Citrus Sinensis ID: 024140

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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--
Protein Sequence
MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRGMFDDRSSILSSVHSSHSSISSSESGSQTGKLENFLLE
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcc
Coil and Loop (DISEMBL)
mlakepgagstfdlpeevlqvlpsdpfeqLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLkddedastgatriakptpneddaavaptgtssvhsqiseggnssfaeerepessrpgisrgfvlasqtstprltppgsppslsasvsptktpkpvsprrhsisfstsrgmfddrssilssvhsshssisssesgsqtgklenflle
Flexible Loop (DISEMBL)
mlakepgagstfdlpeEVLQVLPSDPFEQLDVARKITSIAIstrvsdlesEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLskenealtntvrklqrdvsklevFRKTLvqslkddedastgatriakptpneddaavaptGTSSVHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLTPpgsppslsasvsptktpkpvsprrhsisfstsrgmfddRSSILSSVHSshssisssesgsqtgklenflle
Low Complexity Region (SEG)
MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRGMFDDRssilssvhsshssisssesgsQTGKLENFLLE
Disordered region (IsUnstruct)
****************************QLDVARKITSIAI***************************************************************************VF**********************************************************************************************************************************************************
Disordered Region (DISOPRED)
**************PEEVLQVLPSDPFEQLDVARKITSIAISTR************************************************************V****************************************************************************************************************************************************************L*NFLL*
Disordered Region (DISEMBL)
*********STFDLPEEVLQVLPSDPFEQLDVARKITSIAIST**********************IAELQSQIESIYSSLSD*************KENEALTNTVRKLQRDVSKLEVFRKTLVQS**********ATRIAKPTP***************************************ISRGFVLASQT*********************************ISFSTSRGMFDDRSS**********************KLENFLLE
Disordered Region (DISPRO)
**********TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS***************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRxxxxxxxxxxxxxxxxxxxxxxxxxxxxIESIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVSKLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRGMFDDRSSILSSVHSSHSSISSSESGSQTGKLENFLLE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	272	2.2.26 [Sep-21-2011]
Q93W28	337	Uncharacterized protein A	yes	no	0.897	0.724	0.583	8e-71

>sp|Q93W28|Y4554_ARATH Uncharacterized protein At4g15545 OS=Arabidopsis thaliana GN=At4g15545 PE=1 SV=1

 Score =  266 bits (681), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 151/259 (58%), Positives = 187/259 (72%), Gaps = 15/259 (5%)

Query: 11  TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQ 70
           +FDLP+E+LQVLPSDPFEQLDVARKITSIA+STRVS LESE S LR  LAEK+    ELQ
Sbjct: 21  SFDLPDELLQVLPSDPFEQLDVARKITSIALSTRVSALESESSDLRELLAEKEKEFEELQ 80

Query: 71  SQIESIYSSLSD---KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK 127
           S +ES+ +SLSD   KL  A  +KE L +EN +L+NTV++LQRDVSKLE FRKTL+ SL+
Sbjct: 81  SHVESLEASLSDAFHKLSLADGEKENLIRENASLSNTVKRLQRDVSKLEGFRKTLMMSLQ 140

Query: 128 DDEDASTGATRI-AKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPGISR 186
           DD D + G T+I AKPTPN+DD    P+  SS+ SQ +       A + E ++ +P +S 
Sbjct: 141 DD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQQASEAIEPAATDNENDAPKPSLSA 199

Query: 187 GFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRGMFDDRSSILSS 246
              L SQT+TPRLTPPGSPP LSAS +P  T +P+SPRRHS+SF+T+RGMFDD       
Sbjct: 200 SLPLVSQTTTPRLTPPGSPPILSASGTPKTTSRPISPRRHSVSFATTRGMFDD------- 252

Query: 247 VHSSHSSISSSESGSQTGK 265
              + SSIS SE GSQT +
Sbjct: 253 ---TRSSISISEPGSQTAR 268

Arabidopsis thaliana (taxid: 3702)

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	272
255551573	338	conserved hypothetical protein [Ricinus	0.966	0.778	0.741	5e-90
224107297	346	predicted protein [Populus trichocarpa]	0.959	0.754	0.637	5e-75
449454446	346	PREDICTED: uncharacterized protein LOC10	0.959	0.754	0.587	5e-71
449473478	284	PREDICTED: uncharacterized LOC101204510	0.955	0.915	0.589	6e-71
297804694	335	hypothetical protein ARALYDRAFT_915246 [	0.893	0.725	0.598	1e-70
359477457	332	PREDICTED: uncharacterized protein LOC10	0.841	0.689	0.616	2e-70
18414476	337	uncharacterized protein [Arabidopsis tha	0.897	0.724	0.583	5e-69
357478537	389	hypothetical protein MTR_4g118510 [Medic	0.941	0.658	0.573	9e-69
357478533	344	hypothetical protein MTR_4g118510 [Medic	0.941	0.744	0.573	2e-68
356555589	332	PREDICTED: uncharacterized protein LOC10	0.908	0.743	0.558	3e-68

>gi|255551573|ref|XP_002516832.1| conserved hypothetical protein [Ricinus communis] gi|223543920|gb|EEF45446.1| conserved hypothetical protein [Ricinus communis]

 Score =  337 bits (863), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 201/271 (74%), Positives = 226/271 (83%), Gaps = 8/271 (2%)

Query: 1   MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLA 60
           MLAKE G GSTFDLPEEVLQVLPSDPFEQLDVARKITSIA+STRVS LESE SALR QLA
Sbjct: 1   MLAKESG-GSTFDLPEEVLQVLPSDPFEQLDVARKITSIALSTRVSSLESEFSALRLQLA 59

Query: 61  EKDSRIAELQSQIESIYSSLSD---KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           EKD  IAELQS IES+ +SLSD   KL QA A+KE L KEN +L+N V+KLQRDVSKLEV
Sbjct: 60  EKDHLIAELQSHIESLDASLSDSADKLAQADAEKENLLKENASLSNIVKKLQRDVSKLEV 119

Query: 118 FRKTLVQSLKDDEDASTGAT-RIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEERE 176
           FRKTL++SL+DDE++S+GA   IAKPTP EDDA++ P+ TSS+ SQ SE GNS FAE+RE
Sbjct: 120 FRKTLMKSLQDDEESSSGAIPIIAKPTPTEDDASMLPSRTSSMRSQFSEMGNS-FAEDRE 178

