAEADEAEEEEKEEEAEEESDDDMLFG 106

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 13/25 (52%), Positives = 17/25 (68%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
            E   E +E EEEE+EEE EEE ++
Sbjct: 77  AEAAAEADEAEEEEKEEEAEEESDD 101

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
                  E   E +E EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|217502 pfam03343, SART-1, SART-1 family

 Score = 44.7 bits (106), Expect = 1e-04
 Identities = 21/62 (33%), Positives = 37/62 (59%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E  EE+ E ++E  EE  + EE++E+E  E+ + + E    + +EE+EEE++E +     
Sbjct: 406 EPLEEKPENKDESVEEISDAEEDDEDEEDEDGDGDVEMSAVDNDEEKEEEDKEAIPSTIL 465

Query: 659 EE 660
           EE
Sbjct: 466 EE 467

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 45.4 bits (108), Expect = 1e-04
 Identities = 29/73 (39%), Positives = 40/73 (54%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           Q +I   R+ N+ + +   E + EE E + +E  EE  E EE+ EE++EE E  E E EE
Sbjct: 303 QKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEE 362

Query: 640 EEEEEEEEEEEEE 652
            E E EE E   E
Sbjct: 363 LEAELEELESRLE 375

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 23/73 (31%), Positives = 33/73 (45%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E + QL +  E    +     ++    E E E+ EE + +  +E  E E E EE EE  E
Sbjct: 712 EELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLE 771

Query: 649 EEEEVRGGGKEEI 661
           E EE     + EI
Sbjct: 772 EAEEELAEAEAEI 784

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|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 12/40 (30%), Positives = 14/40 (35%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           EEE+                 E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 43.5 bits (103), Expect = 1e-04
 Identities = 12/40 (30%), Positives = 14/40 (35%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           EEE+                 E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 42.7 bits (101), Expect = 1e-04
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 7/67 (10%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE--EEEEEVRGG 656
           E +EEEE E++ ++ +EE EEEE+ E++  +  E +     E +  +E+  ++E +    
Sbjct: 3   EPDEEEELEDDIDDLDEEAEEEEDGEDLFGDNMERDYRANPELDRYDEDGLDDESDY--- 59

Query: 657 GKEEISL 663
             EE+S 
Sbjct: 60  --EELSA 64

This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. Length = 145

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 18/53 (33%), Positives = 32/53 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E++  +E+  EE E E E++EE +E E+++E +E +    E E +  E + EE
Sbjct: 5   EQKTPQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEAQLAEAQAEE 57

Length = 193

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 25/57 (43%), Positives = 36/57 (63%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           RR ++E EE EE   E EE+ ++EEEE + ++++ +E EEE    EEE    EEE E
Sbjct: 22  RRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELEEENRRLEEEAAASEEERE 78

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 24/60 (40%), Positives = 37/60 (61%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +L  R E+ EE+    ++E EE EE   E EE++++EEEE +  E++ +E EEE    EE
Sbjct: 9   ELEERMEQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELEEENRRLEE 68

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 25/53 (47%), Positives = 29/53 (54%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           EE+    +E  E  +E+     E   EEEEEEEEEEEEE  E E   EE V G
Sbjct: 377 EEDATTIDELREFLKEKGHPVVERWAEEEEEEEEEEEEEAAEAEAPMEEPVPG 429

Length = 470

>gnl|CDD|235562 PRK05687, fliH, flagellar assembly protein H; Validated

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 19/63 (30%), Positives = 22/63 (34%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
               E    E      E  E EE  EEE     EEE E   ++  EE     + E R  G
Sbjct: 25  DPPPEPPPPEPAAPPPEPPEPEEVPEEEAAPLTEEELEAIRQQAHEEGFAAGKAEGRAEG 84

Query: 658 KEE 660
            E 
Sbjct: 85  YEA 87

Length = 246

>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM protein

 Score = 44.7 bits (106), Expect = 1e-04
 Identities = 23/85 (27%), Positives = 33/85 (38%), Gaps = 3/85 (3%)

Query: 578 SDQDEIGSPR-IENIIQLIRRGERE--EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
              +  GS R I +     R   RE     E  + +EE+E   E EE E  +  E     
Sbjct: 108 EPAETAGSLRPIRSSAAAYRDINRELGSFYEYPKTDEEKELLREVEELESRLATEPSPAP 167

Query: 635 EEEEEEEEEEEEEEEEEEVRGGGKE 659
           E EE+    E+  E   +    G+E
Sbjct: 168 ELEEQLALMEKSYELAAKYMPRGQE 192

Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage [Cellular processes, DNA transformation]. Length = 410

>gnl|CDD|221429 pfam12118, SprA-related, SprA-related family

 Score = 44.0 bits (104), Expect = 1e-04
 Identities = 18/78 (23%), Positives = 42/78 (53%)

Query: 577 TSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           +S+    GS   E   +L  +         +E +++  E  +EE   EE  E+++ E  +
Sbjct: 37  SSEASNAGSGSSEQKAKLKGQASTAAGSASQELQKQASESNDEEVVGEEEPEKDQAEAGK 96

Query: 637 EEEEEEEEEEEEEEEEVR 654
           +  ++++E++++EE++VR
Sbjct: 97  QLSQKQQEQQQQEEKQVR 114

This protein is found in bacteria. Proteins in this family are typically between 234 to 465 amino acids in length. There is a conserved GEV sequence motif.Most members are annotated as being SprA-related. Length = 261

>gnl|CDD|220112 pfam09110, HAND, HAND

 Score = 41.5 bits (98), Expect = 1e-04
 Identities = 17/45 (37%), Positives = 29/45 (64%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           ++  + +EE+EEE E + + E+E++   E   EEEEEE++   EE
Sbjct: 64  DDVGDGDEEDEEEREAKRKLEQEKIDNAEPLTEEEEEEKQRLLEE 108

The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein. Length = 109

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 22/46 (47%), Positives = 25/46 (54%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            EE + EE EEE E  E EE  EEV EE  E+ E E   E  +E E
Sbjct: 2   SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 29/62 (46%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E E  EE   E E+E E E + E E E +   E + E+E E E E +E + + E     
Sbjct: 655 AEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEE 714

Query: 658 KE 659
            E
Sbjct: 715 VE 716

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 26/59 (44%), Positives = 31/59 (52%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           E E EE E E E E E  E+E E E  EE EE E+E E E E + E E E + +    E
Sbjct: 709 ETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHE 767

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 44.3 bits (104), Expect = 2e-04
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           RR   EEEE+  ++EE + +  EEEE+    +E E    E  E+ ++  E+   E+
Sbjct: 226 RRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAEAAEKRQKVPEDGLSED 281

Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 20/88 (22%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE------- 639
           R E    L  + E  E+  +EE EE  +E E+ +E  E +QEE+E E +E+ E       
Sbjct: 69  RREGRAVLQEQIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLRE 128

Query: 640 -------------EEEEEEEEEEEEEVR 654
                        EEE+E E EEE ++ 
Sbjct: 129 EIDEFNEERIERKEEEKEREREEELKIL 156

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|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 599 EREEEEEEEEEE-----EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           ERE   E+          + +E+ +E    +   + EEEE  EE +  EEEE+EE   + 
Sbjct: 141 EREILAEKPRVTRFNIVWDNDEDNDEAPPAQPDVDNEEEERLEESDGREEEEDEEVGSDS 200

Query: 654 RGGGKEEIS 662
            G G  E++
Sbjct: 201 YGEGNRELN 209

Length = 279

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

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 13/62 (20%), Positives = 37/62 (59%), Gaps = 2/62 (3%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEE--EEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           R  E+  +E E E +EE++ +++  +    +E+ +E  ++E+    ++E+ +E  E++++
Sbjct: 283 RNKEKRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQRKERGEKKKL 342

Query: 654 RG 655
           + 
Sbjct: 343 KR 344

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|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 9/64 (14%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEE---------EEEEEEEEEEEEEEEEEEEE 649
           + + EEE ++E   E  E E E   + V+ +         E+  +E E E +EE++ +++
Sbjct: 246 DDDGEEESDDESAWEGFESEYEPINKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLKKK 305

Query: 650 EEEV 653
             ++
Sbjct: 306 LAQL 309

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

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 22/67 (32%), Positives = 28/67 (41%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
            +     EE EE  E   EE  E E E  E++ E EE + E E  EE  E   E  E   
Sbjct: 365 EKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLK 424

Query: 656 GGKEEIS 662
              +E+ 
Sbjct: 425 EELKELE 431

Length = 1163

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

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 35/103 (33%), Positives = 54/103 (52%), Gaps = 1/103 (0%)

Query: 562 TNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEE 621
             +L+  R +++      ++E+       +  L R  E  E+  E  E+E EE EEE EE
Sbjct: 781 IEELEEKRQALQEELEELEEELEEAERR-LDALERELESLEQRRERLEQEIEELEEEIEE 839

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
            EE++ E EEE EE E+E EE +EE EE E  +   ++E+   
Sbjct: 840 LEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKEL 882

Length = 1163

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

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 29/66 (43%), Positives = 44/66 (66%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           +++ + + +   E+E EE +EE EE E E+EE E+E +E++EE+EE EEE  E E E  E
Sbjct: 843 KLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAE 902

Query: 647 EEEEEE 652
            +EE E
Sbjct: 903 LKEEIE 908

Length = 1163

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

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 24/66 (36%), Positives = 31/66 (46%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E    L+   E+   E EE +EE EE+     EE EE+ E   EE  E E E  E   
Sbjct: 338 ELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRN 397

Query: 647 EEEEEE 652
           E EE +
Sbjct: 398 ELEELK 403

Length = 1163

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

 Score = 44.4 bits (104), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 43/60 (71%)

Query: 595  IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             ++ E  ++ EEE + + EE ++E EE++++ +E +++EEE+++    ++EEE++ EE+R
Sbjct: 1715 KKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIR 1774

Length = 2084

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 22/76 (28%), Positives = 38/76 (50%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           S  DE      E++   +   E E +   E E   E+  ++E E++EE + EEEE  EE+
Sbjct: 114 SADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEEAGEEK 173

Query: 638 EEEEEEEEEEEEEEEV 653
           E  E+   E++ ++  
Sbjct: 174 ESVEQATREKKFDKSG 189

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 14/57 (24%), Positives = 33/57 (57%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
             E  ++E + + EEE+EE++E+E++++E +  E   ++ + +E   E  + E  + 
Sbjct: 281 DKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKE 337

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 17/55 (30%), Positives = 34/55 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E ++E  ++E + + EEE+EE++E+E+ Q+EEE  E   ++ + +E   E  +  
Sbjct: 279 EPDKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLE 333

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

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

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 21/66 (31%), Positives = 42/66 (63%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           RI + ++ +++ + ++++     +E+ E+  +E EE EE  E E  EE+ +E E++EE+E
Sbjct: 102 RIRDQLRSVKKDDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQE 161

Query: 647 EEEEEE 652
            E EE+
Sbjct: 162 REREEQ 167

Length = 197

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 26/54 (48%), Positives = 33/54 (61%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E+ EEEE EE EE+EEEE EEE EE +   +  EE  E  E+ EE EE  + + 
Sbjct: 77  EDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEELTEASEQLEEHEEGFQAMV 130

Length = 306

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 43.3 bits (102), Expect = 2e-04
 Identities = 28/55 (50%), Positives = 33/55 (60%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           R E    E+ EEEE EE EE+EEEE EEE +E E   +  EE  E  E+ EE EE
Sbjct: 70  RIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEELTEASEQLEEHEE 124

Length = 306

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

 Score = 45.0 bits (106), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 30/57 (52%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           R+++E  ++  EE E   E   + EE++ +E + +E+ ++  E  + +E+ E     
Sbjct: 170 RKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEEN 226

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 = 45.0 bits (106), Expect = 2e-04
 Identities = 12/55 (21%), Positives = 27/55 (49%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
               E+ +++E  ++  EE E   E     EE + +E + +E+ ++  E  + +E
Sbjct: 164 AGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKE 218

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 = 44.6 bits (105), Expect = 2e-04
 Identities = 21/77 (27%), Positives = 39/77 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R E       + E E+EEE   +  +E +EEE+E++ +E + +   +EEEE + E  + E
Sbjct: 248 RDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLE 307

Query: 647 EEEEEEVRGGGKEEISL 663
             + ++     + E  L
Sbjct: 308 RRKVDDEEKLKESEKEL 324

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

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

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 22/67 (32%), Positives = 42/67 (62%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
              +++Q + R E+EE E  ++E E+EEE   +  +E + +E+E++ +EEE +   +EEE
Sbjct: 238 ERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEE 297

Query: 647 EEEEEEV 653
           E + E +
Sbjct: 298 ELKSELL 304

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 = 44.6 bits (105), Expect = 2e-04
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 5/91 (5%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           S +      R++ +I+          + EE + +E + +E+ ++  E  Q +E+ E EEE
Sbjct: 166 SREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYYQLKEKLELEEE 225

Query: 638 -----EEEEEEEEEEEEEEEVRGGGKEEISL 663
                +  +  EE  +  +E+    +EEI  
Sbjct: 226 NLLYLDYLKLNEERIDLLQELLRDEQEEIES 256

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 = 44.2 bits (104), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            +N  +   R +R    +EE          E EE+EE   ++E ++E  EEE++E   E  
Sbjct: 954  DNKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREII 1013

Query: 649  EEEE 652
            EE  
Sbjct: 1014 EETC 1017

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 = 44.2 bits (104), Expect = 2e-04
 Identities = 16/67 (23%), Positives = 32/67 (47%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
              II +++   R E EEE     E+ +++E  ++  E  E   E   + EE + +E + 
Sbjct: 144 KVEIIAMMKPERRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKL 203

Query: 648 EEEEEVR 654
           +E+ +  
Sbjct: 204 KEQAKKA 210

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 = 44.2 bits (104), Expect = 2e-04
 Identities = 24/99 (24%), Positives = 47/99 (47%), Gaps = 22/99 (22%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEE----------------------EEEEEEV 626
           E  +Q ++  E+ ++  E  + +E+ E EEE                       +E+EE+
Sbjct: 195 ELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEI 254

Query: 627 QEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHF 665
           +  ++E E+EEE   +  +E +EEE+ +   +EE+ L  
Sbjct: 255 ESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLA 293

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|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 8/56 (14%), Positives = 33/56 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           GE    E  +      + E+  +++E+E  E++   +++++++++++  + ++++V
Sbjct: 33  GEEVPPEVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDV 88

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 7/61 (11%), Positives = 38/61 (62%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           R    + E+  +++E+EE+E++   +  ++++++++  + ++++ + ++++++      +
Sbjct: 44  RAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDLDDDDDDFLEDDDD 103

Query: 660 E 660
           E
Sbjct: 104 E 104

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 20/60 (33%), Positives = 33/60 (55%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           +++  + +E E++   +     E E    E ++EEEE+EEEEEEE+E+E         EE
Sbjct: 358 KQKWTKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEE 417

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEE 641
                EEEE +EEEEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEE 633
                EEEEEEEEEEEE +EE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEE 631
                EEEEEEEEEEEEEE + EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 44.8 bits (105), Expect = 2e-04
 Identities = 27/54 (50%), Positives = 29/54 (53%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E + EE  EE  EE  EE  EE  EE V+E  EE  EE  EE  EE  EE  EE
Sbjct: 956  EEDAEENVEENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEE 1009

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 44.4 bits (104), Expect = 2e-04
 Identities = 27/54 (50%), Positives = 28/54 (51%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E   EE  EE  EE  EE  EE  EE V+E  EE  EE  EE  EE  EE  EE
Sbjct: 960  EENVEENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEE 1013

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 44.0 bits (103), Expect = 2e-04
 Identities = 27/54 (50%), Positives = 28/54 (51%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E   EE  EE  EE  EE  EE  EE V+E  EE  EE  EE  EE  EE  EE
Sbjct: 964  EENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEE 1017

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 44.0 bits (103), Expect = 2e-04
 Identities = 31/74 (41%), Positives = 38/74 (51%), Gaps = 1/74 (1%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE-EEEVQEEEEEEEEEEEEEEEEEEEE 647
            EN+ + +     E  EE  EE  EE  EE  EE  EE V+E  EE  EE  EE +EE  E
Sbjct: 969  ENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENVE 1028

Query: 648  EEEEEVRGGGKEEI 661
            E EE V    +E +
Sbjct: 1029 EVEENVEEYDEENV 1042

Length = 1136

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 16/58 (27%), Positives = 37/58 (63%), Gaps = 9/58 (15%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEE---------EEEEEEEEEEEEEEEEEEVR 654
           ++E+E+++ ++  +EEE+EE +EE+ +           + + EE+E+ + E+EE+ +R
Sbjct: 25  DDEDEDDDVKDSWDEEEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLR 82

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3 subunit

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 13/66 (19%)

Query: 599 EREEEEEEEEEEEE-------------EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           E +EE+EEE+ +               EE+E+ + E+EE+   E EE+  E+E  E+   
Sbjct: 40  EEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEKGLRELEEDTPEDELAEKLRL 99

Query: 646 EEEEEE 651
            + +EE
Sbjct: 100 RKLQEE 105

This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein eIF3j (HCR1) has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. Length = 242

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

 Score = 43.7 bits (103), Expect = 2e-04
 Identities = 17/70 (24%), Positives = 41/70 (58%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +   +   +E+E+E+E++ EE  + EEE++ E V+ +   ++  +++   +++E  EEE+
Sbjct: 136 EAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEK 195

Query: 653 VRGGGKEEIS 662
            R   +E + 
Sbjct: 196 QRQAAREAVK 205

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|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 41.9 bits (99), Expect = 2e-04
 Identities = 14/30 (46%), Positives = 26/30 (86%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQE 628
           E +E +++EE+EEEE++EE+++E+E E +E
Sbjct: 110 EEDESDDDEEDEEEEDDEEDDDEDESEEEE 139

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 13/30 (43%), Positives = 25/30 (83%)

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +  V  EE+E +++EE+EEEE++EE+++E+
Sbjct: 104 QHLVASEEDESDDDEEDEEEEDDEEDDDED 133

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 44.3 bits (104), Expect = 2e-04
 Identities = 27/61 (44%), Positives = 40/61 (65%), Gaps = 4/61 (6%)

Query: 597 RGEREEEEEEEEEEEEEEEEE----EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           RG ++EEEE+E+ EE EE EE    EEE +++E  E+++E+E + E +E E   E   EE
Sbjct: 103 RGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAEGDENELAGEYIIEE 162

Query: 653 V 653
           V
Sbjct: 163 V 163

Length = 374

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 41.1 bits (97), Expect = 2e-04
 Identities = 13/29 (44%), Positives = 17/29 (58%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
                  EE++EE +EEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.7 bits (96), Expect = 2e-04
 Identities = 14/29 (48%), Positives = 17/29 (58%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
                  E ++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

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

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 36/156 (23%), Positives = 62/156 (39%), Gaps = 14/156 (8%)

Query: 520 VAAKNPTTGTTPFKLCTPEDFKPFVTALMNSEWQSLWDNV----PNTNKLKTIRPSIKVW 575
              ++ +  TT  K       K         +  ++  +         K K       V 
Sbjct: 182 KKTQDTSKETTTEKTEGKTSVKAASLKRNPPKKSNIMSSFFKKKTKEKKEKKEASESTVK 241

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEE----------EEEEEEEEEEEEEEEEEE 625
           + S+++      I         G  E+E+E+E          EEE EE+E+E+ +  ++ 
Sbjct: 242 EESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGERSDSEEETEEKEKEKRKRLKKM 301

Query: 626 VQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           +++E+E+EE E   E   EEEE EE E     K+E 
Sbjct: 302 MEDEDEDEEMEIVPESPVEEEESEEPEPPPLPKKEE 337

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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 41.3 bits (97), Expect = 2e-04
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEE 647
               E + EE+EEE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 16/27 (59%), Positives = 21/27 (77%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEE 638
               EE+ EE+EEE ++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 44.5 bits (105), Expect = 2e-04
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E   ++ E E+EE+ ++++  E E+EE  E E E +E    +E E  + E E 
Sbjct: 201 EEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESES 253

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 16/65 (24%), Positives = 42/65 (64%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           ++ ++ +++E +E  ++++EEE E E+E + +E  E++ ++EEEE+ + E+  + + +  
Sbjct: 153 KKTKKSKKKEAKESSDKDDEEESESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGMLV 212

Query: 656 GGKEE 660
              +E
Sbjct: 213 DSSDE 217

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

>gnl|CDD|235850 PRK06669, fliH, flagellar assembly protein H; Validated

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 25/67 (37%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
              +E+E   EEEEE+ E+  EE  +E +E  EE EE+  E  E  EEE +EE ++    
Sbjct: 30  LSIKEKERLREEEEEQVEQLREEANDEAKEIIEEAEEDAFEIVEAAEEEAKEELLK--KT 87

Query: 659 EEISLHF 665
           +E S   
Sbjct: 88  DEASSII 94

Length = 281

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 44.0 bits (105), Expect = 2e-04
 Identities = 16/55 (29%), Positives = 28/55 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           R+  +I        EE+      E EE +++E+EEEEE+  ++    +E E  E+
Sbjct: 165 RLRELIDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELPEK 219

Length = 619

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.9 bits (95), Expect = 2e-04
 Identities = 12/34 (35%), Positives = 28/34 (82%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           E EE+ + + +EEE+  +E+EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.9 bits (95), Expect = 2e-04
 Identities = 12/34 (35%), Positives = 28/34 (82%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
           E EE+ + + +EEE++++E+EE+++E+  E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.9 bits (95), Expect = 2e-04
 Identities = 11/34 (32%), Positives = 29/34 (85%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           E EE+ + + +EEE++++E+EE++ ++++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.9 bits (95), Expect = 2e-04
 Identities = 11/34 (32%), Positives = 29/34 (85%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           E EE+ + + +EEE++++E +E+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 12/34 (35%), Positives = 28/34 (82%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           E EE+ + + +EEE++++E+EE+  E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.5 bits (94), Expect = 2e-04
 Identities = 12/34 (35%), Positives = 28/34 (82%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           E EE+ + + +EEE  ++E+EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

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

 Score = 44.8 bits (106), Expect = 2e-04
 Identities = 16/64 (25%), Positives = 35/64 (54%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E + +L  + + ++ +EE  + E+  +E +E  EE  +    +EE EE  E  +E ++
Sbjct: 541 LLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEELRERLKELKK 600

Query: 647 EEEE 650
           + +E
Sbjct: 601 KLKE 604

Length = 908

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

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 20/54 (37%), Positives = 33/54 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E  +EE EE+ E+ E   EE EE +E++Q ++ +EE  + E+  +E +E  EE 
Sbjct: 525 EALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEEL 578

Length = 908

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

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
             +++L     +EE EE+ E+ E   EE EE +E+ ++Q+ +EE  + E+  +E +E  E
Sbjct: 518 IELLELEEA-LKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLE 576

Query: 649 EEEEVRGGGKEE 660
           E   +R   +E 
Sbjct: 577 ELRLLRTRKEEL 588

Length = 908

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

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 31/84 (36%), Positives = 45/84 (53%), Gaps = 6/84 (7%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE--- 643
             +  I+ +     E  E+ E+  E  EEE +E ++ EE+QEE+EEEE E+E E  E   
Sbjct: 182 EAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELEQEIEALEERL 241

Query: 644 ---EEEEEEEEEVRGGGKEEISLH 664
              EEE+E  EE++    E  SL 
Sbjct: 242 AELEEEKERLEELKARLLEIESLE 265

Length = 908

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 17/53 (32%), Positives = 22/53 (41%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E E++  E   E   E++  E       +    EEEE EE   EE   EE  E
Sbjct: 134 EAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAEEAPAEEAPAEESAE 186

Length = 186

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

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 17/63 (26%), Positives = 33/63 (52%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           ++EE+   +E + +E++    E+ ++ QE  E  +  EE E+    EE   E+ +   KE
Sbjct: 120 KQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGKVHEETEDSYHVEETASEQYKQDMKE 179

Query: 660 EIS 662
           + S
Sbjct: 180 KAS 182

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

 Score = 43.0 bits (101), Expect = 2e-04
 Identities = 18/64 (28%), Positives = 37/64 (57%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E    E+ +++ +E+  E+E E+ +E V++ E  + E ++  EE+ +EE+   E     K
Sbjct: 166 EETASEQYKQDMKEKASEQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIK 225

Query: 659 EEIS 662
           EE++
Sbjct: 226 EELA 229

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|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 20/46 (43%), Positives = 26/46 (56%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            + E E E  EEEEEE EE EEE E    + +  +   EE +E+EE
Sbjct: 141 PKNEFELELPEEEEEEPEEMEEELEEDAADRDARKRAAEEAKEQEE 186

This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. Length = 363

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 13/25 (52%), Positives = 18/25 (72%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
           E   E +E EEEE+EEE EEE +++
Sbjct: 78  EAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 13/25 (52%), Positives = 16/25 (64%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
             E   E +E EEEE+EEE EEE +
Sbjct: 76  GAEAAAEADEAEEEEKEEEAEEESD 100

Length = 109

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 23/71 (32%), Positives = 34/71 (47%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           + +L R+     ++    E E E+ EE   +  +E+ E E E EE EE  EE EEE  E 
Sbjct: 721 LEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEA 780

Query: 651 EEVRGGGKEEI 661
           E      + +I
Sbjct: 781 EAEIEELEAQI 791

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 24/64 (37%), Positives = 34/64 (53%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E + + I +  +E  E E E EE EE  EE EEE  E + E EE E + E+ +EE + 
Sbjct: 741 EVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKA 800

Query: 647 EEEE 650
             E 
Sbjct: 801 LREA 804

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 25/64 (39%), Positives = 35/64 (54%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           +I  + + + R E E E+ EE   +  +E  E E E EE++E  EE EEE  E E E EE
Sbjct: 727 QISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEE 786

Query: 647 EEEE 650
            E +
Sbjct: 787 LEAQ 790

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|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 13/40 (32%), Positives = 15/40 (37%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           EEE+             V   E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 14/45 (31%), Positives = 16/45 (35%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           EEE+                 E    E E E E EEE E+  G G
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEKKSGMG 159

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 14/29 (48%), Positives = 23/29 (79%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           E+E +EEEE E++ +++ EE EEEE+ E+
Sbjct: 1   EDEPDEEEELEDDIDDLDEEAEEEEDGED 29

This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. Length = 145

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 14/29 (48%), Positives = 23/29 (79%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E+E +EEEE E+++ + +EE EEEE+ E+
Sbjct: 1   EDEPDEEEELEDDIDDLDEEAEEEEDGED 29

This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. Length = 145

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

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 15/56 (26%), Positives = 38/56 (67%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           ++ E+  EE + ++  E+E  ++ E+E  + QE++++ EE E++ + E++++EE+ 
Sbjct: 83  KKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQA 138

Length = 387

>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]

 Score = 44.2 bits (104), Expect = 2e-04
 Identities = 19/90 (21%), Positives = 40/90 (44%)

Query: 574 VWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
           +W+  + ++ G+   E    ++       E++ ++    E+ E E    EE   EEE E+
Sbjct: 332 LWRNLNNEKWGNEEAERKDYILDSSSVPLEKQFDDILYFEKMEIENRNPEESEHEEEVED 391

Query: 634 EEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
            E+E +  +   +++E E       E+ S 
Sbjct: 392 YEDENDHSKRICDDDELENHFRAADEKNSH 421

Length = 776

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

 Score = 44.6 bits (105), Expect = 2e-04
 Identities = 19/70 (27%), Positives = 39/70 (55%), Gaps = 7/70 (10%)

Query: 598  GEREEEEEEEEEEEEEEEEEEEEEE---EEEVQEEEE----EEEEEEEEEEEEEEEEEEE 650
             +  +EE + E++E  ++E+  EE    +E++Q+++     E++E+  E+  EE  +E E
Sbjct: 4016 ADENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENE 4075

Query: 651  EEVRGGGKEE 660
            E    G K +
Sbjct: 4076 ESTEDGVKSD 4085

Length = 4600

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 43.0 bits (102), Expect = 2e-04
 Identities = 18/54 (33%), Positives = 31/54 (57%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E++  +E+  EE E E E++EE +E + E+E +E +    E E +  E + E R
Sbjct: 5   EQKTPQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEAQLAEAQAEER 58

Length = 193

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 42.2 bits (100), Expect = 2e-04
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE--EEEEEEEEEEEEEE 652
           EE++  +E+  EE E E E++EE +  E E+E +E +    E E +  E + EE
Sbjct: 4   EEQKTPQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEAQLAEAQAEE 57

Length = 193

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 21/46 (45%), Positives = 24/46 (52%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            EE + EE EEE E  E EE  EE  EE  E+ E E   E  +E E
Sbjct: 2   SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 42.1 bits (99), Expect = 2e-04
 Identities = 21/46 (45%), Positives = 25/46 (54%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            EE + EE EEE E  E EE V+E  EE  E+ E E   E  +E E
Sbjct: 2   SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|220605 pfam10156, Med17, Subunit 17 of Mediator complex

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 568 IRPSIKVWKTSDQDEIGSPRIENIIQLI---RRGEREEEEEEEEEEEEEEEEEEEEEEEE 624
           I  S++       ++     +E +I+ I   R   R+  EE   EE  +E  + +  EE 
Sbjct: 12  IPLSLRPLIDKPAEDEDPLSLEELIERINQERGSFRDLTEESLREEIAKEAAKIDFSEES 71

Query: 625 EVQEEEEEEEEEEEEEEEEEEEE 647
           + +E++EE++ ++ EE ++  EE
Sbjct: 72  DEEEDDEEDDNDDSEENKDTVEE 94

This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures. Length = 454

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 44.7 bits (106), Expect = 2e-04
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 582 EIGSPRIENIIQ-LIRRGEREEE---EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           E+G  +    I+ L+ RG    E   + +EEE   E+E  EEEE  E    E+  ++ EE
Sbjct: 370 ELGIWKDVERIKALVIRGYPLAEALSKVKEEERPREKEGTEEEERREITVYEKRIKKLEE 429

Query: 638 EEEEEEEEEEEEEEEVR 654
             E  EEE  E + E+ 
Sbjct: 430 TVERLEEENSELKRELE 446

Length = 652

>gnl|CDD|218954 pfam06246, Isy1, Isy1-like splicing family

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           G R+EE+    E E E E+E  E+  EE +E ++E+ + EE+E EE+     +++     
Sbjct: 168 GYRDEEDGVLLEYEAEREKELIEKLVEEWKEIQDEDLQAEEDEREEDIYIPLDDDAEFVA 227

Query: 658 KEEI 661
              +
Sbjct: 228 HVPV 231

Isy1 protein is important in the optimisation of splicing. Length = 253

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 36/68 (52%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E EE EEE + E E   E +  ++E+E   EE+     EE+E+ ++ E+ ++ E+    K
Sbjct: 231 ETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEILKEKK 290

Query: 659 EEISLHFY 666
           +E    F 
Sbjct: 291 DEELFWFE 298

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|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 14/56 (25%), Positives = 33/56 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E  +EEE++       E+ E   E+E+ Q+ + +++  +E EE +++ +++E E +
Sbjct: 7   EINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEVEAQ 62

Length = 196

>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 14/50 (28%), Positives = 29/50 (58%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EE E+E  +EEE++        Q E   E+E+ ++ + +++  +E EE++
Sbjct: 2   EEVEKEINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELK 51

Length = 196

>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682)

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 16/40 (40%), Positives = 26/40 (65%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
               +EEEEEEEE E++++ +E +VQ+ ++ E   E  EE
Sbjct: 92  GHTRQEEEEEEEENEKQQQSDEAQVQQHQQHEHPAENGEE 131

This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length. Length = 133

>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32

 Score = 43.1 bits (101), Expect = 2e-04
 Identities = 27/112 (24%), Positives = 51/112 (45%), Gaps = 14/112 (12%)

Query: 562 TNKLKTIRPSIKVWKTSDQDEIGS--------------PRIENIIQLIRRGEREEEEEEE 607
            N LK   PS +V  T+    I                 R+ N ++ + +         +
Sbjct: 132 PNTLKEAEPSAEVQPTTMTLPIAEHPTITENQSFQPWPERLHNNVEELLQSSLSLGGSVQ 191

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
            +  + ++E+   + +E +QE + EE++ +EE+EEEE EEE ++E   G  +
Sbjct: 192 VKAPKPKQEQLLSKLQEYLQEHKTEEKQPQEEQEEEEVEEEAKQEEGQGTDD 243

This family consists of several mammalian specific proacrosin binding protein sp32 sequences. sp32 is a sperm specific protein which is known to bind with with 55- and 53-kDa proacrosins and the 49-kDa acrosin intermediate. The exact function of sp32 is unclear, it is thought however that the binding of sp32 to proacrosin may be involved in packaging the acrosin zymogen into the acrosomal matrix. Length = 243

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 44.2 bits (105), Expect = 2e-04
 Identities = 11/40 (27%), Positives = 21/40 (52%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
              +  EEE        E++++  E+EEE+++ E+   EE
Sbjct: 260 APPQPPEEEPPPPPPPPEDDDDPPEDEEEQDDAEDRALEE 299

Length = 584

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 12/46 (26%), Positives = 23/46 (50%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           R  R     +  EEE        E++++  ++EEE+++ E+   EE
Sbjct: 254 RATRLPAPPQPPEEEPPPPPPPPEDDDDPPEDEEEQDDAEDRALEE 299

Length = 584

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

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 34/164 (20%), Positives = 64/164 (39%), Gaps = 13/164 (7%)

Query: 517 LVDVAAKNP-----TTGTTPFKLCTPEDFKPFVTALMNSE--WQSLWDNVPNTNKLKTIR 569
           LV  + KNP       GT  F +   E     + +L N+    + L      ++ +    
Sbjct: 740 LVQYSQKNPYQVYTEEGTKKFNILLQEIAYDVIVSLFNNPNAEKILIITEILSDGINNSD 799

Query: 570 PSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEE 629
            + +        E+    IE+  + ++    + EE     EE E   EE++  ++E++ E
Sbjct: 800 INDRP------QELIDQIIESEEERLKALRIQREEMLMRPEELELINEEQKNLKQEIKLE 853

Query: 630 EEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHFYVLYVLSK 673
             E +E EEE +   E + E  E +   K+   L      ++  
Sbjct: 854 LSEIQEAEEEIQNINENKNEFVEFKNDPKKLNKLIIAKDVLIKL 897

Length = 925

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 44.3 bits (105), Expect = 2e-04
 Identities = 14/53 (26%), Positives = 18/53 (33%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E  E   E ++E  + EE  E  E V  E E   +       E   E E    
Sbjct: 944 EHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTA 996

Length = 1068

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

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 18/65 (27%), Positives = 29/65 (44%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
            R    E  +E  +  E+E+  E EEE+ E    +EE ++ + E +  EE  +E E    
Sbjct: 4   LREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPA 63

Query: 656 GGKEE 660
              E 
Sbjct: 64  ASGEG 68

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|222160 pfam13476, AAA_23, AAA domain

 Score = 42.5 bits (100), Expect = 2e-04
 Identities = 24/72 (33%), Positives = 42/72 (58%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
            + + S +    + L    ER EE + + +E++E  EE E+E EE   E++  E+  EE+
Sbjct: 124 DELLKSDKEILPLLLYLGQERLEELKFKRKEKKERLEELEKELEELEDEKDLLEKLLEEK 183

Query: 640 EEEEEEEEEEEE 651
           E+++E EE +EE
Sbjct: 184 EKKKELEELKEE 195

Length = 204

>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E  ++ +R  ER +E  E E   +EE+  ++    E +  E   +  E+  +  E+  E+
Sbjct: 399 EETVEELR--ERAKEALETEALAQEEKLADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQ 456

Query: 649 EEEEVRGGGKEE 660
             +E+     +E
Sbjct: 457 AVDELIDIEGDE 468

Length = 470

>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 17/62 (27%), Positives = 26/62 (41%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
             EE  E E  +EE  EE  E  +E  E E   +EE+  ++    E  + E      ++ 
Sbjct: 387 PVEELLEIEGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRELAFKLAEKG 446

Query: 661 IS 662
           I 
Sbjct: 447 IK 448

Length = 470

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 44.2 bits (104), Expect = 3e-04
 Identities = 24/85 (28%), Positives = 37/85 (43%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           + +    + E   + +      E E  E+E E E  EE EE E+E   E E + E E E 
Sbjct: 700 EAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEG 759

Query: 640 EEEEEEEEEEEEEVRGGGKEEISLH 664
           + +E E E E E      ++E  + 
Sbjct: 760 DRKETEHEGETEAEGKEDEDEGEIQ 784

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 43.5 bits (103), Expect = 3e-04
 Identities = 33/60 (55%), Positives = 39/60 (65%), Gaps = 8/60 (13%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHFYVLYV 670
           E E  E EEEEEEEEV E +EE+E EEEEEEE EE  +EEE   G G     ++ YV +V
Sbjct: 164 EVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE---GTG-----VNKYVYFV 215

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 43.5 bits (103), Expect = 3e-04
 Identities = 24/38 (63%), Positives = 28/38 (73%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
           +R GE EEEEEE  E +EE+E EEEEEEE E   +EEE
Sbjct: 167 LREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 43.1 bits (101), Expect = 3e-04
 Identities = 20/56 (35%), Positives = 34/56 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++++E   E EE +++ EE  +  EEE Q  ++EE + +  EEEE+   +EE E R
Sbjct: 207 QKQQEAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERR 262

Length = 431

>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 21/53 (39%), Positives = 29/53 (54%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E + + +   E EE  E+E EEE  EEE E E  +EE  +  E E + +E EE
Sbjct: 6   EQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEE 58

Length = 191

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.4 bits (103), Expect = 3e-04
 Identities = 23/65 (35%), Positives = 35/65 (53%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E   +  +  +R  EE+ EE+EE  +EE  EEE E E   E++ E+EE E+E  E+  
Sbjct: 224 EAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRR 283

Query: 647 EEEEE 651
            +  E
Sbjct: 284 MKRLE 288

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|218258 pfam04774, HABP4_PAI-RBP1, Hyaluronan / mRNA binding family

 Score = 40.5 bits (95), Expect = 3e-04
 Identities = 20/52 (38%), Positives = 31/52 (59%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
            ++E  E  EE+ E +E+ E EE++  EEE  +E   EEEEV     +E++L
Sbjct: 30  VKDEIAELTEEQGEEEEKNEVEEKQAVEEEANKEGVVEEEEVEEEEDKEMTL 81

This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. Length = 106

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 40.2 bits (94), Expect = 3e-04
 Identities = 19/42 (45%), Positives = 27/42 (64%)

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
           ++ ++ EE EE +EEEEEEEEEE+E E E V    + E  + 
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIE 93

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 29/86 (33%), Positives = 39/86 (45%), Gaps = 11/86 (12%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEE-----------EEEEEEEEEEEEEVQEEEEEEEEE 636
            E  I+ ++    E  EE EE +EE           E E     E  EE++ E EE EE 
Sbjct: 265 AEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEER 324

Query: 637 EEEEEEEEEEEEEEEEVRGGGKEEIS 662
            EE +E+ E  +EE E R    EE+ 
Sbjct: 325 LEELKEKIEALKEELEERETLLEELE 350

Length = 1163

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

 Score = 44.0 bits (103), Expect = 3e-04
 Identities = 21/76 (27%), Positives = 45/76 (59%)

Query: 576  KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
            K +++D+  + R     +       EE  +  EEE++ + EE ++ EE +++ EE ++ E
Sbjct: 1570 KKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAE 1629

Query: 636  EEEEEEEEEEEEEEEE 651
            EE+++ E+ +++E EE
Sbjct: 1630 EEKKKVEQLKKKEAEE 1645

Length = 2084

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

 Score = 44.0 bits (103), Expect = 3e-04
 Identities = 18/61 (29%), Positives = 39/61 (63%)

Query: 600  REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
            ++ EE + + EE ++ EEE+++ E+  ++E EE+++ EE ++ EEE + +  E     +E
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEE 1672

Query: 660  E 660
            +
Sbjct: 1673 D 1673

Length = 2084

>gnl|CDD|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 43.4 bits (102), Expect = 3e-04
 Identities = 7/62 (11%), Positives = 17/62 (27%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
                ++     +   E+  EE E    + E +     + E        +   +  G  +
Sbjct: 156 NPSPNQQPSSFLQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPTSSPPPQSPPDEPGEPQ 215

Query: 659 EE 660
             
Sbjct: 216 SP 217

Length = 413

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 11/52 (21%), Positives = 25/52 (48%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +  E +++ EEEE    +   E+ +   EE++  E E  E   ++  + ++ 
Sbjct: 231 KEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSDDA 282

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 16/60 (26%), Positives = 31/60 (51%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           Q   R  R+     +  EE  +E E  + E+ E +++ +E+E++++ EEEE    +   E
Sbjct: 193 QAFARVVRDMLSSMDMAEELGDEPESADSEDNEDEDDPKEDEDDDQGEEEESGSSDSLSE 252

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 40.8 bits (96), Expect = 3e-04
 Identities = 16/54 (29%), Positives = 29/54 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            E  ++EE+ E E+ E+ E++E E   E    + EEE  +E++ +     EE +
Sbjct: 80  EEENDDEEDAETEDTEDVEDDEWEGFPEPTVTDYEEEYIDEDKYKTTVTVEELD 133

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 43.7 bits (103), Expect = 3e-04
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E   ++  EE+ +EE+ ++++ +  E+ +   EE E  +E EE+E E  + E E
Sbjct: 219 AEETGDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGE 273

Length = 620

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 19/55 (34%), Positives = 31/55 (56%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EE  ++  EE+ +EE+ +++  +  E+ E   EE E  +E EE+E E   G  EE
Sbjct: 220 EETGDDGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEE 274

Length = 620

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 27/55 (49%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE--EEEEEEEEEEE 652
           R E    E+ EEEE EE EE+EEEE  +E EE E   +  EE  E  E+ EE EE
Sbjct: 70  RIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEELTEASEQLEEHEE 124

Length = 306

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

 Score = 44.2 bits (104), Expect = 3e-04
 Identities = 24/64 (37%), Positives = 39/64 (60%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E+E ++E+EE EE E+E +E E +   EEEEEE+ E+ +E+ E+ EEE   + +   +  
Sbjct: 328 EKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERL 387

Query: 661 ISLH 664
            S  
Sbjct: 388 SSAA 391

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 = 44.2 bits (104), Expect = 3e-04
 Identities = 22/66 (33%), Positives = 36/66 (54%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E  ++ +      EEEEEE+ E+ +E+ E+ EEE    ++ E E      + +EEE E
Sbjct: 340 ELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELE 399

Query: 647 EEEEEE 652
            + EEE
Sbjct: 400 LKNEEE 405

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 = 43.8 bits (103), Expect = 3e-04
 Identities = 28/83 (33%), Positives = 44/83 (53%)

Query: 572 IKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEE 631
            K+    +++E    + E +  L    + E E  EEE+   E+EE+ +EEE EE+  E +
Sbjct: 785 EKLKVEEEKEEKLKAQEEELRALEEELKEEAELLEEEQLLIEQEEKIKEEELEELALELK 844

Query: 632 EEEEEEEEEEEEEEEEEEEEEVR 654
           EE++ E+  EEE E  EEE    
Sbjct: 845 EEQKLEKLAEEELERLEEEITKE 867

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 = 43.8 bits (103), Expect = 3e-04
 Identities = 23/92 (25%), Positives = 44/92 (47%)

Query: 563 NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
              K  +   +  K    ++      +      +  E  +  E++ +E+EEEEE+   ++
Sbjct: 701 EIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKK 760

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EEE +E+ E   +E+E  EEEE+ E+ + E  
Sbjct: 761 EEEEEEKSELSLKEKELAEEEEKTEKLKVEEE 792

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 = 43.8 bits (103), Expect = 3e-04
 Identities = 22/67 (32%), Positives = 43/67 (64%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           +      +++   + +++ E+E ++E+EE EE E+E +E E + E  +EEEE+ E+ +E+
Sbjct: 309 RKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEK 368