Query: 177 PE-SSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRG 235
            + SSRPG+S G +LASQTSTPR TPPGSPPS SASVSPT+T KPVSPRRHS+SFSTSRG
Sbjct: 179 IDASSRPGMSHGPLLASQTSTPRFTPPGSPPSFSASVSPTRTSKPVSPRRHSMSFSTSRG 238

Query: 236 MFDDR-SSILSSVHSSHSSISSSESGSQTGK 265
           M DDR S   S   S HSSISSSE+GS TG+
Sbjct: 239 MPDDRSSLFSSIPSSQHSSISSSETGSHTGR 269

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224107297|ref|XP_002314437.1| predicted protein [Populus trichocarpa] gi|222863477|gb|EEF00608.1| predicted protein [Populus trichocarpa]

 Score =  286 bits (733), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 179/281 (63%), Positives = 215/281 (76%), Gaps = 20/281 (7%)

Query: 1   MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLA 60
           ML+KE G GS FDLPE+VLQVLPSDPF+QLDVARKITSIA+STRVS LESE S LR++LA
Sbjct: 1   MLSKESG-GSAFDLPEDVLQVLPSDPFQQLDVARKITSIALSTRVSALESESSLLRAKLA 59

Query: 61  EKDSRIAELQSQIE---SIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           EKD  IA LQ+QIE   S  S  SDKL +A  +KE L KEN +L+NTV+KLQRDVSKLEV
Sbjct: 60  EKDDFIAHLQAQIESLDSSLSDSSDKLSRATQEKENLLKENASLSNTVKKLQRDVSKLEV 119

Query: 118 FRKTLVQSLKDDEDASTGATR-IAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEERE 176
           FRKTLVQSL++DE++S GA + IAKPTPNEDDA + P+  SS+ S++ E GN SFAE+RE
Sbjct: 120 FRKTLVQSLQEDEESSAGAPQIIAKPTPNEDDATLPPSRYSSIQSKVPEMGN-SFAEDRE 178

Query: 177 PE------------SSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPR 224
            +            + RPGI +  +LASQT+TPR TPPGSPPS SASVSPT+T KPVSP+
Sbjct: 179 TDVLMLLHLVIFMAAPRPGIPQ-ILLASQTNTPRFTPPGSPPSFSASVSPTRTSKPVSPK 237

Query: 225 RHSISFSTSRGMFDDRSSILSSVHSSHSSISSSESGSQTGK 265
           R S+SFS +R M DDRS   SS+ SS  S  SS++GSQ G+
Sbjct: 238 RQSMSFSITRSM-DDRSPAFSSLSSSQHSSMSSDAGSQAGR 277

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454446|ref|XP_004144966.1| PREDICTED: uncharacterized protein LOC101217996 [Cucumis sativus] gi|449515179|ref|XP_004164627.1| PREDICTED: uncharacterized protein LOC101231402 [Cucumis sativus]

 Score =  273 bits (698), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 165/281 (58%), Positives = 207/281 (73%), Gaps = 20/281 (7%)

Query: 1   MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLA 60
           M  +E G  + F LP+EVLQVLPSDPF+QLDVARKITSIA+STRVS LESE SAL +Q++
Sbjct: 1   MREEESGVAN-FGLPDEVLQVLPSDPFDQLDVARKITSIALSTRVSALESESSALLAQIS 59

Query: 61  EKDSRIAELQSQIESIYSSLSDK---LGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           EKD+ IAELQSQIES+ ++LS K   L +A+ +KE L +EN +L+NTV+KL RDVSKLEV
Sbjct: 60  EKDALIAELQSQIESLDAALSQKSEVLTRAEQEKETLLQENASLSNTVKKLTRDVSKLEV 119

Query: 118 FRKTLVQSLKDDEDASTGATRIAK---------PTPN--EDDAAVAPTGTSSVHSQISEG 166
           FRKTL+QSL ++E+++      AK         P+ +  EDD A+ P+  SS+ S  SE 
Sbjct: 120 FRKTLMQSLNEEENSTATGGPEAKVKIESQESLPSASVVEDDLALPPSKYSSIQSNTSET 179

Query: 167 GNSSFAEEREPE--SSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPR 224
            N S  EE E +  +SRP IS   +LASQTSTPRLTPPGSPP  SASVSPT+T KPVSP+
Sbjct: 180 VN-SVKEEHEADVATSRPRISNSLLLASQTSTPRLTPPGSPPISSASVSPTRTSKPVSPK 238

Query: 225 RHSISFSTSRGMFDDRSSILSSVHSSHSSISSSESGSQTGK 265
           RHS+SFS SRGMF DR+S+ SS   +HSS+SS   G+ TG+
Sbjct: 239 RHSMSFSVSRGMF-DRTSMYSST-GNHSSVSSPHGGTHTGR 277

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449473478|ref|XP_004153893.1| PREDICTED: uncharacterized LOC101204510 [Cucumis sativus]

 Score =  273 bits (698), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 165/280 (58%), Positives = 206/280 (73%), Gaps = 20/280 (7%)

Query: 1   MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLA 60
           M  +E G  + F LP+EVLQVLPSDPF+QLDVARKITSIA+STRVS LESE SAL +Q++
Sbjct: 1   MREEESGVAN-FGLPDEVLQVLPSDPFDQLDVARKITSIALSTRVSALESESSALLAQIS 59

Query: 61  EKDSRIAELQSQIESIYSSLSDK---LGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           EKD+ IAELQSQIES+ ++LS K   L +A+ +KE L +EN +L+NTV+KL RDVSKLEV
Sbjct: 60  EKDALIAELQSQIESLDAALSQKSEVLTRAEQEKETLLQENASLSNTVKKLTRDVSKLEV 119

Query: 118 FRKTLVQSLKDDEDASTGATRIAK---------PTPN--EDDAAVAPTGTSSVHSQISEG 166
           FRKTL+QSL ++E+++      AK         P+ +  EDD A+ P+  SS+ S  SE 
Sbjct: 120 FRKTLMQSLNEEENSTATGGPEAKVKIESQESLPSASVVEDDLALPPSKYSSIQSNTSET 179

Query: 167 GNSSFAEEREPE--SSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPR 224
            N S  EE E +  +SRP IS   +LASQTSTPRLTPPGSPP  SASVSPT+T KPVSP+
Sbjct: 180 VN-SVKEEHEADVATSRPRISNSLLLASQTSTPRLTPPGSPPISSASVSPTRTSKPVSPK 238

Query: 225 RHSISFSTSRGMFDDRSSILSSVHSSHSSISSSESGSQTG 264
           RHS+SFS SRGMF DR+S+ SS   +HSS+SS   G+ TG
Sbjct: 239 RHSMSFSVSRGMF-DRTSMYSST-GNHSSVSSPHGGTHTG 276

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804694|ref|XP_002870231.1| hypothetical protein ARALYDRAFT_915246 [Arabidopsis lyrata subsp. lyrata] gi|297316067|gb|EFH46490.1| hypothetical protein ARALYDRAFT_915246 [Arabidopsis lyrata subsp. lyrata]

 Score =  272 bits (695), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 155/259 (59%), Positives = 191/259 (73%), Gaps = 16/259 (6%)

Query: 11  TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQ 70
           +FDLP+E+LQVLPSDPFEQLDVARKITSIA+STRVS LESE S LR  LAE+D  IAELQ
Sbjct: 20  SFDLPDELLQVLPSDPFEQLDVARKITSIALSTRVSALESESSDLRELLAERDKEIAELQ 79

Query: 71  SQIESIYSSLSD---KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK 127
           S +ES+ +SLSD   KL  A  +KE L +EN +L+NTV++LQRDVSKLE FRKTL+ SL+
Sbjct: 80  SHVESLDASLSDAFHKLSLADGEKENLIRENASLSNTVKRLQRDVSKLEGFRKTLMMSLQ 139

Query: 128 DDEDASTGATR-IAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPGISR 186
           DD D + G T+ IAKPTPN+DD    P+  SS+ SQ SE    +   + E ++ +P +S 
Sbjct: 140 DD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQASEAIEPA-TTDNENDAPKPSLSA 197

Query: 187 GFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRGMFDDRSSILSS 246
            F L SQT+TPRLTPPGSPP LSAS +P  T +P+SPRRHS+SF+T+RGMFDD       
Sbjct: 198 SFPLVSQTTTPRLTPPGSPPILSASGTPKTTSRPLSPRRHSVSFATTRGMFDD------- 250

Query: 247 VHSSHSSISSSESGSQTGK 265
              + SSIS SE GSQT +
Sbjct: 251 ---TRSSISISEPGSQTTR 266

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359477457|ref|XP_002278619.2| PREDICTED: uncharacterized protein LOC100252741 [Vitis vinifera] gi|297736943|emb|CBI26144.3| unnamed protein product [Vitis vinifera]

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 159/258 (61%), Positives = 188/258 (72%), Gaps = 29/258 (11%)

Query: 1   MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLA 60
           M AKEPG  S FDLPEEVL+VLPSDPFEQLDVARKITSIA+S RVS LESE SALRS+LA
Sbjct: 1   MFAKEPGTPS-FDLPEEVLEVLPSDPFEQLDVARKITSIALSARVSALESEASALRSKLA 59

Query: 61  EKDSRIAELQSQIESIYSSLSD---KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           +KD+ +A+L  QIES+  +LSD   KL  A+ +KE L KEN +L+NTV+KL RDVSKLE 
Sbjct: 60  DKDALVADLHDQIESLDHALSDAADKLFLAEQEKENLLKENASLSNTVKKLNRDVSKLES 119

Query: 118 FRKTLVQSLKDDEDASTGATRIA------------KPTPNEDDAAVAPTGTSSVHSQISE 165
           FRKTL+ SLK+DE++S  + ++                  EDDA    +  SS  SQ SE
Sbjct: 120 FRKTLMLSLKEDEESSGASPQVVAKQMAAQSSLSSASMTGEDDAT---SRYSSTRSQYSE 176

Query: 166 GGNSSFAEEREPESSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRR 225
            GNS FAE+RE ++SR GIS GF+LASQT+TPRLTPPGSPP+LSASVSP         RR
Sbjct: 177 IGNS-FAEDRETDASRAGISHGFLLASQTNTPRLTPPGSPPTLSASVSP---------RR 226

Query: 226 HSISFSTSRGMFDDRSSI 243
           HSIS STSRGMFDDR S+
Sbjct: 227 HSISLSTSRGMFDDRPSV 244

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18414476|ref|NP_567470.1| uncharacterized protein [Arabidopsis thaliana] gi|14517356|gb|AAK62569.1| AT4g15540/dl3810w [Arabidopsis thaliana] gi|15982813|gb|AAL09754.1| AT4g15540/dl3810w [Arabidopsis thaliana] gi|16323276|gb|AAL15372.1| AT4g15540/dl3810w [Arabidopsis thaliana] gi|21592639|gb|AAM64588.1| unknown [Arabidopsis thaliana] gi|22531186|gb|AAM97097.1| expressed protein [Arabidopsis thaliana] gi|23198008|gb|AAN15531.1| expressed protein [Arabidopsis thaliana] gi|332658223|gb|AEE83623.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  266 bits (681), Expect = 5e-69,   Method: Compositional matrix adjust.
 Identities = 151/259 (58%), Positives = 187/259 (72%), Gaps = 15/259 (5%)

Query: 11  TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQ 70
           +FDLP+E+LQVLPSDPFEQLDVARKITSIA+STRVS LESE S LR  LAEK+    ELQ
Sbjct: 21  SFDLPDELLQVLPSDPFEQLDVARKITSIALSTRVSALESESSDLRELLAEKEKEFEELQ 80

Query: 71  SQIESIYSSLSD---KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK 127
           S +ES+ +SLSD   KL  A  +KE L +EN +L+NTV++LQRDVSKLE FRKTL+ SL+
Sbjct: 81  SHVESLEASLSDAFHKLSLADGEKENLIRENASLSNTVKRLQRDVSKLEGFRKTLMMSLQ 140

Query: 128 DDEDASTGATRI-AKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPGISR 186
           DD D + G T+I AKPTPN+DD    P+  SS+ SQ +       A + E ++ +P +S 
Sbjct: 141 DD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQQASEAIEPAATDNENDAPKPSLSA 199

Query: 187 GFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRGMFDDRSSILSS 246
              L SQT+TPRLTPPGSPP LSAS +P  T +P+SPRRHS+SF+T+RGMFDD       
Sbjct: 200 SLPLVSQTTTPRLTPPGSPPILSASGTPKTTSRPISPRRHSVSFATTRGMFDD------- 252

Query: 247 VHSSHSSISSSESGSQTGK 265
              + SSIS SE GSQT +
Sbjct: 253 ---TRSSISISEPGSQTAR 268

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357478537|ref|XP_003609554.1| hypothetical protein MTR_4g118510 [Medicago truncatula] gi|355510609|gb|AES91751.1| hypothetical protein MTR_4g118510 [Medicago truncatula]