Query: 640 EEEEEEE 646
            E+ EEE
Sbjct: 369 LEQLEEE 375

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|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 22/42 (52%), Positives = 30/42 (71%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++E++ EE + EE +E E+ EEEE EEEE EEE E EEE+  
Sbjct: 3   DKEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQE 44

Length = 193

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEE 638
                EEEEEEE +EEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 17/25 (68%), Positives = 18/25 (72%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEE 632
                EEEEEEEEEEEEE +E EEE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 18/25 (72%), Positives = 19/25 (76%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEE 629
                EEEEEEEEEEEEEEEE +EE
Sbjct: 71  AAAAAEEEEEEEEEEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 19/27 (70%), Positives = 19/27 (70%), Gaps = 2/27 (7%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEE 636
                EEEEEEEEEEE  EEEEE EEE
Sbjct: 71  AAAAAEEEEEEEEEEE--EEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P

 Score = 40.4 bits (95), Expect = 3e-04
 Identities = 19/27 (70%), Positives = 19/27 (70%), Gaps = 2/27 (7%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEE 639
                EEEEEEEE  EEEEEEEE EEE
Sbjct: 71  AAAAAEEEEEEEE--EEEEEEEESEEE 95

This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome. Length = 105

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 44.0 bits (103), Expect = 3e-04
 Identities = 27/54 (50%), Positives = 30/54 (55%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E + EE  EE+ EE  EE  EE  EE V+E  EE  EE  EE  EE  EE  EE
Sbjct: 948  EEDAEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVEENVEENVEE 1001

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 44.0 bits (103), Expect = 3e-04
 Identities = 29/75 (38%), Positives = 37/75 (49%)

Query: 579  DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
            + +E     +E + + +   + E  EE EE  EE  EE  EE  EE  +E  EE EE  E
Sbjct: 1018 NVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIE 1077

Query: 639  EEEEEEEEEEEEEEV 653
            E  EE  EE  EE V
Sbjct: 1078 ENIEENVEENVEENV 1092

Length = 1136

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

 Score = 43.7 bits (103), Expect = 3e-04
 Identities = 15/59 (25%), Positives = 36/59 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++ E+ +EE ++ + +EE +E+   +E+E+ +E++ EE  + EEE++ E    +    +
Sbjct: 119 KKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKK 177

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|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 43.5 bits (102), Expect = 3e-04
 Identities = 23/54 (42%), Positives = 36/54 (66%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++EEEE+E+ EE EE EE E  EEE  ++E+ E+++E+E + E +E E   E  
Sbjct: 106 QKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAEGDENELAGEYI 159

Length = 374

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 15/29 (51%), Positives = 17/29 (58%)

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
                  EE +EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 14/29 (48%), Positives = 17/29 (58%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
                  EE+ +EEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 13/29 (44%), Positives = 17/29 (58%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
                   +++EEEEEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
                  EE++EEEEEEEE+EE   EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEKEE--SEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
                  EE++EEEEEEEE+  EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEEEEK--EESEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
                  EE++EEEEEE  EE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEEEEE--EEKEESEEEAAA 99

Length = 106

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
                  EE++EEE  EEEEE+EE EEE   
Sbjct: 71  AAAAAAAEEKKEEE--EEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 40.6 bits (95), Expect = 3e-04
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEE 633
               EE+ EE+EEE+++EE +EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 40.6 bits (95), Expect = 3e-04
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEE 644
               EE+  ++EEE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 40.2 bits (94), Expect = 3e-04
 Identities = 15/27 (55%), Positives = 22/27 (81%)

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEE 649
               +E+ EE+EEE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 43.8 bits (103), Expect = 3e-04
 Identities = 14/51 (27%), Positives = 30/51 (58%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            ++E +E +E+EE +E  E+  E+E + +  +EE+ E+ +E E +   +  
Sbjct: 945 SDDESDETDEDEESDESSEDLSEDESENDSSDEEDGEDWDELESKAAYDSR 995

Length = 1001

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.1 bits (93), Expect = 3e-04
 Identities = 11/34 (32%), Positives = 28/34 (82%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E EE+ + + +EEE++++  EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.1 bits (93), Expect = 3e-04
 Identities = 12/34 (35%), Positives = 28/34 (82%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           E EE+ + + +EEE++  E+EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

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

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 27/76 (35%), Positives = 42/76 (55%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E +++ I     E  E  EE E+ E+E +E EE +EE++E E+E E  E  + + EE+
Sbjct: 201 ELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEK 260

Query: 647 EEEEEEVRGGGKEEIS 662
             E EE     K+EI 
Sbjct: 261 IRELEERIEELKKEIE 276

Length = 880

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

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 17/63 (26%), Positives = 39/63 (61%), Gaps = 3/63 (4%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEE---EEEEEEEEEEEEEEEEEE 649
           +L +R   E+  ++ E+  ++ EE++++ EE + ++  E   + E E E++ +EE +++ 
Sbjct: 93  ELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKKAKEEAKKQA 152

Query: 650 EEE 652
           EEE
Sbjct: 153 EEE 155

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 40.5 bits (95), Expect = 3e-04
 Identities = 13/27 (48%), Positives = 18/27 (66%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEE 624
           G     E +E EEEE+EEE EEE +++
Sbjct: 76  GAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 29/72 (40%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R E++++   R ER EE  E+ EE   E  E  EE+ E  +E  E   E E E EE+ E 
Sbjct: 500 RAEDLVEAEDRIERLEERREDLEELIAERRETIEEKRERAEELRERAAELEAEAEEKREA 559

Query: 647 ----EEEEEEVR 654
               EEE EE R
Sbjct: 560 AAEAEEEAEEAR 571

Length = 880

>gnl|CDD|234366 TIGR03825, FliH_bacil, flagellar assembly protein FliH

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 587 RIENIIQLIRRGERE-EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
               I         E E+E  +EE+E E+  E+ E E  ++ E+ E +     E+ E+E 
Sbjct: 16  ERGIIPLRQVTDVPETEQELADEEQEFEQILEKAEAEAAQIIEQAEAQAAAIREQIEQER 75

Query: 646 EEEEEEEVR 654
            + EEE  R
Sbjct: 76  AQWEEERER 84

This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes. Length = 255

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 41.8 bits (99), Expect = 3e-04
 Identities = 18/47 (38%), Positives = 26/47 (55%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
             EE++  +E+  EE E E E QEE +E E E+E +E +    E E 
Sbjct: 2   SNEEQKTPQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEA 48

Length = 193

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 43.7 bits (103), Expect = 3e-04
 Identities = 27/70 (38%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQE--EEEEEEEEEEEEEEEEEE 646
           E +   I     ++   EE+    +E  E  +E+   V E   EEEEEEEEEEEEE  E 
Sbjct: 360 ERVKDAIPEDLYDKIATEEDATTIDELREFLKEKGHPVVERWAEEEEEEEEEEEEEAAEA 419

Query: 647 EEEEEEVRGG 656
           E   EE   G
Sbjct: 420 EAPMEEPVPG 429

Length = 470

>gnl|CDD|220112 pfam09110, HAND, HAND

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 17/43 (39%), Positives = 27/43 (62%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
               +EE+EEE E + + E+E+ +  E + EEEEEE++   EE
Sbjct: 66  VGDGDEEDEEEREAKRKLEQEKIDNAEPLTEEEEEEKQRLLEE 108

The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein. Length = 109

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 43.8 bits (104), Expect = 3e-04
 Identities = 19/68 (27%), Positives = 31/68 (45%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E  E EE EEE + E E   E +   QE+E   EE+     EE+E+ ++ E++      +
Sbjct: 228 ETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEILK 287

Query: 661 ISLHFYVL 668
                 + 
Sbjct: 288 EKKDEELF 295

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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 14/62 (22%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE---EEEEEEEEEEEEEEEEEEEEEE 652
            R  ++ E  E+   ++E+++    E +    +E+   ++E +    EE+  +E E+EE 
Sbjct: 653 TRESQQAEVTEKARTQDEQQQAPRRERQRRRNDEKRQAQQEAKALNVEEQSVQETEQEER 712

Query: 653 VR 654
           V+
Sbjct: 713 VQ 714

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 13/53 (24%), Positives = 18/53 (33%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           +E  E  E   E ++E  + EE  E  E    E E   +       E   E  
Sbjct: 940 QEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVE 992

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 15/54 (27%), Positives = 19/54 (35%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E  E  E   E ++E  + EE  E  EV   E E   +       E   E E  
Sbjct: 941 EVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETV 994

Length = 1068

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

 Score = 43.5 bits (103), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 32/60 (53%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            +  E+E+  E EEE+ E +  +EE+ + + E +  EE  +E E +     E  GG +EE
Sbjct: 16  RKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAASGEGGGGEEEE 75

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|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 43.7 bits (104), Expect = 3e-04
 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 589 ENIIQ-LIRRG-EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           E I Q L+  G    EE      EE  E E  +EE  EE++E  +E  E E   +EE+  
Sbjct: 366 EEIAQLLVEEGFSSLEELAYVPVEELLEIEGFDEETVEELRERAKEALETEALAQEEKLA 425

Query: 647 EEEEE 651
           ++   
Sbjct: 426 DDLLS 430

Length = 470

>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 8/85 (9%)

Query: 566 KTIRPSIKVWKTSDQ--DEIGSPR--IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEE 621
             +R + K   T  Q   ++ S    I N   L    + E +E ++EEE   +E EE E+
Sbjct: 36  SELRDAEKERDTYKQYLSKLESQNVEISNYEAL----DSELDELKKEEERLLDELEELEK 91

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEE 646
           E++++  E  E +EE+E+ E EE +
Sbjct: 92  EDDDLDGELVELQEEKEQLENEELQ 116

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. Length = 356

>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740)

 Score = 43.5 bits (102), Expect = 3e-04
 Identities = 21/41 (51%), Positives = 29/41 (70%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
            EEEEE E EE+EE  E+E  +V +E+ EEEEEEE +  ++
Sbjct: 140 LEEEEEVEMEEDEEYYEKEPGKVVDEKSEEEEEEELKTMKD 180

This family consists of several uncharacterized plant proteins of unknown function. Length = 565

>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 26/70 (37%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE--EEEEEVQEEEEEEEEEEEEEEEEEE 645
           +E +I+ I R   EE EE  EE  EE E+ +EE   E EE  EE   + E+E E E +  
Sbjct: 4   LEKLIKKILREAEEEAEEILEEAREEAEKIKEEAKREAEEAIEEILRKAEKEAERERQRI 63

Query: 646 EEEEEEEVRG 655
                 E R 
Sbjct: 64  ISSALLEARR 73

Length = 194

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 42.5 bits (101), Expect = 3e-04
 Identities = 23/34 (67%), Positives = 23/34 (67%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE 630
           R  R  E  EEEEEE EEEEEEEEEEE E  E E
Sbjct: 225 RQGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 26/41 (63%), Positives = 30/41 (73%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           E E  E EEEEEEEE  E +EE+E +EEEEEE EE  +EEE
Sbjct: 164 EVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 43.1 bits (101), Expect = 4e-04
 Identities = 23/63 (36%), Positives = 41/63 (65%), Gaps = 2/63 (3%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            +E E+ +++++E   E EE +++ EE ++  EEEE+  ++EE + +  EEEE+ R   K
Sbjct: 199 GKEFEKLKQKQQEAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRR--LK 256

Query: 659 EEI 661
           EEI
Sbjct: 257 EEI 259

Length = 431

>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription]

 Score = 41.7 bits (98), Expect = 4e-04
 Identities = 17/62 (27%), Positives = 42/62 (67%), Gaps = 2/62 (3%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE--EEEEEEEEEEEEVRGGGK 658
            E+++ + +++E +  EE +E+E +  E++EEEE++E +   +E ++E+E+++E+     
Sbjct: 95  TEKKDIKAKDKEVDAFEEGDEDELDYDEDKEEEEDDEVDSLDDENDDEDEDDDEIVEILI 154

Query: 659 EE 660
           E+
Sbjct: 155 ED 156

Length = 175

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

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 22/59 (37%), Positives = 28/59 (47%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
               E E E     E  EE E E EE EE   + +E+ E  +EE EE E   EE E+ +
Sbjct: 295 EEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLL 353

Length = 1163

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

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 31/70 (44%), Positives = 41/70 (58%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           QL  R E  EEE EE EEE EE +E  EE EEE++  EE   + +EE EE EE+ +  +E
Sbjct: 734 QLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQE 793

Query: 653 VRGGGKEEIS 662
                +EE+ 
Sbjct: 794 ELEELEEELE 803

Length = 1163

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

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 33/80 (41%), Positives = 43/80 (53%), Gaps = 4/80 (5%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE----EEEEEE 642
            +E + + +   E+E EE + E EE  EE EE +EE  E++EE EE E E     E  EE
Sbjct: 254 ELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEE 313

Query: 643 EEEEEEEEEEVRGGGKEEIS 662
            E E EE EE     KE+I 
Sbjct: 314 LENELEELEERLEELKEKIE 333

Length = 1163

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

 Score = 43.6 bits (102), Expect = 4e-04
 Identities = 20/62 (32%), Positives = 40/62 (64%), Gaps = 3/62 (4%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            ++ EE + + EE ++ EEE+++ E+ + +E EE+++ EE ++ EEE + +  EE +   K
Sbjct: 1613 KKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAK---K 1669

Query: 659  EE 660
             E
Sbjct: 1670 AE 1671

Length = 2084

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 15/55 (27%), Positives = 34/55 (61%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
             ++E + + EEE+EE++E+E++++EEE  +   ++ + +E   E  + E  +E 
Sbjct: 284 AVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKEL 338

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.1 bits (101), Expect = 4e-04
 Identities = 15/55 (27%), Positives = 34/55 (61%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            ++E  ++E + + EEE+EE++E+E+++ +EE  E   ++ + +E   E  + E 
Sbjct: 280 PDKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLES 334

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.1 bits (101), Expect = 4e-04
 Identities = 20/76 (26%), Positives = 38/76 (50%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           +D +E          ++I   +  +   E E   E+  ++E E++EE+  EEEE  EE+E
Sbjct: 115 ADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEEAGEEKE 174

Query: 638 EEEEEEEEEEEEEEEV 653
             E+   E++ ++  V
Sbjct: 175 SVEQATREKKFDKSGV 190

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.1 bits (101), Expect = 4e-04
 Identities = 17/54 (31%), Positives = 32/54 (59%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            + EEE+EE++E+E++++EEE  E   ++ + +E   E  + E  +E    E R
Sbjct: 291 SKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKELSSFEKR 344

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.1 bits (101), Expect = 4e-04
 Identities = 16/56 (28%), Positives = 33/56 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           + EEE+EE++E+E++++EEE  E   +  + +E   E  + E  +E    E+ + +
Sbjct: 292 KPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKELSSFEKRQAK 347

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT

 Score = 42.5 bits (100), Expect = 4e-04
 Identities = 10/52 (19%), Positives = 24/52 (46%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           + + ++++ EEEE    +   E+ +   E  E  E E  E   ++  + ++ 
Sbjct: 231 KEDEDDDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSDDA 282

This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. Length = 282

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

 Score = 43.0 bits (101), Expect = 4e-04
 Identities = 13/65 (20%), Positives = 31/65 (47%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           ++G+R  +++ +E + ++ ++E  EE+          + EE E++   E   + E E   
Sbjct: 259 KKGKRGGDDDADEYDSDDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDE 318

Query: 656 GGKEE 660
             +E 
Sbjct: 319 DSEES 323

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

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

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 23/72 (31%), Positives = 41/72 (56%)

Query: 582 EIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E+     E I    +  E+EEE   +  +E +EEE+E++ +EEE++   +EEEE + E  
Sbjct: 245 ELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELL 304

Query: 642 EEEEEEEEEEEV 653
           + E  + ++EE 
Sbjct: 305 KLERRKVDDEEK 316

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 = 43.4 bits (102), Expect = 4e-04
 Identities = 21/76 (27%), Positives = 46/76 (60%)

Query: 577 TSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
             ++ E     +E   +++ +  +E +EEE+E++ +EEE +   +EEEE++ E  + E  
Sbjct: 250 EQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERR 309

Query: 637 EEEEEEEEEEEEEEEE 652
           + ++EE+ +E E+E +
Sbjct: 310 KVDDEEKLKESEKELK 325

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|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 42.7 bits (100), Expect = 4e-04
 Identities = 23/52 (44%), Positives = 37/52 (71%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           EEE   ++EEEE+E+ EE++E EE E  EEE +++E+ E+++E+E    G E
Sbjct: 100 EEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAEGDE 151

Length = 374

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.8 bits (93), Expect = 4e-04
 Identities = 15/24 (62%), Positives = 21/24 (87%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEE 621
            E + EE+EEE+++EEE+EEEEEE
Sbjct: 74  AEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional

 Score = 42.0 bits (98), Expect = 4e-04
 Identities = 21/59 (35%), Positives = 36/59 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           R+ + +E +  + +E  E E+ ++E EE   Q+ E+  EE E++ EE  E+EEE EE +
Sbjct: 6   RKNKAKEPKRRDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENEEQK 64

Length = 193

>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional

 Score = 41.6 bits (97), Expect = 4e-04
 Identities = 21/54 (38%), Positives = 35/54 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +R + +E  E E+ ++E EE  E++ E   EE E++ EE  E+EEE EE++ +E
Sbjct: 14  KRRDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENEEQKPKE 67

Length = 193

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 43.5 bits (102), Expect = 4e-04
 Identities = 15/54 (27%), Positives = 30/54 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E   ++E +E +E+EE +E  E+  E+  E +  +EE+ E+ +E E +   +  
Sbjct: 942 EASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDGEDWDELESKAAYDSR 995

Length = 1001

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.1 bits (93), Expect = 4e-04
 Identities = 11/34 (32%), Positives = 29/34 (85%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           E EE+ + + +EEE+++ ++EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.1 bits (93), Expect = 4e-04
 Identities = 11/34 (32%), Positives = 29/34 (85%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           E EE+ + +  +EE++++E+EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 40.1 bits (93), Expect = 4e-04
 Identities = 10/34 (29%), Positives = 29/34 (85%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           E EE+ + + +EEE++++E+ ++++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.8 bits (92), Expect = 4e-04
 Identities = 11/34 (32%), Positives = 28/34 (82%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
           E EE+ + + +EEE++++E+EE+++  ++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.8 bits (92), Expect = 4e-04
 Identities = 11/34 (32%), Positives = 28/34 (82%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           E EE+ + + +EE  +++E+EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

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

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 28/75 (37%), Positives = 42/75 (56%)

Query: 585 SPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           S  +  + + + + E+E +E EE +EE EE E+E E  E   ++ EE+  E EE  EE +
Sbjct: 213 SSELPELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELK 272

Query: 645 EEEEEEEEVRGGGKE 659
           +E EE EE     KE
Sbjct: 273 KEIEELEEKVKELKE 287

Length = 880

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

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 9/85 (10%)

Query: 585 SPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEE--------EEEEE 636
              I  I + I+  E +EE  EE +++ +E E+  EE EE  +  EE        E  ++
Sbjct: 320 EEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKK 379

Query: 637 EEEEEEEEEEEEEEEEVRGGGKEEI 661
                  E+ E+E EE+    KEEI
Sbjct: 380 RLTGLTPEKLEKELEELE-KAKEEI 403

Length = 880

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

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 28/64 (43%), Positives = 38/64 (59%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           + +++L      E EEE   E+EE E  EE EE E+E++E EEE  E  E EE  +EE E
Sbjct: 473 KELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELE 532

Query: 649 EEEE 652
           E+ E
Sbjct: 533 EKLE 536

Length = 908

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

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 29/73 (39%), Positives = 37/73 (50%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           + E    R E + +L R  E  EE+ E  EE E E EE EEE E      EE EE  E+ 
Sbjct: 265 ELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKL 324

Query: 640 EEEEEEEEEEEEE 652
           +  EE  E+ EE+
Sbjct: 325 KSLEERLEKLEEK 337

Length = 908

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 41.7 bits (98), Expect = 4e-04
 Identities = 19/56 (33%), Positives = 24/56 (42%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +    E E++  E   E   E++  E   V  EE    EEEE EE   EE   EE 
Sbjct: 129 KKAALEAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAEEAPAEEAPAEES 184

Length = 186

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

 Score = 42.2 bits (99), Expect = 4e-04
 Identities = 15/63 (23%), Positives = 33/63 (52%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           EEE +E+ +   E+    ++EE+   +E + +E++    E+ ++ +E  E  +   + E 
Sbjct: 102 EEEVKEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGKVHEETED 161

Query: 662 SLH 664
           S H
Sbjct: 162 SYH 164

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

 Score = 42.2 bits (99), Expect = 4e-04
 Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE--EEEEEEEEEEEEEEVRGGGK 658
           EE E   EEE +    + +++ EEEV+E+ +   E+    ++EE+   +E + +      
Sbjct: 80  EEAEPHAEEEGQLAVRKTKQKVEEEVKEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLL 139

Query: 659 EEIS 662
            E S
Sbjct: 140 AEDS 143

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|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.9 bits (101), Expect = 4e-04
 Identities = 13/55 (23%), Positives = 33/55 (60%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +E+E +++ E++ EE E++   E+   +E E+    E+  ++ E+  ++ EE+ +
Sbjct: 65  KEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQK 119

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (94), Expect = 4e-04
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
                  E   E +E EEEE+EEE +EE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (94), Expect = 4e-04
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
                  E   E +E EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 13/30 (43%), Positives = 24/30 (80%)

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + E +EEEE E+ E E+EE+EEE+++++ +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|225887 COG3351, FlaD, Putative archaeal flagellar protein D/E [Cell motility and secretion]

 Score = 41.8 bits (98), Expect = 4e-04
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 585 SPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
               E I +L       + ++ ++E  EE  E  E+ +E  + E+ +  EEE  E+E+  
Sbjct: 21  EELKEKIEEL-----PIQAKKSDDELVEELPERYEQTKENSLIEKVDSIEEEISEKEKVM 75

Query: 645 EEEEEEEE 652
            E+ +E  
Sbjct: 76  SEKLKEPA 83

Length = 214

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +++ +L    E+ EE   +  +E  E E E EE EE ++E EEE  E E E EE E + E
Sbjct: 733 KDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIE 792

Query: 649 EEEEVRGGGKEEIS 662
           + +E     +E + 
Sbjct: 793 QLKEELKALREALD 806

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|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 41.9 bits (99), Expect = 4e-04
 Identities = 11/40 (27%), Positives = 14/40 (35%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           EEE+                 E    + E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 43.5 bits (103), Expect = 4e-04
 Identities = 24/54 (44%), Positives = 30/54 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E   E+ ++ EE  EE  EE  E E E++E  E  E+  EE EE EEE EE  E
Sbjct: 345 ESLREDADDLEERAEELREEAAELESELEEAREAVEDRREEIEELEEEIEELRE 398

Length = 880

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

 Score = 43.0 bits (101), Expect = 4e-04
 Identities = 16/59 (27%), Positives = 41/59 (69%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           R+ + E+  EE + ++  E+E  ++ E+E ++ +E++++ EE E++ + E++++EE+ R
Sbjct: 81  RKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQAR 139

Length = 387

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

 Score = 43.0 bits (101), Expect = 4e-04
 Identities = 14/64 (21%), Positives = 37/64 (57%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           +  E+E  ++ E+E  + +E++++ EE E+  + E++++EE+  +   E++++ E     
Sbjct: 96  QAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAK 155

Query: 656 GGKE 659
              E
Sbjct: 156 AAAE 159

Length = 387

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 41.8 bits (99), Expect = 4e-04
 Identities = 17/47 (36%), Positives = 26/47 (55%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             EE++  +E+  EE E E  Q+EE +E E E+E +E +    E E 
Sbjct: 2   SNEEQKTPQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEA 48

Length = 193

>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 599 EREEEEEEEEEE-----EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E E+E  +EEE+        E+ E   E+E+  Q + +++  +E EE +++ +++E E
Sbjct: 3   EVEKEINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEVE 60

Length = 196

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

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE-EEEEEEEEEEEEE 645
           R   + +L RR  + EE  + + E  +++EE  E++E+E+  +E+  +E+EEE EE   E
Sbjct: 74  RRNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAE 133

Query: 646 EEEEEEEVRGGGKEE 660
           + EE E + G  +EE
Sbjct: 134 QREELERISGLTQEE 148

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|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 589 ENIIQLIRRGEREEEE--EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           + + +L    E E E   +E+ EE   + EEE     E  +   E++   E E E+EE  
Sbjct: 177 KKLAELKAEEEEELERALKEKREELLSKLEEELLARLESKEAALEKQLRLEFEREKEELR 236

Query: 647 EEEEEEVR 654
           ++ EE++R
Sbjct: 237 KKYEEKLR 244

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|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 39.1 bits (92), Expect = 4e-04
 Identities = 13/26 (50%), Positives = 17/26 (65%)

Query: 632 EEEEEEEEEEEEEEEEEEEEEVRGGG 657
                 EEE++EEEEEEEE++  G G
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDDDMGFG 86

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

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

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 33/74 (44%), Positives = 43/74 (58%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           + EI     E      +  E EEE EE E+E EE +EE EE E E+ + E+E +E EEE+
Sbjct: 827 EQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEK 886

Query: 640 EEEEEEEEEEEEEV 653
           EE EEE  E E E+
Sbjct: 887 EELEEELRELESEL 900

Length = 1163

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

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 31/75 (41%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 588 IENIIQLIRR-GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           +   ++ + R  E  + E    EEE E+ +   EE EEE++E EEE EE +E  EE EEE
Sbjct: 707 LRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEE 766

Query: 647 EEEEEEVRGGGKEEI 661
            E  EE     KEEI
Sbjct: 767 LESLEEALAKLKEEI 781

Length = 1163

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

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E +++ +   +   E EE +EE EE+     EE EE  +   EE  E E E  E   E
Sbjct: 341 ERETLLEELE--QLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNE 398

Query: 647 EEEEEE 652
            EE + 
Sbjct: 399 LEELKR 404

Length = 1163

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 43.1 bits (101), Expect = 5e-04
 Identities = 19/66 (28%), Positives = 40/66 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E +E ++E  ++E + + EEE+EE++E +++++EEE  E   ++ + +E   E V     
Sbjct: 276 EDDEPDKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESP 335

Query: 659 EEISLH 664
           +E+S  
Sbjct: 336 KELSSF 341

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 40.4 bits (95), Expect = 5e-04
 Identities = 22/63 (34%), Positives = 41/63 (65%), Gaps = 6/63 (9%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEE-----EEEEEEVQEE-EEEEEEEEEEEEEEEEEEEE 649
           R+ +R ++ +EE +E+E EE  EE     EE ++E++++ +E +E  +  EEE ++EE+ 
Sbjct: 30  RKQQRRKKAQEEAKEKEREERIEERKRIREERKQELEKQLKERKEALKLLEEENDDEEDA 89

Query: 650 EEE 652
           E E
Sbjct: 90  ETE 92

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 21/49 (42%), Positives = 27/49 (55%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
              ++E   E    E+ EEEE EE EE+ +EE EEE EE E   +  EE
Sbjct: 63  FGEDDEGRIEVRISEDGEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEE 111

Length = 306

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

 Score = 43.4 bits (102), Expect = 5e-04
 Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 1/99 (1%)

Query: 564 KLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEE 623
           K +      K  +   + E  S +   + +     E    EE     + E E EE   EE
Sbjct: 886 KDELESKEEKEKEEKKELEEESQKDNLLEEKENEIEERIAEEAIILLKYESEPEELLLEE 945

Query: 624 EEVQEEEEE-EEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
            + +E+EE+ +EEEEE  +     +EE   V      E 
Sbjct: 946 ADEKEKEEDNKEEEEERNKRLLLAKEELGNVNLMAIAEF 984

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 = 43.0 bits (101), Expect = 5e-04
 Identities = 20/92 (21%), Positives = 40/92 (43%)

Query: 562 TNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEE 621
                      +      Q+ +   + E         + EE   +  +E +EEE+E++ +
Sbjct: 226 NLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEEILAQVLKENKEEEKEKKLQ 285

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           EEE     +EEEE + E  + E  + ++EE++
Sbjct: 286 EEELKLLAKEEEELKSELLKLERRKVDDEEKL 317

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|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 42.4 bits (99), Expect = 5e-04
 Identities = 23/54 (42%), Positives = 36/54 (66%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           EEE   ++EEEE+E+ EE E  EE E  EEE +++E+ E+++E+E +  G   E
Sbjct: 100 EEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAEGDENE 153

Length = 374

>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 14/24 (58%), Positives = 17/24 (70%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEE 621
              E++EEEEEEEE+EE EEE   
Sbjct: 76  AAEEKKEEEEEEEEKEESEEEAAA 99

Length = 106

>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 16/55 (29%), Positives = 34/55 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
             +    +++  +  + + ++ ++EE+  ++ +  EE+E +E+EEEEE EEEEE 
Sbjct: 226 SSDAAASQDDGPKGSDVKNKKSDDEEDDDQDGDYVEEKELKEDEEEEETEEEEEE 280

PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Length = 285

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEE 630
               EE+ EE+EEE+++EEE+E +EEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEE 642
               EE+ EE +EE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 5e-04
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEE 643
               EE+ E +EEE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 43.1 bits (101), Expect = 5e-04
 Identities = 17/68 (25%), Positives = 33/68 (48%)

Query: 581 DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           D+      E + +     + E +E +E+EE +E  E+  E+E E    +EE+ E+ +E E
Sbjct: 928 DDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSSDEEDGEDWDELE 987

Query: 641 EEEEEEEE 648
            +   +  
Sbjct: 988 SKAAYDSR 995

Length = 1001

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

 Score = 43.1 bits (102), Expect = 5e-04
 Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 13/74 (17%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEE-------------EEEEEEEVQEEEEEEEEEEEE 639
             I    RE E EEE +EEE EE  +             E+E E +  ++E + E +E++
Sbjct: 392 AEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKK 451

Query: 640 EEEEEEEEEEEEEV 653
           E +EEEE E+EEE 
Sbjct: 452 ESDEEEELEDEEEA 465

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|218177 pfam04615, Utp14, Utp14 protein

 Score = 42.7 bits (101), Expect = 5e-04
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEE-------EEEEEEEEVQEEEEEEEEEEEEEE 641
             I +L R  E EEE +EEE EE  ++         E  E+E E ++ ++E + E +E++
Sbjct: 392 AEIEELRRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNEFKEKK 451

Query: 642 EEEEEEEEEEEVRGGGKEEIS 662
           E +EEEE E+E     ++  +
Sbjct: 452 ESDEEEELEDEEEAKVEKVAN 472

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|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.8 bits (92), Expect = 5e-04
 Identities = 10/34 (29%), Positives = 29/34 (85%)

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           E EE+ + + +E +++++E+EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.8 bits (92), Expect = 5e-04
 Identities = 10/34 (29%), Positives = 29/34 (85%)

Query: 615 EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E EE+ + + + +E++++E+EE+++E+++E+++E
Sbjct: 7   EGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

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

 Score = 43.1 bits (102), Expect = 5e-04
 Identities = 24/76 (31%), Positives = 39/76 (51%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           ++E  I+ +     E ++E EE EE+ +E +E +E+ EE  +  E  EE  +E  E E+ 
Sbjct: 256 KLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDELREIEKR 315

Query: 647 EEEEEEVRGGGKEEIS 662
               EE   G +E I 
Sbjct: 316 LSRLEEEINGIEERIK 331

Length = 880

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 42.6 bits (100), Expect = 5e-04
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           E  + E E E   EEE  EE ++E E E E+EE+  +E+ E+ ++E+   G  ++ 
Sbjct: 206 EPFQLESEVEASPEEENYEEYEDETELEVEDEEKALDEQTEDPQQEDALAGDAKKA 261

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 42.6 bits (100), Expect = 5e-04
 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 7/67 (10%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE-------EEEEEEVRGGG 657
           E E E   EEE  EE E+E E++ E+EE+  +E+ E+ ++E+       +  EEE   G 
Sbjct: 211 ESEVEASPEEENYEEYEDETELEVEDEEKALDEQTEDPQQEDALAGDAKKALEEEEEKGE 270

Query: 658 KEEISLH 664
           + E + +
Sbjct: 271 RPENATY 277

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

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

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           ++E +       E EE +E+ + ++ +EE  + E+  +E++E  EE       +EE EE 
Sbjct: 534 KLEKLEN--LLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKEELEEL 591

Query: 647 EEEEEEVR 654
            E  +E++
Sbjct: 592 RERLKELK 599

Length = 908

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

 Score = 43.2 bits (102), Expect = 5e-04
 Identities = 27/82 (32%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E     +R    E E+E  E EEE  E  E EE  +E  EE+ E+ E   EE EE +E
Sbjct: 491 SREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKE 550

Query: 647 ----EEEEEEVRGGGKEEISLH 664
               ++ +EE+R        L 
Sbjct: 551 KLQLQQLKEELRQLEDRLQELK 572

Length = 908

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

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 14/56 (25%), Positives = 34/56 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            ++E+E +++ E++ EE E++   E+  Q+E E+    E+  ++ E+  ++ EE +
Sbjct: 63  AKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQAEEKQ 118

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

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

 Score = 42.5 bits (100), Expect = 5e-04
 Identities = 14/61 (22%), Positives = 37/61 (60%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           IQ  ++   ++E+E +++ E++ EE E++   E+ +++E E+    E+  ++ E+  ++ 
Sbjct: 55  IQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAAKQA 114

Query: 652 E 652
           E
Sbjct: 115 E 115

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|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 18/42 (42%), Positives = 27/42 (64%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            ++  E+EE E++  +  EE+E   EE+E E  EEEE+EE E
Sbjct: 31  AQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.1 bits (102), Expect = 5e-04
 Identities = 29/64 (45%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R E + Q     E  ++ EE E +E + E EE EEE EE+QEE E  EE  EE  EE EE
Sbjct: 415 RRERLQQ--EIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELREELEE 472

Query: 647 EEEE 650
            E+ 
Sbjct: 473 AEQA 476

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|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 41.4 bits (98), Expect = 5e-04
 Identities = 18/54 (33%), Positives = 30/54 (55%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +E+  EE E E E++EE +E E E+  +E +    E E +  E + EE +  +R
Sbjct: 10  QEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEAQLAEAQAEERDSVLR 63

Length = 193

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 42.9 bits (101), Expect = 5e-04
 Identities = 24/55 (43%), Positives = 29/55 (52%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           EE+    +E  E  +E+    V+   EEEEEEEEEEEEE  E E   E    G E
Sbjct: 377 EEDATTIDELREFLKEKGHPVVERWAEEEEEEEEEEEEEAAEAEAPMEEPVPGFE 431

Length = 470

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 41.0 bits (96), Expect = 5e-04
 Identities = 21/46 (45%), Positives = 25/46 (54%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            EE + EE EEE E  E EE  EE V+E  E+ E E   E  +E E
Sbjct: 2   SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional

 Score = 41.4 bits (97), Expect = 5e-04
 Identities = 15/58 (25%), Positives = 33/58 (56%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EE E+E  +EEE++       E+++   E+E+ ++ + +++  +E EE + +   KE 
Sbjct: 2   EEVEKEINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEV 59

Length = 196

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 43.1 bits (102), Expect = 5e-04
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
              +  EEE        E++    E+EEE+++ E+   EE
Sbjct: 260 APPQPPEEEPPPPPPPPEDDDDPPEDEEEQDDAEDRALEE 299

Length = 584

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 42.7 bits (101), Expect = 5e-04
 Identities = 11/40 (27%), Positives = 20/40 (50%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
              +  EEE        E+++   E+EEE+++ E+   EE
Sbjct: 260 APPQPPEEEPPPPPPPPEDDDDPPEDEEEQDDAEDRALEE 299

Length = 584

>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 42.5 bits (101), Expect = 5e-04
 Identities = 14/56 (25%), Positives = 25/56 (44%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E E  +EE  EE  E  +E  E E    +E+  ++    E  + E   +  E+ ++
Sbjct: 393 EIEGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRELAFKLAEKGIK 448

Length = 470

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

 Score = 43.3 bits (103), Expect = 5e-04
 Identities = 21/53 (39%), Positives = 25/53 (47%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EEEE  +EE + E EEE + E EE    E EEE + E       EE  E    
Sbjct: 39  EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAA 91

Length = 746

>gnl|CDD|217503 pfam03344, Daxx, Daxx Family

 Score = 42.6 bits (100), Expect = 6e-04
 Identities = 24/65 (36%), Positives = 30/65 (46%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           GE EEEEEE E +   EEE E   E +   EE EE+ E    E        E ++ RG  
Sbjct: 467 GEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRNSEMAGISRMSEGQQPRGSS 526

Query: 658 KEEIS 662
            +  S
Sbjct: 527 VQPES 531

The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis, but precise role played by Daxx remains to be determined. Daxx forms a complex with Axin. Length = 715

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 43.1 bits (101), Expect = 6e-04
 Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 4/65 (6%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE----EEEEEEEEEEE 652
           +G+   E + E E E E  E++E E + E Q ++ E ++E  E+E     + E +++E+ 
Sbjct: 792 KGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKG 851

Query: 653 VRGGG 657
           V GGG
Sbjct: 852 VDGGG 856

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 43.1 bits (101), Expect = 6e-04
 Identities = 23/62 (37%), Positives = 34/62 (54%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E  I+    GE  E+E E E E + E E E + +E E + E E E +E+E+E E +  E+
Sbjct: 729 EGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGED 788

Query: 649 EE 650
            E
Sbjct: 789 GE 790

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 42.7 bits (100), Expect = 6e-04
 Identities = 22/67 (32%), Positives = 34/67 (50%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
             G+R+E E E E E E +E+E+E E +     E + +E  E + E E E E  E++   
Sbjct: 757 TEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHE 816

Query: 656 GGKEEIS 662
           G  E  +
Sbjct: 817 GQSETQA 823

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 26/41 (63%), Positives = 29/41 (70%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           E E  E EEEEEEEE  E +EE + EEEEEEE EE  +EEE
Sbjct: 164 EVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 40.8 bits (95), Expect = 6e-04
 Identities = 20/53 (37%), Positives = 34/53 (64%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EEEE++E+EE+E  ++++EE E   +EE E    E E+  ++ E+E  E + R
Sbjct: 95  EEEEKQEQEEQERIQKQKEEAEARAREEAERMRLEREKHFQQIEQERLERKKR 147

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family

 Score = 40.8 bits (95), Expect = 6e-04
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 3/73 (4%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEE---EEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           +  R+ E EE++E+EE+E  ++++EE E    EE E    E E+  ++ E+E  E ++  
Sbjct: 89  KAKRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRLEREKHFQQIEQERLERKKRL 148

Query: 650 EEEVRGGGKEEIS 662
           EE ++   K E+S
Sbjct: 149 EEIMKRTRKSEVS 161

The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Length = 171

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 41.6 bits (98), Expect = 6e-04
 Identities = 9/65 (13%), Positives = 32/65 (49%)

Query: 584 GSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
            + +  N+       E ++EE+E + +  EE+    + ++ +   + +  +++ ++++ E
Sbjct: 82  DADKSTNLDASNEGDEDDDEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSE 141

Query: 644 EEEEE 648
           +E   
Sbjct: 142 DETAA 146

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 41.9 bits (98), Expect = 6e-04
 Identities = 18/82 (21%), Positives = 35/82 (42%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           ++ ++  P  +   + + R    E+          + +E+ +E      + + EEEE  E
Sbjct: 124 EKSDVEEPSEKVDEEDVEREILAEKPRVTRFNIVWDNDEDNDEAPPAQPDVDNEEEERLE 183

Query: 639 EEEEEEEEEEEEEEVRGGGKEE 660
           E +  EEEE+EE      G+  
Sbjct: 184 ESDGREEEEDEEVGSDSYGEGN 205

Length = 279

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

 Score = 42.8 bits (101), Expect = 6e-04
 Identities = 23/54 (42%), Positives = 27/54 (50%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E +EE EE+     EE EE  E   EE+ E E E  E   E EE + E E  EE
Sbjct: 358 EAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEE 411

Length = 1163

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 40.7 bits (95), Expect = 6e-04
 Identities = 16/48 (33%), Positives = 24/48 (50%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           E +EEE E+ E+  +EE+EE EE EEE     +      +   +E   
Sbjct: 32  EEDEEEMEDWEDSLDEEDEEAEEVEEETAASSKAPSSSSKSSSQETIS 79

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 42.7 bits (100), Expect = 6e-04
 Identities = 16/55 (29%), Positives = 32/55 (58%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
              +E  ++E + + EEE+EE++E+E++  EEE  E   ++ + +E   E  + E
Sbjct: 279 EPDKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLE 333

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|114603 pfam05887, Trypan_PARP, Procyclic acidic repetitive protein (PARP)

 Score = 40.3 bits (93), Expect = 6e-04
 Identities = 28/51 (54%), Positives = 28/51 (54%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
              EE EEE E EEE EEE E EE  EE  E E E E E E E E E E E
Sbjct: 71  EPEEEGEEEPEPEEEGEEEPEPEETGEEEPEPEPEPEPEPEPEPEPEPEPE 121

This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. Length = 145

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

 Score = 43.0 bits (101), Expect = 6e-04
 Identities = 22/66 (33%), Positives = 39/66 (59%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           IE + + ++  E + E EEEEEE+ E+ +E+ E+ EEE+  +++ E E      + +EEE
Sbjct: 338 IEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEE 397

Query: 648 EEEEEV 653
            E +  
Sbjct: 398 LELKNE 403

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 = 43.0 bits (101), Expect = 6e-04
 Identities = 20/73 (27%), Positives = 36/73 (49%)

Query: 581  DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
             E     +E   +  +  + +EEEEE  +     +EE        + E EE+EE   ++E
Sbjct: 936  SEPEELLLEEADEKEKEEDNKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDE 995

Query: 641  EEEEEEEEEEEEV 653
             ++E  EEE++E+
Sbjct: 996  LKKERLEEEKKEL 1008

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|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 42.9 bits (100), Expect = 6e-04
 Identities = 31/75 (41%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 580  QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEE--EEEEEEVQEEEEEEEEEE 637
            ++ +     EN+ ++    E  +EE  EE EE  EE  EE  EE  EE  EE  EE EE 
Sbjct: 1016 EENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEEN 1075

Query: 638  EEEEEEEEEEEEEEE 652
             EE  EE  EE  EE
Sbjct: 1076 IEENIEENVEENVEE 1090

Length = 1136

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 6e-04
 Identities = 16/27 (59%), Positives = 21/27 (77%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEE 637
               EE+ EE+EEE+ +EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 6e-04
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEE 629
               EE+ EE+EEE+++EEE+EE +EE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 42.6 bits (100), Expect = 6e-04
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E  EE  ++ E E+EE+ ++++  E ++EE+ E E E +E    +E E  +     G+EE
Sbjct: 198 ELAEEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEE 257

Query: 661 IS 662
           + 
Sbjct: 258 MV 259

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

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

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 15/88 (17%), Positives = 47/88 (53%)

Query: 557 DNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEE 616
            N  + +        I V   +D D+      +     I   + +E+++E++++++ ++E
Sbjct: 109 KNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDE 168

Query: 617 EEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           +EE++E +E+++  ++++   +E++ E 
Sbjct: 169 DEEKKEAKELEKLSDDDDFVWDEDDSEA 196

Length = 509

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

 Score = 42.8 bits (101), Expect = 6e-04
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEE--EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
             E + + + + E   EE EE +E+   ++ +EE  + E+ +QE +E  EE       +E
Sbjct: 527 LKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRKE 586

Query: 645 EEEEEEEEVR 654
           E EE  E ++
Sbjct: 587 ELEELRERLK 596

Length = 908

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

 Score = 42.8 bits (101), Expect = 6e-04
 Identities = 23/62 (37%), Positives = 31/62 (50%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
               ++ ++  E E  E E   EE EE+ E  EE E E++E EEE E      EE EE  
Sbjct: 262 ESLELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELL 321

Query: 648 EE 649
           E+
Sbjct: 322 EK 323

Length = 908

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 40.9 bits (96), Expect = 6e-04
 Identities = 17/51 (33%), Positives = 22/51 (43%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E++  E   E   E++  E      +E    EEEE EE   EE   EE  E
Sbjct: 136 EKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAEEAPAEEAPAEESAE 186

Length = 186

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

 Score = 41.5 bits (97), Expect = 6e-04
 Identities = 12/61 (19%), Positives = 29/61 (47%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           +E+ +   E+    ++EE+   +E ++ E++    E+ ++ +E  E  +  EE       
Sbjct: 106 KEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGKVHEETEDSYHV 165

Query: 660 E 660
           E
Sbjct: 166 E 166

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 39.7 bits (93), Expect = 6e-04
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
                      E +E EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 6e-04
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
                  E   + +E EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

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

 Score = 42.9 bits (102), Expect = 6e-04
 Identities = 25/68 (36%), Positives = 47/68 (69%), Gaps = 2/68 (2%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE--EE 645
           I ++ +L R  E++ EE E   +E E+ +EE EE++E++QEEE++  EE E+E ++  +E
Sbjct: 522 IASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKE 581

Query: 646 EEEEEEEV 653
            ++E +E+
Sbjct: 582 AKKEADEI 589

Length = 782

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

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 22/68 (32%), Positives = 34/68 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            IE  I+ + + E + +E  EE EE+    E+E E  +   +E E   EE EE+  + EE
Sbjct: 720 EIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEE 779

Query: 647 EEEEEEVR 654
              + E R
Sbjct: 780 ALNDLEAR 787

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

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 28/88 (31%), Positives = 46/88 (52%), Gaps = 5/88 (5%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEE----EEEEEEEEEEEEEEEEEVQEEEEEE 633
           S+   I + R++ + Q +    R+  E E+E    E+EEE+ +E  EE EE++   E+E 
Sbjct: 695 SELRRIEN-RLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEI 753

Query: 634 EEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           E  + E +E E   EE EE     +E +
Sbjct: 754 ENVKSELKELEARIEELEEDLHKLEEAL 781

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|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 41.6 bits (98), Expect = 6e-04
 Identities = 12/40 (30%), Positives = 14/40 (35%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           EEE+                 E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 26/60 (43%), Positives = 28/60 (46%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           L  R E  EE   E  E  EE+ E  EE  E   E E E EE+ E   E EEE EE  E 
Sbjct: 514 LEERREDLEELIAERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREE 573

Length = 880

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

 Score = 42.2 bits (99), Expect = 6e-04
 Identities = 16/76 (21%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 587 RIENIIQLIRRGEREEEE--EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           + E + + ++  +  E+E  ++ E+E  + +E++++ EE E Q + E++++EE+  +   
Sbjct: 84  KEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAA 143

Query: 645 EEEEEEEEVRGGGKEE 660
           E++++ E  +     E
Sbjct: 144 EQKKKAEAAKAKAAAE 159

Length = 387

>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 = 6e-04
 Identities = 24/117 (20%), Positives = 55/117 (47%), Gaps = 19/117 (16%)

Query: 547  LMNSEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEE 606
            L NS  + LWD     + L+T + S +    +++ ++ S   +N         +  E+++
Sbjct: 3899 LSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDN---------KALEDKD 3949

Query: 607  EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE----------EEEEEEEEEEV 653
             +E+E+EEE  ++   ++E+Q + +E   +   E E          +E+E +  ++ 
Sbjct: 3950 RQEKEDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKLDEKEGDVSKDS 4006

Length = 4600

>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 = 6e-04
 Identities = 17/62 (27%), Positives = 33/62 (53%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            E++E  ++E+  EE    +E+ ++++     E++E+  E+  EE  +E EE  E      
Sbjct: 4026 EKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSD 4085

Query: 659  EE 660
            EE
Sbjct: 4086 EE 4087

Length = 4600

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 41.7 bits (98), Expect = 6e-04
 Identities = 23/62 (37%), Positives = 33/62 (53%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            + R  +  EE EE   E EE+ ++EEEE +   ++ +E EEE    EEE    EEE E 
Sbjct: 20  DMRRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELEEENRRLEEEAAASEEERER 79

Query: 653 VR 654
           + 
Sbjct: 80  LE 81

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 42.5 bits (101), Expect = 6e-04
 Identities = 17/62 (27%), Positives = 28/62 (45%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           EE  E E  +EE  EE  E  +E ++ E   +EE+  ++    E  + E   +   K   
Sbjct: 389 EELLEIEGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRELAFKLAEKGIK 448

Query: 662 SL 663
           +L
Sbjct: 449 TL 450

Length = 470

>gnl|CDD|219761 pfam08243, SPT2, SPT2 chromatin protein

 Score = 39.9 bits (93), Expect = 6e-04
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
            +QDEI     E I  +  +G +    +  +E++  +  E    E   +Q+EE       
Sbjct: 37  EEQDEIPYDSDE-IWAIFGKGRKRSYYDRYDEDDALDNMEATFME---IQKEERRSARMA 92

Query: 638 EEEEEEEEEEEEEEEVR 654
             E+E E   EEEEE R
Sbjct: 93  RLEDERELAREEEEEKR 109

This family includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation. Length = 116

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 38.5 bits (90), Expect = 6e-04
 Identities = 17/40 (42%), Positives = 25/40 (62%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           ++E + EEE+ EEEEE  + EE +E E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

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

 Score = 42.9 bits (101), Expect = 6e-04
 Identities = 21/62 (33%), Positives = 39/62 (62%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E I  LI +    E+E E++ E  E+  +E+E+ ++E+++E EE +E E  ++ E E+E 
Sbjct: 511 EEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEA 570

Query: 649 EE 650
           +E
Sbjct: 571 QE 572

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|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 42.5 bits (100), Expect = 7e-04
 Identities = 16/58 (27%), Positives = 31/58 (53%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             E E+EEE E        + +++E   E ++E+EE++EE E   + E  + E+  ++
Sbjct: 9   ANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEISKREKARLK 66

Length = 1033

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 39.1 bits (91), Expect = 7e-04
 Identities = 19/44 (43%), Positives = 28/44 (63%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           ++  E EE +E +EEEEEEEEEE+E E E   ++E      E++
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIEDL 95

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 12/75 (16%), Positives = 30/75 (40%)

Query: 586 PRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            + +   +  R  + E+E    +E++++ EE  ++   ++ Q EE   +     + + E 
Sbjct: 92  LQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEA 151

Query: 646 EEEEEEEVRGGGKEE 660
           E +           E
Sbjct: 152 EAKRAAAAAKKAAAE 166

Length = 387

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

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 13/65 (20%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE---EEE 649
           +L ++   E+E  ++ E+E    +E++++ EE  ++   ++++ EE   +       + E
Sbjct: 91  ELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAE 150

Query: 650 EEEVR 654
            E  R
Sbjct: 151 AEAKR 155

Length = 387

>gnl|CDD|222571 pfam14153, Spore_coat_CotO, Spore coat protein CotO

 Score = 41.0 bits (96), Expect = 7e-04
 Identities = 22/52 (42%), Positives = 33/52 (63%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
            +E+EEE+E  +E  + +EEE++ E EE E+E+E  E E E+      KEEI
Sbjct: 36  ADEKEEEKENSDEHVKSKEEEQKIEYEEAEKEKEAGEPEREDIAEQQEKEEI 87

Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. Length = 185

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

 Score = 42.8 bits (101), Expect = 7e-04
 Identities = 28/64 (43%), Positives = 35/64 (54%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E + +L  R E  EEE E  EE   + +EE EE EE+ Q  +EE EE EEE EE E   +
Sbjct: 751 EELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLD 810

Query: 649 EEEE 652
             E 
Sbjct: 811 ALER 814

Length = 1163

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 30/63 (47%), Positives = 34/63 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           GE EE EE EE+EEEE EEE EE E      EE  E  E+ EE EE  +   E+ V  G 
Sbjct: 79  GEEEEVEEGEEDEEEEGEEESEEFEPLGDTPEELTEASEQLEEHEEGFQAMVEQAVERGL 138

Query: 658 KEE 660
             E
Sbjct: 139 SAE 141

Length = 306

>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 29/64 (45%), Positives = 34/64 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            E E EE EE+EEEE EEE EE E   +  EE  E  E+ EE EE  +   E+   RG  
Sbjct: 80  EEEEVEEGEEDEEEEGEEESEEFEPLGDTPEELTEASEQLEEHEEGFQAMVEQAVERGLS 139

Query: 658 KEEI 661
            E I
Sbjct: 140 AETI 143

Length = 306

>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein

 Score = 42.4 bits (100), Expect = 7e-04
 Identities = 19/55 (34%), Positives = 34/55 (61%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           +++  + +E E++   +     E E+   E ++EEEE+EEEEEEE+E+E   +E 
Sbjct: 358 KQKWTKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPSKEH 412

This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. Length = 794

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

 Score = 42.6 bits (100), Expect = 7e-04
 Identities = 16/62 (25%), Positives = 39/62 (62%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            + +  +E + E  +EEE+E+E+ +EE ++++E+ +EE ++ + +EE +E+        +
Sbjct: 90  AKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKE 149

Query: 659 EE 660
           +E
Sbjct: 150 KE 151

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|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEEEE 648
                ++ EE+EEE+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 14/25 (56%), Positives = 20/25 (80%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
               EE+ EE+EEE+++EEE+EEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEE 95

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.4 bits (92), Expect = 7e-04
 Identities = 14/25 (56%), Positives = 20/25 (80%)

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEEE 652
               EE+ EE+EEE+++EEE+EEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEE 95

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]

 Score = 42.7 bits (100), Expect = 7e-04
 Identities = 16/56 (28%), Positives = 30/56 (53%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
              +E +E +E+EE +E  E+  E+E E    +EE+ E+ +E E +   +    + R
Sbjct: 945  SDDESDETDEDEESDESSEDLSEDESENDSSDEEDGEDWDELESKAAYDSRPGKRR 1000

Length = 1001

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

 Score = 42.3 bits (100), Expect = 7e-04
 Identities = 10/49 (20%), Positives = 38/49 (77%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           + ++++E+++E++++++ ++E+EE++E +E E+  ++++   +E++ E 
Sbjct: 148 DDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEA 196

Length = 509

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

 Score = 42.8 bits (101), Expect = 7e-04
 Identities = 28/68 (41%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           +IE + +L R  E EE EEE E      EE EE  E+ +  EE  E+ EE+ E+ E E E
Sbjct: 289 KIERLEELER--EIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELE 346

Query: 647 EEEEEEVR 654
           E  EE+  
Sbjct: 347 ELAEEKNE 354

Length = 908

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

 Score = 42.4 bits (100), Expect = 7e-04
 Identities = 27/66 (40%), Positives = 36/66 (54%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E  I+ +   ERE EE EEE E      EE EE  E+++  EE  E+ EE+ E+ E E
Sbjct: 285 ELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESE 344

Query: 647 EEEEEE 652
            EE  E
Sbjct: 345 LEELAE 350

Length = 908

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

 Score = 41.5 bits (97), Expect = 7e-04
 Identities = 20/96 (20%), Positives = 44/96 (45%)

Query: 560 PNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEE 619
               +L+++   I V K  +      P+++    L+     + +E  E  +  EE E+  
Sbjct: 104 EVKEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGKVHEETEDSY 163

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
             EE   ++ +++ +E+  E+E E+ +E  E+  R 
Sbjct: 164 HVEETASEQYKQDMKEKASEQENEDSKEPVEKAERT 199

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

 Score = 41.5 bits (97), Expect = 7e-04
 Identities = 14/58 (24%), Positives = 31/58 (53%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
                +++ +E+  E+E E+ +E  E+ E    E ++  EE+ +EE+   E+ +  +E
Sbjct: 169 ASEQYKQDMKEKASEQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIKE 226

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 7e-04
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEE 625
               E   E +E EEEE+EEE EEE
Sbjct: 74  AAGAEAAAEADEAEEEEKEEEAEEE 98

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 7e-04
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEEE 652
               E   E +E EEEE+EEE EEE
Sbjct: 74  AAGAEAAAEADEAEEEEKEEEAEEE 98

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 7e-04
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
                  E   E +E +EEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|217502 pfam03343, SART-1, SART-1 family

 Score = 42.4 bits (100), Expect = 7e-04
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 16/81 (19%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEE----------------EEEEEEEEEEEEEEVQEEEEE 632
           E+I + I     E+EEE  E  +                +E  EE+ E ++E V+E  + 
Sbjct: 366 EDIARQIAEERSEDEEEAAENNDNGIVIDETSEFVRSLQKEPLEEKPENKDESVEEISDA 425

Query: 633 EEEEEEEEEEEEEEEEEEEEV 653
           EE++E+EE+E+ + + E   V
Sbjct: 426 EEDDEDEEDEDGDGDVEMSAV 446

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 17/42 (40%), Positives = 28/42 (66%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            ++  E+EE E++  +E+ ++E   EE+E E  EEEE+EE E
Sbjct: 31  AQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 40.4 bits (95), Expect = 7e-04
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 7/61 (11%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEV---QEEEEEEEEEEEEEEEEEEE----EEEEE 651
           E E +EEEE E++ ++ +EE EEEE+      +  E +     E +  +E+    E + E
Sbjct: 1   EDEPDEEEELEDDIDDLDEEAEEEEDGEDLFGDNMERDYRANPELDRYDEDGLDDESDYE 60

Query: 652 E 652
           E
Sbjct: 61  E 61

This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. Length = 145

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 42.7 bits (101), Expect = 7e-04
 Identities = 30/82 (36%), Positives = 37/82 (45%), Gaps = 11/82 (13%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE--------- 639
           E+   L  R E   EE  E E E EE  E  E+  EE++E EEE EE  E          
Sbjct: 349 EDADDLEERAEELREEAAELESELEEAREAVEDRREEIEELEEEIEELRERFGDAPVDLG 408

Query: 640 --EEEEEEEEEEEEEVRGGGKE 659
             E+  EE  EE +E+R    E
Sbjct: 409 NAEDFLEELREERDELREREAE 430

Length = 880

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

 Score = 42.2 bits (99), Expect = 7e-04
 Identities = 15/99 (15%), Positives = 44/99 (44%), Gaps = 9/99 (9%)

Query: 562 TNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEE 621
             + K      +  K     E          + +++ E+E  + +E++++ EE E++ + 
Sbjct: 79  QQRKKKEEQVAEELKPKQAAEQ---------ERLKQLEKERLKAQEQQKQAEEAEKQAQL 129

Query: 622 EEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E+++ +E+  +   E++++ E  + +   E  +     E
Sbjct: 130 EQKQQEEQARKAAAEQKKKAEAAKAKAAAEAAKLKAAAE 168

Length = 387

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 41.7 bits (98), Expect = 7e-04
 Identities = 25/60 (41%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE-EEEEEEEEEEEEEEEEEVR 654
           +  E  EE   E EE+ ++EEEE +  E++  E EEE    EEE    EEE E  E EV 
Sbjct: 26  KELEEYEETALELEEKLKQEEEEAQLLEKKADELEEENRRLEEEAAASEEERERLEAEVD 85

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 27/74 (36%), Positives = 31/74 (41%), Gaps = 12/74 (16%)

Query: 555 LWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEE 614
           L+D +       TI    +  K     E G P +E       R   EEEEEEEEEEEE  
Sbjct: 370 LYDKIATEEDATTIDELREFLK-----EKGHPVVE-------RWAEEEEEEEEEEEEEAA 417

Query: 615 EEEEEEEEEEEVQE 628
           E E   EE     E
Sbjct: 418 EAEAPMEEPVPGFE 431

Length = 470

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 42.7 bits (101), Expect = 7e-04
 Identities = 18/59 (30%), Positives = 30/59 (50%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           +E  E EE EEE + E E   E +  ++E+E   EE+     EE+E+ ++ E     + 
Sbjct: 227 KETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEI 285

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|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain

 Score = 40.7 bits (96), Expect = 7e-04
 Identities = 22/57 (38%), Positives = 36/57 (63%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           G R+  + E+ + E E+E ++ EEE+EE+++   E E + E  E+ EEEE + EE R
Sbjct: 111 GMRKALQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKR 167

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains. Length = 189

>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168)

 Score = 40.0 bits (94), Expect = 7e-04
 Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 27/96 (28%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE----------------------- 632
           RR E E  E  +E+ ++E E+EE +++ EE + ++EE                       
Sbjct: 45  RRREYERLELMDEKWKKETEDEEFQQKREEKKRKDEEKTAKKRAKRQKKKQKKKKKKKAK 104

Query: 633 ----EEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
               +EE+E  +  EE  +EEEE      +E + + 
Sbjct: 105 KGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIM 140

This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 142

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 42.3 bits (99), Expect = 8e-04
 Identities = 23/64 (35%), Positives = 29/64 (45%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           R GE  E   E E E  EE   E E+E E   + E E E E   E + E+E E E E + 
Sbjct: 644 RTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKE 703

Query: 656 GGKE 659
              +
Sbjct: 704 ADHK 707

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 42.0 bits (99), Expect = 8e-04
 Identities = 26/41 (63%), Positives = 29/41 (70%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           E E  E EEEEEEEE  E +EE+  EEEEEEE EE  +EEE
Sbjct: 164 EVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

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

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 21/62 (33%), Positives = 28/62 (45%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           + + +L    E  EE+     EE EE  E   EE  E++ E  E   E EE + E E  E
Sbjct: 351 QLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLE 410

Query: 649 EE 650
           E 
Sbjct: 411 ER 412

Length = 1163

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

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 21/55 (38%), Positives = 26/55 (47%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            +EE EE+     EE EE  E   EE  + E E  E   E EE + E E  EE +
Sbjct: 359 AKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERL 413

Length = 1163

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

 Score = 42.3 bits (99), Expect = 8e-04
 Identities = 17/64 (26%), Positives = 28/64 (43%)

Query: 588  IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
             E   +  +R    +EE          E EE+EE   + + ++E  EEE++E   E  EE
Sbjct: 956  KEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKELLREIIEE 1015

Query: 648  EEEE 651
              + 
Sbjct: 1016 TCQR 1019

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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 42.2 bits (99), Expect = 8e-04
 Identities = 14/57 (24%), Positives = 35/57 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++ + + +EE ++ + +EE +E+   +E+E ++E++ EE  + EEE++ E    +  
Sbjct: 118 KKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSR 174

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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 42.2 bits (99), Expect = 8e-04
 Identities = 14/62 (22%), Positives = 33/62 (53%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            + +EE +E+   +E+E+E+E++ EE    EEE++ E    +   ++  +++   +    
Sbjct: 131 RKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEP 190

Query: 659 EE 660
            E
Sbjct: 191 PE 192

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|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.0 bits (90), Expect = 8e-04
 Identities = 10/38 (26%), Positives = 27/38 (71%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEE 629
           +  +   E  + + +EEE++++E+EE+++E+++E  +E
Sbjct: 3   LHFLEGEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

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

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 23/69 (33%), Positives = 40/69 (57%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E + + I   E+E E  E  + + EE+  E EE  EE+++E EE EE+ +E +E +E+
Sbjct: 232 ELEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEK 291

Query: 647 EEEEEEVRG 655
            EE  ++  
Sbjct: 292 AEEYIKLSE 300

Length = 880

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 39.3 bits (92), Expect = 8e-04
 Identities = 13/32 (40%), Positives = 17/32 (53%)

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
                  E   E  E EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha subunit

 Score = 41.7 bits (98), Expect = 8e-04
 Identities = 20/55 (36%), Positives = 31/55 (56%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           L+  G  +      ++  E+EE E++  +E+E  E   EE+E E  EEEE+EE E
Sbjct: 18  LLTFGNGKGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGE 72

The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. Length = 281

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.8 bits (96), Expect = 8e-04
 Identities = 12/40 (30%), Positives = 14/40 (35%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           EEE+                 E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

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

 Score = 42.7 bits (100), Expect = 8e-04
 Identities = 15/61 (24%), Positives = 34/61 (55%)

Query: 601  EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            E +EE + E++E  ++E+  EE   + E+ ++++  +  E++E+  E+  EE     +E 
Sbjct: 4018 ENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEES 4077

Query: 661  I 661
             
Sbjct: 4078 T 4078

Length = 4600

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 41.3 bits (97), Expect = 8e-04
 Identities = 23/50 (46%), Positives = 32/50 (64%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           EE E E++E EE  E+ EE+    Q+E EE EE   E EE+ ++EEEE +
Sbjct: 1   EEAEREQQELEERMEQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQ 50

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|220112 pfam09110, HAND, HAND

 Score = 39.2 bits (92), Expect = 8e-04
 Identities = 17/45 (37%), Positives = 28/45 (62%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           ++  + +EE+EEE E + +  QE+ +  E   EEEEEE++   EE
Sbjct: 64  DDVGDGDEEDEEEREAKRKLEQEKIDNAEPLTEEEEEEKQRLLEE 108

The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein. Length = 109

>gnl|CDD|218954 pfam06246, Isy1, Isy1-like splicing family

 Score = 41.5 bits (98), Expect = 8e-04
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHFYV 667
            +EE+    E E E E+E+ E+  EE +E ++E+ + EE+E EE++     ++     +V
Sbjct: 170 RDEEDGVLLEYEAEREKELIEKLVEEWKEIQDEDLQAEEDEREEDIYIPLDDDAEFVAHV 229

Isy1 protein is important in the optimisation of splicing. Length = 253

>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740)

 Score = 42.3 bits (99), Expect = 8e-04
 Identities = 21/41 (51%), Positives = 28/41 (68%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
            EEEEE E EE+EE  E+E  + V E+ EEEEEEE +  ++
Sbjct: 140 LEEEEEVEMEEDEEYYEKEPGKVVDEKSEEEEEEELKTMKD 180

This family consists of several uncharacterized plant proteins of unknown function. Length = 565

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

 Score = 42.5 bits (101), Expect = 8e-04
 Identities = 21/51 (41%), Positives = 25/51 (49%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           EEEE  +EE + E EEE + E EE    E EEE + E       EE  E  
Sbjct: 39  EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAA 89

Length = 746

>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family

 Score = 40.7 bits (96), Expect = 8e-04
 Identities = 15/55 (27%), Positives = 30/55 (54%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            +   E+ ++E EE ++   E + + E+ +   EE EE  E  EE ++ E+E ++
Sbjct: 67  LKTRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKK 121

This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Length = 188

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

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 24/68 (35%), Positives = 37/68 (54%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           ER E EEE + E E   E +  ++E+E   EE+       EE E+ ++ +E EE+R  GK
Sbjct: 250 ERVESEEETDVEIETASETKGTKQEQEGSTEEDPSPSLFSEEREDPDKIDETEEIRVNGK 309

Query: 659 EEISLHFY 666
           E+I    +
Sbjct: 310 EKIKKDLF 317

Length = 1832

>gnl|CDD|224581 COG1667, COG1667, Uncharacterized protein conserved in archaea [Function unknown]

 Score = 41.4 bits (97), Expect = 8e-04
 Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE----EEEEEEEEEEEEE 643
            E I++L  + E        EEE E E EE +  E EE+ E+      E EE E   +E 
Sbjct: 101 FEKILEL-NKDECVLSVPITEEEVENEMEELKSSEREELLEKYGIRVPEIEEIERILDEA 159

Query: 644 EEEEEEEEEVRGGGKEEI 661
              +   EE+    +EE+
Sbjct: 160 VGSDYFSEEIEEPSREEL 177

Length = 254

>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812)

 Score = 39.6 bits (93), Expect = 8e-04
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
           ++ D I   R++ ++  I   ER E +   +EE++ +EEE + + EE  + E E+++
Sbjct: 72  AEVDAIARSRVQPVLDEID--ERAEAQRARDEEKKLDEEEAKRQHEEAKEREREKKK 126

This is a family of fungal proteins whose function is not known. Length = 126

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 41.9 bits (99), Expect = 8e-04
 Identities = 10/48 (20%), Positives = 22/48 (45%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
             +  +  E+ + +E   E  +E+ + EEE  + +  EEE   +   +
Sbjct: 2   TLKVHDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQ 49

Length = 325

>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional

 Score = 39.5 bits (92), Expect = 8e-04
 Identities = 14/46 (30%), Positives = 24/46 (52%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           + +   E+E  E E EE  +E+ E    +E +    E E++EE+E 
Sbjct: 4   DMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEP 49

Length = 130

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

 Score = 42.3 bits (99), Expect = 9e-04
 Identities = 23/75 (30%), Positives = 43/75 (57%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           + + +L +  ++E+EE EE E+E +E E + E EEEE ++ E+ +E+ E+ EEE   +++
Sbjct: 322 KELKKLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKK 381

Query: 649 EEEEVRGGGKEEISL 663
            E E      +    
Sbjct: 382 LESERLSSAAKLKEE 396

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 42.2 bits (99), Expect = 9e-04
 Identities = 15/56 (26%), Positives = 28/56 (50%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            E +++E+E E  E+ E E E + E+ E  E+E++ E  E     ++       +V
Sbjct: 656 EETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDKAVRRALPKV 711

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

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

 Score = 42.4 bits (100), Expect = 9e-04
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEE--EEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            E + + +     + E   EE EE +E+   ++ +EE  ++++  +E +E  EE      
Sbjct: 524 EEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRT 583

Query: 646 EEEEEEEVR 654
            +EE EE+R
Sbjct: 584 RKEELEELR 592

Length = 908

>gnl|CDD|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional

 Score = 40.7 bits (95), Expect = 9e-04
 Identities = 15/59 (25%), Positives = 34/59 (57%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           EE E+E  +EEE++       E+ E   E+E+ ++ + +++  +E EE +++++    E
Sbjct: 2   EEVEKEINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEVE 60

Length = 196

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

 Score = 41.9 bits (99), Expect = 9e-04
 Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 7/86 (8%)

Query: 572 IKVWKTSDQDEIGSPRI----ENIIQLIRRGE---REEEEEEEEEEEEEEEEEEEEEEEE 624
           I   K  +  +     I    E + QL ++      EEEEE E   +E+ EE   + EEE
Sbjct: 149 IDSIKEDNLKDDLESLIASAKEELDQLSKKLAELKAEEEEELERALKEKREELLSKLEEE 208

Query: 625 EVQEEEEEEEEEEEEEEEEEEEEEEE 650
            +   E +E   E++   E E E+EE
Sbjct: 209 LLARLESKEAALEKQLRLEFEREKEE 234

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|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 41.5 bits (98), Expect = 9e-04
 Identities = 19/54 (35%), Positives = 30/54 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ER + E  E E+E   E+++EEE+  E QE   +E  ++  E+ E E E+   E
Sbjct: 209 ERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLAE 262

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 23/62 (37%), Positives = 32/62 (51%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
             E EE E+E E E E + E E E +  + E E E E E +E+E+E E +  E+    G 
Sbjct: 735 GEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGD 794

Query: 659 EE 660
           E 
Sbjct: 795 EG 796

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 41.6 bits (97), Expect = 0.001
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 4/60 (6%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE----EEEEEEEEEEEEEEEEEE 652
           + +++E   E EE +++ EE  +  EEEE + ++EE +    EEEE+   +EE E    E
Sbjct: 206 KQKQQEAALELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAE 265

Length = 431

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 41.6 bits (97), Expect = 0.001
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           R +  EEEE+  ++EE + +  EEEE+  ++EE E    E  E+ ++  E+   E+
Sbjct: 226 RRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIERRRAEAAEKRQKVPEDGLSED 281

Length = 431

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

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 31/67 (46%), Positives = 41/67 (61%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            E + +L    E  E+E EE +EE EE E E+EE E+E++E EEE+EE EEE  E E E 
Sbjct: 841 EEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESEL 900

Query: 648 EEEEEVR 654
            E +E  
Sbjct: 901 AELKEEI 907

Length = 1163

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

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 30/60 (50%), Positives = 37/60 (61%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
            +E EE EEE    EEE EE +EE++E E+E EE + E EE  EE EE +E     KEEI
Sbjct: 238 RKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEI 297

Length = 1163

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

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 1/77 (1%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEE-EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            +E + + +R    E E E  E   E EE + E E  EE ++   E  E+ +EE +E E 
Sbjct: 373 ELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEA 432

Query: 646 EEEEEEEVRGGGKEEIS 662
           E EE +       EE+ 
Sbjct: 433 ELEELQTELEELNEELE 449

Length = 1163

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

 Score = 42.1 bits (98), Expect = 0.001
 Identities = 20/76 (26%), Positives = 45/76 (59%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            ++E EE+++ EE ++ EEE + + EE  +E EE++++ EE +++EEE+++     +   K
Sbjct: 1709 KKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEK 1768

Query: 659  EEISLHFYVLYVLSKG 674
            +   +      V+ + 
Sbjct: 1769 KAEEIRKEKEAVIEEE 1784

Length = 2084

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 18/64 (28%), Positives = 38/64 (59%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
            + + EEE+EE++E+E++++EEE  E  + + + +E   E  + E  +E    E+ +   
Sbjct: 289 ADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKELSSFEKRQAKL 348

Query: 658 KEEI 661
           K++I
Sbjct: 349 KQQI 352

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 41.5 bits (97), Expect = 0.001
 Identities = 17/68 (25%), Positives = 38/68 (55%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
            +   ++E + + EEE+EE++E+E++++EE   E   ++ + +E   E  + E  +E+  
Sbjct: 281 DKEAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKELSS 340

Query: 656 GGKEEISL 663
             K +  L
Sbjct: 341 FEKRQAKL 348

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

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

 Score = 40.5 bits (95), Expect = 0.001
 Identities = 19/47 (40%), Positives = 26/47 (55%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
                E+E+EE EEE EEE+EE  +E E+  EE+ E   E+E     
Sbjct: 80  DKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITNPS 126

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|223003 PHA03169, PHA03169, hypothetical protein; Provisional

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 12/54 (22%), Positives = 18/54 (33%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
           E+   + E + E  EE    E+EE  +        E          G  +E  S
Sbjct: 63  EQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELAS 116

Length = 413

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 21/63 (33%), Positives = 43/63 (68%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E E+E++++EE++EEEEEEEEE +  + ++EE+E  E+   E+ E ++ +  + +  G  
Sbjct: 158 EDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFTYEKSEVDKTDCFKFIEAGAG 217

Query: 659 EEI 661
           +++
Sbjct: 218 DDV 220

Length = 2849

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

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 11/68 (16%), Positives = 30/68 (44%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R   I +       + +++E  ++  EE E   E   +  + + +E + +E+ ++  E  
Sbjct: 155 RRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQAKKALEYY 214

Query: 647 EEEEEEVR 654
           + +E+   
Sbjct: 215 QLKEKLEL 222

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

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

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 27/86 (31%), Positives = 45/86 (52%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
                 E      E +  L ++ + +EEEEE+   ++EEEEEE+ E   + +E  EEEE+
Sbjct: 724 LADKVQEAQDKINEELKLLEQKIKEKEEEEEKSRLKKEEEEEEKSELSLKEKELAEEEEK 783

Query: 636 EEEEEEEEEEEEEEEEEVRGGGKEEI 661
            E+ + EEE+EE+ + +       E 
Sbjct: 784 TEKLKVEEEKEEKLKAQEEELRALEE 809

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

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

 Score = 41.9 bits (98), Expect = 0.001
 Identities = 29/97 (29%), Positives = 50/97 (51%)

Query: 563 NKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE 622
            +LK+    ++  K  D++++     E         + +EE EE E+E +E E + E EE
Sbjct: 297 EELKSELLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKELEIKREAEE 356

Query: 623 EEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           EEE Q E+ +E+ E+ EEE   +++ E E +    K 
Sbjct: 357 EEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

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

>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid)

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 9/57 (15%), Positives = 34/57 (59%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
           EE   E  +      + E+  +++E+EE+E++   ++++++++++++     +++ L
Sbjct: 34  EEVPPEVAKSRAPAADAEDAAKKDEDEEDEDDVVLDDDDDDDDDDDLPDLDDDDVDL 90

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. Length = 104

>gnl|CDD|131972 TIGR02926, AhaH, ATP synthase archaeal, H subunit

 Score = 38.3 bits (89), Expect = 0.001
 Identities = 23/61 (37%), Positives = 32/61 (52%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +  I   R   RE  EE EEE  +  EE  +E EEE  +E E+  EE E+E E  + + +
Sbjct: 23  KQRIAEAREEARELLEEAEEEASKLGEEIIKEAEEEIEKEAEKIREEGEKEIEAMKSKAK 82

Query: 649 E 649
           E
Sbjct: 83  E 83

he A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The hydrophilic A1 "stalk" complex (AhaABCDEFG) is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. It is unclear precisely where AhaH fits into these complexes. Length = 85

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

 Score = 41.8 bits (98), Expect = 0.001
 Identities = 16/65 (24%), Positives = 34/65 (52%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           +  E+E++ EE  + EEE++ E    +    +  +++   +++E  EEE++ +   E   
Sbjct: 146 KEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVK 205

Query: 656 GGKEE 660
           G  EE
Sbjct: 206 GKPEE 210

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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 41.8 bits (98), Expect = 0.001
 Identities = 16/72 (22%), Positives = 42/72 (58%), Gaps = 7/72 (9%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEE-------EEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           ++ ++E+ +EE ++ + +EE +E       E+E+E++V+E  + EEE++ E    +   +
Sbjct: 117 KKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPK 176

Query: 649 EEEEVRGGGKEE 660
           +  + +   K++
Sbjct: 177 KPPKKKPPNKKK 188

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|222581 pfam14181, YqfQ, YqfQ-like protein

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
            ++EEEE EEE  +E E+E   E + E +E+++ E  + + E+E+      K + S
Sbjct: 94  SDDEEEETEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPS 149

The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. Length = 155

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 39.0 bits (91), Expect = 0.001
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 615 EEEEEEEEEEEVQEEEEEEEEEEEEEE 641
               EE+ EE+ +E+++EEE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEE 632
               EE+ EE+EEE+++EEE +EEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 15/27 (55%), Positives = 21/27 (77%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEE 636
               EE+ EE+EEE++ +EE+EEEEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 14/27 (51%), Positives = 21/27 (77%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEE 631
               EE+ EE+EEE+++EEE+ +EEEE
Sbjct: 71  AAAAEEKAEEKEEEKKKEEEKEEEEEE 97

This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. Length = 106

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

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 22/52 (42%), Positives = 37/52 (71%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E + E +E++E +EEEE E+EEE +V++   +  +  E+ ++EEEEEE +EE
Sbjct: 442 ENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEE 493

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|218177 pfam04615, Utp14, Utp14 protein

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 22/52 (42%), Positives = 36/52 (69%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            + E +E++E +EEEE E+EEE + E+V  +  +  E+ ++EEEEEE +EE 
Sbjct: 443 NKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEEN 494

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|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 39.0 bits (90), Expect = 0.001
 Identities = 10/33 (30%), Positives = 27/33 (81%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE 630
           GE + + + +EEE++++E+EE+++E+++  ++E
Sbjct: 8   GEEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 38.6 bits (89), Expect = 0.001
 Identities = 10/25 (40%), Positives = 25/25 (100%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEV 626
           +EEE++++E+EE+++E+++E+++EV
Sbjct: 17  DEEEDDDDEDEEDDDEDDDEDDDEV 41

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 21/95 (22%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEE-------------EE 624
           +D ++   PR++ +    R+ +R   +E E E  +E+  EEE +              EE
Sbjct: 27  TDSEDDMEPRLKPV--FTRKKDRITIQEREREAAKEKALEEEAKRKAEERKRETLKIVEE 84

Query: 625 EVQEEEEEEEEEEEEE------EEEEEEEEEEEEV 653
           EV++E E ++     E      + ++E EEEE E 
Sbjct: 85  EVKKELELKKRNTLLEANIDDVDTDDENEEEEYEA 119

This family represents the C-terminus (approximately 300 residues) of proteins that are involved as binding partners for Prp19 as part of the nuclear pore complex. The family in Drosophila is necessary for pre-mRNA splicing, and the human protein has been found in purifications of the spliceosome. In the past this family was thought, erroneously, to be associated with microfibrillin. Length = 277

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 20/55 (36%), Positives = 31/55 (56%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           E  + E E E   EEE  EE   E E E E+EE+  +E+ E+ ++E+ + G  K+
Sbjct: 206 EPFQLESEVEASPEEENYEEYEDETELEVEDEEKALDEQTEDPQQEDALAGDAKK 260

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

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

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 21/63 (33%), Positives = 35/63 (55%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
             +EE EE+ E+ E   EE EE +E+   ++ +EE  + E+  +E +E  EE  +    K
Sbjct: 526 ALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRLLRTRK 585

Query: 659 EEI 661
           EE+
Sbjct: 586 EEL 588

Length = 908

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

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 2/103 (1%)

Query: 550 SEWQSLWDNVPNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEE 609
            E + + D +    K + +   +K  +   + +     +E  +  +     +  E  EEE
Sbjct: 154 KERKEILDELFGLEKYEKLSELLK--EVIKEAKAKIEELEGQLSELLEDIEDLLEALEEE 211

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +E ++ EE +EE+EE + E+E E  EE   E EEE+E  EE 
Sbjct: 212 LKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEEL 254

Length = 908

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

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 27/77 (35%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 587 RIENIIQLIRR-GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            +E +++ ++   ER E+ EE+ E+ E E EE  EE+ E  +  EE  +E EE  EE E+
Sbjct: 316 ELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEK 375

Query: 646 EEEEEEEVRGGGKEEIS 662
           E E+  E     +E I 
Sbjct: 376 ELEKALERLKQLEEAIQ 392

Length = 908

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

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 3/92 (3%)

Query: 564 KLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEE---EEEEEEE 620
           KL   R      +  + ++     +E + QL    +  +EE  E     E   EE EE E
Sbjct: 357 KLLEERLKELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEELE 416

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +E EE++ E EE EEE ++ EE+  + E +E 
Sbjct: 417 KELEELERELEELEEEIKKLEEQINQLESKEL 448

Length = 908

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

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 27/66 (40%), Positives = 32/66 (48%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R+  I  L     +  EEE  E E   EE EE+ E  EE++ E EE EEE E      EE
Sbjct: 257 RLLEIESLELEALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEE 316

Query: 647 EEEEEE 652
            EE  E
Sbjct: 317 LEELLE 322

Length = 908

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 18/52 (34%), Positives = 22/52 (42%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E E++  E   E   E++  E      EE    EEEE EE   EE   EE  
Sbjct: 134 EAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAEEAPAEEAPAEESA 185

Length = 186

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

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 15/59 (25%), Positives = 33/59 (55%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           +E+  E+E E+ +E  E+ E  +   ++  EE+ +EE+   E+ +  +EE  +   +E+
Sbjct: 178 KEKASEQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIKEELAKEPVEEQ 236

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

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 17/54 (31%), Positives = 31/54 (57%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E+E E+ +E  E+ E  + E ++  EE  +EE+   E+ +  +EE  +E  EE+
Sbjct: 183 EQENEDSKEPVEKAERTKAETDDVTEEDYDEEDNPVEDSKAIKEELAKEPVEEQ 236

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

 Score = 40.7 bits (95), Expect = 0.001
 Identities = 16/62 (25%), Positives = 32/62 (51%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGG 657
           G+  EE E+    EE   E+ +++ +E+  E+E E+ +E  E+ E  + E ++       
Sbjct: 153 GKVHEETEDSYHVEETASEQYKQDMKEKASEQENEDSKEPVEKAERTKAETDDVTEEDYD 212

Query: 658 KE 659
           +E
Sbjct: 213 EE 214

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|234017 TIGR02794, tolA_full, TolA protein

 Score = 41.4 bits (97), Expect = 0.001
 Identities = 11/55 (20%), Positives = 33/55 (60%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++++   ++E+E +++ E++ EE E+ +  E+  ++E E+    E+  ++ E+  
Sbjct: 57  QQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAEQAA 111

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
                  E   E +E EEE +EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 38.5 bits (90), Expect = 0.001
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
                  E   E +  EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 14/27 (51%), Positives = 22/27 (81%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEE 625
           E EEEEE E+ E E+EE+EEE+++++ 
Sbjct: 47  EWEEEEEGEDLESEDEEDEEEDDDDDM 73

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

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

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 21/81 (25%), Positives = 39/81 (48%)

Query: 581 DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
             +   RI  I   + + E E    E    E E++      E+E +++E +E +E+  + 
Sbjct: 786 ARLSHSRIPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDL 845

Query: 641 EEEEEEEEEEEEVRGGGKEEI 661
           +E+ +  E+E E   G KEE+
Sbjct: 846 KEQIKSIEKEIENLNGKKEEL 866

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

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 17/63 (26%), Positives = 31/63 (49%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            IEN+       E E EE E    + E    + ++E +E++ +  E E + EE E + E+
Sbjct: 855 EIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEK 914

Query: 647 EEE 649
           + +
Sbjct: 915 KRK 917

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|217502 pfam03343, SART-1, SART-1 family

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 18/54 (33%), Positives = 36/54 (66%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++E  EE+ E ++E  EE  + EE++E +E+E+ + + E    + +EE+EEE++
Sbjct: 404 QKEPLEEKPENKDESVEEISDAEEDDEDEEDEDGDGDVEMSAVDNDEEKEEEDK 457

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.4 bits (100), Expect = 0.001
 Identities = 29/63 (46%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 591 IIQLIRRGER-EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           I +L  R ER E+  E  ++E EE  ++ EE E +E+Q E EE EEE EE +EE E  EE
Sbjct: 402 IERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEEELEELQEELERLEE 461

Query: 650 EEE 652
             E
Sbjct: 462 ALE 464

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 19/66 (28%), Positives = 30/66 (45%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E  ++ +R+   E   +     ++    E E E+ EE   +  +E  E E E EE EE
Sbjct: 709 ELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEE 768

Query: 647 EEEEEE 652
             EE E
Sbjct: 769 RLEEAE 774

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|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 17/46 (36%), Positives = 29/46 (63%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
             E++EEEEEEEE+E   + +    E EE+    ++E+ E++EE+ 
Sbjct: 178 RREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDN 223

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
             E++EEEEEEEE+E   +      E EE+    ++E+ E++EE+ +       G 
Sbjct: 178 RREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPSPKSGS 233

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 12/40 (30%), Positives = 14/40 (35%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           EEE+                 E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 12/40 (30%), Positives = 15/40 (37%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           EEE+               + E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 29/81 (35%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEV-----------------------------QEEEE 631
                 E    E E E E EEE E+                              Q+E+ 
Sbjct: 130 CSVNMTECTGPEPEPEPEPEEEPEKKSGMGPLLLVLAVALIGGGAYYYFKFYKPKQQEKG 189

Query: 632 EEEEEEEEEEEEEEEEEEEEE 652
             +++ +E +  +E+EEE++E
Sbjct: 190 APDDDLDEYDYGDEDEEEDDE 210

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 12/40 (30%), Positives = 14/40 (35%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           EEE+                 E    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 31/83 (37%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEE-------------------------------EVQEE 629
                E    E E E E EEE E+                               + +  
Sbjct: 131 SVNMTECTGPEPEPEPEPEEEPEKKSGMGPLLLVLAVALIGGGAYYYFKFYKPKQQEKGA 190

Query: 630 EEEEEEEEEEEEEEEEEEEEEEE 652
            +++ +E +  +E+EEE++E   
Sbjct: 191 PDDDLDEYDYGDEDEEEDDEPPW 213

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

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

 Score = 41.5 bits (97), Expect = 0.001
 Identities = 15/61 (24%), Positives = 40/61 (65%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
           + E++ +++EE+  EE + ++  E+E  ++ E+E  + +E++++ EE E++ ++    +E
Sbjct: 76  KGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQE 135

Query: 660 E 660
           E
Sbjct: 136 E 136

Length = 387

>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 5/85 (5%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
              E++ ++    E+ E E    EE + EEE E+ E+E +  +   +++E E      +E
Sbjct: 358 VPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDENDHSKRICDDDELENHFRAADE 417

Query: 661 ISLHFYVLY-----VLSKGKIAGLF 680
            + H  V +      +++G   G+F
Sbjct: 418 KNSHLVVGFRNERSYVTRGNSIGVF 442

Length = 776

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

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 14/60 (23%), Positives = 31/60 (51%)

Query: 601  EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            +E+ ++++  +  E++E+  E+  E   +E EE  E+  + +EE E+ E  E +      
Sbjct: 4044 DEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDNHP 4103

Length = 4600

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 15/47 (31%), Positives = 26/47 (55%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
             EE++  +E+  EE E E E++ + +E E E+E +E +    E E 
Sbjct: 2   SNEEQKTPQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEA 48