 Score =  266 bits (679), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 156/272 (57%), Positives = 195/272 (71%), Gaps = 16/272 (5%)

Query: 8   AGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIA 67
            G  FDLPE+V+QVLPSDPFEQLDVARKITSIA+STRV  LE E S LR++ AEKD  IA
Sbjct: 6   GGLNFDLPEDVMQVLPSDPFEQLDVARKITSIALSTRVKALELESSELRAKTAEKDELIA 65

Query: 68  ELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ 124
           ELQSQ+ES+  SLS   D L +A+ DKE L KEN +L+NTVRKL RDVSKLEVFRKTL+Q
Sbjct: 66  ELQSQLESLDVSLSQTADNLVRAEQDKENLLKENASLSNTVRKLNRDVSKLEVFRKTLMQ 125

Query: 125 SLKDDEDASTGATRIA-----------KPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAE 173
           SL++DED S GA  I                 ++ A+  P+ +SS+   +S+  NS +AE
Sbjct: 126 SLQEDEDNSGGAPDIVARIQSQSSLTSTSQYGDNGASFQPSISSSM-PHVSDSENS-YAE 183

Query: 174 EREPESSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTS 233
           ++E +  RP +    ++ASQ +TP +TP GSPPSLSASVSPT+T +P+SPRRHSISFSTS
Sbjct: 184 DQESDDIRPRVPYNLLVASQRTTPLITPTGSPPSLSASVSPTRTSRPMSPRRHSISFSTS 243

Query: 234 RGMFDDRSSILSSVHSSHSSISSSESGSQTGK 265
           RG  DDRSS+ SS+     S S S +GSQ+G+
Sbjct: 244 RGTHDDRSSVFSSIGHGSISSSDSVTGSQSGR 275

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357478533|ref|XP_003609552.1| hypothetical protein MTR_4g118510 [Medicago truncatula] gi|355510607|gb|AES91749.1| hypothetical protein MTR_4g118510 [Medicago truncatula]

 Score =  265 bits (676), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 156/272 (57%), Positives = 195/272 (71%), Gaps = 16/272 (5%)

Query: 8   AGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIA 67
            G  FDLPE+V+QVLPSDPFEQLDVARKITSIA+STRV  LE E S LR++ AEKD  IA
Sbjct: 6   GGLNFDLPEDVMQVLPSDPFEQLDVARKITSIALSTRVKALELESSELRAKTAEKDELIA 65

Query: 68  ELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ 124
           ELQSQ+ES+  SLS   D L +A+ DKE L KEN +L+NTVRKL RDVSKLEVFRKTL+Q
Sbjct: 66  ELQSQLESLDVSLSQTADNLVRAEQDKENLLKENASLSNTVRKLNRDVSKLEVFRKTLMQ 125

Query: 125 SLKDDEDASTGATRIA-----------KPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAE 173
           SL++DED S GA  I                 ++ A+  P+ +SS+   +S+  NS +AE
Sbjct: 126 SLQEDEDNSGGAPDIVARIQSQSSLTSTSQYGDNGASFQPSISSSM-PHVSDSENS-YAE 183

Query: 174 EREPESSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTS 233
           ++E +  RP +    ++ASQ +TP +TP GSPPSLSASVSPT+T +P+SPRRHSISFSTS
Sbjct: 184 DQESDDIRPRVPYNLLVASQRTTPLITPTGSPPSLSASVSPTRTSRPMSPRRHSISFSTS 243

Query: 234 RGMFDDRSSILSSVHSSHSSISSSESGSQTGK 265
           RG  DDRSS+ SS+     S S S +GSQ+G+
Sbjct: 244 RGTHDDRSSVFSSIGHGSISSSDSVTGSQSGR 275

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555589|ref|XP_003546113.1| PREDICTED: uncharacterized protein LOC100776071 [Glycine max]

 Score =  264 bits (675), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 157/281 (55%), Positives = 195/281 (69%), Gaps = 34/281 (12%)

Query: 1   MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLA 60
           ML  E  +GS  DLPEE+L VLPSDP+EQLDVARKITS+A+STRV  L+SE SALR++LA
Sbjct: 1   MLVSE-SSGSKVDLPEELLNVLPSDPYEQLDVARKITSVALSTRVDALQSESSALRAELA 59

Query: 61  EKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           +++  IAELQSQ+ESI ++LS   DKL +A  DKE L KEN +L+NTVRKL RDVSKLE 
Sbjct: 60  DRNRLIAELQSQVESIDAALSEAADKLARADQDKENLLKENASLSNTVRKLTRDVSKLET 119

Query: 118 FRKTLVQSLKDDEDASTGATRIAKPTPNE----------DDAAVAPTGTSSVHSQI--SE 165
           FRKTL++SL++DED S G    A    ++          DD A +   + +   +I  S+
Sbjct: 120 FRKTLMKSLREDEDTSEGTPDTAAKLHSQASFTSTSQFGDDDASSTLSSRTSSMRINTSD 179

Query: 166 GGNSSFAEEREPESSRPGISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKT-PKPVSPR 224
            GN   AE+RE + S+   S   +LASQTSTPR+TPPGSPPS+SA VSPT+T  KPVSPR
Sbjct: 180 MGN-YLAEDRESDGSKSRASHNLLLASQTSTPRITPPGSPPSMSALVSPTRTSSKPVSPR 238

Query: 225 RHSISFSTSRGMFDDRSSILSSVHSSHSSISSSESGSQTGK 265
           RH+ISFSTSRGMFDDRSS+                GSQTG+
Sbjct: 239 RHAISFSTSRGMFDDRSSV----------------GSQTGR 263

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	272
TAIR|locus:505006472	337	AT4G15545 "AT4G15545" [Arabido	0.845	0.682	0.605	1.1e-66
TAIR|locus:2017933	325	AT1G16520 "AT1G16520" [Arabido	0.797	0.667	0.390	6.2e-30
TAIR|locus:2205230	310	AT1G56080 "AT1G56080" [Arabido	0.742	0.651	0.368	2.1e-29
UNIPROTKB|E7EMV0	863	DIAPH1 "Protein diaphanous hom	0.705	0.222	0.248	3.2e-05
MGI|MGI:96687	487	Krt12 "keratin 12" [Mus muscul	0.558	0.312	0.254	4.2e-05
UNIPROTKB|E7ERW8	1215	DIAPH1 "Protein diaphanous hom	0.705	0.158	0.248	4.8e-05
UNIPROTKB|E9PHQ0	1260	DIAPH1 "Protein diaphanous hom	0.705	0.152	0.248	5.1e-05
UNIPROTKB|E7ET75	1264	DIAPH1 "Protein diaphanous hom	0.705	0.151	0.248	5.1e-05
UNIPROTKB|E9PEZ3	1269	DIAPH1 "Protein diaphanous hom	0.705	0.151	0.248	5.1e-05
UNIPROTKB|O60610	1272	DIAPH1 "Protein diaphanous hom	0.705	0.150	0.248	5.1e-05

TAIR|locus:505006472 AT4G15545 "AT4G15545" [Arabidopsis thaliana (taxid:3702)]

 Score = 678 (243.7 bits), Expect = 1.1e-66, P = 1.1e-66
 Identities = 143/236 (60%), Positives = 177/236 (75%)

Query:     9 GS-TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIA 67
             GS +FDLP+E+LQVLPSDPFEQLDVARKITSIA+STRVS LESE S LR  LAEK+    
Sbjct:    18 GSRSFDLPDELLQVLPSDPFEQLDVARKITSIALSTRVSALESESSDLRELLAEKEKEFE 77

Query:    68 ELQSQIESIYSSLSD---KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ 124
             ELQS +ES+ +SLSD   KL  A  +KE L +EN +L+NTV++LQRDVSKLE FRKTL+ 
Sbjct:    78 ELQSHVESLEASLSDAFHKLSLADGEKENLIRENASLSNTVKRLQRDVSKLEGFRKTLMM 137

Query:   125 SLKDDEDASTGATRI-AKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPG 183
             SL+DD D + G T+I AKPTPN+DD    P+  SS+ SQ +       A + E ++ +P 
Sbjct:   138 SLQDD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQQASEAIEPAATDNENDAPKPS 196

Query:   184 ISRGFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSRGMFDD 239
             +S    L SQT+TPRLTPPGSPP LSAS +P  T +P+SPRRHS+SF+T+RGMFDD
Sbjct:   197 LSASLPLVSQTTTPRLTPPGSPPILSASGTPKTTSRPISPRRHSVSFATTRGMFDD 252

GO:0006833 "water transport" evidence=RCA

GO:0009637 "response to blue light" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0042744 "hydrogen peroxide catabolic process" evidence=RCA

GO:0046777 "protein autophosphorylation" evidence=RCA

TAIR|locus:2017933 AT1G16520 "AT1G16520" [Arabidopsis thaliana (taxid:3702)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 89/228 (39%), Positives = 132/228 (57%)

Query:    12 FDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQ- 70
             F+LPEEVL V+P DPFEQLD+ARKITS+AI++RVS+L+SE   LR +L  K+S + EL+ 
Sbjct:     8 FELPEEVLSVIPMDPFEQLDLARKITSMAIASRVSNLDSEVVELRQKLLGKESVVRELEE 67

Query:    71 --SQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD 128
               S++E        +L     D   L+KE ++L  TV KL RD++KLE F++ L++SL D
Sbjct:    68 KASRLERDCREADSRLKVVLEDNMNLTKEKDSLAMTVTKLTRDLAKLETFKRQLIKSLSD 127

Query:   129 DEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREP--ESSRPGISR 186
             +    T    I   T ++  +     G  + HS I +  + S  +   P  E+S+   ++
Sbjct:   128 ESGPQTEPVDIR--TCDQPGSYPGKDGRINAHS-IKQAYSGS-TDTNNPVVEASKYTGNK 183

Query:   187 GFVLASQTSTPRLTPPGSPPSLSASVSPTKTPKPVSPRRHSISFSTSR 234
              F + S  S PRLTP  +P  +S SVSP       SP+R S + S ++
Sbjct:   184 -FSMTSYIS-PRLTPTATPKIISTSVSPRGYSAAGSPKRTSGAVSPTK 229

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2205230 AT1G56080 "AT1G56080" [Arabidopsis thaliana (taxid:3702)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 81/220 (36%), Positives = 123/220 (55%)

Query:     8 AGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIA 67
             +G  F+L +E+L V+P+DP++QLD+ARKITS+AI++RVS+LES+ S LR +L EKD  + 
Sbjct:     4 SGGDFNLSDEILAVIPTDPYDQLDLARKITSMAIASRVSNLESQVSGLRQKLLEKDRLVH 63

Query:    68 ELQSQIES---IYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ 124
             EL+ ++ S   +Y      L     +  +L++E ++L  T +KL RD +KLE F++ L+Q
Sbjct:    64 ELEDRVSSFERLYHEADSSLKNVVDENMKLTQERDSLAITAKKLGRDYAKLEAFKRQLMQ 123

Query:   125 SLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPESSRPGI 184
             SL DD  + T             D  + P G    +S  S   N   +E R+ +S  P  
Sbjct:   124 SLNDDNPSQTETA----------DVRMVPRGKDE-NSNGSYSNNEGLSEARQRQSMTPQF 172

Query:   185 SRGFVLASQTSTPR-LTPPGSPPSLSASVSPTKTPKPVSP 223
             S  F   + + TP+ L+   SP S SA+ SP       SP
Sbjct:   173 SPAF---TPSGTPKILSTAASPRSYSAASSPKLFSGAASP 209

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|E7EMV0 DIAPH1 "Protein diaphanous homolog 1" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 3.2e-05, P = 3.2e-05
 Identities = 50/201 (24%), Positives = 84/201 (41%)

Query:    29 QLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQ 88
             Q+++   I  +   T+V   E++ + L  +L  + +   ELQ +++ + S    KL   Q
Sbjct:   449 QIEIEGLIDQMIDKTKVEKSEAKAAELEKKLDSELTARHELQVEMKKMESDFEQKLQDLQ 508

Query:    89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD--DEDASTGATRIAKPTPNE 146
              +K+ L  E + +    + L+ +VS+L      L + L+D   E AS  A  I  P    
Sbjct:   509 GEKDALHSEKQQIATEKQDLEAEVSQLTGEVAKLTKELEDAKKEMASLSAAAITVPPSVP 568

Query:   147 DDAAVAPT----GTSS--VHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLT 200
               A V P     G S   +    + G +++      P    P +  G  ++S  S P  T
Sbjct:   569 SRAPVPPAPPLPGDSGTIIPPPPAPGDSTTPPPPPPPPPPPPPLPGGVCISSPPSLPGGT 628