Length = 193

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 19/46 (41%), Positives = 24/46 (52%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
           I+ + + ++       E   EEEEEEEEEEEEE  E E   EE   
Sbjct: 383 IDELREFLKEKGHPVVERWAEEEEEEEEEEEEEAAEAEAPMEEPVP 428

Length = 470

>gnl|CDD|221429 pfam12118, SprA-related, SprA-related family

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 16/56 (28%), Positives = 35/56 (62%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            +++  E  +EE   EEE E+++ E   Q  ++++E++++EE++  E +  + EVR
Sbjct: 69  LQKQASESNDEEVVGEEEPEKDQAEAGKQLSQKQQEQQQQEEKQVRELKARDREVR 124

This protein is found in bacteria. Proteins in this family are typically between 234 to 465 amino acids in length. There is a conserved GEV sequence motif.Most members are annotated as being SprA-related. Length = 261

>gnl|CDD|220112 pfam09110, HAND, HAND

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 17/45 (37%), Positives = 29/45 (64%), Gaps = 2/45 (4%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEE--EEEEEEEEEEEEE 651
           ++  + +EE+EEE E + + E+E+ +  E   EEEEEE++   EE
Sbjct: 64  DDVGDGDEEDEEEREAKRKLEQEKIDNAEPLTEEEEEEKQRLLEE 108

The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein. Length = 109

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 20/46 (43%), Positives = 23/46 (50%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EE + EE EEE E  E EE  E   EE  E+ E E   E  +E E
Sbjct: 2   SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 19/68 (27%), Positives = 32/68 (47%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           E EE EEE + E E   E +  ++ QE   EE+     EE+E+ ++ E+ +     KE+ 
Sbjct: 231 ETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEILKEKK 290

Query: 662 SLHFYVLY 669
               +   
Sbjct: 291 DEELFWFE 298

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|184536 PRK14145, PRK14145, heat shock protein GrpE; Provisional

 Score = 40.3 bits (94), Expect = 0.001
 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 5/59 (8%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE-----EEEEEEEEE 652
           E+E  +EEE++       E+ E   E+ Q ++ + +++  +E EE     +++E E +E
Sbjct: 5   EKEINKEEEKDVNNLSSNEQMEGPPEDEQAQQNQPQQQTVDEIEELKQKLQQKEVEAQE 63

Length = 196

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 14/47 (29%), Positives = 22/47 (46%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
              +  EEE        E  ++  E+EEE+++ E+   EE   E VR
Sbjct: 260 APPQPPEEEPPPPPPPPEDDDDPPEDEEEQDDAEDRALEEIVLEAVR 306

Length = 584

>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 11/40 (27%), Positives = 19/40 (47%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
              +  EEE        E+  +  E+EEE+++ E+   EE
Sbjct: 260 APPQPPEEEPPPPPPPPEDDDDPPEDEEEQDDAEDRALEE 299

Length = 584

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 42.3 bits (100), Expect = 0.001
 Identities = 12/53 (22%), Positives = 29/53 (54%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E+   ++E+++    E +    +E+ + Q+E +    EE+  +E E+EE  ++
Sbjct: 663 EKARTQDEQQQAPRRERQRRRNDEKRQAQQEAKALNVEEQSVQETEQEERVQQ 715

Length = 1068

>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740)

 Score = 41.6 bits (97), Expect = 0.001
 Identities = 24/68 (35%), Positives = 36/68 (52%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           D++ + S      I    R     +   EEEEE E EE+EE  E+E  +  +E+ EEEEE
Sbjct: 113 DEENLPSSIAPPEIDPEPRKPIVPDLVLEEEEEVEMEEDEEYYEKEPGKVVDEKSEEEEE 172

Query: 639 EEEEEEEE 646
           EE +  ++
Sbjct: 173 EELKTMKD 180

This family consists of several uncharacterized plant proteins of unknown function. Length = 565

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 40.9 bits (97), Expect = 0.001
 Identities = 21/33 (63%), Positives = 23/33 (69%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +    E  +EEEEE EEEEEEEEEEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 40.9 bits (97), Expect = 0.001
 Identities = 22/34 (64%), Positives = 23/34 (67%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
           R+    E  EEEEEE EEEEEEEEEE  EE E E
Sbjct: 225 RQGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 40.9 bits (97), Expect = 0.001
 Identities = 22/33 (66%), Positives = 23/33 (69%)

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +    E  EEEEEE EEEEEEEEEEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 601 EEEEEEEEEEEEEEEEEEEEE 621
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 602 EEEEEEEEEEEEEEEEEEEEE 622
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 603 EEEEEEEEEEEEEEEEEEEEE 623
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 604 EEEEEEEEEEEEEEEEEEEEE 624
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 605 EEEEEEEEEEEEEEEEEEEEE 625
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 628 EEEEEEEEEEEEEEEEEEEEE 648
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 629 EEEEEEEEEEEEEEEEEEEEE 649
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 630 EEEEEEEEEEEEEEEEEEEEE 650
                 EEE++EEEEEEEE++
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           ++E + EEE+ EEEEE  + E ++E E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 17/40 (42%), Positives = 25/40 (62%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           ++E + EEE+ EEEEE  + EE +E E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family

 Score = 40.7 bits (96), Expect = 0.001
 Identities = 14/53 (26%), Positives = 32/53 (60%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +   E+ ++E EE ++   E + ++++ ++  EE EE  E  EE ++ E+E++
Sbjct: 68  KTRLEKLKKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELK 120

This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Length = 188

>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812)

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 13/37 (35%), Positives = 24/37 (64%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           +E  E +   +EE++ +EEE + Q EE +E E E+++
Sbjct: 90  DERAEAQRARDEEKKLDEEEAKRQHEEAKEREREKKK 126

This is a family of fungal proteins whose function is not known. Length = 126

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 11/46 (23%), Positives = 21/46 (45%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             +  +  E+ + +E   EV +E+   EEE  + +  EEE   +  
Sbjct: 2   TLKVHDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA 47

Length = 325

>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional

 Score = 39.1 bits (91), Expect = 0.001
 Identities = 16/45 (35%), Positives = 24/45 (53%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            E+E  E E EE  EE+ E    +EV+    E E++EE+E  +  
Sbjct: 9   YEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRP 53

Length = 130

>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 15/57 (26%), Positives = 29/57 (50%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            E+  E E  + E  E E+E   E+++E ++  E +E   +E  ++  E+ E E  +
Sbjct: 202 KEKAIEAERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREK 258

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|227504 COG5177, COG5177, Uncharacterized conserved protein [Function unknown]

 Score = 42.0 bits (98), Expect = 0.001
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 7/69 (10%)

Query: 599 EREEEEEEEEEEEEE-----EEEEEEEEEEEEVQEEEEE--EEEEEEEEEEEEEEEEEEE 651
           E EEEE+ +  +EE      ++++ +E + EEV  +EE   ++ E  EE   EEEE +  
Sbjct: 394 EDEEEEDGQCNDEESTMSAIDDDDPKENDNEEVAGDEESAIDDNEGFEELSPEEEERQLR 453

Query: 652 EVRGGGKEE 660
           E R   KE+
Sbjct: 454 EFRDMEKED 462

Length = 769

>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

 Score = 42.0 bits (98), Expect = 0.001
 Identities = 15/54 (27%), Positives = 28/54 (51%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
                  EE +   EE+     E+V+ E    EE+++++EE + ++E E E +G
Sbjct: 459 RASLMTMEETQRHSEEDLVNRFEDVRYEHVAGEEDDDDDEELQAQKELELEAQG 512

Length = 591

>gnl|CDD|221179 pfam11711, Tim54, Inner membrane protein import complex subunit Tim54

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 17/55 (30%), Positives = 20/55 (36%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           G  +  E  E   +E   E E E         E  EE  E   EE E+  EEE  
Sbjct: 193 GPLDPPEPPEPTVDEAAPETEVEATPAAESPAEPAEETAETTPEETEDAPEEENN 247

Mitochondrial function depends on the import of hundreds of different proteins synthesised in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targetting information, into the inner membrane. Length = 377

>gnl|CDD|221179 pfam11711, Tim54, Inner membrane protein import complex subunit Tim54

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 19/62 (30%), Positives = 23/62 (37%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E  E   +E   E E E     E   +  EE  E   EE E+  EEE  +       K  
Sbjct: 199 EPPEPTVDEAAPETEVEATPAAESPAEPAEETAETTPEETEDAPEEENNKPVKPPVPKPY 258

Query: 661 IS 662
           IS
Sbjct: 259 IS 260

Mitochondrial function depends on the import of hundreds of different proteins synthesised in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targetting information, into the inner membrane. Length = 377

>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex subunit beta; Reviewed

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 27/63 (42%), Positives = 38/63 (60%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E + + I    R++   EE+ ++ EE ++  +E+E  V E    EEEEEEEEEEEEEEE 
Sbjct: 361 ERVKEFIPEELRDKIATEEDVKDIEELKKFLKEKEHPVVERWAAEEEEEEEEEEEEEEEP 420

Query: 649 EEE 651
             E
Sbjct: 421 VAE 423

Length = 463

>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex subunit beta; Reviewed

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 19/32 (59%), Positives = 20/32 (62%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE 630
           ER   EEEEEEEEEEEEEEE   E   +   E
Sbjct: 400 ERWAAEEEEEEEEEEEEEEEPVAEVMMMPAPE 431

Length = 463

>gnl|CDD|184538 PRK14149, PRK14149, heat shock protein GrpE; Provisional

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 4/58 (6%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE----EEEEEEVR 654
           E  +E +   ++E E EE+    +E Q EE++E  E+E E +E+ E    E  E+ +R
Sbjct: 4   EHNQEHDHLSQKEPESEEKACACKEQQGEEKQEASEKEGEIKEDFELKYKEMHEKYLR 61

Length = 191

>gnl|CDD|218576 pfam05395, DARPP-32, Protein phosphatase inhibitor 1/DARPP-32

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 14/51 (27%), Positives = 23/51 (45%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
              EE +  EEE+E +  +E      E E  E ++ EE      ++ + EV
Sbjct: 95  GSLEENQASEEEDELDSPDELGYPTGETESTEAQDSEEPGSCPTQDAQSEV 145

This family consists of several mammalian protein phosphatase inhibitor 1 (IPP-1) and dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) proteins. Protein phosphatase inhibitor-1 is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. It has been demonstrated that DARPP-32, if phosphorylated, can inhibit protein-phosphatase-1. DARPP-32 has a key role in many neurotransmitter pathways throughout the brain and has been shown to be involved in controlling receptors, ion channels and other physiological factors including the brain's response to drugs of abuse, such as cocaine, opiates and nicotine. DARPP-32 is reciprocally regulated by the two neurotransmitters that are most often implicated in schizophrenia - dopamine and glutamate. Dopamine activates DARPP-32 through the D1 receptor pathway and disables DARPP-32 through the D2 receptor. Glutamate, acting through the N-methyl-d-aspartate receptor, renders DARPP-32 inactive. A mutant form of DARPP-32 has been linked with gastric cancers. Length = 170

>gnl|CDD|218576 pfam05395, DARPP-32, Protein phosphatase inhibitor 1/DARPP-32

 Score = 39.9 bits (93), Expect = 0.001
 Identities = 13/52 (25%), Positives = 22/52 (42%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
              EE +  EEE+E +  +E      E E  E ++ EE      ++ +   G
Sbjct: 95  GSLEENQASEEEDELDSPDELGYPTGETESTEAQDSEEPGSCPTQDAQSEVG 146

This family consists of several mammalian protein phosphatase inhibitor 1 (IPP-1) and dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) proteins. Protein phosphatase inhibitor-1 is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. It has been demonstrated that DARPP-32, if phosphorylated, can inhibit protein-phosphatase-1. DARPP-32 has a key role in many neurotransmitter pathways throughout the brain and has been shown to be involved in controlling receptors, ion channels and other physiological factors including the brain's response to drugs of abuse, such as cocaine, opiates and nicotine. DARPP-32 is reciprocally regulated by the two neurotransmitters that are most often implicated in schizophrenia - dopamine and glutamate. Dopamine activates DARPP-32 through the D1 receptor pathway and disables DARPP-32 through the D2 receptor. Glutamate, acting through the N-methyl-d-aspartate receptor, renders DARPP-32 inactive. A mutant form of DARPP-32 has been linked with gastric cancers. Length = 170

>gnl|CDD|204032 pfam08703, PLC-beta_C, PLC-beta C terminal

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 25/104 (24%), Positives = 52/104 (50%), Gaps = 9/104 (8%)

Query: 562 TNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEE 621
             +++  +   K  +  ++ EI    I+ ++Q I+R       EE ++  +E+ EE++ E
Sbjct: 77  LERIQEAKTKEKHAQEREKTEINRSHIQEVVQSIKR------LEEAQKRRQEKLEEKQAE 130

Query: 622 EEEEVQEEE---EEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
             +++QEEE   + E   E E + +   +E +E ++   KE  S
Sbjct: 131 ILQQIQEEEPKLQAEATAEYEAKLKRLPQEVQEYLQECRKEGSS 174

This domain corresponds to the alpha helical C terminal domain of phospholipase C beta. Length = 181

>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 12/80 (15%)

Query: 36  DLLII--GRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPA 93
           D+++   G+S+ L  LLQR Q        WS  +G   +  P KS  +     +  R   
Sbjct: 150 DIVLFSEGKSRKLQELLQRLQE-------WSKESGLKIN--PSKSKVMLIGN-KKKRLKD 199

Query: 94  LSYNGIQLKFVTSTKFLGLT 113
           ++ NG  ++ V + K+LG+T
Sbjct: 200 ITLNGTPIEAVETFKYLGVT 219

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities. Length = 220

>gnl|CDD|227615 COG5296, COG5296, Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]

 Score = 41.6 bits (97), Expect = 0.001
 Identities = 17/63 (26%), Positives = 30/63 (47%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +++L +  EREE    E   E +  ++ +E EE E   +EE      EE  E+    ++ 
Sbjct: 148 LLELKKTREREERLYSERHIELQRFKDYKELEESEQGLQEEYTPSYAEEAVEDISRTDDF 207

Query: 651 EEV 653
            E+
Sbjct: 208 AEL 210

Length = 521

>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 22/57 (38%), Positives = 35/57 (61%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            L++   R++E+ E  + + EE EE  EE+ E V+E +E++EE E   E  EEE +E
Sbjct: 338 NLVQTALRQQEKIERYQADLEELEERLEEQNEVVEEADEQQEENEARAEAAEEEVDE 394

Length = 1486

>gnl|CDD|218328 pfam04921, XAP5, XAP5, circadian clock regulator

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 26/87 (29%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEE-----------------------EEEEEEEEE 638
            +++EEE+E+E E+E++  +E  E  E                          EE+E E 
Sbjct: 14  GDDDEEEDEDEGEDEKKVPKESSEPDEANVNPNKKKIGKNPSVDTSFLPDKAREEKEAEL 73

Query: 639 EEEEEEEEEEEEEEVRGGGKEEISLHF 665
            EE  EE  +++E V+    EEI + F
Sbjct: 74  REELREEFLKKQEAVKE---EEIEITF 97

This protein is found in a wide range of eukaryotes. It is a nuclear protein and is suggested to be DNA binding. In plants, this family is essential for correct circadian clock functioning by acting as a light-quality regulator coordinating the activities of blue and red light signalling pathways during plant growth - inhibiting growth in red light but promoting growth in blue light. Length = 233

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

 Score = 40.7 bits (96), Expect = 0.002
 Identities = 18/62 (29%), Positives = 37/62 (59%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EEE E     ++  ++ ++  E+ E + EEE++E++++    +++EEEEEEE     +E+
Sbjct: 396 EEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455

Query: 661 IS 662
             
Sbjct: 456 EE 457

Length = 482

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

 Score = 40.7 bits (96), Expect = 0.002
 Identities = 17/59 (28%), Positives = 36/59 (61%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            EEE E     ++  ++ ++  E+ +++ EEE++E++++    +++EEEEE     KEE
Sbjct: 395 TEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEE 453

Length = 482

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 25/85 (29%), Positives = 36/85 (42%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           +   + EI +   ++  +        E E E E  E+E E E  EE EE   E E E E 
Sbjct: 692 EQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEG 751

Query: 636 EEEEEEEEEEEEEEEEEVRGGGKEE 660
           + E E E + +E E E       +E
Sbjct: 752 KHEVETEGDRKETEHEGETEAEGKE 776

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 24/44 (54%), Positives = 29/44 (65%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
            +   E  E EEEEEEEE  E +EE+E EEEE +E EE  +EEE
Sbjct: 161 YVAEVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 25/41 (60%), Positives = 29/41 (70%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           E E  E EEEEEEEE  E +EE+E EE +EEE EE  +EEE
Sbjct: 164 EVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 26/41 (63%), Positives = 28/41 (68%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           E E  E EEEEEEEE  E +E  E EEEEEEE EE  +EEE
Sbjct: 164 EVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 41.0 bits (97), Expect = 0.002
 Identities = 17/43 (39%), Positives = 19/43 (44%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE 630
              + Q I   E     E EEE EE E   EEE E +   EEE
Sbjct: 290 RRELEQQIEEKEERRAAEREEELEEGERLREEEAERQARIEEE 332

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|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 41.7 bits (98), Expect = 0.002
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 6/69 (8%)

Query: 599 EREEEEEEEEEE------EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +  EEE+EEE E        + +++E   E+E+  EE++EE E   + E  + E+   +E
Sbjct: 8   QANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEISKREKARLKE 67

Query: 653 VRGGGKEEI 661
           ++   K+EI
Sbjct: 68  LKKQKKQEI 76

Length = 1033

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 40.8 bits (95), Expect = 0.002
 Identities = 18/55 (32%), Positives = 30/55 (54%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E  +EE + +  +E  EE+EE++E EE +   E   +E  E E+  EE+  + E
Sbjct: 304 AEAHKEEVQSDRPDEIGEEKEEDDENEENERHTELLADELNELEKGIEEKRRQME 358

Length = 392

>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription]

 Score = 40.5 bits (94), Expect = 0.002
 Identities = 18/51 (35%), Positives = 28/51 (54%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           EE + +  +E  EE+EE++E EE E   E   +E  E E+  EE+  + E 
Sbjct: 309 EEVQSDRPDEIGEEKEEDDENEENERHTELLADELNELEKGIEEKRRQMES 359

Length = 392

>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II)

 Score = 40.8 bits (95), Expect = 0.002
 Identities = 28/107 (26%), Positives = 37/107 (34%), Gaps = 49/107 (45%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE---------------- 638
           ++ G    EE  + +  EEE EEE   EEE  ++ +  E+EE E                
Sbjct: 44  VQSGSDSSEENGDGDSSEEEGEEETSNEEENNEDSDGNEDEEAEAENTTLSTVTLGYGGD 103

Query: 639 ---------------------------------EEEEEEEEEEEEEE 652
                                            E+EEEEEEEEEEE 
Sbjct: 104 ATPGTGNIGLAALQLPKKAGNAGKKATKEDESDEDEEEEEEEEEEEA 150

Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralised connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. Length = 291

>gnl|CDD|218303 pfam04874, Mak16, Mak16 protein C-terminal region

 Score = 37.9 bits (88), Expect = 0.002
 Identities = 20/42 (47%), Positives = 26/42 (61%)

Query: 621 EEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEIS 662
           ++  E +E EE +EEEEEEEEEE+E E E        +EEI 
Sbjct: 52  KKALEAEESEENDEEEEEEEEEEDEGEIEYVSDDEELEEEIE 93

The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. Length = 97

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

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 26/68 (38%), Positives = 36/68 (52%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E + + +R  E E  E +EE E+  E  EE E + E ++ E  E EEE EEE E+  E
Sbjct: 885 EKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLE 944

Query: 647 EEEEEEVR 654
            E E E+ 
Sbjct: 945 TELEREIE 952

Length = 1163

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

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 27/66 (40%), Positives = 38/66 (57%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E +   +   E E EE EEE EE +E  EE EEE E ++E   + +EE EE EE+ + 
Sbjct: 731 ELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQA 790

Query: 647 EEEEEE 652
            +EE E
Sbjct: 791 LQEELE 796

Length = 1163

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

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 30/62 (48%), Positives = 38/62 (61%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           EEE    EEE EE +EE EE E+E++E + E EE  EE EE +EE  E +E     + EI
Sbjct: 245 EEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEELEGEI 304

Query: 662 SL 663
           SL
Sbjct: 305 SL 306

Length = 1163

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

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 28/76 (36%), Positives = 42/76 (55%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +  + + + + +   EE EEE EE EEE EE +E  EE++EE E  EE   + +EE EE
Sbjct: 724 ELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEE 783

Query: 647 EEEEEEVRGGGKEEIS 662
            EE+ +      EE+ 
Sbjct: 784 LEEKRQALQEELEELE 799

Length = 1163

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

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 22/56 (39%), Positives = 25/56 (44%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           E  +EE EE+     EE EE  E   E   E E E  E   E EE + E E  E R
Sbjct: 357 EEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEER 412

Length = 1163

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

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 572 IKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEE 631
            +  +  +  E+ +  +  I   +   +RE E  EE  E   E  E+ +EE +E++ E E
Sbjct: 378 FEALR-EELAELEA-ELAEIRNELEELKREIESLEERLERLSERLEDLKEELKELEAELE 435

Query: 632 EEEEEEEEEEEEEEEEEEEEE 652
           E + E EE  EE EE EE+ E
Sbjct: 436 ELQTELEELNEELEELEEQLE 456

Length = 1163

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

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 22/70 (31%), Positives = 30/70 (42%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +L    E  EE  E   EE  E E E  E   E++E + E E  EE  E   E  E+ +E
Sbjct: 366 KLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKE 425

Query: 653 VRGGGKEEIS 662
                + E+ 
Sbjct: 426 ELKELEAELE 435

Length = 1163

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

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 19/59 (32%), Positives = 36/59 (61%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            +E+E ++ +++E  E EE +EEE +    E++E++ + E+E+EE EEE E       +
Sbjct: 46  ADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEESSD 104

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 = 39.7 bits (93), Expect = 0.002
 Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 9/69 (13%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQE---------EEEEEEEEEEEEEEEEEEEEEEE 651
           ++   +E+E ++ +++E  E EE + +E         E++ + E+E+EE EEE EEE+EE
Sbjct: 42  DQAAADEQEAKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENEEEDEE 101

Query: 652 EVRGGGKEE 660
                 KE 
Sbjct: 102 SSDENEKET 110

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|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa)

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 17/78 (21%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEE-----EEVQEE------------EEEEEEEEEEEEE 642
           R+++  ++ +EE +E+E EE  EE     EE ++E            +  EEE ++EE+ 
Sbjct: 30  RKQQRRKKAQEEAKEKEREERIEERKRIREERKQELEKQLKERKEALKLLEEENDDEEDA 89

Query: 643 EEEEEEEEEEVRGGGKEE 660
           E E+ E+ E+    G  E
Sbjct: 90  ETEDTEDVEDDEWEGFPE 107

Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. Length = 134

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

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 13/72 (18%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
             EI +         I + E  EE EEE+ EEE    ++ ++ ++   ++   ++++ + 
Sbjct: 305 SPEIPAK------PEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDS 358

Query: 640 EEEEEEEEEEEE 651
            ++ ++ + + E
Sbjct: 359 GDDSDDSDIDGE 370

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

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

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 17/72 (23%), Positives = 32/72 (44%)

Query: 579  DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
            ++++    + E   +  R    +EE          E EE+EE   ++  ++E  EEE++E
Sbjct: 948  EKEKEEDNKEEEEERNKRLLLAKEELGNVNLMAIAEFEEKEERYNKDELKKERLEEEKKE 1007

Query: 639  EEEEEEEEEEEE 650
               E  EE  + 
Sbjct: 1008 LLREIIEETCQR 1019

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

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

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 24/93 (25%), Positives = 46/93 (49%)

Query: 560 PNTNKLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEE 619
               ++K     IK      + E      + + +   +   E +  E++ +E+EEEEE+ 
Sbjct: 697 RRQEEIKKKEQRIKEELKKLKLEKEELLADKVQEAQDKINEELKLLEQKIKEKEEEEEKS 756

Query: 620 EEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             ++EE +EE+ E   +E+E  EEEE+ E+ + 
Sbjct: 757 RLKKEEEEEEKSELSLKEKELAEEEEKTEKLKV 789

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

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

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 26/65 (40%), Positives = 38/65 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E+EE EE E+E +E E + E EEEEEE  E+ +E+ E+ EEE   +++ E E        
Sbjct: 334 EKEEIEELEKELKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLSSAAKL 393

Query: 659 EEISL 663
           +E  L
Sbjct: 394 KEEEL 398

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|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 21/45 (46%), Positives = 28/45 (62%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           ++E++ EE + +E EE E+ EEEE EEEE EEE E E       E
Sbjct: 3   DKEQKTEEPDAEETEEAEKSEEEEAEEEEPEEENELEEEQQEIAE 47

Length = 193

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 10/51 (19%), Positives = 33/51 (64%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +E +EE    EE+ ++++++  +   +  +++   +++ +EE+ +EE++E+
Sbjct: 74  DEIDEEIIPLEEKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEEDDED 124

Length = 129

>gnl|CDD|235033 PRK02363, PRK02363, DNA-directed RNA polymerase subunit delta; Reviewed

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 11/52 (21%), Positives = 34/52 (65%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +E +EE    EE+ ++++++  + +    +++   +++ +EE+ +EE++E+E
Sbjct: 74  DEIDEEIIPLEEKFDKKKKKFMDGDDDIIDDDILPDDDFDEEDLDEEDDEDE 125

Length = 129

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

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 14/67 (20%), Positives = 34/67 (50%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
            + + ++ EE  + EEE++ E    +   +   +++   +++E  EEE++ +   E V+G
Sbjct: 147 EKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKG 206

Query: 656 GGKEEIS 662
             +E   
Sbjct: 207 KPEEPDV 213

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|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 16/70 (22%), Positives = 41/70 (58%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            ++ + +G  +    + +  +E + E  +EEE+E+ Q +EE+++++E+ +EE ++ + +E
Sbjct: 76  AVKRVEKGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKE 135

Query: 651 EEVRGGGKEE 660
           E       +E
Sbjct: 136 EAKEKRPPKE 145

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|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 12/53 (22%), Positives = 40/53 (75%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E  EEE+++EE+++++++E+E++++++  E++E+E++++    ++   ++  E
Sbjct: 48  EAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGNE 100

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 30/111 (27%), Positives = 53/111 (47%), Gaps = 16/111 (14%)

Query: 557 DNVPNTNK--LKTIRPSIKVWKTSDQDEIGSPRIEN---IIQLIRRGEREEEEEEEEEEE 611
           D  P++ K  +   R  I+     D D + S  I++     +++R   R  E  EE  ++
Sbjct: 148 DAPPHSAKALVDLWRNDIEAKAGKDLDRL-SAAIDDQQAFARVVREMLRSMELAEEMGDD 206

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE----------EEEEEEEEEE 652
            E E+EE+ ++++  + E+EE+ E E E +E          + E E  EEE
Sbjct: 207 TESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEE 257

This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin]. Length = 600

>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            +    +EEEEE  E   +E  E   E++  +E +EE +EEE+ R
Sbjct: 15  PKPPSPKEEEEEALELAIQEAHENALEKKLLDELDEELDEEEDDR 59

It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Length = 192

>gnl|CDD|220102 pfam09073, BUD22, BUD22

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 18/77 (23%), Positives = 45/77 (58%), Gaps = 2/77 (2%)

Query: 588 IENIIQLIR--RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           +E+I++ +    G   + ++ + +++ ++ +++E +E  +  +EEE E E+E + EE  E
Sbjct: 129 LESIMEGLDKILGIETKAKKGKAKKKTKKSKKKEAKESSDKDDEEESESEDESKSEESAE 188

Query: 646 EEEEEEEVRGGGKEEIS 662
           ++ ++EE      E+ S
Sbjct: 189 DDSDDEEEEDSDSEDYS 205

BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. Length = 424

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

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 23/75 (30%), Positives = 43/75 (57%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           R+  + + I   E   +E EE+EE  EE +++ +E E+ ++E EE  E  EE + ++EE 
Sbjct: 315 RLSRLEEEINGIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEEL 374

Query: 647 EEEEEEVRGGGKEEI 661
           E  ++ + G   E++
Sbjct: 375 ERLKKRLTGLTPEKL 389

Length = 880

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 19/55 (34%), Positives = 32/55 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E+ E+  +++ +E +    E  + E EV+   EEE  EE E+E E E E+EE+ +
Sbjct: 187 EQHEQPADDDPDEWKISASEPFQLESEVEASPEEENYEEYEDETELEVEDEEKAL 241

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 20/54 (37%), Positives = 27/54 (50%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +    + E   E+EEEEE    E E   QEE   EEE  +E + E E  E+ E+
Sbjct: 138 QENNLDAEPAREDEEEEESFSAEFEHPAQEETAGEEERTDEPKVEHEAHEQHEQ 191

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

>gnl|CDD|234055 TIGR02907, spore_VI_D, stage VI sporulation protein D

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 8/73 (10%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE----EEEEEEEEEEEEEEEEEVRG 655
           +EE   EEE  +E + E E  E+ E+  +++ +E +    E  + E E E   EEE    
Sbjct: 166 QEETAGEEERTDEPKVEHEAHEQHEQPADDDPDEWKISASEPFQLESEVEASPEEENYEE 225

Query: 656 GGKEEISLHFYVL 668
              E        +
Sbjct: 226 YEDE----TELEV 234

SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation [Cellular processes, Sporulation and germination]. Length = 338

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

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 3/67 (4%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E+ ++   +   + E EE  +   EE EE+ EE E E++ E +  E EE+ EE+ EE 
Sbjct: 634 ELESELE---KLNLQAELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEEL 690

Query: 647 EEEEEEV 653
           E+ EEE+
Sbjct: 691 EQLEEEL 697

Length = 908

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

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 29/85 (34%), Positives = 42/85 (49%), Gaps = 16/85 (18%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEE----------------EEEEEEEEEVQEEE 630
           ++E ++Q +   E E E EE EEE E E E                EE EE+ EE++ E 
Sbjct: 611 QLEELLQSLELSEAENELEEAEEELESELEKLNLQAELEELLQAALEELEEKVEELEAEI 670

Query: 631 EEEEEEEEEEEEEEEEEEEEEEVRG 655
             E +  E EE+ EE+ EE E++  
Sbjct: 671 RRELQRIENEEQLEEKLEELEQLEE 695

Length = 908

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

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 26/64 (40%), Positives = 35/64 (54%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           +   E  E E EE EEE   E+EE E  +E EE E+E  E EEE  E  E EE ++   +
Sbjct: 473 KELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELE 532

Query: 659 EEIS 662
           E++ 
Sbjct: 533 EKLE 536

Length = 908

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

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 13/60 (21%), Positives = 30/60 (50%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
            E+    ++EE+   +E + +E++ +  E+ ++ +E  E  +  EE E+   V     E+
Sbjct: 113 LEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGKVHEETEDSYHVEETASEQ 172

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 615 EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
                  E     +E EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
                  E   E  + EEEE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
                  E   E +E EEEE +EE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
           G         E   E +E EEEE+EEE  +E +++
Sbjct: 68  GAAAAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
                  E   E +E EEEE+EE  EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEEEEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 14/30 (46%), Positives = 22/30 (73%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEE 630
           + E EEEEE E+ E E+EE+EEE++  + +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|225887 COG3351, FlaD, Putative archaeal flagellar protein D/E [Cell motility and secretion]

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 582 EIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           +      E + +L    ER E+ +E    E+ +  EEE  E+E+V  E+ +E  +     
Sbjct: 33  QAKKSDDELVEELP---ERYEQTKENSLIEKVDSIEEEISEKEKVMSEKLKEPAQMSSTS 89

Query: 642 EEEEEEEEEEEVRGG 656
           EEEE++ + EE+   
Sbjct: 90  EEEEKKAKLEEIPED 104

Length = 214

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

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE---EEE 643
           R+E + + +   E+E E  + E +E E   EE EE+  +++E   + E         E +
Sbjct: 738 RLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQ 797

Query: 644 EEEEEEEEEVR 654
            E  + EEEV 
Sbjct: 798 AELSKLEEEVS 808

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

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 18/82 (21%), Positives = 36/82 (43%)

Query: 582 EIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E     I+ + +     + + +  E+E E    ++EE EEE EE++    + E    + +
Sbjct: 829 EYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLK 888

Query: 642 EEEEEEEEEEEVRGGGKEEISL 663
           +E +E E +        EE+  
Sbjct: 889 KERDELEAQLRELERKIEELEA 910

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|217502 pfam03343, SART-1, SART-1 family

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 18/63 (28%), Positives = 34/63 (53%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
             E+ E ++E  EE  + EE++E+EE+   + + E    + +EE+EEE++E        +
Sbjct: 408 LEEKPENKDESVEEISDAEEDDEDEEDEDGDGDVEMSAVDNDEEKEEEDKEAIPSTILEE 467

Query: 659 EEI 661
           E  
Sbjct: 468 EPT 470

SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognised by T cells. Length = 603

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.6 bits (98), Expect = 0.002
 Identities = 25/76 (32%), Positives = 33/76 (43%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E    L  R E  E      E   E+ EE+ EE  E+++    E EE EE  EE E E E
Sbjct: 817 EEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELE 876

Query: 649 EEEEVRGGGKEEISLH 664
                R   +E ++L 
Sbjct: 877 ALLNERASLEEALALL 892

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 25/74 (33%), Positives = 34/74 (45%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            I  + Q  +         E + EE E + EE E + +E+ EE  E EE+ EE +EE E 
Sbjct: 296 EISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELES 355

Query: 647 EEEEEEVRGGGKEE 660
            E E E      EE
Sbjct: 356 LEAELEELEAELEE 369

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE-EEEEEEEEEEEEEEEEE 649
           +  L  + E   E+ E    E EE EE  EE E E++    E    EE       E EE 
Sbjct: 840 LEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEEL 899

Query: 650 EEEVRGGGKE 659
            EE+R    +
Sbjct: 900 SEELRELESK 909

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|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
             E++EEEEEEEE+E   +      + EE+    ++E+ E++EE+ +     + G
Sbjct: 178 RREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPSPKSG 232

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 11/40 (27%), Positives = 13/40 (32%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           EEE+                      E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366)

 Score = 40.0 bits (94), Expect = 0.002
 Identities = 11/40 (27%), Positives = 14/40 (35%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           EEE+                 +    E E E E EEE E+
Sbjct: 115 EEEDAAAPTCSCCPVCSVNMTECTGPEPEPEPEPEEEPEK 154

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. Length = 213

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

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 14/60 (23%), Positives = 40/60 (66%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E++ +++EE+  EE + ++  E+E +++ E+E  + +E++++ EE E++ +  +   +E+
Sbjct: 78  EQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQ 137

Length = 387

>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 4/61 (6%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           E+  +E      E   E +EE EE+  E E + EE  E+ E E E E E+       +E+
Sbjct: 8   EDIRDEARARASEIRAEADEEAEEIIAEAEADAEEILEDREAEAEREIEQLRE----QEL 63

Query: 662 S 662
           S
Sbjct: 64  S 64

Length = 188

>gnl|CDD|234366 TIGR03825, FliH_bacil, flagellar assembly protein FliH

 Score = 40.6 bits (95), Expect = 0.002
 Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 585 SPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEV-----QEEEEEEEEEEEE 639
            P  E  I  +R+     E E+E  +EE+E E+  E+ E E      Q E +     E+ 
Sbjct: 12  IPAQERGIIPLRQVTDVPETEQELADEEQEFEQILEKAEAEAAQIIEQAEAQAAAIREQI 71

Query: 640 EEEEEEEEEEEEEVRGGGKEE 660
           E+E  + EEE E +    K+E
Sbjct: 72  EQERAQWEEERERLIQEAKQE 92

This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes. Length = 255

>gnl|CDD|218771 pfam05835, Synaphin, Synaphin protein

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 33/97 (34%), Positives = 42/97 (43%), Gaps = 23/97 (23%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEE--------------EEEEE 624
            +DE      E   + I+   RE EEE + +  + EEE E               EE+EE
Sbjct: 23  KEDEGDESDAEEEDEEIQEALREAEEERKAKHRKMEEEREVMRQGIRDKYGIKKKEEDEE 82

Query: 625 EVQEEEEEEE---------EEEEEEEEEEEEEEEEEE 652
           E Q   EEEE          EE   E  EE+EEEEE+
Sbjct: 83  EPQAAAEEEEGRLGRKKKTPEELAAEAGEEDEEEEEK 119

This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerisation of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles. Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin transmembrane regions that reside in opposing membranes prior to fusion. Length = 139

>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 16/65 (24%), Positives = 31/65 (47%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
              E++ ++    E+ E E    EE E +EE E+ E+E +  +   +++E E   R   +
Sbjct: 358 VPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDENDHSKRICDDDELENHFRAADE 417

Query: 659 EEISL 663
           +   L
Sbjct: 418 KNSHL 422

Length = 776

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

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 18/59 (30%), Positives = 36/59 (61%), Gaps = 2/59 (3%)

Query: 603  EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
            EE+  E E++  E+     E + V +E++ +  E+++ +E+E+EEE  ++V  G  +EI
Sbjct: 3913 EEDLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDV--GIDDEI 3969

Length = 4600

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

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 16/62 (25%), Positives = 36/62 (58%)

Query: 602  EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
            EE    +E+ ++++  +  E++E++ E+  EE  +E EE  E+  + +EE  +G   E+ 
Sbjct: 4038 EENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQ 4097

Query: 662  SL 663
            ++
Sbjct: 4098 AI 4099

Length = 4600

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

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 15/52 (28%), Positives = 30/52 (57%)

Query: 601  EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E++E+  E+  EE  +E EE  E+ V+ +EE E+ E  E++  +   + + +
Sbjct: 4057 EDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDNHPKMDAK 4108

Length = 4600

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +E+  EE E E E++EE +E E   E +E +    E E +  E + EE +
Sbjct: 9   PQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEAQLAEAQAEERD 59

Length = 193

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E   +L       EEE E  E E +E   E  + EEE +++E E  + ++E  E +E  E
Sbjct: 61  EENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQELREAQEAHE 120

Query: 649 EEEE 652
              +
Sbjct: 121 RARQ 124

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQE-EEEEEEEEEEEEEEEEEEEEEEEEV 653
                  EE+ ++EEEE +  E++ +E EEE +  EEE    EEE E  E E +E   EV
Sbjct: 32  EETALELEEKLKQEEEEAQLLEKKADELEEENRRLEEEAAASEEERERLEAEVDEATAEV 91

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 25/65 (38%), Positives = 33/65 (50%), Gaps = 6/65 (9%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE------EEEEEEE 649
            + E EE +  E++ +E EEE    EEE    EEE E  E E +E        EEE E++
Sbjct: 42  LKQEEEEAQLLEKKADELEEENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKK 101

Query: 650 EEEVR 654
           E E R
Sbjct: 102 EAETR 106

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 20/52 (38%), Positives = 27/52 (51%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           E E    EEE    EEE E  E E +E   E  + EEE E++E E  + ++E
Sbjct: 60  EEENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQE 111

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|220112 pfam09110, HAND, HAND

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 17/45 (37%), Positives = 29/45 (64%), Gaps = 2/45 (4%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEE--EEEEEEEEEEEEE 652
           ++  + +EE+EEE E  ++ E+E+ +  E   EEEEEE++   EE
Sbjct: 64  DDVGDGDEEDEEEREAKRKLEQEKIDNAEPLTEEEEEEKQRLLEE 108

The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein. Length = 109

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 20/45 (44%), Positives = 23/45 (51%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           E  + EE EEE E  E EE  EE  EE  E+ E E   E  +E E
Sbjct: 3   EEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 20/46 (43%), Positives = 23/46 (50%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            EE + EE EEE E  E E   EE  EE  E+ E E   E  +E E
Sbjct: 2   SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANERADEFE 47

Length = 177

>gnl|CDD|237628 PRK14156, PRK14156, heat shock protein GrpE; Provisional

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 19/41 (46%), Positives = 22/41 (53%)

Query: 614 EEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            EE + EE EEEV+  E EE  EE  EE  E+ E E    R
Sbjct: 2   SEEIKNEEVEEEVEATETEETVEEVVEETPEKSELELANER 42

Length = 177

>gnl|CDD|218734 pfam05758, Ycf1, Ycf1

 Score = 41.1 bits (97), Expect = 0.002
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           +E  E EE EEE + E E   E +  ++E+E   EE+     EE+E+ ++       E +
Sbjct: 227 KETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEEKEDPDKTEDLDKLEIL 286

Query: 662 SL 663
             
Sbjct: 287 KE 288

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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 13/53 (24%), Positives = 18/53 (33%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            +E  E  E   E ++E  + EE     E    E E   +       E   EV
Sbjct: 939 AQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEV 991

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 14/52 (26%), Positives = 18/52 (34%)

Query: 601  EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             E ++E  + EE  E  E    E EV  +       E   E E     E E 
Sbjct: 950  VEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEV 1001

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 14/61 (22%), Positives = 21/61 (34%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           Q+I   +    +E  E  E   E ++E  + EE  E  E    E E   +       E  
Sbjct: 929 QVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVA 988

Query: 653 V 653
            
Sbjct: 989 A 989

Length = 1068

>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 14/52 (26%), Positives = 18/52 (34%)

Query: 601  EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E ++E  + EE  E  E    E E V +       E   E E     E E  
Sbjct: 951  EPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVA 1002

Length = 1068

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

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEE-EEEEEEEEEEEEEEEEEEEEEEEVRGGGKE 659
            E+E+  E EEE+ E +  +EE +++  E +  EE  +E E +     E         + 
Sbjct: 19  TEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAASGEGGGGEEEEEEA 78

Query: 660 EISLHFYVLYVLSKGKIA 677
           +     +  Y+       
Sbjct: 79  KAEAAEFRAYLRGGDDAL 96

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

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 8/70 (11%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE--------EEEEEEEEEEEEEE 650
           E  E   E  +E  +  E+E+  E EE + E +  +EE        +  EE  +E E + 
Sbjct: 3   ELREALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKP 62

Query: 651 EEVRGGGKEE 660
                GG  E
Sbjct: 63  AASGEGGGGE 72

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|236410 PRK09202, nusA, transcription elongation factor NusA; Validated

 Score = 40.6 bits (96), Expect = 0.002
 Identities = 15/54 (27%), Positives = 22/54 (40%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             EE  E E  +EE  EE  E  +E    E   +EE+  ++    E  + E   
Sbjct: 387 PVEELLEIEGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRELAF 440

Length = 470

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 40.1 bits (95), Expect = 0.002
 Identities = 23/38 (60%), Positives = 25/38 (65%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
           I  G +    E  EEEEEE EEEEEEEEEEE +E E E
Sbjct: 221 ILEGRQGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

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

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 20/56 (35%), Positives = 25/56 (44%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EEEE  +EE + E EEE + E +E    E EEE + E       EE        E 
Sbjct: 39  EEEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEA 94

Length = 746

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

 Score = 41.0 bits (97), Expect = 0.002
 Identities = 20/60 (33%), Positives = 25/60 (41%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EEE  +EE + E EEE + E EE    E EEE + E       EE  E         +  
Sbjct: 40  EEEARKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAARPA 99

Length = 746

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 17/38 (44%), Positives = 22/38 (57%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           E + EEE+ EEEEE  + EE +E E+    EE   E E
Sbjct: 28  ELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 17/40 (42%), Positives = 25/40 (62%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           ++E + EEE+ EEEEE   +EE +E E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 17/40 (42%), Positives = 24/40 (60%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           ++E + EEE+ EEEEE  + EE +E E  +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           ++E + EEE+ EEEEE  + EE  + E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 23/61 (37%), Positives = 39/61 (63%), Gaps = 2/61 (3%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE--EE 652
           +R+  + E+ + E E+E ++ EEE+EE E+ V E E + E  E+ EEEE + EE+   +E
Sbjct: 112 MRKALQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADE 171

Query: 653 V 653
           +
Sbjct: 172 I 172

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains. Length = 189

>gnl|CDD|224581 COG1667, COG1667, Uncharacterized protein conserved in archaea [Function unknown]