Query:   201 PPGSPPSLSASVS-PTKTPKP 220
                 PP LS   + P   P P
Sbjct:   629 AISPPPPLSGDATIPPPPPLP 649

GO:0003779 "actin binding" evidence=IEA

GO:0017048 "Rho GTPase binding" evidence=IEA

GO:0030036 "actin cytoskeleton organization" evidence=IEA

MGI|MGI:96687 Krt12 "keratin 12" [Mus musculus (taxid:10090)]

 Score = 124 (48.7 bits), Expect = 4.2e-05, P = 4.2e-05
 Identities = 41/161 (25%), Positives = 76/161 (47%)

Query:    22 LPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS 81
             L S   E  D+ R + ++ I  + S L  + S+L   LAE +       SQ++ +  SL 
Sbjct:   331 LQSSKSEVTDLKRMVQNLEIELQ-SQLAMK-SSLEGSLAETEGGYCCQLSQVQQLIGSLE 388

Query:    82 DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDASTGATRIAK 141
             ++L Q +AD ER + +++ L     +L+ ++   E +R+ L    + D    + +  ++K
Sbjct:   389 EQLQQVRADAERQNADHQRLLGVKARLEMEI---ETYRRLLEGDSQGDGFDESSSLSVSK 445

Query:   142 PTPNEDDAAVAPTGTSSVHSQISEGGN----SSFAEEREPE 178
             P     D++  P  T  + + + E  N    SS  +E E E
Sbjct:   446 PQTPSVDSSKDPNKTRKIKTVVQEIVNGEVVSSQVQELEEE 486

GO:0005198 "structural molecule activity" evidence=IEA

GO:0005882 "intermediate filament" evidence=IEA

GO:0060429 "epithelium development" evidence=IMP

GO:0061303 "cornea development in camera-type eye" evidence=IMP

UNIPROTKB|E7ERW8 DIAPH1 "Protein diaphanous homolog 1" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 4.8e-05, P = 4.8e-05
 Identities = 50/201 (24%), Positives = 84/201 (41%)

Query:    29 QLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQ 88
             Q+++   I  +   T+V   E++ + L  +L  + +   ELQ +++ + S    KL   Q
Sbjct:   404 QIEIEGLIDQMIDKTKVEKSEAKAAELEKKLDSELTARHELQVEMKKMESDFEQKLQDLQ 463

Query:    89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD--DEDASTGATRIAKPTPNE 146
              +K+ L  E + +    + L+ +VS+L      L + L+D   E AS  A  I  P    
Sbjct:   464 GEKDALHSEKQQIATEKQDLEAEVSQLTGEVAKLTKELEDAKKEMASLSAAAITVPPSVP 523

Query:   147 DDAAVAPT----GTSS--VHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLT 200
               A V P     G S   +    + G +++      P    P +  G  ++S  S P  T
Sbjct:   524 SRAPVPPAPPLPGDSGTIIPPPPAPGDSTTPPPPPPPPPPPPPLPGGVCISSPPSLPGGT 583

Query:   201 PPGSPPSLSASVS-PTKTPKP 220
                 PP LS   + P   P P
Sbjct:   584 AISPPPPLSGDATIPPPPPLP 604

GO:0003779 "actin binding" evidence=IEA

GO:0017048 "Rho GTPase binding" evidence=IEA

GO:0030036 "actin cytoskeleton organization" evidence=IEA

UNIPROTKB|E9PHQ0 DIAPH1 "Protein diaphanous homolog 1" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 5.1e-05, P = 5.1e-05
 Identities = 50/201 (24%), Positives = 84/201 (41%)

Query:    29 QLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQ 88
             Q+++   I  +   T+V   E++ + L  +L  + +   ELQ +++ + S    KL   Q
Sbjct:   449 QIEIEGLIDQMIDKTKVEKSEAKAAELEKKLDSELTARHELQVEMKKMESDFEQKLQDLQ 508

Query:    89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD--DEDASTGATRIAKPTPNE 146
              +K+ L  E + +    + L+ +VS+L      L + L+D   E AS  A  I  P    
Sbjct:   509 GEKDALHSEKQQIATEKQDLEAEVSQLTGEVAKLTKELEDAKKEMASLSAAAITVPPSVP 568

Query:   147 DDAAVAPT----GTSS--VHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLT 200
               A V P     G S   +    + G +++      P    P +  G  ++S  S P  T
Sbjct:   569 SRAPVPPAPPLPGDSGTIIPPPPAPGDSTTPPPPPPPPPPPPPLPGGVCISSPPSLPGGT 628

Query:   201 PPGSPPSLSASVS-PTKTPKP 220
                 PP LS   + P   P P
Sbjct:   629 AISPPPPLSGDATIPPPPPLP 649

GO:0003779 "actin binding" evidence=IEA

GO:0017048 "Rho GTPase binding" evidence=IEA

GO:0030036 "actin cytoskeleton organization" evidence=IEA

UNIPROTKB|E7ET75 DIAPH1 "Protein diaphanous homolog 1" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 5.1e-05, P = 5.1e-05
 Identities = 50/201 (24%), Positives = 84/201 (41%)

Query:    29 QLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQ 88
             Q+++   I  +   T+V   E++ + L  +L  + +   ELQ +++ + S    KL   Q
Sbjct:   449 QIEIEGLIDQMIDKTKVEKSEAKAAELEKKLDSELTARHELQVEMKKMESDFEQKLQDLQ 508

Query:    89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD--DEDASTGATRIAKPTPNE 146
              +K+ L  E + +    + L+ +VS+L      L + L+D   E AS  A  I  P    
Sbjct:   509 GEKDALHSEKQQIATEKQDLEAEVSQLTGEVAKLTKELEDAKKEMASLSAAAITVPPSVP 568

Query:   147 DDAAVAPT----GTSS--VHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLT 200
               A V P     G S   +    + G +++      P    P +  G  ++S  S P  T
Sbjct:   569 SRAPVPPAPPLPGDSGTIIPPPPAPGDSTTPPPPPPPPPPPPPLPGGVCISSPPSLPGGT 628

Query:   201 PPGSPPSLSASVS-PTKTPKP 220
                 PP LS   + P   P P
Sbjct:   629 AISPPPPLSGDATIPPPPPLP 649

GO:0003779 "actin binding" evidence=IEA

GO:0017048 "Rho GTPase binding" evidence=IEA

GO:0030036 "actin cytoskeleton organization" evidence=IEA

UNIPROTKB|E9PEZ3 DIAPH1 "Protein diaphanous homolog 1" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 5.1e-05, P = 5.1e-05
 Identities = 50/201 (24%), Positives = 84/201 (41%)