 Score = 40.2 bits (94), Expect = 0.002
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEE------EEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           EEE E E EE +  E EE  E+      E E  E   +E    +   EE EE   EE ++
Sbjct: 120 EEEVENEMEELKSSEREELLEKYGIRVPEIEEIERILDEAVGSDYFSEEIEEPSREELLK 179

Query: 655 GGGKEEISLHF 665
             G +E   ++
Sbjct: 180 KLGIKEPDENW 190

Length = 254

>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812)

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 12/36 (33%), Positives = 22/36 (61%)

Query: 619 EEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +E  E +   +EE++ +EEE + + EE +E E E +
Sbjct: 90  DERAEAQRARDEEKKLDEEEAKRQHEEAKEREREKK 125

This is a family of fungal proteins whose function is not known. Length = 126

>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812)

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 12/37 (32%), Positives = 24/37 (64%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           +E  E +   +EE++ +EEE + + EE +E E E+++
Sbjct: 90  DERAEAQRARDEEKKLDEEEAKRQHEEAKEREREKKK 126

This is a family of fungal proteins whose function is not known. Length = 126

>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812)

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 12/37 (32%), Positives = 24/37 (64%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +E  E +   +EE+++ EEE + + EE +E E E+++
Sbjct: 90  DERAEAQRARDEEKKLDEEEAKRQHEEAKEREREKKK 126

This is a family of fungal proteins whose function is not known. Length = 126

>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex subunit beta; Reviewed

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           EE+ ++ EE ++  +E+E   V+    EEEEEEEEEEEEEEE   E  +
Sbjct: 378 EEDVKDIEELKKFLKEKEHPVVERWAAEEEEEEEEEEEEEEEPVAEVMM 426

Length = 463

>gnl|CDD|184538 PRK14149, PRK14149, heat shock protein GrpE; Provisional

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 15/50 (30%), Positives = 32/50 (64%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++E  +E +   ++E E EE+    +E++ EE++E  E+E E +E+ E++
Sbjct: 2   KDEHNQEHDHLSQKEPESEEKACACKEQQGEEKQEASEKEGEIKEDFELK 51

Length = 191

>gnl|CDD|184538 PRK14149, PRK14149, heat shock protein GrpE; Provisional

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 16/55 (29%), Positives = 33/55 (60%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++E  +E +   ++E E EE+    + Q+ EE++E  E+E E +E+ E + +E+ 
Sbjct: 2   KDEHNQEHDHLSQKEPESEEKACACKEQQGEEKQEASEKEGEIKEDFELKYKEMH 56

Length = 191

>gnl|CDD|218576 pfam05395, DARPP-32, Protein phosphatase inhibitor 1/DARPP-32

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 14/60 (23%), Positives = 26/60 (43%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +Q I     + +   EE +  EEE+E +  +E      E E  E ++ EE      ++ +
Sbjct: 83  LQRIVESHLQSQGSLEENQASEEEDELDSPDELGYPTGETESTEAQDSEEPGSCPTQDAQ 142

This family consists of several mammalian protein phosphatase inhibitor 1 (IPP-1) and dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) proteins. Protein phosphatase inhibitor-1 is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. It has been demonstrated that DARPP-32, if phosphorylated, can inhibit protein-phosphatase-1. DARPP-32 has a key role in many neurotransmitter pathways throughout the brain and has been shown to be involved in controlling receptors, ion channels and other physiological factors including the brain's response to drugs of abuse, such as cocaine, opiates and nicotine. DARPP-32 is reciprocally regulated by the two neurotransmitters that are most often implicated in schizophrenia - dopamine and glutamate. Dopamine activates DARPP-32 through the D1 receptor pathway and disables DARPP-32 through the D2 receptor. Glutamate, acting through the N-methyl-d-aspartate receptor, renders DARPP-32 inactive. A mutant form of DARPP-32 has been linked with gastric cancers. Length = 170

>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 7/35 (20%), Positives = 31/35 (88%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           E EE E+++++E++++++++++  +++++++E++E
Sbjct: 46  EGEEPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80

Length = 80

>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 7/35 (20%), Positives = 31/35 (88%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           E EE E+++++E+++++++++++  ++++++E++E
Sbjct: 46  EGEEPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80

Length = 80

>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional

 Score = 37.5 bits (87), Expect = 0.002
 Identities = 13/60 (21%), Positives = 39/60 (65%), Gaps = 4/60 (6%)

Query: 581 DEIGSPRIENIIQ----LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
             I   R E +I+     I R    E EE E+++++E++++++++++++  +++++E++E
Sbjct: 21  ASIMEARTEALIEEEKVEIARSVMIEGEEPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80

Length = 80

>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 11/49 (22%), Positives = 36/49 (73%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EEE+ E       E EE E+++++E  +++++++++++++++++E++E
Sbjct: 32  IEEEKVEIARSVMIEGEEPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80

Length = 80

>gnl|CDD|218637 pfam05558, DREPP, DREPP plasma membrane polypeptide

 Score = 40.0 bits (93), Expect = 0.002
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 8/60 (13%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE--------EEEEEEEEEEEEEEV 653
           EE++ EEE    E E++   +E+E+  EEE++EEE          +  E + EE   +  
Sbjct: 132 EEKKPEEEAPAAETEKKPAVKEKEIVVEEEKKEEEAVPVAAAPSTKAPETKVEETPAKAP 191

This family contains several plant plasma membrane proteins termed DREPPs as they are developmentally regulated plasma membrane polypeptides. Length = 201

>gnl|CDD|221733 pfam12720, DUF3807, Protein of unknown function (DUF3807)

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 8/81 (9%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE- 650
           I  + R    +EE E EEE E +   +      E   + +E E++   ++ +   ++E  
Sbjct: 62  IHALLRERELKEEAEAEEEGEVDASPDAGAVAGESSADRKEAEQQGAAQKRKSCRDKERK 121

Query: 651 -------EEVRGGGKEEISLH 664
                         K + SL 
Sbjct: 122 SAKDPRGGTQDVVDKSQASLD 142

This is a family of conserved fungal proteins of unknown function. Length = 169

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/24 (58%), Positives = 19/24 (79%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEE 624
           EEE+ E+EEE E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/24 (58%), Positives = 19/24 (79%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEE 625
           EEE+ E+EEE E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/24 (58%), Positives = 19/24 (79%)

Query: 628 EEEEEEEEEEEEEEEEEEEEEEEE 651
           EEE+ E+EEE E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/24 (58%), Positives = 19/24 (79%)

Query: 629 EEEEEEEEEEEEEEEEEEEEEEEE 652
           EEE+ E+EEE E+EEE EE+ E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 15/25 (60%), Positives = 19/25 (76%)

Query: 630 EEEEEEEEEEEEEEEEEEEEEEEVR 654
           EEE+ E+EEE E+EEE EE+ E  R
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVKR 46

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/24 (58%), Positives = 18/24 (75%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEE 631
           EEE+ E+EEE E+EEE E Q E +
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEVK 45

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

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

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 9/56 (16%), Positives = 43/56 (76%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             E E+ ++E EE+++ + ++++ +++  +++++++++++++ E+++E+E E+++ 
Sbjct: 68  AEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLE 123

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

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

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 8/56 (14%), Positives = 42/56 (75%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + E EE+++ + ++++ ++++++++++++ +++++ E+++E+E E++ E+  +   
Sbjct: 75  KKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLEDLTKSYS 130

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

>gnl|CDD|221620 pfam12527, DUF3727, Protein of unknown function (DUF3727)

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 19/45 (42%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
           L  RGE  E EE+E  E EEE++++E+E EEE +       E++E
Sbjct: 12  LTVRGELPEPEEDEILELEEEDDDDEDE-EEEYELLASFYHEDQE 55

This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length. Length = 100

>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 8/49 (16%), Positives = 13/49 (26%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
                E +     E    ++++   E    E      E       EEE 
Sbjct: 107 NAALAEADGGPTAEATTPKKKKAAAEAAAAEAAAPAAEAAAAAAAEEEA 155

Length = 155

>gnl|CDD|218482 pfam05178, Kri1, KRI1-like family

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 588 IENIIQLIRR--GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           IE  ++ I++  G R  +  EE+  + + + E+ +EE  ++  ++  EEE+EEE+   ++
Sbjct: 26  IEEKLEKIKKVAGLRGADLSEEDLADGDFDPEKWDEEMAKLFGDDYYEEEDEEEKPTWDD 85

Query: 646 EEEEEEEVRGGGKE 659
           +E+  + V    +E
Sbjct: 86  DEDIGDLVPDEDEE 99

The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus. Length = 99

>gnl|CDD|205480 pfam13300, DUF4078, Domain of unknown function (DUF4078)

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 18/47 (38%), Positives = 29/47 (61%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +EEE +E+ EE E+  EE E  ++E EE +E+ +   EE  ++ EE 
Sbjct: 41  DEEERKEQMEELEKAREETERERKEREERKEKRKRAIEERRKKIEER 87

This family is found from fungi to humans, but its exact function is not known. Length = 88

>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein

 Score = 39.4 bits (92), Expect = 0.002
 Identities = 12/59 (20%), Positives = 32/59 (54%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            ++ +++++E+  EEE++ E ++++ EE E   +  EE  + +E        + + E+ 
Sbjct: 65  TKKSKKKDKEKLTEEEKKPESDDDKTEENENDPDNNEESGDSQESASANSLSDIDNEDD 123

Length = 198

>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 409 ITKVYSTWSYLKLCKK-DITFMWCPSHCGIKGNEIVDVAAKN 449
            TK Y  +   K+ KK  I+F+   +H G K NE+ D  AK 
Sbjct: 91  GTKEYKEF-MDKIKKKIKISFVKVKAHSGDKYNELADKLAKK 131

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. Length = 133

>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal domain

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 14/53 (26%), Positives = 32/53 (60%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +    + + ++EE E+E+E+EE   +   E ++E  E E+++ E +  +EE++
Sbjct: 71  KLRRDKLKAKKEEAEKEKEKEERFMKALAEAEKERAELEKKKAEAKLMKEEKK 123

This domain is found in a number of different types of plant proteins including NAM-like proteins. Length = 147

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 38.5 bits (89), Expect = 0.002
 Identities = 13/54 (24%), Positives = 33/54 (61%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           RR E+E   + E+++ E   +E+ +EE+++ ++ EE+ +   E+ ++  ++ E 
Sbjct: 18  RRCEQETRGQREQQQCERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEP 71

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein

 Score = 40.0 bits (94), Expect = 0.003
 Identities = 25/41 (60%), Positives = 29/41 (70%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           E E  E EEEEEEEE  E +EE+E  +EEEEE EE  +EEE
Sbjct: 164 EVELREGEEEEEEEEVGEADEEDEGEEEEEEEPEEVPKEEE 204

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. Length = 481

>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]

 Score = 40.0 bits (93), Expect = 0.003
 Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 19/83 (22%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEE-------------------EEEEEEEEEEEEVQE 628
           + N    I + E+ + EE  E+ +EE                    + +E+ +E    Q 
Sbjct: 113 VNNEYPGITKLEKSDVEEPSEKVDEEDVEREILAEKPRVTRFNIVWDNDEDNDEAPPAQP 172

Query: 629 EEEEEEEEEEEEEEEEEEEEEEE 651
           + + EEEE  EE +  EEEE+EE
Sbjct: 173 DVDNEEEERLEESDGREEEEDEE 195

Length = 279

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

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 26/74 (35%), Positives = 37/74 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            ++N ++ +     E   + EE E + EE + E    EE  E+ +   EE EEE EE EE
Sbjct: 692 SLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEE 751

Query: 647 EEEEEEVRGGGKEE 660
           E EE + R    EE
Sbjct: 752 ELEELQERLEELEE 765

Length = 1163

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 40.4 bits (94), Expect = 0.003
 Identities = 14/56 (25%), Positives = 31/56 (55%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
               +  + + EEE+EE++E+E++++EEE      ++ + +E   E  + E  +E 
Sbjct: 283 EAVKKEADSKPEEEDEEDDEQEDDQDEEEPPEAAMDKVKLDEPVLEGVDLESPKEL 338

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein

 Score = 40.4 bits (94), Expect = 0.003
 Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 22/94 (23%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
            +++E  S   E I          E E   E+  ++E E++EE++ EE +  EE+E  E+
Sbjct: 119 EEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEEAGEEKESVEQ 178

Query: 638 EEEE----------------------EEEEEEEE 649
              E                      E  E EEE
Sbjct: 179 ATREKKFDKSGVDDKFFKLDEMNEFLEATEAEEE 212

This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. Length = 613

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

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 12/52 (23%), Positives = 31/52 (59%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E   + E E++E+ EE EEE+ EEE    ++ ++ ++ + ++   ++++ + 
Sbjct: 307 EIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDS 358

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

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

 Score = 40.7 bits (95), Expect = 0.003
 Identities = 23/72 (31%), Positives = 46/72 (63%), Gaps = 6/72 (8%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEE------EEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           + E I+  + +  +EEE+E++ +EEE      EEEE + E  + E ++ ++EE+ +E E+
Sbjct: 263 KEEEILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEK 322

Query: 641 EEEEEEEEEEEE 652
           E ++ E+E ++E
Sbjct: 323 ELKKLEKELKKE 334

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 = 0.003
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           EN+ +LI     E + +E + +E+ ++  E  + +E+++ EEE     +  +  EE  + 
Sbjct: 184 ENLAELIID-LEELKLQELKLKEQAKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDL 242

Query: 649 EEEEVRGGGKEEISL 663
            +E +R   +E  S 
Sbjct: 243 LQELLRDEQEEIESS 257

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|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 40.9 bits (95), Expect = 0.003
 Identities = 29/62 (46%), Positives = 32/62 (51%)

Query: 599  EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
            E  EE  EE +EE  EE EE  EE +E   EE EE  EE  EE  EE  EE +E      
Sbjct: 1013 ENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEI 1072

Query: 659  EE 660
            EE
Sbjct: 1073 EE 1074

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 40.9 bits (95), Expect = 0.003
 Identities = 30/80 (37%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 573 KVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
           K  K  D  ++ S  I + I LI +  + + E   E  +E  E   EE+ EE V+E+ EE
Sbjct: 903 KKAKKKDAKDL-SGNIAHEINLINKELKNQNENVPEHLKEHAEANIEEDAEENVEEDAEE 961

Query: 633 EEEEEEEEEEEEEEEEEEEE 652
             EE  EE  EE  EE  EE
Sbjct: 962 NVEENVEENVEENVEENVEE 981

Length = 1136

>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 40.5 bits (94), Expect = 0.003
 Identities = 28/62 (45%), Positives = 34/62 (54%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            ENI + +   + E  EE EE  EE +EE  EE EE   +  EE  EE  EE +EE  EE 
Sbjct: 1013 ENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEI 1072

Query: 649  EE 650
            EE
Sbjct: 1073 EE 1074

Length = 1136

>gnl|CDD|216403 pfam01271, Granin, Granin (chromogranin or secretogranin)

 Score = 40.4 bits (94), Expect = 0.003
 Identities = 11/67 (16%), Positives = 24/67 (35%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           RG  +   E E  EE EE+E +     +E++     +    +      + +  +   R  
Sbjct: 299 RGRSQNRAERERSEESEEKELDRASPYQEIEITANLQIPPSDLIRMLRKGDGRKPRGRVE 358

Query: 657 GKEEISL 663
            +  +  
Sbjct: 359 EEGALEA 365

Length = 585

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

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 22/53 (41%), Positives = 35/53 (66%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E + E +E++E +EEEE E+EEE + E    +  +  E+ ++EEEEEE +EE 
Sbjct: 442 ENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEEN 494

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|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 24/59 (40%), Positives = 37/59 (62%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           +  EREE+E ++ EEE ++  EE  E E+ ++E  +E EE E++  EEE EE  EE + 
Sbjct: 612 KELEREEKELKKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLE 670

Length = 880

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

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 27/66 (40%), Positives = 33/66 (50%), Gaps = 9/66 (13%)

Query: 596 RRGEREEEEEE---------EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
              E E+E  E         EEE   E+EE E  EE EE+++E  E EEE  E  E EE 
Sbjct: 467 LPEEHEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEA 526

Query: 647 EEEEEE 652
            +EE E
Sbjct: 527 LKEELE 532

Length = 908

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

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 36/97 (37%), Positives = 48/97 (49%), Gaps = 8/97 (8%)

Query: 564 KLKTIRPSIKVWKTSDQDEIGSPRIENIIQLIRRGE------REEEEEEEEEEEEEEEEE 617
           +L+ +   IK  K  +Q      +   I +L   GE      +E  EE E+E  E  E E
Sbjct: 425 ELEELEEEIK--KLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELE 482

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            EE EEE  +E+EE E  EE EE E+E  E EEE + 
Sbjct: 483 LEELEEELSREKEEAELREEIEELEKELRELEEELIE 519

Length = 908

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

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 24/73 (32%), Positives = 30/73 (41%)

Query: 590 NIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
              Q     E+E E  EE   E EEE+E  EE +  + E E  E E  +  EEE  E E 
Sbjct: 222 QEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELER 281

Query: 650 EEEVRGGGKEEIS 662
             E      E + 
Sbjct: 282 LLEELEEKIERLE 294

Length = 908

>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional

 Score = 39.0 bits (91), Expect = 0.003
 Identities = 15/51 (29%), Positives = 24/51 (47%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + ++  ++   E E++  E   E V E++  E      EE    EEEE EE
Sbjct: 123 KAKKAAKKAALEAEKKVNEARAEAVAEKKAAEAAAVAAEEAAAAEEEEAEE 173

Length = 186

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

 Score = 39.9 bits (93), Expect = 0.003
 Identities = 15/67 (22%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 599 EREEE---EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE--EEEEEEEEEEEEEEEEEEV 653
             E E   EEE +    + +++ EEE +E++Q   E+    ++EE+   +E + +E++ +
Sbjct: 79  PEEAEPHAEEEGQLAVRKTKQKVEEEVKEQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFL 138

Query: 654 RGGGKEE 660
                ++
Sbjct: 139 LAEDSDD 145

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|234017 TIGR02794, tolA_full, TolA protein

 Score = 39.8 bits (93), Expect = 0.003
 Identities = 12/53 (22%), Positives = 30/53 (56%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            R++E E+    E+  ++ E+  ++ E ++++ EE + ++  E + + E E E
Sbjct: 89  ARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAE 141

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|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
                  E   E +E EE  EE+EEE EEE +++
Sbjct: 71  AAAAAGAEAAAEADEAEE--EEKEEEAEEESDDD 102

Length = 109

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 14/30 (46%), Positives = 22/30 (73%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEE 631
           + E EEEEE E+ E E+EE+EEE+  ++ +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 13/30 (43%), Positives = 24/30 (80%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           + E EEEEE E+ E ++EE+EEE+++++ +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 595 IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE-EEV 653
           +   E + +E  EE  E EE+ EE +EE E ++ E EE E E EE E   EE EE+ E +
Sbjct: 325 LEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETL 384

Query: 654 RG 655
           R 
Sbjct: 385 RS 386

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 24/73 (32%), Positives = 31/73 (42%), Gaps = 5/73 (6%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE-----EEEEEE 641
           R+E++ + I     + E    E EE EE  EE E E E +  E    EE       E EE
Sbjct: 839 RLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEE 898

Query: 642 EEEEEEEEEEEVR 654
             EE  E E +  
Sbjct: 899 LSEELRELESKRS 911

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|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 6/59 (10%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEE------EEEEEEEVQEEEEEEEEEEEEEEEEEE 645
            ++    R E++EEEEEEEE+E   +      E EE+    ++E+ E++EE+ +     
Sbjct: 171 SMLEALFRREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPSP 229

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|184539 PRK14150, PRK14150, heat shock protein GrpE; Provisional

 Score = 38.7 bits (91), Expect = 0.003
 Identities = 16/47 (34%), Positives = 26/47 (55%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
             EE++  +E+  EE E E E+ +E +E E E+E +E +    E E 
Sbjct: 2   SNEEQKTPQEQVSEEIEAEVEQQEEADEAELEDELDEADARIAELEA 48

Length = 193

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 21/53 (39%), Positives = 33/53 (62%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           E  E E++E EE  E+ EE+    ++E++E EE   E EE+ ++EEEE +  E
Sbjct: 1   EEAEREQQELEERMEQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQLLE 53

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 25/60 (41%), Positives = 38/60 (63%), Gaps = 4/60 (6%)

Query: 597 RGEREEEEEEEEEEEEEEE----EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
             ERE++E EE  E+ EE+    ++E EE EE   E EE+ ++EEEE +  E++ +E EE
Sbjct: 2   EAEREQQELEERMEQMEEDMRRAQKELEEYEETALELEEKLKQEEEEAQLLEKKADELEE 61

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 39.3 bits (92), Expect = 0.003
 Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE-EEEVR 654
           EEE    EEE    EEE E  E EV E   E  + EEE E++E E  + ++E+R
Sbjct: 60  EEENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQELR 113

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 22/57 (38%), Positives = 28/57 (49%)

Query: 581 DEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           D+I +      I  +R   +E+     E   EEEEEEEEEEEEE  + E   EE   
Sbjct: 372 DKIATEEDATTIDELREFLKEKGHPVVERWAEEEEEEEEEEEEEAAEAEAPMEEPVP 428

Length = 470

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 21/63 (33%), Positives = 32/63 (50%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           + + + + + EE   E+E  EEEE  E    E+   + EE  E  EEE  E + E EE +
Sbjct: 390 LAEALSKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELK 449

Query: 651 EEV 653
            E+
Sbjct: 450 REI 452

Length = 652

>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32

 Score = 39.6 bits (92), Expect = 0.003
 Identities = 16/56 (28%), Positives = 34/56 (60%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
              + +  + ++E+   + +E  +E + EE++ +EE+EEEE EEE ++  G G ++
Sbjct: 188 GSVQVKAPKPKQEQLLSKLQEYLQEHKTEEKQPQEEQEEEEVEEEAKQEEGQGTDD 243

This family consists of several mammalian specific proacrosin binding protein sp32 sequences. sp32 is a sperm specific protein which is known to bind with with 55- and 53-kDa proacrosins and the 49-kDa acrosin intermediate. The exact function of sp32 is unclear, it is thought however that the binding of sp32 to proacrosin may be involved in packaging the acrosin zymogen into the acrosomal matrix. Length = 243

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

 Score = 40.0 bits (94), Expect = 0.003
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE--EEEEEVQEEEEEEEEEEEEEEEEE 644
            +  + + +R+   +E+  E EEE+ E +  +EE  + + E+   EE  +E E +     
Sbjct: 7   ALAELAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAASG 66

Query: 645 EEEEEEEEVRGGGKEEISLHFYV 667
           E    EEE      E      Y+
Sbjct: 67  EGGGGEEEEEEAKAEAAEFRAYL 89

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|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.8 bits (94), Expect = 0.003
 Identities = 20/33 (60%), Positives = 22/33 (66%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +    E  EE +EE EEEEEEEEEEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.8 bits (94), Expect = 0.003
 Identities = 20/33 (60%), Positives = 22/33 (66%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           +    E  EEEEEE EEEEEE +EEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.8 bits (94), Expect = 0.003
 Identities = 20/33 (60%), Positives = 22/33 (66%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           +    E  EEEEEE EEE +EEEEEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.4 bits (93), Expect = 0.003
 Identities = 20/33 (60%), Positives = 22/33 (66%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +    E   +EEEE EEEEEEEEEEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein

 Score = 37.2 bits (87), Expect = 0.003
 Identities = 11/21 (52%), Positives = 14/21 (66%)

Query: 606 EEEEEEEEEEEEEEEEEEEEV 626
                 EEE++EEEEEEEE+ 
Sbjct: 61  AAAAAAEEEKKEEEEEEEEDD 81

This family includes archaebacterial L12, eukaryotic P0, P1 and P2. Length = 88

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

 Score = 40.6 bits (96), Expect = 0.003
 Identities = 17/53 (32%), Positives = 21/53 (39%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            +EE + E EEE + E EE    E EE  + E       EE  E     E   
Sbjct: 44  RKEEAKREAEEEAKAEAEEAAAAEAEEEAKAEAAAAAPAEEAAEAAAAAEAAA 96

Length = 746

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

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 24/92 (26%), Positives = 50/92 (54%), Gaps = 3/92 (3%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE---E 644
           IE +  L +  E++ E  E+  +E+E+ ++E E+E EE++E E  ++ E E+E +E    
Sbjct: 517 IEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKA 576

Query: 645 EEEEEEEEVRGGGKEEISLHFYVLYVLSKGKI 676
            ++E E  +R   +++I     +  +    K+
Sbjct: 577 LKKEVESIIRELKEKKIHKAKEIKSIEDLVKL 608

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|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812)

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 12/37 (32%), Positives = 24/37 (64%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
           +E  E +   +EE++ +EEE  ++ EE +E E E+++
Sbjct: 90  DERAEAQRARDEEKKLDEEEAKRQHEEAKEREREKKK 126

This is a family of fungal proteins whose function is not known. Length = 126

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 40.3 bits (95), Expect = 0.003
 Identities = 10/46 (21%), Positives = 19/46 (41%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
             +  +  E+ + +E   E   E+   EEE  + +  EEE   +  
Sbjct: 2   TLKVHDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGA 47

Length = 325

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 39.9 bits (94), Expect = 0.003
 Identities = 10/48 (20%), Positives = 21/48 (43%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
             +  +  E+ + +E   E  +E+   EEE  + +  EEE   +   +
Sbjct: 2   TLKVHDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQ 49

Length = 325

>gnl|CDD|177755 PLN00152, PLN00152, DNA-directed RNA polymerase; Provisional

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 15/51 (29%), Positives = 26/51 (50%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           + +   E+E  E E EE  EE+ +    +E +    E E++EE+E  +  R
Sbjct: 4   DMDMGYEDEPSEPEIEEGAEEDSESNNNDEVKGSIGENEDKEEQEPVQRPR 54

Length = 130

>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 39.6 bits (93), Expect = 0.003
 Identities = 17/56 (30%), Positives = 29/56 (51%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
             E E  + E  E E+E   E+++EEE   E +E   +E  ++  E+ E E E++ 
Sbjct: 205 AIEAERAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLL 260

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (93), Expect = 0.003
 Identities = 15/58 (25%), Positives = 28/58 (48%)

Query: 590 NIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           ++     R      EE +   EE+     E+   E V  EE+++++EE + ++E E E
Sbjct: 452 SVDSYDPRASLMTMEETQRHSEEDLVNRFEDVRYEHVAGEEDDDDDEELQAQKELELE 509

Length = 591

>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex subunit beta; Reviewed

 Score = 40.4 bits (95), Expect = 0.003
 Identities = 17/29 (58%), Positives = 18/29 (62%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEE 631
             EEEEEEEEEEEEEEE   E  +    E
Sbjct: 403 AAEEEEEEEEEEEEEEEPVAEVMMMPAPE 431

Length = 463

>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 9/53 (16%), Positives = 14/53 (26%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + E       E +     E    +++    E    E      E       EEE
Sbjct: 102 KLELFNAALAEADGGPTAEATTPKKKKAAAEAAAAEAAAPAAEAAAAAAAEEE 154

Length = 155

>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein

 Score = 39.0 bits (91), Expect = 0.003
 Identities = 15/75 (20%), Positives = 37/75 (49%)

Query: 576 KTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           K   +    +PR     +  ++ ++E+  EEE++ E ++++ EE E + +  EE  + +E
Sbjct: 49  KQPKKKRPTTPRKPATTKKSKKKDKEKLTEEEKKPESDDDKTEENENDPDNNEESGDSQE 108

Query: 636 EEEEEEEEEEEEEEE 650
                   + + E++
Sbjct: 109 SASANSLSDIDNEDD 123

Length = 198

>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal domain

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 16/55 (29%), Positives = 35/55 (63%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E+   ++ + ++EE E+E+E+EE   +   E E+E  E E+++ E +  +EE+++
Sbjct: 70  EKLRRDKLKAKKEEAEKEKEKEERFMKALAEAEKERAELEKKKAEAKLMKEEKKI 124

This domain is found in a number of different types of plant proteins including NAM-like proteins. Length = 147

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 38.5 bits (89), Expect = 0.003
 Identities = 16/65 (24%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 597 RGEREEEE-EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           RG+RE+++ E   +E+ +EE++++ + EE+ Q   E+ ++  ++ E       ++   R 
Sbjct: 25  RGQREQQQCERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEPRHRPTCQQRCERR 84

Query: 656 GGKEE 660
             KE+
Sbjct: 85  YEKEQ 89

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|218003 pfam04281, Tom22, Mitochondrial import receptor subunit Tom22

 Score = 38.4 bits (90), Expect = 0.003
 Identities = 9/46 (19%), Positives = 25/46 (54%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            E E+E  +E+    +   +EE  +++E++ + + +  ++ + E E
Sbjct: 5   TEVEDETFQEKPAAPKNLAQEESDDDDEDDTDTDSDISDDSDFENE 50

The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins. The N terminal region of Tom22 has been shown to have chaperone-like activity, and the C terminal region faces the intermembrane face. Length = 136

>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and more complex than their prokaryotic counterparts and unlike prokaryote, RNase H are essential in higher eukaryote

 Score = 38.3 bits (90), Expect = 0.003
 Identities = 28/105 (26%), Positives = 36/105 (34%), Gaps = 26/105 (24%)

Query: 366 AELIAIFLCLEAILDSPSG--KFLIVTDS--------------------RSSLAALSNVR 403
           AEL A+   L  I +   G  K +I TDS                     S    ++N  
Sbjct: 46  AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105

Query: 404 FINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAK 448
            I  L   +      L+     + F   P H GI GNE  D  AK
Sbjct: 106 LIKELDKLLEE----LEERGIRVKFWHVPGHSGIYGNEEADRLAK 146

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at the N-terminal called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Length = 150

>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 40.2 bits (94), Expect = 0.003
 Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E  +    + E   E E+ E   E+  +EE+ + E+EVQ  +  E  E      E ++E 
Sbjct: 275 EAEVAA-WKAETRREAEQAEILAEQAIQEEKAQAEQEVQHAKALEAREMRVGLIERQKET 333

Query: 649 EEEE 652
           E E 
Sbjct: 334 ELEP 337

Length = 548

>gnl|CDD|220438 pfam09845, DUF2072, Zn-ribbon containing protein (DUF2072)

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR--GGGKEEISL 663
           E +  + +  EE+  EE++ E +EE  E +++ E+ EE E  E VR  G G  E++L
Sbjct: 35  ERKRPKPDVPEEKPVEEIERETDEELLEVKQDREQGEEGERIESVRILGPGSYELNL 91

This archaeal protein has no known function. Length = 121

>gnl|CDD|223783 COG0711, AtpF, F0F1-type ATP synthase, subunit b [Energy production and conversion]

 Score = 38.4 bits (90), Expect = 0.003
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 586 PRIENII----QLIRRGEREEEEEEEEEEEEEEEEEEE-EEEEEEVQEEEEEEEEEEEEE 640
             I   +      I     E E  +EE +    E E+E EE  E+  E  E+ ++E E+ 
Sbjct: 29  KPILKALDERQAKIADDLAEAERLKEEAQALLAEYEQELEEAREQASEIIEQAKKEAEQI 88

Query: 641 EEEEEEEEEEEEVR 654
            EE + E EEE  R
Sbjct: 89  AEEIKAEAEEELER 102

Length = 161

>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein

 Score = 40.2 bits (94), Expect = 0.003
 Identities = 14/44 (31%), Positives = 22/44 (50%)

Query: 615 EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           EEE  ++E + ++E E EE      EEE  + +   +E R   K
Sbjct: 242 EEESIDDELDVLREIEAEEAGIGPIEEEVVDSQAANDEPRRVFK 285

Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent relicensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. Length = 397

>gnl|CDD|183731 PRK12766, PRK12766, 50S ribosomal protein L32e; Provisional

 Score = 39.4 bits (92), Expect = 0.003
 Identities = 19/36 (52%), Positives = 23/36 (63%)

Query: 625 EVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EV EE E E E+E  EEEEEE+ + E E+R  G  E
Sbjct: 60  EVSEETEAEVEDEGGEEEEEEDADVETELRPRGLTE 95

Length = 232

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 40.0 bits (93), Expect = 0.004
 Identities = 22/60 (36%), Positives = 26/60 (43%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           E E   E   EE E   E E E  E    E E+E E E + E E E E   E +G  + E
Sbjct: 637 EAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEQEGE 696

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon

 Score = 40.0 bits (93), Expect = 0.004
 Identities = 23/84 (27%), Positives = 36/84 (42%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           S  DE      ++   L+ R  R EE  +E   E  E ++E +    +    E     +E
Sbjct: 43  SVPDEESKTSTDDEAALLERLARREERRDERFSEALERQKEFKPTSTDQSLSEPSRRMQE 102

Query: 638 EEEEEEEEEEEEEEEVRGGGKEEI 661
           +   E E  EEEE+E     +EE+
Sbjct: 103 DSGAENETVEEEEKEESREEREEV 126

Length = 431

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 39.9 bits (94), Expect = 0.004
 Identities = 23/85 (27%), Positives = 33/85 (38%), Gaps = 21/85 (24%)

Query: 592 IQLIRRGEREEEEEEEEE---------------------EEEEEEEEEEEEEEEEVQEEE 630
            +++ +   +EE E+E                       EE    E EEE EE E   EE
Sbjct: 262 ERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQIEEKEERRAAEREEELEEGERLREE 321

Query: 631 EEEEEEEEEEEEEEEEEEEEEEVRG 655
           E E +   EEE +   +E  E + G
Sbjct: 322 EAERQARIEEERQRLLKEHAEALLG 346

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|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 15/76 (19%), Positives = 41/76 (53%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
              +      E  ++ + R    + +++E   E+E+E+EE++EE E   + E  + E+  
Sbjct: 5   VNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEISKREKAR 64

Query: 639 EEEEEEEEEEEEEEVR 654
            +E ++++++E +++ 
Sbjct: 65  LKELKKQKKQEIQKIL 80

Length = 1033

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

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 16/67 (23%), Positives = 30/67 (44%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +  +   + + E E +  + E    E+  EE   + EE++ + EE + E    EEE E+
Sbjct: 675 ELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQ 734

Query: 647 EEEEEEV 653
            +   E 
Sbjct: 735 LQSRLEE 741

Length = 1163

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

 Score = 40.1 bits (93), Expect = 0.004
 Identities = 20/67 (29%), Positives = 40/67 (59%)

Query: 595  IRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            +R+ E  ++ EE   EE  +  EEE++ + E  ++ EE + + EE ++ EEE+++ E+++
Sbjct: 1580 LRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLK 1639

Query: 655  GGGKEEI 661
                EE 
Sbjct: 1640 KKEAEEK 1646

Length = 2084

>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890)

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           E EE+EEE E+ E+  +EE+EE EE     EEE     +      +   +E   +
Sbjct: 30  EVEEDEEEMEDWEDSLDEEDEEAEE----VEEETAASSKAPSSSSKSSSQETISI 80

This family is conserved in dsDNA adenoviruses of vertebrates. The function is not known. Length = 172

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

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 20/47 (42%), Positives = 30/47 (63%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
            +G+ E+E+EE EEE EEE+EE  +E E+E +E+ E   E+E     
Sbjct: 80  DKGDAEKEDEESEEENEEEDEESSDENEKETEEKTESNVEKEITNPS 126

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|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen; Provisional

 Score = 40.2 bits (93), Expect = 0.004
 Identities = 28/63 (44%), Positives = 34/63 (53%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            EN+ + I     E +EE  EE EE  EE +EE  EE  +  EE  EE  EE  EE +EE 
Sbjct: 1009 ENVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEEN 1068

Query: 649  EEE 651
             EE
Sbjct: 1069 VEE 1071

Length = 1136

>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional

 Score = 39.7 bits (92), Expect = 0.004
 Identities = 22/61 (36%), Positives = 40/61 (65%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLHFY 666
           EEE   ++EEEE+E+ EE  + EE E  EEE +++E+ E+++E+E    G + E++  + 
Sbjct: 100 EEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKESDAEGDENELAGEYI 159

Query: 667 V 667
           +
Sbjct: 160 I 160

Length = 374

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 40.0 bits (93), Expect = 0.004
 Identities = 14/50 (28%), Positives = 38/50 (76%), Gaps = 2/50 (4%)

Query: 615 EEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
           +E EEE  EEE  +++EE+++++++E+E++++++++E+      ++ +LH
Sbjct: 43  KEAEEEAMEEE--DDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLH 90

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 39.6 bits (92), Expect = 0.004
 Identities = 12/54 (22%), Positives = 40/54 (74%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           E   EEE+++EE+++++++E+E+++++  +E++E+E++++    ++   ++  E
Sbjct: 47  EEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGNE 100

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|240413 PTZ00423, PTZ00423, glideosome-associated protein 45; Provisional

 Score = 38.9 bits (90), Expect = 0.004
 Identities = 22/59 (37%), Positives = 36/59 (61%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           +E +  + +E  E E+ ++E EE+ E++ E+  EE E++ EE  E+EEE      KEEI
Sbjct: 11  KEPKRRDIDELAEREKLKKEVEEIPEQKPEDIVEELEDQPEEPPEQEEENEEQKPKEEI 69

Length = 193

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

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 20/54 (37%), Positives = 35/54 (64%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +  + E +E++E +EEEE E+EEE +  +   +  +  E+ ++EEEEEE +EE 
Sbjct: 441 KENKNEFKEKKESDEEEELEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEEN 494

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|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 596 RRGEREEEEEEEEEEEE--EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
             G + + EE+  E EE  EE ++E EE EE+V+E +E +E+ EE  +  E  EE  +E+
Sbjct: 250 LEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLDEL 309

Query: 654 RGGGKEEISL 663
           R   K    L
Sbjct: 310 REIEKRLSRL 319

Length = 880

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

 Score = 40.5 bits (95), Expect = 0.004
 Identities = 28/57 (49%), Positives = 33/57 (57%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            E+E  E  E E EE EEE   E+EE E++EE EE E+E  E EEE  E  E EE  
Sbjct: 471 HEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEAL 527

Length = 908

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

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 25/68 (36%), Positives = 39/68 (57%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           ++E +   IRR  +  E EE+ EE+ EE E+ EEE E+  +E EE  ++  E E+  EE 
Sbjct: 662 KVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEEL 721

Query: 647 EEEEEEVR 654
           E  + E+ 
Sbjct: 722 ESRKAELE 729

Length = 908

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

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 26/73 (35%), Positives = 41/73 (56%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
             + +L++    E EE+ EE E E   E +  E EE+++E+ EE E+ EEE E+  EE E
Sbjct: 646 AELEELLQAALEELEEKVEELEAEIRRELQRIENEEQLEEKLEELEQLEEELEQLREELE 705

Query: 649 EEEEVRGGGKEEI 661
           E  +  G  ++ I
Sbjct: 706 ELLKKLGEIEQLI 718

Length = 908

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

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 26/67 (38%), Positives = 36/67 (53%)

Query: 586 PRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
             +E + + I R E  E E EE EEE E      EE EE +++ +  EE  E+ EE+ E+
Sbjct: 281 RLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEK 340

Query: 646 EEEEEEE 652
            E E EE
Sbjct: 341 LESELEE 347

Length = 908

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

 Score = 39.1 bits (91), Expect = 0.004
 Identities = 13/64 (20%), Positives = 29/64 (45%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E+ +   E+    ++EE+   +E + +  +    E+ ++ +E  E  +  EE E     +
Sbjct: 107 EQLQSLLEKIVVSKQEEDGPGKEPQLDEDKFLLAEDSDDRQETLEAGKVHEETEDSYHVE 166

Query: 659 EEIS 662
           E  S
Sbjct: 167 ETAS 170

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|234017 TIGR02794, tolA_full, TolA protein

 Score = 39.4 bits (92), Expect = 0.004
 Identities = 13/57 (22%), Positives = 31/57 (54%), Gaps = 4/57 (7%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE----EEEEEEVR 654
           E+  ++E E+    E+  ++ E+  ++ EE++++ EE + ++  E     E E E +
Sbjct: 87  EQARQKELEQRAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEAEAEKK 143

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|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 13/30 (43%), Positives = 22/30 (73%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEE 633
           + E EEEEE E+ E E+EE+EE  ++++ +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 36.4 bits (85), Expect = 0.004
 Identities = 12/30 (40%), Positives = 23/30 (76%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           + E EEEEE E+ E E+EE+ +E+++++ +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 13/30 (43%), Positives = 23/30 (76%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           + E EEEEE E+ E E+EE +EE+++++ +
Sbjct: 45  DAEWEEEEEGEDLESEDEEDEEEDDDDDMD 74

The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. Length = 76

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

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 13/83 (15%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           +++IG    E     I   ER   E+E E E+ EE   + E E +++  E EE E E EE
Sbjct: 293 KEKIGELEAE-----IASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEE 347

Query: 640 E--------EEEEEEEEEEEEVR 654
           E        EE  E +EE E++R
Sbjct: 348 ERKRRDKLTEEYAELKEELEDLR 370

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 22/64 (34%), Positives = 32/64 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +  +   + + E    +  +E  E E E EE EE  EE +EE  E E E EE E + E+
Sbjct: 734 DLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQ 793

Query: 647 EEEE 650
            +EE
Sbjct: 794 LKEE 797

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 22/74 (29%), Positives = 33/74 (44%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E + + +    R+     ++    E E E+ EE   ++ +E  E E E EE EE  EE
Sbjct: 713 ELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEE 772

Query: 647 EEEEEEVRGGGKEE 660
            EEE        EE
Sbjct: 773 AEEELAEAEAEIEE 786

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 32/69 (46%), Positives = 39/69 (56%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           L+ R E   EE EE +EE +E EEE EE   E+QE EE+ EE   E  E EEE EE ++ 
Sbjct: 230 LVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKE 289

Query: 654 RGGGKEEIS 662
                 EIS
Sbjct: 290 LYALANEIS 298

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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 27/63 (42%), Positives = 37/63 (58%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E EE  ++ EE E +E + E EE EEE++E +EE E  EE  EE  EE EE E+     +
Sbjct: 422 EIEELLKKLEEAELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQALDAAE 481

Query: 659 EEI 661
            E+
Sbjct: 482 REL 484

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|218115 pfam04502, DUF572, Family of unknown function (DUF572)

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            R E++EEEEEEEE+E   +      E EE +   ++E+ E++EE+ +     
Sbjct: 177 FRREKKEEEEEEEEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPSP 229

Family of eukaryotic proteins with undetermined function. Length = 321

>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEE------EEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
            E EE E++ ++ +EE EEEE+ E+      E + +   E +  +E+  ++E + EE   
Sbjct: 5   DEEEELEDDIDDLDEEAEEEEDGEDLFGDNMERDYRANPELDRYDEDGLDDESDYEELSA 64

Query: 652 EVR 654
             R
Sbjct: 65  AAR 67

This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. Length = 145

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE- 646
           IE++ + I   ERE EE  EE  +  E  EE EEE +++  E   ++ + E  E   EE 
Sbjct: 260 IEDLRETIAETEREREELAEEVRDLRERLEELEEERDDLLAEAGLDDADAEAVEARREEL 319

Query: 647 EEEEEEVR 654
           E+ +EE+R
Sbjct: 320 EDRDEELR 327

Length = 880

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 31/81 (38%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEE--------EEEEEVQEEEE 631
           Q   GSP +E I +   R   EE E E E+ EEE EE EE         E E+ ++  EE
Sbjct: 459 QPVEGSPHVETIEE--DRERVEELEAELEDLEEEVEEVEERLERAEDLVEAEDRIERLEE 516

Query: 632 EEEEEEEEEEEEEEEEEEEEE 652
             E+ EE   E  E  EE+ E
Sbjct: 517 RREDLEELIAERRETIEEKRE 537

Length = 880

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 24/54 (44%), Positives = 28/54 (51%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
             RE+ ++ EE  EE  EE  E E E E   E  E+  EE EE EEE EE  E 
Sbjct: 346 SLREDADDLEERAEELREEAAELESELEEAREAVEDRREEIEELEEEIEELRER 399

Length = 880

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 29/70 (41%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 596 RRGEREE--EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
            R E +E  EE EE  EE E  E E E+  E + E E E EE  EE  +  E  EE EE 
Sbjct: 235 TRDEADEVLEEHEERREELETLEAEIEDLRETIAETEREREELAEEVRDLRERLEELEEE 294

Query: 654 RGGGKEEISL 663
           R     E  L
Sbjct: 295 RDDLLAEAGL 304

Length = 880

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

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 14/78 (17%), Positives = 40/78 (51%)

Query: 575 WKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
           +      +  + + E   +       EE + ++  E+E  ++ E+E  + + Q+++ EE 
Sbjct: 64  YGRIQSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEA 123

Query: 635 EEEEEEEEEEEEEEEEEE 652
           E++ + E++++EE+  + 
Sbjct: 124 EKQAQLEQKQQEEQARKA 141

Length = 387

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

 Score = 39.5 bits (92), Expect = 0.004
 Identities = 12/58 (20%), Positives = 37/58 (63%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           + ++   ++ E++ +++EE+  EE + ++  E+E  ++ E+E  + +E++++ EE  +
Sbjct: 68  QSQQSSAKKGEQQRKKKEEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEK 125

Length = 387

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

 Score = 40.4 bits (94), Expect = 0.004
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 589  ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQ---EEEEEEEEEEEEEEEEEE 645
            E+I   +   +  EE   EE+   + + +E E  E E       ++    E E  + EEE
Sbjct: 3825 EDITNTLNEDDDLEELANEEDTANQSDLDESEARELESDMNGVTKDSVVSENENSDSEEE 3884

Query: 646  EEEEEEEV 653
             ++ +EEV
Sbjct: 3885 NQDLDEEV 3892

Length = 4600

>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family

 Score = 39.3 bits (92), Expect = 0.004
 Identities = 20/55 (36%), Positives = 27/55 (49%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
            EE    EEE E  E E +E   E    EEE E++E E  + ++E  E +E   R
Sbjct: 67  EEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQELREAQEAHER 121

This family of proteins contain a band 4.1 domain (pfam00373), at their amino terminus. This family represents the rest of these proteins. Length = 244

>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM protein

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 19/99 (19%), Positives = 32/99 (32%), Gaps = 1/99 (1%)

Query: 553 QSLWDNVPNTNKLKTIRPSI-KVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEE 611
           Q L D+   ++K      S    +     +   +      I+      R+   E     E
Sbjct: 79  QDLADSFEKSDKESQDYSSSDSGFDEEPDEPAETAGSLRPIRSSAAAYRDINRELGSFYE 138

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
             + +EE+E   E  + E     E     E EE+    E
Sbjct: 139 YPKTDEEKELLREVEELESRLATEPSPAPELEEQLALME 177

Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage [Cellular processes, DNA transformation]. Length = 410

>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682)

 Score = 37.9 bits (88), Expect = 0.004
 Identities = 15/40 (37%), Positives = 25/40 (62%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
               +EEEEEEEE E++++ +E Q ++ ++ E   E  EE
Sbjct: 92  GHTRQEEEEEEEENEKQQQSDEAQVQQHQQHEHPAENGEE 131

This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length. Length = 133

>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682)

 Score = 37.9 bits (88), Expect = 0.004
 Identities = 15/39 (38%), Positives = 25/39 (64%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
             R+EEEEEEEE E++++ +E + ++ +  E   E  EE
Sbjct: 93  HTRQEEEEEEEENEKQQQSDEAQVQQHQQHEHPAENGEE 131

This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length. Length = 133

>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740)

 Score = 40.0 bits (93), Expect = 0.004
 Identities = 20/41 (48%), Positives = 28/41 (68%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
            EEEEE E EE+EE  E+E  +  +E+ EEEEEEE +  ++
Sbjct: 140 LEEEEEVEMEEDEEYYEKEPGKVVDEKSEEEEEEELKTMKD 180

This family consists of several uncharacterized plant proteins of unknown function. Length = 565

>gnl|CDD|224308 COG1390, NtpE, Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]

 Score = 38.9 bits (91), Expect = 0.004
 Identities = 22/56 (39%), Positives = 30/56 (53%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEISLH 664
           E+  ++   E EEE EE+ EE  EE E+ +EE + E EE  EE +R   KE     
Sbjct: 5   EKLIKKILREAEEEAEEILEEAREEAEKIKEEAKREAEEAIEEILRKAEKEAERER 60

Length = 194

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.4 bits (93), Expect = 0.004
 Identities = 21/33 (63%), Positives = 23/33 (69%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           +    E  EEEEEE +EEEEEEEEEE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.4 bits (93), Expect = 0.004
 Identities = 20/33 (60%), Positives = 22/33 (66%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           +    E  EEEEEE EEEEEEE +EE EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.4 bits (93), Expect = 0.004
 Identities = 20/33 (60%), Positives = 22/33 (66%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE 635
           +    E  EEEEEE EEEEEEEE +E EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional

 Score = 39.0 bits (92), Expect = 0.004
 Identities = 20/33 (60%), Positives = 22/33 (66%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
           +    E  EEEEEE EEEEEEEEE + EE E E
Sbjct: 226 QGRLAEAAEEEEEEAEEEEEEEEEEEAEEAEAE 258

Length = 258

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           ++E + EEE+ EEEE   + EE +E E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           ++E + EEE+ EEEEE  + +E +E E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|205206 pfam13025, DUF3886, Protein of unknown function (DUF3886)

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           ++E + EEE+ EEEEE ++ EE +E E+ +  EE   E E
Sbjct: 26  KKELKAEEEKREEEEEARKREERKEREKNKSFEELLNESE 65

This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. Length = 70

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 39.6 bits (93), Expect = 0.004
 Identities = 9/48 (18%), Positives = 20/48 (41%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
             +  +  E+ + +E   E  + +   EEE  + +  EEE   +   +
Sbjct: 2   TLKVHDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQ 49

Length = 325

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 39.6 bits (93), Expect = 0.004
 Identities = 10/44 (22%), Positives = 20/44 (45%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
            +  E+ + +E   E  +E+   EEE  + +  EEE   +   +
Sbjct: 6   HDLNEDADFDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQ 49

Length = 325

>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain

 Score = 39.6 bits (93), Expect = 0.004
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 12/76 (15%)

Query: 597 RGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEE---------EEEEEEEEEEEE---EE 644
           R + E  E E+E   E+++EEE+  E +E   +E         E E E+   E+E   E 
Sbjct: 210 RAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLAEQERMLEH 269

Query: 645 EEEEEEEEVRGGGKEE 660
           + +E+EE ++ G K E
Sbjct: 270 KLQEQEELLKEGFKTE 285

Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297

>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (93), Expect = 0.004
 Identities = 13/51 (25%), Positives = 24/51 (47%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
                  EE +   EE+     E+   E    EE+++++EE + ++E E E
Sbjct: 459 RASLMTMEETQRHSEEDLVNRFEDVRYEHVAGEEDDDDDEELQAQKELELE 509

Length = 591

>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]

 Score = 40.1 bits (93), Expect = 0.004
 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEE-EEEEEEEEEEEEEEEEEVRGGG 657
                  EE +   EE+     ++   E    EE+++++EE + ++E E+   G
Sbjct: 459 RASLMTMEETQRHSEEDLVNRFEDVRYEHVAGEEDDDDDEELQAQKELELEAQG 512

Length = 591

>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex subunit beta; Reviewed

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 19/32 (59%), Positives = 20/32 (62%)

Query: 632 EEEEEEEEEEEEEEEEEEEEEVRGGGKEEISL 663
             EEEEEEEEEEEEEEE   EV      E+ L
Sbjct: 403 AAEEEEEEEEEEEEEEEPVAEVMMMPAPEMQL 434

Length = 463

>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 10/59 (16%), Positives = 38/59 (64%)

Query: 586 PRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
             +E   + +   E+ E       E EE E+++++E++++  +++++++++++++E++E
Sbjct: 22  SIMEARTEALIEEEKVEIARSVMIEGEEPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80

Length = 80

>gnl|CDD|218637 pfam05558, DREPP, DREPP plasma membrane polypeptide

 Score = 38.9 bits (90), Expect = 0.004
 Identities = 18/54 (33%), Positives = 27/54 (50%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           EE++ EEE    E E++  V+E+E   EEE++EEE          +      EE
Sbjct: 132 EEKKPEEEAPAAETEKKPAVKEKEIVVEEEKKEEEAVPVAAAPSTKAPETKVEE 185

This family contains several plant plasma membrane proteins termed DREPPs as they are developmentally regulated plasma membrane polypeptides. Length = 201

>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 15/23 (65%), Positives = 19/23 (82%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEV 626
           EEE+ E+EEE E+EEE EE+ EV
Sbjct: 22  EEEKREDEEENEDEEEGEEQSEV 44

This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family includes the signal peptide. Length = 46

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

 Score = 38.5 bits (90), Expect = 0.004
 Identities = 10/59 (16%), Positives = 45/59 (76%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +L    E+ ++E EE+++ + ++++ +++++++  +++++++++ E+++E+E E++ E+
Sbjct: 66  ELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDKLED 124

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

>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional

 Score = 38.1 bits (89), Expect = 0.004
 Identities = 8/48 (16%), Positives = 13/48 (27%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
               E +     E    ++++   E    E      E       EEE 
Sbjct: 108 AALAEADGGPTAEATTPKKKKAAAEAAAAEAAAPAAEAAAAAAAEEEA 155

Length = 155

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 38.2 bits (88), Expect = 0.004
 Identities = 14/57 (24%), Positives = 33/57 (57%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++ +R+ +E ++  +++E+    +++ + E +E+ +E    E E   +E EEE  EE
Sbjct: 90  QQQQRQYQECQQRCQQQEQRPRRQQQCQRECREQYQEHGRGEGENINQEGEEERSEE 146

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 37.8 bits (87), Expect = 0.004
 Identities = 12/55 (21%), Positives = 31/55 (56%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +R   +E   + E+++ E   +E+ +EE++ Q + EE+ +   E+ ++  ++ E 
Sbjct: 17  QRRCEQETRGQREQQQCERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEP 71

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|218003 pfam04281, Tom22, Mitochondrial import receptor subunit Tom22

 Score = 38.0 bits (89), Expect = 0.004
 Identities = 9/45 (20%), Positives = 25/45 (55%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            E E+E  +E+    +   QEE ++++E++ + + +  ++ + E 
Sbjct: 5   TEVEDETFQEKPAAPKNLAQEESDDDDEDDTDTDSDISDDSDFEN 49

The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins. The N terminal region of Tom22 has been shown to have chaperone-like activity, and the C terminal region faces the intermembrane face. Length = 136

>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 2/75 (2%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           ++    P+  +    I   +R+ +EE +      E    + E   E   E EE E  E+ 
Sbjct: 331 KETELEPQERSY--FINAAQRQAQEEAKAAANIAEAIGAQAEAAVETARETEEAERAEQA 388

Query: 640 EEEEEEEEEEEEEVR 654
                 E  E+E+V 
Sbjct: 389 ALVAAAEAAEQEQVE 403

Length = 548

>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation factor RRN3

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 12/39 (30%), Positives = 29/39 (74%)

Query: 616 EEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++ ++EEEE V  +E++++E++  + ++++EEE + EV 
Sbjct: 223 DDIDDEEEERVLADEDDDDEDDMFDMDDDDEEESDPEVE 261

This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. Length = 554

>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 14/51 (27%), Positives = 24/51 (47%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           L+ R  R  E E +        E  E EEE +  ++ + ++ EE ++  EE
Sbjct: 259 LLPRATRLPEPEPQPPPPPPPPEPPEPEEEPDEPDQTDPDDGEETDQIPEE 309

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll]. Length = 589

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

 Score = 40.0 bits (94), Expect = 0.004
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
              I   R  E E E +++  E+  E+E+  EE E+ + EE +E   + EE +++ E+ E
Sbjct: 303 LKEIHEARLNEEERELKKKFTEKIREKEKRLEELEQNLIEERKELNSKLEEIQKKLEDLE 362

Query: 649 EEEE 652
           +  E
Sbjct: 363 KRLE 366

Length = 373

>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2)

 Score = 40.3 bits (94), Expect = 0.004
 Identities = 18/74 (24%), Positives = 33/74 (44%)

Query: 578 SDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEE 637
           +D+ E  +      I+   R E E+   +E EE+      EEE++ ++ + E ++   EE
Sbjct: 681 TDESEENAENKVASIEGEHRKEIEDLLFDESEEDNIVGMIEEEKDADDFKNEWQDISLEE 740

Query: 638 EEEEEEEEEEEEEE 651
            E  E     E+  
Sbjct: 741 LEALEANLLAEQNS 754

All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1034

>gnl|CDD|218598 pfam05470, eIF-3c_N, Eukaryotic translation initiation factor 3 subunit 8 N-terminus

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 20/60 (33%), Positives = 38/60 (63%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E E+EEEEE+E+++++  ++E+E+E+ V   EE     E   +  +E++EE+E+     K
Sbjct: 136 ESEDEEEEEDEDDDDDGSDDEDEDEDGVGATEEVAASSESGVDRVKEDDEEDEDADLSKK 195

The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA. Length = 593

>gnl|CDD|222977 PHA03089, PHA03089, late transcription factor VLTF-4; Provisional

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 16/72 (22%), Positives = 32/72 (44%)

Query: 572 IKVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEE 631
           I   KTS + +    + +   +  ++ + +EE  E   EE  + EE EE +++   E  +
Sbjct: 45  IPSKKTSKKKKTTPRKKKTTKKTKKKKKEKEEVPELAAEELSDSEENEENDKKVDYELPK 104

Query: 632 EEEEEEEEEEEE 643
            +    E   E+
Sbjct: 105 VQNTAAEVNHED 116

Length = 191

>gnl|CDD|147845 pfam05914, RIB43A, RIB43A

 Score = 39.6 bits (93), Expect = 0.004
 Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 592 IQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           +  IR+G +E++ +E+E   EEE+  E+E + + + +       E +E    +E  ++
Sbjct: 282 LAAIRKG-QEQQLQEKERRREEEQLREKEWDRQAINQARAAVLLERQERRLRKELRKQ 338

This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialised set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterized in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialised protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organising their three-dimensional structure. Human RIB43A homologues could represent a structural requirement in centriole replication in dividing cells. Length = 379

>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional

 Score = 40.2 bits (94), Expect = 0.004
 Identities = 21/57 (36%), Positives = 36/57 (63%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGG 656
           +E +E++EE++EE+ EE + EE +EE +EEE+    E  E+   E  ++  +EV  G
Sbjct: 277 KELKEKKEEKDEEKSEEVKTEEVDEEFEEEEKGFYYELYEKVNIEANKKFIKEVIAG 333

Length = 1627

>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release factors

 Score = 37.1 bits (87), Expect = 0.004
 Identities = 18/36 (50%), Positives = 23/36 (63%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           E  EEEE++E  E  EEE EE++ E EEE EE  + 
Sbjct: 1   ELLEEEEDDEMRELAEEELEELEAELEEELEELLKL 36

Length = 116

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	682
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.88
PRK06548	161	ribonuclease H; Provisional	99.87
PRK08719	147	ribonuclease H; Reviewed	99.85
PRK00203	150	rnhA ribonuclease H; Reviewed	99.82
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.82
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.7
KOG3752|consensus	371		99.7
PRK13907	128	rnhA ribonuclease H; Provisional	99.68
PRK07708	219	hypothetical protein; Validated	99.58
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.41
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	99.14
cd01650	220	RT_nLTR_like RT_nLTR: Non-LTR (long terminal repea	98.86
cd01651	226	RT_G2_intron RT_G2_intron: Reverse transcriptases	98.14
cd01648	119	TERT TERT: Telomerase reverse transcriptase (TERT)	98.11
cd00304	98	RT_like RT_like: Reverse transcriptase (RT, RNA-de	98.0
PF00078	214	RVT_1: Reverse transcriptase (RNA-dependent DNA po	97.92
cd03487	214	RT_Bac_retron_II RT_Bac_retron_II: Reverse transcr	97.9
cd01646	158	RT_Bac_retron_I RT_Bac_retron_I: Reverse transcrip	97.83
cd03714	119	RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) oc	96.7
cd01709	346	RT_like_1 RT_like_1: A subfamily of reverse transc	96.33
cd01645	213	RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from r	96.26
cd03715	210	RT_ZFREV_like RT_ZFREV_like: A subfamily of revers	95.22
PF09004	42	DUF1891: Domain of unknown function (DUF1891); Int	92.92
cd01647	177	RT_LTR RT_LTR: Reverse transcriptases (RTs) from r	88.54
KOG1832|consensus	1516		86.1
KOG4768|consensus	796		83.3

>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]

Probab=99.88  E-value=1.8e-22  Score=182.08  Aligned_cols=127  Identities=20%  Similarity=0.206  Sum_probs=105.2

Q ss_pred             CeEEEEeCCCCC--CCCceEEEEEc-c-e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhh
Q psy3428         327 SHTICYTDGSKT--PTTTGCAYSVG-N-V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALS  400 (682)
Q Consensus       327 ~~~~iytDgS~~--~~~~G~g~~~~-~-~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~  400 (682)
                      ..+.||||||+.  +|..|+|+|+. . .  ..+.... .+||++||+.|++.||+++.+.+...|.|+|||++|+++|.
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~   80 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT   80 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence            368999999975  46799998875 1 1  2333344 89999999999999999999888999999999999999997


Q ss_pred             cCCCC-----------cH-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCC
Q psy3428         401 NVRFI-----------NP-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGT  454 (682)
Q Consensus       401 ~~~~~-----------~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  454 (682)
                      .+..+           .| ..++++..+.++..+...|.+.|||||+|.++||+||+||+.|+...
T Consensus        81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            43111           12 35688999999998888999999999999999999999999998765

>PRK06548 ribonuclease H; Provisional

Probab=99.87  E-value=9.5e-22  Score=181.33  Aligned_cols=129  Identities=23%  Similarity=0.261  Sum_probs=99.8

Q ss_pred             CCeEEEEeCCCCCC--CCceEEEEEcceeeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhh---
Q psy3428         326 TSHTICYTDGSKTP--TTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALS---  400 (682)
Q Consensus       326 ~~~~~iytDgS~~~--~~~G~g~~~~~~~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~---  400 (682)
                      +..+.||||||+..  +..|+|+++............+||++|||+|++.||+.+.. ....|.|+|||++|++++.   
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~   81 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWV   81 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHH
Confidence            45699999999764  56889988764322222234689999999999999986643 4457999999999999997   


Q ss_pred             ------cCCCC--cHH-HHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCCC
Q psy3428         401 ------NVRFI--NPL-ITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTP  456 (682)
Q Consensus       401 ------~~~~~--~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~  456 (682)
                            +++..  .++ .+++++.+..+... ..|.|.|||||+|++|||.||+||++|+.....
T Consensus        82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~~  145 (161)
T PRK06548         82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFST  145 (161)
T ss_pred             HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhcc
Confidence                  33332  233 47888888887766 579999999999999999999999999865543

>PRK08719 ribonuclease H; Reviewed

Probab=99.85  E-value=4.5e-21  Score=175.84  Aligned_cols=121  Identities=22%  Similarity=0.276  Sum_probs=94.2

Q ss_pred             CeEEEEeCCCCCCCC-----ceEEEEEcc----e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHH
Q psy3428         327 SHTICYTDGSKTPTT-----TGCAYSVGN----V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSS  395 (682)
Q Consensus       327 ~~~~iytDgS~~~~~-----~G~g~~~~~----~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~  395 (682)
                      ..++||||||+..++     +|+|+++..    .  .....+....||++||+.|++.||+.+.+.    ..|+|||++|
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            468999999985432     589987642    1  234445566899999999999999998652    3799999999


Q ss_pred             HHhhh--------cCCCCc---H-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCccc
Q psy3428         396 LAALS--------NVRFIN---P-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTT  452 (682)
Q Consensus       396 i~~l~--------~~~~~~---~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  452 (682)
                      ++++.        ++...+   + ..+++++.+..+.. ...|.|.|||||+|++|||.||+||++|++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            99983        333222   2 23677888877766 477999999999999999999999999875

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.82  E-value=4.1e-20  Score=171.58  Aligned_cols=125  Identities=19%  Similarity=0.224  Sum_probs=94.5

Q ss_pred             eEEEEeCCCCCC--CCceEEEEEc--ceee-eecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         328 HTICYTDGSKTP--TTTGCAYSVG--NVVR-STLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       328 ~~~iytDgS~~~--~~~G~g~~~~--~~~~-~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      .+.||||||+..  +..|+|+++.  +... ........||+.|||.|++.||+.+..  ...+.|+|||++++++|..+
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            489999999864  4588888764  2221 112234679999999999999998864  46799999999999999752


Q ss_pred             ---------CCC--cHH-HHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCC
Q psy3428         403 ---------RFI--NPL-ITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTT  455 (682)
Q Consensus       403 ---------~~~--~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  455 (682)
                               ...  .++ .+++++.+..+... ..|.|.|||||+|++||+.||+|||+|+....
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence                     111  122 24566666666544 78999999999999999999999999987653

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=99.82  E-value=1e-20  Score=172.54  Aligned_cols=117  Identities=34%  Similarity=0.405  Sum_probs=88.4

Q ss_pred             CeEEEEeCCCCCC--CCceEEEEEc-ceeeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhc--
Q psy3428         327 SHTICYTDGSKTP--TTTGCAYSVG-NVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSN--  401 (682)
Q Consensus       327 ~~~~iytDgS~~~--~~~G~g~~~~-~~~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~--  401 (682)
                      ..+.||||||+.+  +..|+|+++. +......++ ..+++.||+.||..||+ +.  ..+.+.|+|||++++..+..  
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~--~~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-AL--EHRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-TH--STSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hh--hcccccccccHHHHHHHHHHhc
Confidence            4689999999653  3457776554 333444455 88999999999999999 44  33899999999999998866  


Q ss_pred             ---CCCCc----HHHHHHHHHHHHHHhcCCceEEEEecCCCCC-chhHHHHHHhcCcc
Q psy3428         402 ---VRFIN----PLITKVYSTWSYLKLCKKDITFMWCPSHCGI-KGNEIVDVAAKNPT  451 (682)
Q Consensus       402 ---~~~~~----~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~a~  451 (682)
                         .....    ++..+|++.+    ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence               33222    3444555433    55789999999999999 69999999999886

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner

Probab=99.70  E-value=2.3e-16  Score=142.11  Aligned_cols=122  Identities=29%  Similarity=0.322  Sum_probs=98.2

Q ss_pred             EEEeCCCCCCC--CceEEEEEccee--ee---ecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         330 ICYTDGSKTPT--TTGCAYSVGNVV--RS---TLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       330 ~iytDgS~~~~--~~G~g~~~~~~~--~~---~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      .+|||||...+  ++|+|+++.+..  ..   .......+++.+|+.|++.||+.+...+..++.|++||+.++..+.+.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            48999998764  689998876421  11   112257899999999999999999988899999999999999999987


Q ss_pred             CC-CcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcc
Q psy3428         403 RF-INPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPT  451 (682)
Q Consensus       403 ~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  451 (682)
                      .. .......++..+..+...+..+.|.|||+|+|+.+|+.||.|||.|+
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            65 23344555555666666788999999999999999999999999874

One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

>KOG3752|consensus

Probab=99.70  E-value=6.5e-17  Score=163.13  Aligned_cols=128  Identities=25%  Similarity=0.240  Sum_probs=100.6

Q ss_pred             CCCeEEEEeCCCCCCC-----CceEEEEEcc---eeeeecCC-CCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHH
Q psy3428         325 YTSHTICYTDGSKTPT-----TTGCAYSVGN---VVRSTLLN-PVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSS  395 (682)
Q Consensus       325 ~~~~~~iytDgS~~~~-----~~G~g~~~~~---~~~~~~~~-~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~  395 (682)
                      +.+..++|||||+..+     .+|+|++++.   ...+..+. ..+|||.|||.|+..||+.+.+.+..+|+|.|||+++
T Consensus       209 ~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~  288 (371)
T KOG3752|consen  209 EIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYF  288 (371)
T ss_pred             cccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHH
Confidence            3456899999998763     3899999974   24455554 7899999999999999999998888899999999999


Q ss_pred             HHhhhcCCCC-----------cH------HHHHHHHHHHHHHhc--CCceEEEEecCCCCCchhHHHHHHhcCccc
Q psy3428         396 LAALSNVRFI-----------NP------LITKVYSTWSYLKLC--KKDITFMWCPSHCGIKGNEIVDVAAKNPTT  452 (682)
Q Consensus       396 i~~l~~~~~~-----------~~------~~~~i~~~~~~l~~~--~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  452 (682)
                      +++|+.+...           ++      ..+..+..+..|...  +..|.+.|||||.|+.|||+||.||++++.
T Consensus       289 i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  289 INSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            9998643211           11      123444555555443  689999999999999999999999999854

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.68  E-value=1.6e-16  Score=143.76  Aligned_cols=120  Identities=18%  Similarity=0.139  Sum_probs=98.8

Q ss_pred             EEEEeCCCCCC--CCceEEEEEcceeee--e-cCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcCC
Q psy3428         329 TICYTDGSKTP--TTTGCAYSVGNVVRS--T-LLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVR  403 (682)
Q Consensus       329 ~~iytDgS~~~--~~~G~g~~~~~~~~~--~-~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~~  403 (682)
                      +.||||||+..  +.+|+|+++.+....  . ......+|+.||+.|++.||+.+...+..+|.|++||+.+++.+.+..
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~   81 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY   81 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence            67999999864  569999988643221  1 122457999999999999999999988889999999999999999876


Q ss_pred             CCcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCccc
Q psy3428         404 FINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTT  452 (682)
Q Consensus       404 ~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~  452 (682)
                      ...+....+++.+..+...+..+.|.|||+    ++|+.||.||+.|+.
T Consensus        82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~  126 (128)
T PRK13907         82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL  126 (128)
T ss_pred             hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence            555556777888888888888899999995    689999999998864

>PRK07708 hypothetical protein; Validated

Probab=99.58  E-value=2.1e-14  Score=140.16  Aligned_cols=128  Identities=13%  Similarity=0.070  Sum_probs=99.1

Q ss_pred             CCCeEEEEeCCCCC--CCCceEEEEEcc--e--ee----eecCCCCCchHHHHHHHHHHHHHHHHcCCCCc--EEEEcCC
Q psy3428         325 YTSHTICYTDGSKT--PTTTGCAYSVGN--V--VR----STLLNPVNSIFSAELIAIFLCLEAILDSPSGK--FLIVTDS  392 (682)
Q Consensus       325 ~~~~~~iytDgS~~--~~~~G~g~~~~~--~--~~----~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~--v~i~sDs  392 (682)
                      .++.+++|+|||..  ++++|+|+++..  .  ..    ...++..+||+.||+.|++.||+.+...+.+.  |.|++||
T Consensus        70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS  149 (219)
T PRK07708         70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS  149 (219)
T ss_pred             CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence            45679999999974  567999988752  1  11    12455568999999999999999999887654  8999999


Q ss_pred             HHHHHhhhcCC-CCcHHHHHHHHHHHHHHhcC-CceEEEEecCCCCCchhHHHHHHhcCcccCCCC
Q psy3428         393 RSSLAALSNVR-FINPLITKVYSTWSYLKLCK-KDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTP  456 (682)
Q Consensus       393 ~~~i~~l~~~~-~~~~~~~~i~~~~~~l~~~~-~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~  456 (682)
                      +.+++.+.+.. ..++..+.+.+.+..+..+. ..+.|.|||    +..|+.||+||++|+.....
T Consensus       150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVI  211 (219)
T ss_pred             HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCC
Confidence            99999998765 34555666666666555443 357889998    78899999999999986544

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.41  E-value=1.5e-12  Score=140.06  Aligned_cols=123  Identities=17%  Similarity=0.164  Sum_probs=100.4

Q ss_pred             eEEEEeCCCCCC--CCceEEEEEccee-------eeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHh
Q psy3428         328 HTICYTDGSKTP--TTTGCAYSVGNVV-------RSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAA  398 (682)
Q Consensus       328 ~~~iytDgS~~~--~~~G~g~~~~~~~-------~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~  398 (682)
                      .+.||||||+..  +.+|+|+++.+..       ....++ .+||+.||+.|++.||+.+.+.+.++|.|++||+.+++.
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~   80 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ   80 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence            478999999765  4689998876321       122233 789999999999999999999888999999999999999


Q ss_pred             hhcCCC-CcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCC
Q psy3428         399 LSNVRF-INPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTT  455 (682)
Q Consensus       399 l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  455 (682)
                      +.+... +++-...++..+..+..++..+.|.|||    ..+|+.||.||+.|+....
T Consensus        81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~~  134 (372)
T PRK07238         81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIP----RARNAHADRLANEAMDAAA  134 (372)
T ss_pred             hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECC----chhhhHHHHHHHHHHHhhc
Confidence            987653 4555667777778888888999999999    4789999999999976554

>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B

Probab=99.14  E-value=9.8e-11  Score=98.04  Aligned_cols=85  Identities=16%  Similarity=0.143  Sum_probs=70.0

Q ss_pred             hHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcCCCCcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHH
Q psy3428         363 IFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEI  442 (682)
Q Consensus       363 ~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~  442 (682)
                      +..||+.|+..||+.+.+.+.++|.|.|||+.++..|.+..........+...+..+...+..+.|.|||    ..+|..
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~   76 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV   76 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence            4689999999999999999999999999999999999887544335567777778888889999999999    999999


Q ss_pred             HHHHhcCcc
Q psy3428         443 VDVAAKNPT  451 (682)
Q Consensus       443 AD~lAk~a~  451 (682)
                      ||.|||.|.
T Consensus        77 A~~LA~~a~   85 (87)
T PF13456_consen   77 ADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999999875

>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT)

Probab=98.86  E-value=2.8e-09  Score=106.11  Aligned_cols=98  Identities=23%  Similarity=0.387  Sum_probs=83.0

Q ss_pred             hhHHHHHHHHhhccc-----------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCC
Q psy3428           8 HKVILMSLLFVGFAV-----------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPG   76 (682)
Q Consensus         8 ~~~~llfllyi~~~~-----------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~   76 (682)
                      ..|++||.+|.+++.           ....+....||| |+++++.+..     ..++..++.+..|+..+|+++|  ++
T Consensus       112 ~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaD-D~~i~~~~~~-----~~~~~~~~~~~~~~~~~gl~in--~~  183 (220)
T cd01650         112 PLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYAD-DIVLFSEGKS-----RKLQELLQRLQEWSKESGLKIN--PS  183 (220)
T ss_pred             cccHHHHHHHHHHHHHHHHhhccccCCCCccceEEecc-ceeeeccCCH-----HHHHHHHHHHHHHHHHcCCEEC--hh
Confidence            356799999988752           245788999999 9999988876     3489999999999999999999  99


Q ss_pred             eeEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428          77 KSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW  114 (682)
Q Consensus        77 Kt~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l  114 (682)
                      ||++++++..... ...+.+++..+..+..+||||+.|
T Consensus       184 Kt~~~~~~~~~~~-~~~~~~~~~~~~~~~~~kyLG~~i  220 (220)
T cd01650         184 KSKVMLIGNKKKR-LKDITLNGTPIEAVETFKYLGVTI  220 (220)
T ss_pred             heEEEEecCCCcc-hhhhhhcCCcccCCCCCeeccccC
Confidence            9999999987654 333788899999999999999975

This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.

>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin

Probab=98.14  E-value=2.5e-06  Score=85.16  Aligned_cols=80  Identities=18%  Similarity=0.157  Sum_probs=65.2

Q ss_pred             hhhHHHHHHHHhhccc----------------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCc
Q psy3428           7 IHKVILMSLLFVGFAV----------------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTI   70 (682)
Q Consensus         7 ~~~~~llfllyi~~~~----------------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~   70 (682)
                      -..|++||.+|+.++.                ....+....||| |+++++.+...      ++..++.+..|+...||.
T Consensus       131 ~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~D-D~~i~~~~~~~------~~~~~~~i~~~~~~~gl~  203 (226)
T cd01651         131 GVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYAD-DFVIGVRGPKE------AEEIKELIREFLEELGLE  203 (226)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecC-ceEEecCCHHH------HHHHHHHHHHHHHHcCCe
Confidence            3456789999987641                126788999999 99999877665      788899999999999999


Q ss_pred             ccCCCCeeEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428          71 FSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW  114 (682)
Q Consensus        71 ~n~~~~Kt~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l  114 (682)
                      +|  ++||++++|+                   .+.+.|||..|
T Consensus       204 ln--~~Kt~i~~~~-------------------~~~~~fLG~~~  226 (226)
T cd01651         204 LN--PEKTRITHFK-------------------SEGFDFLGFTF  226 (226)
T ss_pred             ec--hhhcceeecC-------------------CCCCeeCCeEC
Confidence            99  9999999997                   35677888764

RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).

>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT)

Probab=98.11  E-value=7.7e-06  Score=72.67  Aligned_cols=85  Identities=18%  Similarity=0.020  Sum_probs=63.0

Q ss_pred             hhHHHHHHHHhhccc---------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHH-hHhCCcccCCCCe
Q psy3428           8 HKVILMSLLFVGFAV---------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWS-DLNGTIFSTDPGK   77 (682)
Q Consensus         8 ~~~~llfllyi~~~~---------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~-~~~gl~~n~~~~K   77 (682)
                      --|++||.+|...+.         .........||| |+.+++.+..      .++..++.+..|. .+.||.+|  ++|
T Consensus        25 ~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaD-D~li~~~~~~------~~~~~~~~l~~~l~~~~gl~iN--~~K   95 (119)
T cd01648          25 PLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVD-DFLLITTSLD------KAIKFLNLLLRGFINQYKTFVN--FDK   95 (119)
T ss_pred             chHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeC-cEEEEeCCHH------HHHHHHHHHHHhhHHhhCeEEC--ccc
Confidence            346688999976541         124566788999 9988876643      3688999999997 99999999  999


Q ss_pred             eEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeC
Q psy3428          78 SVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWD  115 (682)
Q Consensus        78 t~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld  115 (682)
                      |++.....              .......+.|||+.|+
T Consensus        96 t~~~~~~~--------------~~~~~~~~~flG~~i~  119 (119)
T cd01648          96 TQINFSFA--------------QLDSSDLIPWCGLLIN  119 (119)
T ss_pred             ceeecccc--------------ccCCCCccCceeEeeC
Confidence            99886542              0123356899999875

Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at

>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family

Probab=98.00  E-value=1.6e-05  Score=67.86  Aligned_cols=80  Identities=19%  Similarity=0.137  Sum_probs=63.5

Q ss_pred             eehhhHHHHHHHHhhcccc-----CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeE
Q psy3428           5 VQIHKVILMSLLFVGFAVT-----GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSV   79 (682)
Q Consensus         5 ~~~~~~~llfllyi~~~~~-----~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~   79 (682)
                      +|.-.|+++|.+|...+..     ..++....|+| |+.+.+...       .++..+..+..|+.++|+.+|  ++||+
T Consensus        14 qG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~D-D~~i~~~~~-------~~~~~~~~l~~~l~~~gl~ln--~~Kt~   83 (98)
T cd00304          14 QGSPLSPALANLYMEKLEAPILKQLLDITLIRYVD-DLVVIAKSE-------QQAVKKRELEEFLARLGLNLS--DEKTQ   83 (98)
T ss_pred             CCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeC-cEEEEeCcH-------HHHHHHHHHHHHHHHcCcEEC--hheeE
Confidence            3455678899998877532     35788999999 999987766       368889999999999999999  99998


Q ss_pred             EEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428          80 CIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW  114 (682)
Q Consensus        80 ~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l  114 (682)
                      .+                    .....++|||+.+
T Consensus        84 ~~--------------------~~~~~~~flG~~~   98 (98)
T cd00304          84 FT--------------------EKEKKFKFLGILV   98 (98)
T ss_pred             Ee--------------------cCCCCeeeeceeC
Confidence            86                    1346688888763

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.

>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons

Probab=97.92  E-value=5.8e-06  Score=81.49  Aligned_cols=78  Identities=26%  Similarity=0.357  Sum_probs=63.7

Q ss_pred             hhHHHHHHHHhhccc-----c-CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEE
Q psy3428           8 HKVILMSLLFVGFAV-----T-GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCI   81 (682)
Q Consensus         8 ~~~~llfllyi~~~~-----~-~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i   81 (682)
                      .-|+++|.+|...+.     . ..++....||| |+.+++.....      ++..++.+.+|+.++||.+|  ++||+++
T Consensus       131 ~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~D-D~~i~~~~~~~------~~~~~~~i~~~~~~~gl~ln--~~Kt~~~  201 (214)
T PF00078_consen  131 PLSPLLFNIYLDDLDRELQQELNPDISYLRYAD-DILIISKSKEE------LQKILEKISQWLEELGLKLN--PEKTKIL  201 (214)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETT-EEEEEESSHHH------HHHHHHHHHHHHHHTTSBCS--STTTSCS
T ss_pred             cccchhhccccccccccccccccccccceEecc-ccEEEECCHHH------HHHHHHHHHHHHHHCCCEEC--hHHEEEE
Confidence            347899999988751     1 26788999999 99999877444      89999999999999999999  9999877


Q ss_pred             EecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428          82 DFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW  114 (682)
Q Consensus        82 ~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l  114 (682)
                      +                    ..+.++|||+.|
T Consensus       202 ~--------------------~~~~~~~lG~~i  214 (214)
T PF00078_consen  202 H--------------------PSDSVKFLGYVI  214 (214)
T ss_dssp             ----------------------ESSEEETTEEE
T ss_pred             e--------------------CCCCEEEEeEEC
Confidence            6                    568899999875

The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....

>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=97.90  E-value=2.8e-05  Score=76.96  Aligned_cols=85  Identities=15%  Similarity=0.073  Sum_probs=66.6

Q ss_pred             ehhhHHHHHHHHhhccc-------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428           6 QIHKVILMSLLFVGFAV-------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS   78 (682)
Q Consensus         6 ~~~~~~llfllyi~~~~-------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt   78 (682)
                      |...|++||.+|..++.       ...++....||| |++|++.+...    ..++..+..+..|+.+.||.+|  ++||
T Consensus       107 G~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaD-D~~i~~~~~~~----~~~~~~~~~i~~~l~~~gL~ln--~~Kt  179 (214)
T cd03487         107 GAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYAD-DITFSSNKKLK----EALDKLLEIIRSILSEEGFKIN--KSKT  179 (214)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEec-cEEEEccccch----hHHHHHHHHHHHHHHHCCceeC--CCce
Confidence            34456799999988642       234678899999 99998877653    3478899999999999999999  9999


Q ss_pred             EEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428          79 VCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK  117 (682)
Q Consensus        79 ~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~  117 (682)
                      +++..+                    ..+.+||+.+...
T Consensus       180 ~i~~~~--------------------~~~~~~G~~i~~~  198 (214)
T cd03487         180 RISSKG--------------------SRQIVTGLVVNNG  198 (214)
T ss_pred             EEccCC--------------------CCcEEEEEEEeCC
Confidence            998653                    3456889888764

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons

Probab=97.83  E-value=3.7e-05  Score=72.11  Aligned_cols=85  Identities=16%  Similarity=0.195  Sum_probs=67.0

Q ss_pred             hhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEE
Q psy3428           7 IHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCI   81 (682)
Q Consensus         7 ~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i   81 (682)
                      -..|++|+.+|+.++.     ....+....||| |+++++.....      ++..++.+..|..+.||.+|  ++||+.+
T Consensus        58 ~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~D-D~~i~~~~~~~------~~~~~~~i~~~l~~~gL~ln--~~Kt~~~  128 (158)
T cd01646          58 PLTSRFLANIYLNDVDHELKSKLKGVDYVRYVD-DIRIFADSKEE------AEEILEELKEFLAELGLSLN--LSKTEIL  128 (158)
T ss_pred             cchHHHHHHHHHHHHHHHHHhccCCceEEEecC-cEEEEcCCHHH------HHHHHHHHHHHHHHCCCEEC--hhhceee
Confidence            3457788888887752     146788999999 99999865433      68899999999999999999  9999999


Q ss_pred             EecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428          82 DFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK  117 (682)
Q Consensus        82 ~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~  117 (682)
                      ++....                 ..+.+||..+...
T Consensus       129 ~~~~~~-----------------~~~~flg~~~~~~  147 (158)
T cd01646         129 PLPEGT-----------------ASKDFLGYRFSPI  147 (158)
T ss_pred             ecCCCC-----------------ccccccceEeehh
Confidence            886532                 5577888877653

The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.

>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons

Probab=96.70  E-value=0.0049  Score=54.65  Aligned_cols=68  Identities=19%  Similarity=0.056  Sum_probs=45.3

Q ss_pred             eeehhhHHHHHHHHhhcccc---CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHH-HHhHhCCcccCCCCeeE
Q psy3428           4 EVQIHKVILMSLLFVGFAVT---GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHK-WSDLNGTIFSTDPGKSV   79 (682)
Q Consensus         4 ~~~~~~~~llfllyi~~~~~---~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~-W~~~~gl~~n~~~~Kt~   79 (682)
                      .+|.-.||.+|--++.-+..   .....+..|+| |+.|.+.+   .+.   .+..+..+.. -++++|+.+|  ++||+
T Consensus        35 p~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~D-Dili~~~~---~~~---~~~~~~~l~~~~l~~~gl~ln--~~K~~  105 (119)
T cd03714          35 PFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLD-DLLIIASS---IKT---SEAVLRHLRATLLANLGFTLN--LEKSK  105 (119)
T ss_pred             CCcccchHHHHHHHHHHHHHHhhcCCeEEEEEec-CeEEEeCc---HHH---HHHHHHHHHHHHHHHcCCccC--hhhcE
Confidence            35666677777666654321   34567889999 99987665   222   2334443333 6889999999  99998


Q ss_pred             E
Q psy3428          80 C   80 (682)
Q Consensus        80 ~   80 (682)
                      +
T Consensus       106 ~  106 (119)
T cd03714         106 L  106 (119)
T ss_pred             e
Confidence            6

Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.

>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs)

Probab=96.33  E-value=0.058  Score=55.89  Aligned_cols=109  Identities=16%  Similarity=0.128  Sum_probs=72.0

Q ss_pred             hhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEEE
Q psy3428           8 HKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCID   82 (682)
Q Consensus         8 ~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i~   82 (682)
                      -.|+||=.+|.+++.     ...+....-||| |+.+++.  . .+    ...++..+.++++..||++|  ++||.++.
T Consensus        89 viSplLaNiyL~~lD~~v~~~~~g~~l~RYaD-D~vi~~~--~-~~----a~~aw~~i~~fl~~lGLelN--~eKT~iV~  158 (346)
T cd01709          89 ALSDVFGELVLFCLDFAVNQATDGGLLYRLHD-DLWFWGQ--P-ET----CAKAWKAIQEFAKVMGLELN--KEKTGSVY  158 (346)
T ss_pred             hhhHHHHHHHHHHHHHHHHhcCCCceEEEEcC-eEEEEcC--H-HH----HHHHHHHHHHHHHHcCceec--cccceEEE
Confidence            356788888877652     225678899999 9999833  2 22    45666688899999999999  99999998


Q ss_pred             ecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC-CCch-------HHHHHHHHH
Q psy3428          83 FNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK-MNWS-------LHIQLLKNR  130 (682)
Q Consensus        83 f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~-L~~~-------~Hi~~~~~k  130 (682)
                      ....++....    .-...=|...++|-=+.||+. .+|.       .||+.....
T Consensus       159 ~~~~~r~~~~----~~~~~LP~g~i~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~Q  210 (346)
T cd01709         159 LSDDTKTRDT----TIDATLPEGPVRWGFLKLDPKTGRWEIDQSQVDAHIDELRKQ  210 (346)
T ss_pred             eccCCccCCC----cccccCCCCCceeeeEEecCCCCcEEeeHHHHHHHHHHHHHH
Confidence            8754331111    011122455677777788864 6675       466555443

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.