Query:    29 QLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQ 88
             Q+++   I  +   T+V   E++ + L  +L  + +   ELQ +++ + S    KL   Q
Sbjct:   458 QIEIEGLIDQMIDKTKVEKSEAKAAELEKKLDSELTARHELQVEMKKMESDFEQKLQDLQ 517

Query:    89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD--DEDASTGATRIAKPTPNE 146
              +K+ L  E + +    + L+ +VS+L      L + L+D   E AS  A  I  P    
Sbjct:   518 GEKDALHSEKQQIATEKQDLEAEVSQLTGEVAKLTKELEDAKKEMASLSAAAITVPPSVP 577

Query:   147 DDAAVAPT----GTSS--VHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLT 200
               A V P     G S   +    + G +++      P    P +  G  ++S  S P  T
Sbjct:   578 SRAPVPPAPPLPGDSGTIIPPPPAPGDSTTPPPPPPPPPPPPPLPGGVCISSPPSLPGGT 637

Query:   201 PPGSPPSLSASVS-PTKTPKP 220
                 PP LS   + P   P P
Sbjct:   638 AISPPPPLSGDATIPPPPPLP 658

GO:0003779 "actin binding" evidence=IEA

GO:0017048 "Rho GTPase binding" evidence=IEA

GO:0030036 "actin cytoskeleton organization" evidence=IEA

UNIPROTKB|O60610 DIAPH1 "Protein diaphanous homolog 1" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 5.1e-05, P = 5.1e-05
 Identities = 50/201 (24%), Positives = 84/201 (41%)

Query:    29 QLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQ 88
             Q+++   I  +   T+V   E++ + L  +L  + +   ELQ +++ + S    KL   Q
Sbjct:   458 QIEIEGLIDQMIDKTKVEKSEAKAAELEKKLDSELTARHELQVEMKKMESDFEQKLQDLQ 517

Query:    89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD--DEDASTGATRIAKPTPNE 146
              +K+ L  E + +    + L+ +VS+L      L + L+D   E AS  A  I  P    
Sbjct:   518 GEKDALHSEKQQIATEKQDLEAEVSQLTGEVAKLTKELEDAKKEMASLSAAAITVPPSVP 577

Query:   147 DDAAVAPT----GTSS--VHSQISEGGNSSFAEEREPESSRPGISRGFVLASQTSTPRLT 200
               A V P     G S   +    + G +++      P    P +  G  ++S  S P  T
Sbjct:   578 SRAPVPPAPPLPGDSGTIIPPPPAPGDSTTPPPPPPPPPPPPPLPGGVCISSPPSLPGGT 637

Query:   201 PPGSPPSLSASVS-PTKTPKP 220
                 PP LS   + P   P P
Sbjct:   638 AISPPPPLSGDATIPPPPPLP 658

GO:0005737 "cytoplasm" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

GO:0003779 "actin binding" evidence=IEA

GO:0005522 "profilin binding" evidence=IEA

GO:0017048 "Rho GTPase binding" evidence=IEA

GO:0030041 "actin filament polymerization" evidence=IEA

GO:0031175 "neuron projection development" evidence=IEA

GO:0043005 "neuron projection" evidence=IEA

GO:0032587 "ruffle membrane" evidence=IEA

GO:0008360 "regulation of cell shape" evidence=IMP

GO:0007010 "cytoskeleton organization" evidence=IMP

GO:0032886 "regulation of microtubule-based process" evidence=IMP

GO:0005102 "receptor binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0044325 "ion channel binding" evidence=IPI

GO:0072686 "mitotic spindle" evidence=IDA

GO:0035372 "protein localization to microtubule" evidence=IMP

GO:0071420 "cellular response to histamine" evidence=IMP

GO:0051279 "regulation of release of sequestered calcium ion into cytosol" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q93W28	Y4554_ARATH	No assigned EC number	0.5830	0.8970	0.7240	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_Genewise1_v1.C_LG_X4241 hypothetical protein (346 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	272
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	8e-05
pfam03962	188	pfam03962, Mnd1, Mnd1 family	1e-04
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	0.001
pfam04156	186	pfam04156, IncA, IncA protein	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004

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

 Score = 44.3 bits (105), Expect = 5e-05
 Identities = 24/109 (22%), Positives = 49/109 (44%), Gaps = 4/109 (3%)

Query: 27  FEQLDVARKITSIA-ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI---YSSLSD 82
             +    R    I  +   + +LE +   L  +L E +  + EL+ ++E +      L D
Sbjct: 818 SLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELED 877

Query: 83  KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDED 131
           +L + + +KE L +E   L + + +L+ ++ KL    + L   L+  E 
Sbjct: 878 ELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEV 926

Length = 1163

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 42.3 bits (100), Expect = 8e-05
 Identities = 26/103 (25%), Positives = 50/103 (48%), Gaps = 17/103 (16%)

Query: 42  STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENE-- 99
             R+ +L+ E + L+ +LAE   ++AELQ +       L  +L   +A+ ERL KE    
Sbjct: 65  RERLPELQQELAELQEELAELQEQLAELQQEN----QELKQELSTLEAELERLQKELARI 120

Query: 100 --------ALTNTVRKLQRDVSKLEVFRKTL---VQSLKDDED 131
                    L    R+L+ ++++L+   + L    + L+++E 
Sbjct: 121 KQLSANAIELDEENRELREELAELKQENEALEAENERLQENEQ 163

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family

 Score = 41.5 bits (98), Expect = 1e-04
 Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 5/88 (5%)

Query: 42  STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEAL 101
           S  ++ L++    L+ +L E   RIAELQ+QIE +     +       ++  L +E + L
Sbjct: 61  SQALNKLKTRLEKLKKELEELKQRIAELQAQIEKLKKGREET-----EERTELLEELKQL 115

Query: 102 TNTVRKLQRDVSKLEVFRKTLVQSLKDD 129
              ++KL+ ++ K E      ++ LK++
Sbjct: 116 EKELKKLKAELEKYEKNDPERIEKLKEE 143

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|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA binding

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 4/78 (5%)

Query: 53  SALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV 112
           S+L  +LAEKD +IA+L  + E     LS K  +     ++L  +N+ L   + +L++ +
Sbjct: 1   SSLEKKLAEKDEQIAQLMEEGE----KLSKKELKHNNTIKKLRAKNKELEKEIAELKKKL 56

Query: 113 SKLEVFRKTLVQSLKDDE 130
            KLE   + L + LK  E
Sbjct: 57  EKLEKELENLEERLKRAE 74

This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. Length = 74

>gnl|CDD|217933 pfam04156, IncA, IncA protein

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 21/90 (23%), Positives = 46/90 (51%)