>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs)

Probab=96.26  E-value=0.0051  Score=60.70  Aligned_cols=67  Identities=16%  Similarity=0.104  Sum_probs=50.7

Q ss_pred             eeehhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428           4 EVQIHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS   78 (682)
Q Consensus         4 ~~~~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt   78 (682)
                      -+|.-.|+.+|-.|+....     ...++....|+| |+.|.+.  +.++    ....+..+...+.++|+.+|  ++||
T Consensus       130 P~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~D-Dili~s~--~~~~----~~~~l~~v~~~l~~~gl~ln--~~K~  200 (213)
T cd01645         130 PQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMD-DILIASD--LEGQ----LREIYEELRQTLLRWGLTIP--PEKV  200 (213)
T ss_pred             CCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcC-CEEEEcC--CHHH----HHHHHHHHHHHHHHCCCEeC--HHHE
Confidence            3566778889988887542     123567889999 9987744  4333    67788888888999999999  9999


Q ss_pred             E
Q psy3428          79 V   79 (682)
Q Consensus        79 ~   79 (682)
                      +
T Consensus       201 ~  201 (213)
T cd01645         201 Q  201 (213)
T ss_pred             e
Confidence            6

RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.

>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT

Probab=95.22  E-value=0.023  Score=55.96  Aligned_cols=81  Identities=19%  Similarity=0.146  Sum_probs=59.5

Q ss_pred             eeeehhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCe
Q psy3428           3 TEVQIHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGK   77 (682)
Q Consensus         3 ~~~~~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~K   77 (682)
                      ..+|.--++.+|-.++....     ...++....|.| |+.|..  ++.++    ....++.+..-+.++|+.+|  ++|
T Consensus       125 lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~D-Dili~s--~~~~e----~~~~l~~v~~~l~~~gl~l~--~~K  195 (210)
T cd03715         125 LPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVD-DLLLAA--DSEED----CLKGTDALLTHLGELGYKVS--PKK  195 (210)
T ss_pred             EeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECC-cEEEec--CCHHH----HHHHHHHHHHHHHHCCCCcC--HHH
Confidence            34666677888877765431     124567889999 998874  45544    56788888888999999999  999


Q ss_pred             eEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428          78 SVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW  114 (682)
Q Consensus        78 t~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l  114 (682)
                      |+..                      +++++|||.++
T Consensus       196 ~~~~----------------------~~~v~fLG~~~  210 (210)
T cd03715         196 AQIC----------------------RAEVKFLGVVW  210 (210)
T ss_pred             eeCC----------------------CCceEEeeEEC
Confidence            9743                      36788999764

An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.

>PF09004 DUF1891: Domain of unknown function (DUF1891); InterPro: IPR015095 This domain is found at the extreme N terminus of eukaryotic alkylated DNA repair protein homologs

Probab=92.92  E-value=0.017  Score=40.04  Aligned_cols=42  Identities=26%  Similarity=0.431  Sum_probs=7.9

Q ss_pred             chHHHHHHHHHHHHHHHHHHhhhcccCCCChHHHHHHHHHhccc
Q psy3428         120 WSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLP  163 (682)
Q Consensus       120 ~~~Hi~~~~~ka~~~~~~L~~l~~~~~g~~~~~~~~ly~a~v~p  163 (682)
                      |+.|+..+.+||...++.||++.  +..+++..+..+|+++|.+
T Consensus         1 W~~n~~~~~KKa~qRlyFLRkl~--k~~~~~~~l~lfY~s~IeS   42 (42)
T PF09004_consen    1 WTSNTTSLYKKAQQRLYFLRKLR--KFNVDSKLLTLFYHSVIES   42 (42)
T ss_dssp             ---------------------------SS-----SHTTTTT---
T ss_pred             CCcchHHHHHHHHhHHHHHHHHH--HccchhHHHHHHHHHHhcC
Confidence            78899999999999999999995  5678999999999988753

; GO: 0008168 methyltransferase activity, 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process; PDB: 2CQ2_A 3THT_C 3THP_A.

>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template

Probab=88.54  E-value=0.67  Score=43.36  Aligned_cols=68  Identities=13%  Similarity=0.097  Sum_probs=44.1

Q ss_pred             eeehhhHHHHHHHHhhcccc-CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEE
Q psy3428           4 EVQIHKVILMSLLFVGFAVT-GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVC   80 (682)
Q Consensus         4 ~~~~~~~~llfllyi~~~~~-~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~   80 (682)
                      .+|.-.++.+|.-.+..+.. ........|.| |+.|...  +.++.    ...+..+..-..++|+.+|  ++||+.
T Consensus        97 p~G~~~s~~~~~~~~~~~l~~~~~~~~~~y~D-Di~i~~~--~~~~~----~~~~~~~~~~l~~~~~~~~--~~K~~~  165 (177)
T cd01647          97 PFGLKNAPATFQRLMNKILGDLLGDFVEVYLD-DILVYSK--TEEEH----LEHLREVLERLREAGLKLN--PEKCEF  165 (177)
T ss_pred             cCCCccHHHHHHHHHHhhhccccccccEEEec-CccccCC--CHHHH----HHHHHHHHHHHHHcCCEeC--HHHcee
Confidence            35555666666666554422 12456778999 9988754  44443    4455555566667999999  999964

RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.

>KOG1832|consensus

Probab=86.10  E-value=0.2  Score=56.88  Aligned_cols=15  Identities=13%  Similarity=0.036  Sum_probs=6.5

Q ss_pred             EEEecCe-EEEEecCCH
Q psy3428          31 CDQDYDL-LIIGRSKDL   46 (682)
Q Consensus        31 ~yAD~D~-~i~~~~~~~   46 (682)
                      .||= |+ +|++.-++.
T Consensus       627 ~~Al-~vL~i~t~iP~i  642 (1516)
T KOG1832|consen  627 QYAL-GVLHIVTSIPDI  642 (1516)
T ss_pred             HHHH-hheeeeEecchH
Confidence            4555 44 333444444

>KOG4768|consensus

Probab=83.30  E-value=4.9  Score=44.53  Aligned_cols=129  Identities=11%  Similarity=0.072  Sum_probs=72.8

Q ss_pred             CCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEEEecCCCCCCCCceeeCCeeeccc
Q psy3428          25 VGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFV  104 (682)
Q Consensus        25 ~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i~f~~~~~~~~~~~~i~g~~I~~~  104 (682)
                      .....+.||| |+.+.+.|.-.+     ....+..+..++.+.||+.|  ++||++.+-....       .+-|..|...
T Consensus       499 kr~~yVRyad-d~ii~v~GS~nd-----~K~ilr~In~f~sslGls~n--~~kt~it~S~eg~-------~flg~nis~t  563 (796)
T KOG4768|consen  499 KRLMYVRYAD-DIIIGVWGSVND-----CKQILRDINNFLSSLGLSNN--SSKTQITVSREGT-------HFLGYNISTT  563 (796)
T ss_pred             ceeeEEEecC-CEEEEEeccHHH-----HHHHHHHHHHHHHhhCcccC--cccceEEeeccce-------eeeeceeccC
Confidence            3455688999 999988885442     45667777788888999999  9999987654321       1111111111


Q ss_pred             c-------ceeEEeEEeCC--CCCchHHHHHHHHHHHHHHHHHHhhh-----cccCCCChHHHHHHHHHhcccceeec
Q psy3428         105 T-------STKFLGLTWDA--KMNWSLHIQLLKNRALNSLNALKMVS-----CKKWGVRRSMLLRFYKSFTLPILDYG  168 (682)
Q Consensus       105 ~-------~~k~LGv~ld~--~L~~~~Hi~~~~~ka~~~~~~L~~l~-----~~~~g~~~~~~~~ly~a~v~p~l~Yg  168 (682)
                      +       .-+--|+-+.+  .+.-+.-|..++.|.+..-....+..     +..-...+.+..-.|.++.+.++.|=
T Consensus       564 P~r~~~~~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnYY  641 (796)
T KOG4768|consen  564 PGRPAAGEGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYCSHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILNYY  641 (796)
T ss_pred             CCCccceeccccceEEeccCCceeecchHHHHHHHHHhcceeecCCcCceeeeeecccCHHHHHHHHHHHhhchhhhh
Confidence            1       11111111211  12344556666665554433333221     00112456677778888888888763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	682
3dlk_A	556	Crystal Structure Of An Engineered Form Of The Hiv-		4e-04
3qo9_A	557	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		5e-04
1hni_A	558	Structure Of Hiv-1 Reverse Transcriptase In A Compl		5e-04
3irx_A	558	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		5e-04
1qe1_A	558	Crystal Structure Of 3tc-Resistant M184i Mutant Of		5e-04
1hys_A	553	Crystal Structure Of Hiv-1 Reverse Transcriptase In		5e-04
1hpz_A	560	Human Immunodeficiency Virus Type 1 Length = 560		5e-04
4dg1_A	549	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		5e-04
2ze2_A	557	Crystal Structure Of L100iK103N MUTANT HIV-1 Revers		5e-04
3ig1_A	555	Hiv-1 Reverse Transcriptase With The Inhibitor Beta		5e-04
1dlo_A	556	Human Immunodeficiency Virus Type 1 Length = 556		5e-04
2i5j_A	552	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		5e-04
2zd1_A	557	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		5e-04
1hvu_A	554	Human Immunodeficiency Virus Type 1 Reverse Transcr		5e-04
1s6p_A	560	Crystal Structure Of Human Immunodeficiency Virus T		5e-04
3qlh_A	555	Hiv-1 Reverse Transcriptase In Complex With Manicol		5e-04
3kle_A	562	Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr		5e-04
3klh_A	564	Crystal Structure Of Azt-Resistant Hiv-1 Reverse Tr		5e-04
2vg5_A	557	Crystal Structures Of Hiv-1 Reverse Transcriptase C		5e-04
1hmv_A	560	The Structure Of Unliganded Reverse Transcriptase F		5e-04
1uwb_A	558	Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558		5e-04
3jsm_A	558	K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linke		5e-04
3hvt_A	556	Structural Basis Of Asymmetry In The Human Immunode		5e-04
1n5y_A	558	Hiv-1 Reverse Transcriptase Crosslinked To Post- Tr		6e-04
1s1w_A	560	Crystal Structure Of V106a Mutant Hiv-1 Reverse Tra		6e-04
1s1t_A	560	Crystal Structure Of L100i Mutant Hiv-1 Reverse Tra		6e-04
3klf_A	557	Crystal Structure Of Wild-Type Hiv-1 Reverse Transc		6e-04
2iaj_A	560	Crystal Structure Of K103nY181C MUTANT HIV-1 Revers		6e-04
1rev_A	560	Hiv-1 Reverse Transcriptase Length = 560		6e-04
1lwe_A	560	Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse		6e-04
1s1x_A	560	Crystal Structure Of V108i Mutant Hiv-1 Reverse Tra		6e-04
3dm2_A	560	Crystal Structure Of Hiv-1 K103n Mutant Reverse Tra		6e-04
1lw0_A	560	Crystal Structure Of T215y Mutant Hiv-1 Reverse Tra		6e-04
1jle_A	560	Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra		6e-04
1lwc_A	560	Crystal Structure Of M184v Mutant Hiv-1 Reverse Tra		6e-04
1rt3_A	560	Azt Drug Resistant Hiv-1 Reverse Transcriptase Comp		6e-04
2jle_A	566	Novel Indazole Nnrtis Created Using Molecular Templ		6e-04
3bgr_A	557	Crystal Structure Of K103nY181C MUTANT HIV-1 Revers		6e-04
3ffi_A	561	Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Len		6e-04
2ynf_A	563	Hiv-1 Reverse Transcriptase Y188l Mutant In Complex		6e-04
1lwf_A	560	Crystal Structure Of A Mutant Hiv-1 Reverse Transcr		6e-04
1jkh_A	560	Crystal Structure Of Y181c Mutant Hiv-1 Reverse Tra		6e-04
3med_A	560	Hiv-1 K103n Reverse Transcriptase In Complex With T		6e-04
3drs_A	563	Hiv Reverse Transcriptase K103n Mutant In Complex W		6e-04
2rki_A	560	Crystal Structure Of Hiv-1 Reverse Transcriptase (R		6e-04
1jlf_A	560	Crystal Structure Of Y188c Mutant Hiv-1 Reverse Tra		6e-04
2rf2_A	563	Hiv Reverse Transcriptase In Complex With Inhibitor		7e-04
3kjv_A	560	Hiv-1 Reverse Transcriptase In Complex With Dna Len		7e-04
3di6_A	561	Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor		7e-04
3dmj_A	560	Crystal Structure Of Hiv-1 V106a And Y181c Mutant R		7e-04
3drr_A	563	Hiv Reverse Transcriptase Y181c Mutant In Complex W		8e-04

>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1 Reverse Transcriptase, Rt69a Length = 556

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 411 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 452
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 453 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 507
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 508 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 550

>pdb|3QO9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti) Length = 557

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 412 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 453
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 454 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 508
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 509 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|1HNI|A Chain A, Structure Of Hiv-1 Reverse Transcriptase In A Complex With The Nonnucleoside Inhibitor Alpha-Apa R 95845 At 2.8 Angstroms Resolution Length = 558

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3IRX|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With The Non-Nucleoside Rt Inhibitor (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-Oxo-2, 3-Dihydrobenzo[d]oxazol-5-Yl)-5- (5-Methyl-1,3,4-Oxadiazol-2-Yl)pent-1-Enyl)-2-Methoxy-3- Methylbenzothioate. Length = 558

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 413 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 454
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 455 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 509
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 510 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|1QE1|A Chain A, Crystal Structure Of 3tc-Resistant M184i Mutant Of Hiv-1 Reverse Transcriptase Length = 558

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In Complex With A Polypurine Tract Rna:dna Length = 553

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1HPZ|A Chain A, Human Immunodeficiency Virus Type 1 Length = 560

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|4DG1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With Polymorphism Mutation K172a And K173a Length = 549

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2ZE2|A Chain A, Crystal Structure Of L100iK103N MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 412 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 453
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 454 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 508
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 509 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta- Thujaplicinol Bound At The Rnase H Active Site Length = 555

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1 Length = 556

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2I5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Dhbnh, An Rnase H Inhibitor Length = 552

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2ZD1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 412 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 453
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 454 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 508
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 509 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|1HVU|A Chain A, Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed With A 33-Base Nucleotide Rna Pseudoknot Length = 554

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S6P|A Chain A, Crystal Structure Of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (Rt) In Complex With Janssen-R100943 Length = 560

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3QLH|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Manicol At The Rnase H Active Site And Tmc278 (rilpivirine) At The Nnrti Binding Pocket Length = 555

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 411 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 452
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 453 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 507
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 508 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 550

>pdb|3KLE|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 562

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 412 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 453
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 454 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 508
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 509 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|3KLH|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse Transcriptase Crosslinked To Post-Translocation Aztmp-Terminated Dna (Complex P) Length = 564

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 412 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 453
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 454 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 508
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 509 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|2VG5|A Chain A, Crystal Structures Of Hiv-1 Reverse Transcriptase Complexes With Thiocarbamate Non-Nucleoside Inhibitors Length = 557

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1HMV|A Chain A, The Structure Of Unliganded Reverse Transcriptase From The Human Immunodeficiency Virus Type 1 Length = 560

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo Length = 558

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3JSM|A Chain A, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To Ds-Dna And Complexed With Tenofovir-Diphosphate As The Incoming Nucleotide Substrate Length = 558

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human Immunodeficiency Virus Type 1 Reverse Transcriptase Heterodimer Length = 556

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1N5Y|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Post- Translocation Aztmp-Terminated Dna (Complex P) Length = 558

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S1W|A Chain A, Crystal Structure Of V106a Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S1T|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse Transcriptase In Complex With Uc-781 Length = 560

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3KLF|A Chain A, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase Crosslinked To A Dsdna With A Bound Excision Product, Aztppppa Length = 557

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 412 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 453
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 454 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 508
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 509 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|2IAJ|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Atp Length = 560

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 452 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 506
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 507 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1REV|A Chain A, Hiv-1 Reverse Transcriptase Length = 560

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1LWE|A Chain A, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse Transcriptase (Rtmn) In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1S1X|A Chain A, Crystal Structure Of V108i Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DM2|A Chain A, Crystal Structure Of Hiv-1 K103n Mutant Reverse Transcriptase In Complex With Gw564511. Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1LW0|A Chain A, Crystal Structure Of T215y Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1JLE|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1LWC|A Chain A, Crystal Structure Of M184v Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1RT3|A Chain A, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed With 1051u91 Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2JLE|A Chain A, Novel Indazole Nnrtis Created Using Molecular Template Hybridization Based On Crystallographic Overlays Length = 566

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3BGR|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt Inhibitor Length = 557

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 71/171 (41%), Gaps = 42/171 (24%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 412 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 453
Query: 342 TGCAYSVGNVVRSTLLNPVNSI-FSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLAAL 399
            G A  V N  R  ++   N+     EL AI+L L+      SG +  IVTDS+ +L  +
Sbjct: 454 LGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQD-----SGLEVNIVTDSQYALGII 508
Query: 400 ------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
                 S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 509 QAQPDKSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 551

>pdb|3FFI|A Chain A, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor Length = 561

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 411 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 452
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 453 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 505
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 506 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 550

>pdb|2YNF|A Chain A, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With Inhibitor Gsk560 Length = 563

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 413 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 454
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 455 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 507
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 508 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|1LWF|A Chain A, Crystal Structure Of A Mutant Hiv-1 Reverse Transcriptase (rtmq+m184v: M41l/d67n/k70r/m184v/t215y) In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1JKH|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse Transcriptase In Complex With Dmp-266(Efavirenz) Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3MED|A Chain A, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc125 Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DRS|A Chain A, Hiv Reverse Transcriptase K103n Mutant In Complex With Inhibitor R8d Length = 563

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 413 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 454
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 455 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 507
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 508 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|2RKI|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In Complex With A Triazole Derived Nnrti Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|1JLF|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse Transcriptase In Complex With Nevirapine Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|2RF2|A Chain A, Hiv Reverse Transcriptase In Complex With Inhibitor 7e (Nnrti) Length = 563

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 413 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 454
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 455 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 507
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 508 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 552

>pdb|3KJV|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Dna Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DI6|A Chain A, Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor Length = 561

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse Transcriptase In Complex With Gw564511 Length = 560

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 410 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 451
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 452 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 504
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 505 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 549

>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With Inhibitor R8e Length = 563

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 71/173 (41%), Gaps = 46/173 (26%)
Query: 285 FTPPWS--NSPPPVDLSLCDGKKSDSAPVVFQSLFREAINTKYTSHTICYTDGSKT-PTT 341
           + P W   N+PP V L      + +  P+V    F              Y DG+    T 
Sbjct: 413 WIPEWEFVNTPPLVKLWY----QLEKEPIVGAETF--------------YVDGAANRETK 454
Query: 342 TGCAYSVGNVVRS---TLLNPVNSIFSAELIAIFLCLEAILDSPSG-KFLIVTDSRSSLA 397
            G A  V N  R    TL +  N     EL AI+L L+      SG +  IVTDS+ +L 
Sbjct: 455 LGKAGYVTNRGRQKVVTLTDTTNQ--KTELQAIYLALQD-----SGLEVNIVTDSQYALG 507
Query: 398 AL------SNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444
            +      S    +N +I ++        + K+ +   W P+H GI GNE VD
Sbjct: 508 IIQAQPDQSESELVNQIIEQL--------IKKEKVYLAWVPAHKGIGGNEQVD 552

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	682
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.87
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.87
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.86
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.85
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.85
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.84
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.83
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.82
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.8
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.76
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.75
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.73
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.72
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.7
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.29
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	99.04
3fsi_A	255	RT, reverse transcriptase domain; transferase/DNA	96.25
1rw3_A	455	POL polyprotein; RNA and DNA dependent DNA polymer	93.6
3kyl_A	596	Telomerase reverse transcriptase; reverse transcri	93.52
2zd1_B	428	P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleosid	89.81
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	89.59
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	88.9

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A

Probab=99.87  E-value=1.6e-22  Score=185.97  Aligned_cols=124  Identities=23%  Similarity=0.277  Sum_probs=95.7

Q ss_pred             CCCeEEEEeCCCCCC--CCceEEEEEcce-eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhc
Q psy3428         325 YTSHTICYTDGSKTP--TTTGCAYSVGNV-VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSN  401 (682)
Q Consensus       325 ~~~~~~iytDgS~~~--~~~G~g~~~~~~-~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~  401 (682)
                      ..+.+.||||||+..  +..|+|+++... .....+ ..+||+.||+.|++.||+.+    ..+|.|+|||++++++|..
T Consensus         9 ~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~~   83 (150)
T 3qio_A            9 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIITQ   83 (150)
T ss_dssp             CTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHHH
T ss_pred             CCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHHH
Confidence            456899999999754  458889887632 222333 47899999999999999985    4899999999999999976


Q ss_pred             CC-----------CCcH-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccC
Q psy3428         402 VR-----------FINP-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTG  453 (682)
Q Consensus       402 ~~-----------~~~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  453 (682)
                      +.           ...+ ..+++++.+..+..++..|.|.|||||+|++|||.||+||++|+..
T Consensus        84 w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           84 WIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            51           1112 2245666555444567899999999999999999999999999875

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*

Probab=99.87  E-value=1.4e-22  Score=188.40  Aligned_cols=129  Identities=21%  Similarity=0.247  Sum_probs=101.6

Q ss_pred             CCCeEEEEeCCCCCCCC-----ceEEEEEcce---eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHH
Q psy3428         325 YTSHTICYTDGSKTPTT-----TGCAYSVGNV---VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSL  396 (682)
Q Consensus       325 ~~~~~~iytDgS~~~~~-----~G~g~~~~~~---~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i  396 (682)
                      +.+.+.||||||+..++     +|+|+++...   ..+..+...+||+.||+.|++.||+.+...+..+|.|+|||++++
T Consensus         4 ~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi   83 (154)
T 2qkb_A            4 MGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTI   83 (154)
T ss_dssp             ETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHH
T ss_pred             CCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHH
Confidence            35689999999986542     7999887632   234445557899999999999999999987889999999999999


Q ss_pred             HhhhcC---------CCCc--H-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCC
Q psy3428         397 AALSNV---------RFIN--P-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGT  454 (682)
Q Consensus       397 ~~l~~~---------~~~~--~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  454 (682)
                      +.|.++         ....  + ..+.+++.+..+... ..|.|.|||||+|++|||.||+|||+|+..+
T Consensus        84 ~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~~-~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           84 NGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQG-MDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHTT-CEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             hhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHcC-CceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            999763         1111  1 234566666665554 5799999999999999999999999998764

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A

Probab=99.86  E-value=3.3e-23  Score=190.46  Aligned_cols=128  Identities=16%  Similarity=0.063  Sum_probs=100.6

Q ss_pred             CCCeEEEEeCCCCCCCCceEEEEEc--ce--eeee-cC--CC--CCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHH
Q psy3428         325 YTSHTICYTDGSKTPTTTGCAYSVG--NV--VRST-LL--NP--VNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSS  395 (682)
Q Consensus       325 ~~~~~~iytDgS~~~~~~G~g~~~~--~~--~~~~-~~--~~--~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~  395 (682)
                      +++.+.||||||+.++.+|+|+++.  +.  ..+. ..  +.  .+||+.||+.|++.||+.+...+. +|.|+|||+.+
T Consensus         3 ~~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i   81 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGI   81 (147)
T ss_dssp             TTSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTH
T ss_pred             CCCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHH
Confidence            4678999999999888899998875  22  1222 22  22  369999999999999999877666 99999999998


Q ss_pred             HHhhhcCCC-CcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCCC
Q psy3428         396 LAALSNVRF-INPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTP  456 (682)
Q Consensus       396 i~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~  456 (682)
                      .+.+.+... ..+....+.+.++.|..   .|.|.|||||+|++|||.||+|||+|+.....
T Consensus        82 ~~w~~~~w~~~~~~~~~~~~l~~~l~~---~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A           82 AFWATGEWKAKNEFTQAYAKLMNQYRG---IYSFEKVKAHSGNEFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             HHHTTSSSSCCHHHHHHHHCGGGGGST---TCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCT
T ss_pred             HHHHhCCCccCCcchHHHHHHHHHhcC---CeeEEEecCcCCCcchHHHHHHHHHHHhcccc
Confidence            888776544 34455556665555543   89999999999999999999999999987654

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}

Probab=99.85  E-value=3e-22  Score=184.44  Aligned_cols=123  Identities=20%  Similarity=0.156  Sum_probs=92.3

Q ss_pred             CeEEEEeCCCCCCC--CceEEEEEcc--e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhh
Q psy3428         327 SHTICYTDGSKTPT--TTGCAYSVGN--V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALS  400 (682)
Q Consensus       327 ~~~~iytDgS~~~~--~~G~g~~~~~--~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~  400 (682)
                      ..++||||||+..+  .+|+|+++..  .  ..+..+ ..+||+.||+.|++.||+.+..  ..+|.|+|||+++++.|.
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~-~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   79 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYD-PATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMN   79 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHH
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCC-CCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHH
Confidence            47899999997654  4889988752  1  122223 3679999999999999999975  589999999999999998


Q ss_pred             c-CC---------C--CcH-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccC
Q psy3428         401 N-VR---------F--INP-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTG  453 (682)
Q Consensus       401 ~-~~---------~--~~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  453 (682)
                      . +.         .  ..+ ..+.+++.+..+... ..|.|.|||||+|++|||.||+|||+|+..
T Consensus        80 ~~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~~-~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           80 EGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTL-HRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             SSHHHHHHHTTCC----CCCTTHHHHHHHHHHHHH-SEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHhh-CceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence            7 21         1  111 124555555555544 479999999999999999999999999864

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=99.85  E-value=1.5e-21  Score=181.75  Aligned_cols=128  Identities=23%  Similarity=0.235  Sum_probs=94.5

Q ss_pred             CCeEEEEeCCCCC--CCCceEEEEEc--cee-eeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhh
Q psy3428         326 TSHTICYTDGSKT--PTTTGCAYSVG--NVV-RSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALS  400 (682)
Q Consensus       326 ~~~~~iytDgS~~--~~~~G~g~~~~--~~~-~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~  400 (682)
                      ...+.||||||+.  +|..|+|+++.  +.. ........+||+.||+.|++.||+.+   ...+|.|+|||+++++.+-
T Consensus        21 ~~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw   97 (165)
T 3p1g_A           21 DADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAH   97 (165)
T ss_dssp             TCSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHH
T ss_pred             CCCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhh
Confidence            3469999999986  56688887654  221 12234567899999999999999999   3689999999999999983


Q ss_pred             cCCCCcHH-HHHHHHHHHHHHhcCCceEEEEecCCCC-----CchhHHHHHHhcCcccCCCC
Q psy3428         401 NVRFINPL-ITKVYSTWSYLKLCKKDITFMWCPSHCG-----IKGNEIVDVAAKNPTTGTTP  456 (682)
Q Consensus       401 ~~~~~~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~g-----i~gNe~AD~lAk~a~~~~~~  456 (682)
                      ....+.++ .+.++..+......+..|.|.|||||+|     ++|||+||+|||+|+..+..
T Consensus        98 ~~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~~  159 (165)
T 3p1g_A           98 VHSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVL  159 (165)
T ss_dssp             SCCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCCC
Confidence            21222221 2344443322233578999999999999     99999999999999876543

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.84  E-value=2.9e-21  Score=179.35  Aligned_cols=125  Identities=19%  Similarity=0.215  Sum_probs=96.1

Q ss_pred             eEEEEeCCCCCC--CCceEEEEEcc--e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhc
Q psy3428         328 HTICYTDGSKTP--TTTGCAYSVGN--V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSN  401 (682)
Q Consensus       328 ~~~iytDgS~~~--~~~G~g~~~~~--~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~  401 (682)
                      .+.||||||+..  +.+|+|+++..  .  ..+..+ ..+||+.||+.|++.||+.+..  ..+|.|+|||+++++.|..
T Consensus         4 ~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (155)
T 1jl1_A            4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQ   80 (155)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHT
T ss_pred             eEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHHH
Confidence            589999999865  44889988752  1  122223 3579999999999999999975  3799999999999999986


Q ss_pred             C---------CCC--cH-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCCC
Q psy3428         402 V---------RFI--NP-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTP  456 (682)
Q Consensus       402 ~---------~~~--~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~  456 (682)
                      +         ...  .+ ..+.+++.+..+... ..|.|.|||||+|++|||.||+|||+|+..+..
T Consensus        81 w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           81 WIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQ-HQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             THHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTT-CEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHhhcccccccCCccCCHHHHHHHHHHHcc-CceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            2         111  11 124566666666544 689999999999999999999999999987654

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A

Probab=99.83  E-value=4.3e-21  Score=178.72  Aligned_cols=123  Identities=20%  Similarity=0.230  Sum_probs=94.1

Q ss_pred             CeEEEEeCCCCCC--CCceEEEEEcc--e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhh
Q psy3428         327 SHTICYTDGSKTP--TTTGCAYSVGN--V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALS  400 (682)
Q Consensus       327 ~~~~iytDgS~~~--~~~G~g~~~~~--~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~  400 (682)
                      ..+.||||||+..  +.+|+|+++..  .  .....+ ..+||+.||+.|++.||+.+..  ..+|.|+|||+++++.|.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHH
Confidence            4689999999864  45899988742  2  112223 3579999999999999999864  389999999999999997


Q ss_pred             c--------CC-CC--cH-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccC
Q psy3428         401 N--------VR-FI--NP-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTG  453 (682)
Q Consensus       401 ~--------~~-~~--~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  453 (682)
                      +        .. ..  .+ ....++..+..+... ..|.|.|||||+|++||+.||+|||+|+..
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQL-HQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHTT-SEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHHcc-CcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            7        22 11  11 124555555555544 689999999999999999999999999987

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A

Probab=99.82  E-value=5.2e-21  Score=179.46  Aligned_cols=126  Identities=19%  Similarity=0.155  Sum_probs=95.8

Q ss_pred             CeEEEEeCCCCCC--CCceEEEEEcc--eeeeec-CCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhc
Q psy3428         327 SHTICYTDGSKTP--TTTGCAYSVGN--VVRSTL-LNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSN  401 (682)
Q Consensus       327 ~~~~iytDgS~~~--~~~G~g~~~~~--~~~~~~-~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~  401 (682)
                      ..+.||||||+..  +.+|+|+++..  ....+. ....+||+.||+.|++.||+.+...  .+|.|+|||+++++.|.+
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~   84 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTE   84 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHS
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhh
Confidence            5789999999865  45899988752  111111 1135799999999999999988653  589999999999999988


Q ss_pred             ----------CCCCc--H-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCC
Q psy3428         402 ----------VRFIN--P-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTT  455 (682)
Q Consensus       402 ----------~~~~~--~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  455 (682)
                                +...+  + ..+.++..+..+... ..|.|.|||||+|++||+.||+|||+|+....
T Consensus        85 ~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~~-~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           85 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTT-SEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             hHHHHHHhcccccccCCccCcHHHHHHHHHHHhc-CeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence                      22211  1 124566666666554 58999999999999999999999999998765

>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}

Probab=99.80  E-value=5.8e-20  Score=170.75  Aligned_cols=126  Identities=22%  Similarity=0.230  Sum_probs=92.6

Q ss_pred             CCeEEEEeCCCCC--CCC-----ceEEEEEcc------eeeeecC-CCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcC
Q psy3428         326 TSHTICYTDGSKT--PTT-----TGCAYSVGN------VVRSTLL-NPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTD  391 (682)
Q Consensus       326 ~~~~~iytDgS~~--~~~-----~G~g~~~~~------~~~~~~~-~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sD  391 (682)
                      ...++||||||+.  |++     +|+|+++..      ....+.. ....+++.||+.|+..||+.+...+ .+|.|+||
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~~-~~v~I~TD   83 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKIP-GPVLVITD   83 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHSS-SCEEEEES
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcCC-CeEEEEeC
Confidence            4568999999975  344     799988641      1222222 2467888999999999998887644 57999999


Q ss_pred             CHHHHHhhhcC---------CC--CcH-HHHHHHHHHHHHHhcCCceEEEEecCCCCC------chhHHHHHHhcCccc
Q psy3428         392 SRSSLAALSNV---------RF--INP-LITKVYSTWSYLKLCKKDITFMWCPSHCGI------KGNEIVDVAAKNPTT  452 (682)
Q Consensus       392 s~~~i~~l~~~---------~~--~~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi------~gNe~AD~lAk~a~~  452 (682)
                      |++++++|..+         ..  +.| ..+++++.+..+......|.|.|||||+|+      +|||+||+||++|+.
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            99999999642         11  112 234666666666666678999999999995      589999999999874

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}

Probab=99.76  E-value=6.9e-19  Score=161.11  Aligned_cols=121  Identities=17%  Similarity=0.192  Sum_probs=99.8

Q ss_pred             eEEEEeCCCCCC--CCceEEEEEcce-------eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHh
Q psy3428         328 HTICYTDGSKTP--TTTGCAYSVGNV-------VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAA  398 (682)
Q Consensus       328 ~~~iytDgS~~~--~~~G~g~~~~~~-------~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~  398 (682)
                      .+.||||||+..  +.+|+|+++...       .....+ ..+||+.||+.|++.||+.+...+.++|.|+|||+++++.
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~   81 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAI-GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQ   81 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccC-CCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHH
Confidence            589999999864  468999887521       112223 3689999999999999999998888999999999999999


Q ss_pred             hhcCC-CCcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccC
Q psy3428         399 LSNVR-FINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTG  453 (682)
Q Consensus       399 l~~~~-~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  453 (682)
                      +.+.. ..++....++..+..+..++..|.|.|||    .++|+.||+|||+|+..
T Consensus        82 i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           82 MSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVP----RARNTYADRLANDAMDA  133 (141)
T ss_dssp             HTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECC----GGGCHHHHHHHHHHHHH
T ss_pred             HhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcC----CcccHHHHHHHHHHHHH
Confidence            98853 55666677777788888888999999999    48999999999998754

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}

Probab=99.75  E-value=1.1e-18  Score=159.62  Aligned_cols=121  Identities=17%  Similarity=0.185  Sum_probs=96.8

Q ss_pred             eEEEEeCCCCCC--CCceEEEEEcc----e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCC----cEEEEcCCHHH
Q psy3428         328 HTICYTDGSKTP--TTTGCAYSVGN----V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSG----KFLIVTDSRSS  395 (682)
Q Consensus       328 ~~~iytDgS~~~--~~~G~g~~~~~----~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~----~v~i~sDs~~~  395 (682)
                      .+.||||||+..  +.+|+|+++..    .  .....++ .+||+.||+.|++.||+.+...+.+    +|.|+|||+++
T Consensus         3 ~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~-~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            3 KIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIG-ETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             EEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEE-EECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             eEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCC-CCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            689999999864  46899988753    1  1222233 5799999999999999999887777    99999999999


Q ss_pred             HHhhhcCCC-CcHHHHHHHHHHHHH-HhcCCceEEEEecCCCCCchhHHHHHHhcCcccC
Q psy3428         396 LAALSNVRF-INPLITKVYSTWSYL-KLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTG  453 (682)
Q Consensus       396 i~~l~~~~~-~~~~~~~i~~~~~~l-~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~  453 (682)
                      ++.+.++.. .++-...++..+..+ ..++..|.|.|||    .++|+.||+|||+|+..
T Consensus        82 i~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~~~~V~----~~~N~~AD~LA~~a~~~  137 (140)
T 3u3g_D           82 VRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIP----REKNARADELVNEAIDK  137 (140)
T ss_dssp             HHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCEEEECC----GGGGHHHHHHHHHHHHH
T ss_pred             HHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEEEEEcC----chhhHHHHHHHHHHHHh
Confidence            999988653 455455666777777 6677899999999    59999999999998753

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A

Probab=99.73  E-value=5.9e-18  Score=156.33  Aligned_cols=121  Identities=17%  Similarity=0.134  Sum_probs=94.6

Q ss_pred             EEEEeCCCCC---CCCceE-EEEEcc--ee---eeecCC---CCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHH
Q psy3428         329 TICYTDGSKT---PTTTGC-AYSVGN--VV---RSTLLN---PVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSL  396 (682)
Q Consensus       329 ~~iytDgS~~---~~~~G~-g~~~~~--~~---~~~~~~---~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i  396 (682)
                      +.||||||+.   ++++|+ |+++..  ..   .....+   ..+||+.||+.|++.||+.+...+..+|.|+|||++++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            5799999986   356885 877653  11   112223   37899999999999999999988888999999999999


Q ss_pred             HhhhcCCC-CcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCC
Q psy3428         397 AALSNVRF-INPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGT  454 (682)
Q Consensus       397 ~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~  454 (682)
                      +.+.++.. .++....+++.+..+.... .|.|.|||+    ++|+.||+|||+|+...
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~~  135 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYELV  135 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHhh
Confidence            99988743 3344566666666666655 599999997    59999999999998654

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=99.72  E-value=6.3e-18  Score=189.69  Aligned_cols=117  Identities=23%  Similarity=0.298  Sum_probs=91.8

Q ss_pred             CCeEEEEeCCCCCCC--CceEEEEEcce-eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         326 TSHTICYTDGSKTPT--TTGCAYSVGNV-VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       326 ~~~~~iytDgS~~~~--~~G~g~~~~~~-~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      .+.+.||||||+..+  .+|+|+++... ...... ..+||+.||+.|++.||+.    ...++.|+|||++|++++.++
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~  508 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ  508 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcc
Confidence            457999999998654  47888887532 222223 3679999999999999998    568999999999999999987


Q ss_pred             CCC--cHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcc
Q psy3428         403 RFI--NPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPT  451 (682)
Q Consensus       403 ~~~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  451 (682)
                      ...  .++.+++.+    +...+..|.|.|||||+|++|||.||+||++|+
T Consensus       509 ~~~~~~~l~~~~~~----~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          509 PTESESKIVNQIIE----EMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CSEESCHHHHHHHH----HHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHH----HhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            533  344444433    333468899999999999999999999999985

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=99.70  E-value=7.6e-18  Score=189.10  Aligned_cols=116  Identities=26%  Similarity=0.345  Sum_probs=89.0

Q ss_pred             CCeEEEEeCCCCCC--CCceEEEEEcce-eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         326 TSHTICYTDGSKTP--TTTGCAYSVGNV-VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       326 ~~~~~iytDgS~~~--~~~G~g~~~~~~-~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      .+.+.||||||+..  +.+|+|+++... ...... ..+||+.||+.|++.||+.+    ..++.|+|||++|++++.++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~  511 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQ  511 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTC
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcC
Confidence            45689999999754  447888887632 222222 46899999999999999998    57999999999999999987


Q ss_pred             CCC--cHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCc
Q psy3428         403 RFI--NPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNP  450 (682)
Q Consensus       403 ~~~--~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a  450 (682)
                      ...  .++.+++.+   .+. ....|.|.|||||+|++|||.||+||++|
T Consensus       512 ~~~~~~~l~~~~~~---~l~-~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          512 PDKSESELVNQIIE---QLI-KKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEESSHHHHHHHH---HHH-HCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CccCCHHHHHHHHH---HHh-cCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            665  244444443   233 34689999999999999999999999986

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*

Probab=99.29  E-value=3.1e-13  Score=121.90  Aligned_cols=119  Identities=12%  Similarity=0.016  Sum_probs=83.9

Q ss_pred             CCCeEEEEeCCCCC--CCCceEEEEEcc--ee--eeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHh
Q psy3428         325 YTSHTICYTDGSKT--PTTTGCAYSVGN--VV--RSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAA  398 (682)
Q Consensus       325 ~~~~~~iytDgS~~--~~~~G~g~~~~~--~~--~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~  398 (682)
                      +...+.||||||+.  ++.+|+|+++..  ..  .+..++ .+||+.||++|++.||+.+.+.+. +|.|+|||++|++.
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~-~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w   85 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIP-IGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKW   85 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEE-EECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccC-CcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHH
Confidence            34678899999975  456899998862  11  112222 579999999999999999998766 99999999999999


Q ss_pred             hhcCCCC-----cHHHHHHHHHHHHHH--hcCCceEEEEecCCCCCchhHHHHH
Q psy3428         399 LSNVRFI-----NPLITKVYSTWSYLK--LCKKDITFMWCPSHCGIKGNEIVDV  445 (682)
Q Consensus       399 l~~~~~~-----~~~~~~i~~~~~~l~--~~~~~v~~~WVpgH~gi~gNe~AD~  445 (682)
                      +.+...+     .....++++.+.++.  .+...+....|+.|++.-||..||.
T Consensus        86 ~~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           86 VKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTCC
T ss_pred             HHcCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCcccc
Confidence            9876522     112344454444332  1124556666777888889988873

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=99.04  E-value=1.2e-10  Score=102.74  Aligned_cols=75  Identities=13%  Similarity=0.088  Sum_probs=56.8

Q ss_pred             CCeEEEEeCCCCC--CCCceEEEEEcc--e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhh
Q psy3428         326 TSHTICYTDGSKT--PTTTGCAYSVGN--V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAAL  399 (682)
Q Consensus       326 ~~~~~iytDgS~~--~~~~G~g~~~~~--~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l  399 (682)
                      +....||||||+.  ||.+|+|+|+..  .  .....+ ..+||+.||++|++.||+.+.+.+.. +.|+|||++|++.+
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi   80 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWV   80 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHH
Confidence            4566899999975  456889655542  1  122222 26899999999999999999875544 89999999999999


Q ss_pred             hcC
Q psy3428         400 SNV  402 (682)
Q Consensus       400 ~~~  402 (682)
                      .++
T Consensus        81 ~~~   83 (134)
T 4htu_A           81 KDK   83 (134)
T ss_dssp             HHT
T ss_pred             HcC
Confidence            764

>3fsi_A RT, reverse transcriptase domain; transferase/DNA MMLV RT, protein-DNA complex, drug-DNA complex; HET: OWL; 1.75A {Moloney murine leukemia virus} SCOP: e.8.1.2 PDB: 1d1u_A 1n4l_A* 1ztt_A 2fjv_A* 2fjw_A 2fjx_A* 2fvp_A 2fvq_A 2fvr_A 2fvs_A 2r2r_A* 2r2s_A* 2r2t_A* 2r2u_A* 1ztw_A* 1i6j_A 1qaj_A* 1d0e_A* 1nnd_A 1mml_A ...

Probab=96.25  E-value=0.0035  Score=62.35  Aligned_cols=83  Identities=13%  Similarity=-0.035  Sum_probs=62.1

Q ss_pred             eeehhhHHHHHHHHhhcccc-----CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428           4 EVQIHKVILMSLLFVGFAVT-----GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS   78 (682)
Q Consensus         4 ~~~~~~~~llfllyi~~~~~-----~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt   78 (682)
                      -||.-.++.+|--+++....     ..++.+..|.| |+.|.+  ++.++    ....+..+.++.+++||.+|  ++||
T Consensus       166 PfGl~~sP~~fq~~m~~il~~~~~~~~~~~v~~Y~D-Dili~s--~~~ee----h~~~l~~v~~~L~~~gl~l~--~~Kc  236 (255)
T 3fsi_A          166 PQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVD-DLLLAA--TSELD----CQQGTRALLQTLGNLGYRAS--AKKA  236 (255)
T ss_dssp             CTTCTTHHHHHHHHHHHHTHHHHHHCTTCEEEEETT-EEEEEE--SSHHH----HHHHHHHHHHHHHHHTCCBC--TTTC
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHHhCcCcEEEEEcC-CeEEEe--CCHHH----HHHHHHHHHHHHHHCCeEEC--HHHh
Confidence            46667788888887775421     24567899999 988764  45544    45668888889999999999  9999


Q ss_pred             EEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428          79 VCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK  117 (682)
Q Consensus        79 ~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~  117 (682)
                      +..                      +..++|||..++.+
T Consensus       237 ~f~----------------------~~~~~fLG~~i~~~  253 (255)
T 3fsi_A          237 QIC----------------------QKQVKYLGYLLKEG  253 (255)
T ss_dssp             EEE----------------------ESEEEETTEEEETT
T ss_pred             ccc----------------------CCceEEEEEEEeCC
Confidence            754                      24678999988765

>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2

Probab=93.60  E-value=0.026  Score=61.07  Aligned_cols=84  Identities=12%  Similarity=-0.057  Sum_probs=58.8

Q ss_pred             eeeehhhHHHHHHHHhhcccc-----CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCe
Q psy3428           3 TEVQIHKVILMSLLFVGFAVT-----GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGK   77 (682)
Q Consensus         3 ~~~~~~~~~llfllyi~~~~~-----~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~K   77 (682)
                      --||.-.+|-+|--+++....     ..+..+..|+| |+.|.  +++.++..    ..+..+.+-++++||.+|  ++|
T Consensus       169 mpfGl~naP~~fq~~m~~~l~~~~~~~~~~~v~~YvD-Dili~--s~~~~e~~----~~l~~v~~~l~~~gl~l~--~~K  239 (455)
T 1rw3_A          169 LPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVD-DLLLA--ATSELDCQ----QGTRALLQTLGNLGYRAS--AKK  239 (455)
T ss_dssp             CCSSCTTHHHHHHHHHHHHHHHHHHTCTTCEEEEETT-EEEEE--ESSHHHHH----HHHHHHHHHHHHHTCCBC--GGG
T ss_pred             cCCCCCCcHHHHHHHHHHHHHHhhhhCCCceEEEEcC-CEEEe--cCCHHHHH----HHHHHHHHHHHHcCCccC--ccc
Confidence            346667778777777665311     24678889999 98776  45565544    445566666678899999  999


Q ss_pred             eEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428          78 SVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK  117 (682)
Q Consensus        78 t~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~  117 (682)
                      |++.                      +..++|||.+++.+
T Consensus       240 ~~f~----------------------~~~~~fLG~~i~~~  257 (455)
T 1rw3_A          240 AQIC----------------------QKQVKYLGYLLKEG  257 (455)
T ss_dssp             CCCS----------------------BSSCEETTEEESSS
T ss_pred             hhhh----------------------ccceeEeeeeccCC
Confidence            9642                      35678999998865

>3kyl_A Telomerase reverse transcriptase; reverse transcriptase; 2.70A {Tribolium castaneum} PDB: 3du5_A 3du6_A

Probab=93.52  E-value=0.059  Score=57.14  Aligned_cols=62  Identities=11%  Similarity=0.001  Sum_probs=40.0

Q ss_pred             hHHHHHHHHhhccc------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEEE
Q psy3428           9 KVILMSLLFVGFAV------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCID   82 (682)
Q Consensus         9 ~~~llfllyi~~~~------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i~   82 (682)
                      -||||-.+|.+++.      ...+...+.||| |..+++.+  .++    .+..+..+..|     +.+|  ++||.+ .
T Consensus       312 ISPLLANIYLheLDkel~~~l~kd~~LVRYAD-DFVIi~~S--ke~----Aerfl~~Lkg~-----leLN--pEKTrI-n  376 (596)
T 3kyl_A          312 LSGCLCELYMAFMDRLYFSNLDKDAFIHRTVD-DYFFCSPH--PHK----VYDFELLIKGV-----YQVN--PTKTRT-N  376 (596)
T ss_dssp             THHHHHHHHHHHHHHHHSTTSCTTSEEEECSS-EEEEEESC--HHH----HHHHHHHHHHH-----SCEE--EEEEEE-C
T ss_pred             hhHHHHHHHHHHHHHHHHHhhccCceEEEEcC-cEEEEECC--HHH----HHHHHHHhhCc-----ceEC--chhcee-e
Confidence            46677777877652      124567889999 99999865  332    23333334444     3999  999975 4


Q ss_pred             ecC
Q psy3428          83 FNR   85 (682)
Q Consensus        83 f~~   85 (682)
                      |..
T Consensus       377 F~~  379 (596)
T 3kyl_A          377 LPT  379 (596)
T ss_dssp             CTT
T ss_pred             ccc
Confidence            433

>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...

Probab=89.81  E-value=0.17  Score=54.04  Aligned_cols=68  Identities=9%  Similarity=-0.041  Sum_probs=40.4

Q ss_pred             eeehhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428           4 EVQIHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS   78 (682)
Q Consensus         4 ~~~~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt   78 (682)
                      .||.-.++.+|-.+++...     ...++.+..|.| |+.|.+.+ +.++.    ...+..+.+-+.++||.+|  ++||
T Consensus       150 PfGl~nsPa~fq~~m~~il~~~~~~~~~~~v~vY~D-DIlI~s~~-~~~eh----~~~l~~v~~~l~~~gL~l~--~~Kc  221 (428)
T 2zd1_B          150 PQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMD-DLYVGSDL-EIGQH----RTKIEELRQHLLRWGLTTP--DKKH  221 (428)
T ss_dssp             CTTCTHHHHHHHHHHHHHHHHHHHHCTTCEEEEETT-EEEEEECS-CHHHH----HHHHHHHHHHHHHHHC---------
T ss_pred             CCCCcchHHHHHHHHHHHHHHHhhcCCCceEEEEec-ceEEecCC-cHHHH----HHHHHHHHHHHHHhCCccC--hhHc
Confidence            4666778888887776541     234567889999 99987632 34443    4455566666778899999  9998


Q ss_pred             E
Q psy3428          79 V   79 (682)
Q Consensus        79 ~   79 (682)
                      +
T Consensus       222 ~  222 (428)
T 2zd1_B          222 Q  222 (428)
T ss_dssp             -
T ss_pred             c
Confidence            6

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=89.59  E-value=0.21  Score=55.34  Aligned_cols=83  Identities=8%  Similarity=-0.015  Sum_probs=57.8

Q ss_pred             eeehhhHHHHHHHHhhcc-----ccCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428           4 EVQIHKVILMSLLFVGFA-----VTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS   78 (682)
Q Consensus         4 ~~~~~~~~llfllyi~~~-----~~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt   78 (682)
                      -||.-.+|.+|--+++..     ...+++.+..|.| |+.|.+.. +.++    ....+..+.+.+.++||.+|  ++||
T Consensus       152 PfGl~nap~~fq~~m~~il~~~~~~~~~~~v~~Y~D-DIli~s~~-~~~e----h~~~l~~v~~~l~~~gl~l~--~~Kc  223 (557)
T 2zd1_A          152 PQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMD-DLYVGSDL-EIGQ----HRTKIEELRQHLLRWGLTTP--DKKH  223 (557)
T ss_dssp             CTTCTTHHHHHHHHHHHHHHHHHHTCTTEEEEEETT-EEEEEECS-CHHH----HHHHHHHHHHHHHTTTCCCC--CSCC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHhhhcCCCceEEEEec-CEEEecCc-hHHH----HHHHHHHHHHHHHHcCCccC--hhhc
Confidence            456667788887777654     2234567889999 99887532 3444    34456777778889999999  9997


Q ss_pred             EEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428          79 VCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK  117 (682)
Q Consensus        79 ~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~  117 (682)
                      +   |                    ..+++|||..++.+
T Consensus       224 ~---f--------------------~~~~~fLG~~i~~~  239 (557)
T 2zd1_A          224 Q---K--------------------EPPFLWMGYELHPD  239 (557)
T ss_dssp             S---C--------------------CSSEEETTEEECSS
T ss_pred             C---C--------------------CCceEEeeEEEccC
Confidence            4   2                    12467888888765

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=88.90  E-value=0.3  Score=54.14  Aligned_cols=83  Identities=8%  Similarity=-0.078  Sum_probs=56.3

Q ss_pred             eeehhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428           4 EVQIHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS   78 (682)
Q Consensus         4 ~~~~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt   78 (682)
                      .||.-.++-+|--+++...     ..+++.+..|.| |+.|.+. .+.++-    ...+..+.+-+.++||.+|  ++||
T Consensus       150 PfGl~napa~fq~~m~~il~~~~~~~~~~~v~~Y~D-DIli~s~-~~~~eh----~~~l~~v~~~l~~~gl~l~--~~K~  221 (555)
T 1mu2_A          150 PQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMD-DILIASD-RTDLEH----DRVVLQLKELLNGLGFSTP--DEKF  221 (555)
T ss_dssp             CTTCTTHHHHHHHHHHHHHHHHHHHCTTSEEEEETT-EEEEEEC-SCHHHH----HHHHHHHHHHHHHTTCBCC--STTE
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHhhCCCcEEEEEec-ceEEecC-CCHHHH----HHHHHHHHHHHHHcCCccC--HHHh
Confidence            4566677877877776541     124567899999 9988653 145543    3445666667788999999  9997


Q ss_pred             EEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428          79 VCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK  117 (682)
Q Consensus        79 ~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~  117 (682)
                      .   +                    +.+++|||..++.+
T Consensus       222 ~---~--------------------~~~~~fLG~~i~~~  237 (555)
T 1mu2_A          222 Q---K--------------------DPPYHWMGYELWPT  237 (555)
T ss_dssp             E---C--------------------SSSEEETTEEECSS
T ss_pred             c---c--------------------CCceeEEeEEEeCC
Confidence            2   1                    13577888887754

---

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	682
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	3e-10
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-10
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	1e-09
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-09
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-09
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	5e-09
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	1e-08
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-08
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	3e-08
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-08
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	5e-08
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	9e-08
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	1e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-06
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-05
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	5e-05
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-04
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-04
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	2e-09
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	3e-09
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	5e-09
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	6e-09
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	9e-09
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	1e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	2e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	2e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	3e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	5e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	8e-08
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	3e-07
d1sa0e_	138	a.137.10.1 (E:) Stathmin 4 {Rat (Rattus norvegicus	5e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	3e-04
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	2e-06
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	8e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	1e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	2e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	3e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	3e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	5e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	5e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	5e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	5e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	8e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	9e-04
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	0.001
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	0.001
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	0.001
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	0.002
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	0.002
d2ayua1	301	d.305.1.1 (A:70-370) Nucleosome assembly protein,	0.003
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	1e-04
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	4e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	2e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	4e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	6e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	6e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	8e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	8e-04
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	0.001
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	0.002
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	0.003
d1ofcx3	102	a.187.1.1 (X:697-798) HAND domain of the nucleosom	0.003
d2ap3a1	185	a.24.27.1 (A:12-196) Hypothetical protein MW0975 (	2e-04
d2ap3a1	185	a.24.27.1 (A:12-196) Hypothetical protein MW0975 (	4e-04
d2ap3a1	185	a.24.27.1 (A:12-196) Hypothetical protein MW0975 (	8e-04
d2ap3a1	185	a.24.27.1 (A:12-196) Hypothetical protein MW0975 (	0.001
d1ulya_	190	a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococ	5e-04
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	0.001
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	0.002
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	0.002
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	0.002
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	0.002
d1qkla_	127	a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId:	0.002
d1s1ta1	110	c.55.3.1 (A:430-539) HIV RNase H (Domain of revers	0.002
d1jfib_	135	a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain	0.002
d1jfib_	135	a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain	0.003
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	0.003

>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 = 59.4 bits (143), Expect = 3e-10
 Identities = 11/68 (16%), Positives = 34/68 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           + +N   + ++    +E  ++  E+ E +  +  +E+E     + +E+E+  +E  ++E 
Sbjct: 227 QRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKES 286

Query: 647 EEEEEEVR 654
              + E++
Sbjct: 287 RIMKNEIQ 294

>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 = 59.0 bits (142), Expect = 4e-10
 Identities = 12/62 (19%), Positives = 32/62 (51%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
              +  +  E++E   +E  ++  E+ E +  ++ +E+E     + +E+E+  +E  ++E
Sbjct: 226 MQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKE 285

Query: 653 VR 654
            R
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 = 57.8 bits (139), Expect = 1e-09
 Identities = 12/66 (18%), Positives = 32/66 (48%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E   +  +  E++E   +E  ++  E+ E +  +  + QE     + +E+E+  +E  ++
Sbjct: 225 EMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQK 284

Query: 649 EEEEVR 654
           E   ++
Sbjct: 285 ESRIMK 290

>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 = 57.1 bits (137), Expect = 2e-09
 Identities = 11/62 (17%), Positives = 32/62 (51%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           Q  R  +   ++  E+ E +  +  +E+E    ++ +E+E+  +E  ++E    + E ++
Sbjct: 236 QKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQD 295

Query: 653 VR 654
           ++
Sbjct: 296 LQ 297

>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 = 55.9 bits (134), Expect = 4e-09
 Identities = 9/65 (13%), Positives = 29/65 (44%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +         ++  E+ E +  +  +E+E     + + QE+  +E  ++E    + E ++
Sbjct: 236 QKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQD 295

Query: 649 EEEEV 653
            + ++
Sbjct: 296 LQTKM 300

>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 = 55.9 bits (134), Expect = 5e-09
 Identities = 15/69 (21%), Positives = 35/69 (50%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++ R+ E+  E++E   +E  ++  E+ E +     +E+E     + +E+E+  +E  ++
Sbjct: 225 EMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQK 284

Query: 653 VRGGGKEEI 661
                K EI
Sbjct: 285 ESRIMKNEI 293

>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 = 54.4 bits (130), Expect = 1e-08
 Identities = 9/66 (13%), Positives = 30/66 (45%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +E   +  +   ++  E+ E +  +  +E+E     +  ++E+  +E  ++E    + E
Sbjct: 233 MMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNE 292

Query: 647 EEEEEE 652
            ++ + 
Sbjct: 293 IQDLQT 298

>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 = 54.0 bits (129), Expect = 2e-08
 Identities = 10/73 (13%), Positives = 32/73 (43%)

Query: 573 KVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
           +       ++      E++ QL  + E +  +  +E+E     + +E+E+  +   ++E 
Sbjct: 227 QRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKES 286

Query: 633 EEEEEEEEEEEEE 645
              + E ++ + +
Sbjct: 287 RIMKNEIQDLQTK 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 = 53.2 bits (127), Expect = 3e-08
 Identities = 13/75 (17%), Positives = 36/75 (48%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           + E+     +     + + E+  E++E   +E  ++  E  E +  +  +E+E     + 
Sbjct: 212 KAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKL 271

Query: 647 EEEEEEVRGGGKEEI 661
           +E+E+ ++ G ++E 
Sbjct: 272 QEQEQLLKEGFQKES 286

>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 = 52.8 bits (126), Expect = 4e-08
 Identities = 14/68 (20%), Positives = 31/68 (45%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            I    Q +   E+E E E  + E  +   +   E + + ++  E++E   +E  ++  E
Sbjct: 191 AILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTE 250

Query: 647 EEEEEEVR 654
           + E + V+
Sbjct: 251 KMENDRVQ 258

>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 = 52.8 bits (126), Expect = 5e-08
 Identities = 14/78 (17%), Positives = 34/78 (43%)

Query: 575 WKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEE 634
             T  + EI   R++            E + + E+  E++E   +E  ++  ++ E +  
Sbjct: 198 TLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRV 257

Query: 635 EEEEEEEEEEEEEEEEEE 652
           +  +E+E     + +E+E
Sbjct: 258 QLLKEQERTLALKLQEQE 275

>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 = 52.1 bits (124), Expect = 9e-08
 Identities = 13/74 (17%), Positives = 32/74 (43%)

Query: 579 DQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEE 638
             D+  + + + I     + E  +   +   E + + E+  E++E   QE  ++  E+ E
Sbjct: 194 QTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKME 253

Query: 639 EEEEEEEEEEEEEE 652
            +  +  +E+E   
Sbjct: 254 NDRVQLLKEQERTL 267

>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 = 51.7 bits (123), Expect = 1e-07
 Identities = 14/81 (17%), Positives = 35/81 (43%)

Query: 580 QDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           Q +      E  I++ R      +   +   E + + E+  E++E   +E  ++  E+ E
Sbjct: 194 QTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKME 253

Query: 640 EEEEEEEEEEEEEVRGGGKEE 660
            +  +  +E+E  +    +E+
Sbjct: 254 NDRVQLLKEQERTLALKLQEQ 274

>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 = 50.9 bits (121), Expect = 2e-07
 Identities = 12/80 (15%), Positives = 30/80 (37%)

Query: 573 KVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
            + +T          IE         +   +   E + + E+  E++E   +E  ++  E
Sbjct: 191 AILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTE 250

Query: 633 EEEEEEEEEEEEEEEEEEEE 652
           + E +  +  +E+E     +
Sbjct: 251 KMENDRVQLLKEQERTLALK 270

>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 = 47.8 bits (113), Expect = 2e-06
 Identities = 14/64 (21%), Positives = 31/64 (48%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           + I+Q  +    +E+E E E  + E  +   +   E  ++ E+  E++E   +E  ++  
Sbjct: 190 DAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLT 249

Query: 649 EEEE 652
           E+ E
Sbjct: 250 EKME 253

>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 = 44.7 bits (105), Expect = 2e-05
 Identities = 13/66 (19%), Positives = 32/66 (48%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
             E++   I + ++   E+E+E E E  + E  +   + + E + + E+  E++E   +E
Sbjct: 184 SKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQE 243

Query: 647 EEEEEE 652
             ++  
Sbjct: 244 HLKQLT 249

>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 = 43.6 bits (102), Expect = 5e-05
 Identities = 11/65 (16%), Positives = 30/65 (46%)

Query: 588 IENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +++   +     + ++   E+E+E E E  + E  +   +   E + + E+  E++E   
Sbjct: 182 LKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSY 241

Query: 648 EEEEE 652
           +E  +
Sbjct: 242 QEHLK 246

>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 = 41.3 bits (96), Expect = 2e-04
 Identities = 11/66 (16%), Positives = 27/66 (40%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
                 + +     + ++   E+E+E E E  + E  +   +   E + + E+  E++E 
Sbjct: 180 TYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKER 239

Query: 647 EEEEEE 652
             +E  
Sbjct: 240 SYQEHL 245

>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 = 41.3 bits (96), Expect = 2e-04
 Identities = 14/80 (17%), Positives = 34/80 (42%)

Query: 573 KVWKTSDQDEIGSPRIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEE 632
            + K   ++     + E I+Q   + +    +   + ++   E+E+E E E    E  + 
Sbjct: 159 DLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQA 218

Query: 633 EEEEEEEEEEEEEEEEEEEE 652
             +   E + + E+  E++E
Sbjct: 219 SAKMLHEMQRKNEQMMEQKE 238

>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 = 40.9 bits (95), Expect = 4e-04
 Identities = 13/66 (19%), Positives = 28/66 (42%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
              I       +E   +   + ++   E+E+E E E V+ E  +   +   E + + E+ 
Sbjct: 174 AEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQM 233

Query: 649 EEEEVR 654
            E++ R
Sbjct: 234 MEQKER 239

>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 = 40.9 bits (95), Expect = 4e-04
 Identities = 11/63 (17%), Positives = 28/63 (44%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           + +E   +   + ++   E+E+E E E  + E  +   +   E + + E+  E+     +
Sbjct: 183 KSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQ 242

Query: 659 EEI 661
           E +
Sbjct: 243 EHL 245

>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 = 54.1 bits (130), Expect = 2e-09
 Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE--EEEEEEE 650
            L  + E E E  ++  EE     +  +E+  +  E  +E  E       E  +E+++  
Sbjct: 68  HLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHA 127

Query: 651 EEVR 654
           EEVR
Sbjct: 128 EEVR 131

>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 = 53.7 bits (129), Expect = 3e-09
 Identities = 14/57 (24%), Positives = 27/57 (47%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++ E  EE  + +E E  +   E+ E E EV ++  EE     +  +E+  ++ E  
Sbjct: 49  KKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESN 105

>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 = 53.0 bits (127), Expect = 5e-09
 Identities = 14/57 (24%), Positives = 25/57 (43%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           RR  +E E  +   E+ E E E  ++  EE     +  +E+  ++ E  +E  E   
Sbjct: 57  RRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHL 113

>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 = 52.6 bits (126), Expect = 6e-09
 Identities = 14/74 (18%), Positives = 31/74 (41%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           ++E   +  +  E E  +   E+ E E E  ++  EE     +  +E+  ++ E  +E  
Sbjct: 50  KLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENR 109

Query: 647 EEEEEEVRGGGKEE 660
           E     +    +E+
Sbjct: 110 EAHLAAMLERLQEK 123

>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 = 52.2 bits (125), Expect = 9e-09
 Identities = 11/60 (18%), Positives = 26/60 (43%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            + +  E      +  +E+  ++ E  +E  E       E  +E+++  EE  + +E +E
Sbjct: 79  VIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKE 138

>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 = 51.8 bits (124), Expect = 1e-08
 Identities = 14/64 (21%), Positives = 27/64 (42%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           E I + +   E   + +E E  +   E+ E E E  +   EE     +  +E+  ++ E 
Sbjct: 45  EEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMES 104

Query: 649 EEEE 652
            +E 
Sbjct: 105 NKEN 108

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 13/62 (20%), Positives = 26/62 (41%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGK 658
           E  +   E+ E E E  ++  EE    ++  +E+  ++ E  +E  E        R   K
Sbjct: 64  ELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEK 123

Query: 659 EE 660
           ++
Sbjct: 124 DK 125

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 11/60 (18%), Positives = 28/60 (46%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           ++I++   E     +  +E+  ++ E  +E  E       E  +E+++  EE  + +E +
Sbjct: 78  EVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELK 137

>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 = 50.7 bits (121), Expect = 3e-08
 Identities = 12/64 (18%), Positives = 26/64 (40%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
               +IQ          +  +E+  ++ E  +E  E       E  +E+++  EE  + +
Sbjct: 75  HEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNK 134

Query: 647 EEEE 650
           E +E
Sbjct: 135 ELKE 138

>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 = 49.9 bits (119), Expect = 5e-08
 Identities = 17/65 (26%), Positives = 30/65 (46%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           RR    EE +++ E  EE  + +E E  + + E+ E E E  ++  EE     +  + + 
Sbjct: 39  RRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKL 98

Query: 656 GGKEE 660
             K E
Sbjct: 99  AQKME 103

>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 = 49.5 bits (118), Expect = 8e-08
 Identities = 11/56 (19%), Positives = 25/56 (44%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           ++ E  EE  + +E E  +   E+ E  +E  ++  EE     +  +E+  ++   
Sbjct: 49  KKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMES 104

>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 = 47.6 bits (113), Expect = 3e-07
 Identities = 11/60 (18%), Positives = 24/60 (40%)

Query: 593 QLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
                  +++ E  EE  + +E E  +   E+   E E  ++  EE     +  +E+  +
Sbjct: 41  DPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQ 100

>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 = 47.2 bits (112), Expect = 5e-07
 Identities = 15/57 (26%), Positives = 26/57 (45%)

Query: 596 RRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           RR +   EE +++ E  EE  + +E E  +   E+ E E E  ++  EE     +  
Sbjct: 38  RRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMA 94

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 44.9 bits (105), Expect = 2e-06
 Identities = 27/119 (22%), Positives = 38/119 (31%), Gaps = 8/119 (6%)

Query: 332 YTDGS--KTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIV 389
           YTDGS  +        Y               +   AEL A  + L         K  I+
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66

Query: 390 TDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAK 448
            DS                 +K+ +      + K+ I   W P+H GI GN+ VD    
Sbjct: 67  VDS--QYVMGIVASQPTESESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 37.6 bits (86), Expect = 8e-04
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 473 MNSEWQNLWDNVPNTNKLKTIRPSIKKDITFMWCPSHCGIKGNELVDVAAK 523
           + +      ++              K+ I   W P+H GI GN+ VD    
Sbjct: 75  IVASQPTESES--KIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 42.7 bits (100), Expect = 1e-04
 Identities = 10/43 (23%), Positives = 23/43 (53%)

Query: 598 GEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           G+ + + E+  + +E  E   E E   + +E+ + + EEE+ +
Sbjct: 72  GQEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.5 bits (97), Expect = 2e-04
 Identities = 13/42 (30%), Positives = 24/42 (57%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
           +E+ + E+  + +E  E   E E  V EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 13/43 (30%), Positives = 25/43 (58%)

Query: 613 EEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRG 655
           +E+ + E+  + +   E   E E   +EEE+ + + EEE+V+G
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVKG 115

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 12/42 (28%), Positives = 25/42 (59%)

Query: 608 EEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           +E+ + E+  + +E  E + E E   +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.4 bits (94), Expect = 5e-04
 Identities = 12/42 (28%), Positives = 25/42 (59%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
           +E+ + E+  + +E  E   E E + +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.4 bits (94), Expect = 5e-04
 Identities = 12/40 (30%), Positives = 24/40 (60%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +E+ + E+  + +E+ E   E E   +EEE+ + + EEE+
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQ 112

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.4 bits (94), Expect = 5e-04
 Identities = 12/42 (28%), Positives = 25/42 (59%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
           +E+ + E+  + +E  E   E E+  +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.0 bits (93), Expect = 5e-04
 Identities = 10/44 (22%), Positives = 22/44 (50%)

Query: 618 EEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           +E+ + E++ + +E  E   E E   +EEE+ + +      + I
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVKGI 116

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.6 bits (92), Expect = 8e-04
 Identities = 11/42 (26%), Positives = 23/42 (54%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           +E+ + E+  + +E  E   E     +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.6 bits (92), Expect = 9e-04
 Identities = 11/42 (26%), Positives = 24/42 (57%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
           +E+ + E+  + +E  E   E +   +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.2 bits (91), Expect = 0.001
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 587 RIENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEE 636
           +   II    + + E+  + +E  E   E E   +EEE+ Q + EEE+ +
Sbjct: 65  QRSRIISGQEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.8 bits (90), Expect = 0.001
 Identities = 11/42 (26%), Positives = 24/42 (57%)

Query: 607 EEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           +E+ + E+  + +E  E   + E   +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.8 bits (90), Expect = 0.001
 Identities = 12/42 (28%), Positives = 24/42 (57%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +E+ + E+  + +E  E   E E   +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.8 bits (90), Expect = 0.002
 Identities = 12/42 (28%), Positives = 25/42 (59%)

Query: 611 EEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           +E+ + E+  + +E V+   E E   +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.5 bits (89), Expect = 0.002
 Identities = 11/44 (25%), Positives = 24/44 (54%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           +E+ + E+  + +E      E E   +EEE+ + + EEE+ + +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVKGI 116

>d2ayua1 d.305.1.1 (A:70-370) Nucleosome assembly protein, NAP {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: NAP-like
superfamily: NAP-like
family: NAP-like
domain: Nucleosome assembly protein, NAP
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.7 bits (87), Expect = 0.003
 Identities = 11/42 (26%), Positives = 23/42 (54%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEE 647
           +E+ + E+  + +E  E     E   +EEE+ + + EEE+ +
Sbjct: 73  QEQPKPEQIAKGQEIVESLNETELLVDEEEKAQNDSEEEQVK 114

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

 Score = 42.6 bits (99), Expect = 1e-04
 Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 11/71 (15%)

Query: 591 IIQLIRRGEREEEEE-----------EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
           I  L+ +  R E EE           +   EE+          E   ++ +++E+E+EE+
Sbjct: 29  ITYLLEQYNRVEAEEARLSDLITGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEED 88

Query: 640 EEEEEEEEEEE 650
            +++  +++  
Sbjct: 89  GDDDSADDDNS 99

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

 Score = 40.7 bits (94), Expect = 4e-04
 Identities = 11/79 (13%), Positives = 32/79 (40%)

Query: 591 IIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           +  LI        EE+          E  +E+ ++ ++E+EE+ +++  +++   + E  
Sbjct: 46  LSDLITGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELA 105

Query: 651 EEVRGGGKEEISLHFYVLY 669
            E     + +  +    + 
Sbjct: 106 REKFAELRAQYVVTRDTIK 124

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 10/40 (25%), Positives = 21/40 (52%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEE 640
           +  E   +  + + EE+ + +E E + EEE +E+E    +
Sbjct: 60  KNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 9/41 (21%), Positives = 20/41 (48%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEE 643
            +  E   +  + + EE+ + +E +   EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEE 641
            +  E   +  + + EE+ + +E E   EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 9/41 (21%), Positives = 19/41 (46%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEE 644
            +  E   +  + + EE+ + +  E   EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.1 bits (86), Expect = 8e-04
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEE 646
            +  E   +  + + EE+ ++ E E   EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.1 bits (86), Expect = 8e-04
 Identities = 9/41 (21%), Positives = 20/41 (48%)

Query: 599 EREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEE 639
            +  E   +  + + EE+ + +E E   +EE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 610 EEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
            +  E   +  + + E Q + +E E   EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 9/41 (21%), Positives = 19/41 (46%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEE 642
            +  E   +  + + EE+ + +E     EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 609 EEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
            +  E   +  + + EE ++ +E E   EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d1ofcx3 a.187.1.1 (X:697-798) HAND domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 102

class: All alpha proteins
fold: HAND domain of the nucleosome remodeling ATPase ISWI
superfamily: HAND domain of the nucleosome remodeling ATPase ISWI
family: HAND domain of the nucleosome remodeling ATPase ISWI
domain: HAND domain of the nucleosome remodeling ATPase ISWI
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 9/41 (21%), Positives = 20/41 (48%)

Query: 612 EEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
            +  E   +  + + +E+ + +E E   EEE +E+E    +
Sbjct: 59  PKNTELGSDATKVQREEQRKIDEAEPLTEEEIQEKENLLSQ 99

>d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]} Length = 185

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: MW0975(SA0943)-like
family: MW0975(SA0943)-like
domain: Hypothetical protein MW0975 (SA0943)
species: Staphylococcus aureus [TaxId: 1280]

 Score = 40.4 bits (93), Expect = 2e-04
 Identities = 7/57 (12%), Positives = 31/57 (54%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEEI 661
           +++E +   ++ ++ +++EE ++   ++  E +E++++  E+   ++    G   + 
Sbjct: 3   DKKEIKAYLKQVDKIKDDEEPIKTVGKKIAELDEKKKKLTEDVNSKDTAVRGKAVKD 59

>d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]} Length = 185

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: MW0975(SA0943)-like
family: MW0975(SA0943)-like
domain: Hypothetical protein MW0975 (SA0943)
species: Staphylococcus aureus [TaxId: 1280]

 Score = 39.7 bits (91), Expect = 4e-04
 Identities = 7/50 (14%), Positives = 29/50 (58%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           +++E +   ++ ++ +++EE  + V ++  E +E++++  E+   ++   
Sbjct: 3   DKKEIKAYLKQVDKIKDDEEPIKTVGKKIAELDEKKKKLTEDVNSKDTAV 52

>d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]} Length = 185

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: MW0975(SA0943)-like
family: MW0975(SA0943)-like
domain: Hypothetical protein MW0975 (SA0943)
species: Staphylococcus aureus [TaxId: 1280]

 Score = 38.9 bits (89), Expect = 8e-04
 Identities = 6/60 (10%), Positives = 29/60 (48%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           +++E +   ++ ++ +++EE  +   ++  E +E++++  E+   ++            +
Sbjct: 3   DKKEIKAYLKQVDKIKDDEEPIKTVGKKIAELDEKKKKLTEDVNSKDTAVRGKAVKDLIK 62

>d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]} Length = 185

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: MW0975(SA0943)-like
family: MW0975(SA0943)-like
domain: Hypothetical protein MW0975 (SA0943)
species: Staphylococcus aureus [TaxId: 1280]

 Score = 38.1 bits (87), Expect = 0.001
 Identities = 6/61 (9%), Positives = 28/61 (45%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVRGGGKEE 660
           ++E +   ++ ++ +++EE  +    +  E +E++++  E+   ++     +      + 
Sbjct: 4   KKEIKAYLKQVDKIKDDEEPIKTVGKKIAELDEKKKKLTEDVNSKDTAVRGKAVKDLIKN 63

Query: 661 I 661
            
Sbjct: 64  A 64

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]} Length = 190

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

 Score = 39.6 bits (92), Expect = 5e-04
 Identities = 13/65 (20%), Positives = 27/65 (41%)

Query: 594 LIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEV 653
           L+   +R  ++E +      +  EE+E+  ++   E+     E     E   +EE  E +
Sbjct: 123 LLNIMDRMSQKEFDATVRISKYIEEKEDALKDFSNEDIIHAIEWLSTAELARDEEYLELL 182

Query: 654 RGGGK 658
           +  G 
Sbjct: 183 KRLGS 187

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 10/48 (20%), Positives = 25/48 (52%)

Query: 601 EEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
           + E+  + ++ ++ EE+E  ++ E  +EE +E  E     E  +  ++
Sbjct: 3   DNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQK 50

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 11/48 (22%), Positives = 25/48 (52%)

Query: 602 EEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEE 649
           + E+  + ++ ++ EE+E  ++ E  EEE +E  E     E  +  ++
Sbjct: 3   DNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQK 50

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 10/48 (20%), Positives = 24/48 (50%)

Query: 603 EEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEE 650
           + E+  + ++ ++ EE+E  ++    EEE +E  E     E  +  ++
Sbjct: 3   DNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQK 50

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 12/49 (24%), Positives = 23/49 (46%)

Query: 606 EEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEEVR 654
           + E+  + ++ ++ EE+E     E  EEE +E  E     E  +  + R
Sbjct: 3   DNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKR 51

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 10/48 (20%), Positives = 26/48 (54%)

Query: 604 EEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEE 651
           + E+  + ++ ++ EE+E  ++++  EEE +E  E     E  +  ++
Sbjct: 3   DNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQK 50

>d1qkla_ a.143.1.2 (A:) RPB6 {Human (Homo sapiens) [TaxId: 9606]} Length = 127

class: All alpha proteins
fold: RPB6/omega subunit-like
superfamily: RPB6/omega subunit-like
family: RPB6
domain: RPB6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 11/48 (22%), Positives = 24/48 (50%)

Query: 605 EEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEEEEEE 652
           + E+  + ++ ++ EE+E  +  E  EEE +E  E     E  +  ++
Sbjct: 3   DNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQK 50

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/107 (19%), Positives = 39/107 (36%), Gaps = 12/107 (11%)

Query: 332 YTDGS--KTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIV 389
           Y DG+  +        Y      +  +     +    EL AI+L L+        +  IV
Sbjct: 12  YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDS----GLEVNIV 67

Query: 390 TDSRSSLAALSNVRFINPLITKVYSTWSYLKLC--KKDITFMWCPSH 434
           TDS+ +L  +       P  ++       ++    K+ +   W P+H
Sbjct: 68  TDSQYALGIIQA----QPDQSESELVNQIIEQLIKKEKVYLAWVPAH 110

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} Length = 135

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, beta chain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 8/46 (17%), Positives = 18/46 (39%)

Query: 600 REEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEE 645
           +    +  +     E     EEE    Q+E   +  +++ E  ++E
Sbjct: 87  KTVALKRRKASSRLENLGIPEEELLRQQQELFAKARQQQAELAQQE 132

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} Length = 135

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, beta chain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 9/60 (15%), Positives = 26/60 (43%)

Query: 589 ENIIQLIRRGEREEEEEEEEEEEEEEEEEEEEEEEEEVQEEEEEEEEEEEEEEEEEEEEE 648
            + I  ++   +E +    +  +     E     EEE+  +++E   +  +++ E  ++E
Sbjct: 73  GSYISEVKEVLQECKTVALKRRKASSRLENLGIPEEELLRQQQELFAKARQQQAELAQQE 132

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

 Score = 36.5 bits (83), Expect = 0.003
 Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 4/47 (8%)

Query: 416 WSYLKLCKKDITFMWCPSHCGIKGNEIVD----VAAKNPTTGTTPFK 458
                L +  I + W   H G   NE  D     AA NPT   T ++
Sbjct: 104 RLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGYQ 150

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	682
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.88
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.83
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.82
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.69
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.45
d1ztwa1	255	MMLV reverse transcriptase {Moloney murine leukemi	94.28

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=99.88  E-value=1.7e-23  Score=185.31  Aligned_cols=119  Identities=24%  Similarity=0.257  Sum_probs=88.7

Q ss_pred             CCeEEEEeCCCCCC--CCceEEEEEcce-eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         326 TSHTICYTDGSKTP--TTTGCAYSVGNV-VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       326 ~~~~~iytDgS~~~--~~~G~g~~~~~~-~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      ++...+|||||+..  +.+|+|+++... .....++ .+||+.|||.||++||+.    ....+.|+|||++++..+.+.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~~-~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEecC-CCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcC
Confidence            34578999999764  346777776643 3333333 579999999999999985    367899999999999999887


Q ss_pred             CCCcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcc
Q psy3428         403 RFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPT  451 (682)
Q Consensus       403 ~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~  451 (682)
                      ...+.. ......+..+.. ...|.|.|||||+|++|||+||+||++|+
T Consensus        80 ~~~~~~-~~~~~~~~~~~~-~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          80 PTESES-KIVNQIIEEMIK-KEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEESC-HHHHHHHHHHHH-CSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             Cccccc-hHHHHHHHHhhh-cceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            654310 112222333333 46899999999999999999999999985

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

Probab=99.83  E-value=7.6e-22  Score=179.87  Aligned_cols=125  Identities=18%  Similarity=0.142  Sum_probs=91.3

Q ss_pred             eEEEEeCCCCCCC--CceEEEEEcc---eeeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         328 HTICYTDGSKTPT--TTGCAYSVGN---VVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       328 ~~~iytDgS~~~~--~~G~g~~~~~---~~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      .++||||||+.++  .+|+|+++..   ..........+||++||+.|++.||+++.  ....+.|++||++++..+...
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~--~~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALK--EPCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCC--SCCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhcc--CCceEEEecchhhhhcccccc
Confidence            5789999998764  4788987642   11122222456999999999999999864  356899999999999887543


Q ss_pred             C---------CC---cHH-HHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCC
Q psy3428         403 R---------FI---NPL-ITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTT  455 (682)
Q Consensus       403 ~---------~~---~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~  455 (682)
                      .         ..   .++ ..+++..+..+. ....|.|.|||||+|++|||.||+|||+|+....
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~-~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~~  145 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAM-APHRVRFHFVKGHTGHPENERVDREARRQAQSQA  145 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH-TTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHh-hhcccceEEccCCCCCcchHHHHHHHHHHHHHhc
Confidence            1         10   111 134455554444 3478999999999999999999999999987653

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

Probab=99.82  E-value=5.3e-21  Score=175.44  Aligned_cols=128  Identities=18%  Similarity=0.197  Sum_probs=92.6

Q ss_pred             eEEEEeCCCCCCC--CceEEEEEc--ceeeeec-CCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         328 HTICYTDGSKTPT--TTGCAYSVG--NVVRSTL-LNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       328 ~~~iytDgS~~~~--~~G~g~~~~--~~~~~~~-~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      .|.||||||+..+  .+|+|+++.  +....+. ....+|++.||++|++.||+++.  ....+.|++||++++..+...
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~--~~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALK--EHAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCC--SCCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhc--ccceEEEeecceeeEEcccch
Confidence            4899999997654  589998764  2222111 12457899999999999999875  356799999999999887543


Q ss_pred             C---------CC--cH-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCCCCc
Q psy3428         403 R---------FI--NP-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTPFK  458 (682)
Q Consensus       403 ~---------~~--~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~~~  458 (682)
                      .         ..  .+ ....++..+..+. ....|.|+|||||+|++|||+||+|||+|+..+....
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~-~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d  146 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTLED  146 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCC
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHh-hcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCc
Confidence            2         11  11 1123444444443 3468999999999999999999999999998776543

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=99.69  E-value=1.6e-17  Score=141.40  Aligned_cols=100  Identities=23%  Similarity=0.349  Sum_probs=73.4

Q ss_pred             CCeEEEEeCCCCCC--CCceEEEEEcce-eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428         326 TSHTICYTDGSKTP--TTTGCAYSVGNV-VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV  402 (682)
Q Consensus       326 ~~~~~iytDgS~~~--~~~G~g~~~~~~-~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~  402 (682)
                      .+...+|||||+..  +..|+|++.... .....++ .+||++|||.||+.||+..    ..++.|+|||+++++++..+
T Consensus         6 ~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~~-~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~~   80 (110)
T d1s1ta1           6 VGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQ   80 (110)
T ss_dssp             TTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEES-SCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHHC
T ss_pred             CCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEecc-cCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhcC
Confidence            34568999999654  346777776532 3333333 5799999999999999853    56899999999999999887


Q ss_pred             CCCc--HHHHHHHHHHHHHHhcCCceEEEEecCC
Q psy3428         403 RFIN--PLITKVYSTWSYLKLCKKDITFMWCPSH  434 (682)
Q Consensus       403 ~~~~--~~~~~i~~~~~~l~~~~~~v~~~WVpgH  434 (682)
                      ....  ++.+++.+.   + .....|.|.|||||
T Consensus        81 ~~~~~~~l~~~il~~---l-~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          81 PDQSESELVNQIIEQ---L-IKKEKVYLAWVPAH  110 (110)
T ss_dssp             CSEESCHHHHHHHHH---H-HHCSEEEEEECCSS
T ss_pred             ccccchHHHHHHHHH---H-hcCCceEEEEeCCC
Confidence            6543  344444432   3 34578999999999

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.45  E-value=6.6e-15  Score=126.88  Aligned_cols=113  Identities=12%  Similarity=0.058  Sum_probs=82.2

Q ss_pred             EEEeCCCCC--CCCceEEEEEcce---e-eeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcCC
Q psy3428         330 ICYTDGSKT--PTTTGCAYSVGNV---V-RSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVR  403 (682)
Q Consensus       330 ~iytDgS~~--~~~~G~g~~~~~~---~-~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~~  403 (682)
                      .||||||+.  ||.+|+|+|+...   . .+..+ +.+||++||++|++.||+.+...+ .++.|+|||++|+..+.++.
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~-~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~   83 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKK   83 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCE-EEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCc-CccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCc
Confidence            389999975  4568999887532   1 12122 467999999999999999998754 57999999999999997654


Q ss_pred             CC-----cHHHHHHHHHHHHHH--hcCCceEEEEecCCCCCchhHHHH
Q psy3428         404 FI-----NPLITKVYSTWSYLK--LCKKDITFMWCPSHCGIKGNEIVD  444 (682)
Q Consensus       404 ~~-----~~~~~~i~~~~~~l~--~~~~~v~~~WVpgH~gi~gNe~AD  444 (682)
                      .+     ....+++++.+.++.  -+...+.+.||+.|+..-||..||
T Consensus        84 ~kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          84 AKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             eecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            22     123345555554421  223568899999999888998887

>d1ztwa1 e.8.1.2 (A:24-278) MMLV reverse transcriptase {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Multi-domain proteins (alpha and beta)
fold: DNA/RNA polymerases
superfamily: DNA/RNA polymerases
family: Reverse transcriptase
domain: MMLV reverse transcriptase
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=94.28  E-value=0.019  Score=54.49  Aligned_cols=81  Identities=14%  Similarity=-0.025  Sum_probs=54.2

Q ss_pred             ehhhHHHHHHHHhhcc-----ccCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEE
Q psy3428           6 QIHKVILMSLLFVGFA-----VTGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVC   80 (682)
Q Consensus         6 ~~~~~~llfllyi~~~-----~~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~   80 (682)
                      |.-.++-.|--++...     ....++.+..|.| |+.|.  +.+.++.    ...++.+.+-++++|+.+|  ++||++
T Consensus       168 Gl~~spa~fq~~~~~il~~~~~~~~~~~~~~Y~D-Dili~--s~t~~eh----~~~l~~vl~~l~~~gl~~~--~~K~~~  238 (255)
T d1ztwa1         168 GFKNSPTLFDEALHRDLADFRIQHPDLILLQYVD-DLLLA--ATSELDC----QQGTRALLQTLGNLGYRAS--AKKAQI  238 (255)
T ss_dssp             TCTTHHHHHHHHHHHHTHHHHHHCTTCEEEEETT-EEEEE--ESSHHHH----HHHHHHHHHHHHHHTCCBC--TTTCEE
T ss_pred             hcccchhhhHHHHHHHHHHhhccCCceEEEEEee-eeecc--CCCHHHH----HHHHHHHHHHHHHCcCEeC--HHHeEC
Confidence            3444555554444332     1235667888999 99886  4566554    4555555666678999999  999986


Q ss_pred             EEecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428          81 IDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK  117 (682)
Q Consensus        81 i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~  117 (682)
                      .                      .++++|||.+++..
T Consensus       239 ~----------------------~~~v~fLG~~I~~G  253 (255)
T d1ztwa1         239 C----------------------QKQVKYLGYLLKEG  253 (255)
T ss_dssp             E----------------------ESEEEETTEEEETT
T ss_pred             C----------------------CCCcEEeEEEEeCC
Confidence            4                      35688999998753