Query: 44  RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN 103
            +S+L+ + S L+ +L + + RIAEL+S++E +   L       ++ +ERL    E++  
Sbjct: 80  ELSELKQQLSELQEELEDLEERIAELESELEDLKEDLQLLRELLKSLEERLESLEESIKE 139

Query: 104 TVRKLQRDVSKLEVFRKTLVQSLKDDEDAS 133
             ++L+     L    + L + L+  ++  
Sbjct: 140 LAKELRELRQDLREEVEELREELERLQENL 169

Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Length = 186

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 26/108 (24%), Positives = 52/108 (48%), Gaps = 4/108 (3%)

Query: 27  FEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI---YSSLSDK 83
            E+L              +  L++E  +L   L E   ++ EL+ Q+E +    ++L ++
Sbjct: 673 EEELAELEAQLEKL-EEELKSLKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEE 731

Query: 84  LGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDED 131
           L Q Q+  E L +E E L   + +LQ  + +LE   ++L ++L   ++
Sbjct: 732 LEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKE 779

Length = 1163

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 20/111 (18%), Positives = 55/111 (49%), Gaps = 10/111 (9%)

Query: 38  SIAISTRVSDLESEHSALRSQLAEK-------DSRIAELQSQIESIYS---SLSDKLGQA 87
            + +  ++ +LE+E ++L   +AEK       + R+A+L+++I+ + +    L  ++ + 
Sbjct: 289 QLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEE 348

Query: 88  QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDASTGATR 138
           +  +++L++E   L   +  L+ ++ +++         LKD  +      R
Sbjct: 349 RKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKR 399

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 = 38.1 bits (89), Expect = 0.004
 Identities = 27/90 (30%), Positives = 51/90 (56%), Gaps = 4/90 (4%)

Query: 41  ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEA 100
           +  R+  L+ E S+L+S+L   ++R+ EL  ++    S  S K+G+ + + E+L +E E 
Sbjct: 679 LRERLEGLKRELSSLQSELRRIENRLDELSQEL----SDASRKIGEIEKEIEQLEQEEEK 734

Query: 101 LTNTVRKLQRDVSKLEVFRKTLVQSLKDDE 130
           L   + +L+ D+S LE   + +   LK+ E
Sbjct: 735 LKERLEELEEDLSSLEQEIENVKSELKELE 764

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 = 38.1 bits (89), Expect = 0.004
 Identities = 25/112 (22%), Positives = 53/112 (47%), Gaps = 3/112 (2%)

Query: 24  SDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYS---SL 80
           S       + R+     +  ++ +LE + + L   LAE    + EL+ ++E +      L
Sbjct: 665 SAKTNSSILERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEEL 724

Query: 81  SDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDA 132
           S ++   + D  RL  E E L   + +L +++++LE   + L + L++ E+ 
Sbjct: 725 SRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEE 776

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	272
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	96.87
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	96.86
PRK11637	428	AmiB activator; Provisional	96.84
PRK10884	206	SH3 domain-containing protein; Provisional	96.73
PF06637	442	PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 Th	96.62
COG2433	652	Uncharacterized conserved protein [Function unknow	96.59
PRK11637	428	AmiB activator; Provisional	96.53
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	96.42
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	96.36
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	96.16
PRK09039	343	hypothetical protein; Validated	96.14
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	95.97
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	95.67
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	95.66
PHA02562	562	46 endonuclease subunit; Provisional	95.51
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	95.49
PF10186	302	Atg14: UV radiation resistance protein and autopha	95.47
PF05700	221	BCAS2: Breast carcinoma amplified sequence 2 (BCAS	95.33
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	95.22
PRK03918	880	chromosome segregation protein; Provisional	95.19
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	95.05
PF03148	384	Tektin: Tektin family; InterPro: IPR000435 Tektin	95.01
KOG3990	305	consensus Uncharacterized conserved protein [Funct	95.01
PRK02224	880	chromosome segregation protein; Provisional	94.87
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	94.71
KOG0288	459	consensus WD40 repeat protein TipD [General functi	94.63
PF09755	310	DUF2046: Uncharacterized conserved protein H4 (DUF	94.61
PF08647	96	BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR01395	94.52
PRK10884	206	SH3 domain-containing protein; Provisional	94.51
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	94.47
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	94.42
PHA02562	562	46 endonuclease subunit; Provisional	94.42
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	94.35
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	94.33
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	94.26
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	94.18
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	94.02
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	93.96
KOG2685	421	consensus Cystoskeletal protein Tektin [Cytoskelet	93.95
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	93.9
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	93.9
PF11180	192	DUF2968: Protein of unknown function (DUF2968); In	93.81
COG4026	290	Uncharacterized protein containing TOPRIM domain,	93.81
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	93.79
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	93.73
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	93.53
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	93.45
COG4942	420	Membrane-bound metallopeptidase [Cell division and	93.32
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	93.18
PF10186	302	Atg14: UV radiation resistance protein and autopha	93.15
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	93.12
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	93.11
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	93.1
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	92.94
PF00038	312	Filament: Intermediate filament protein; InterPro:	92.92
PRK03918	880	chromosome segregation protein; Provisional	92.91
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	92.91
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	92.9
PF04899	70	MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 Th	92.87
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	92.82
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	92.72
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	92.7
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	92.67
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	92.63
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	92.61
KOG3433	203	consensus Protein involved in meiotic recombinatio	92.6
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	92.58
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	92.55
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	92.53
PRK02224	880	chromosome segregation protein; Provisional	92.53
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	92.53
KOG0249	916	consensus LAR-interacting protein and related prot	92.32
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	92.3
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	92.23
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	92.18
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	92.14
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	92.06
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	91.97
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	91.81
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	91.72
KOG4010	208	consensus Coiled-coil protein TPD52 [General funct	91.71
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	91.68
PF02050	123	FliJ: Flagellar FliJ protein; InterPro: IPR012823	91.62
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	91.55
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	91.47
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	91.45
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	91.34
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	91.34
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	91.21
TIGR02231	525	conserved hypothetical protein. This family consis	91.18
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	91.17
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	91.16
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	91.15
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	91.13
PF13863	126	DUF4200: Domain of unknown function (DUF4200)	91.07
PRK10361	475	DNA recombination protein RmuC; Provisional	91.05
PF15290	305	Syntaphilin: Golgi-localised syntaxin-1-binding cl	90.95
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	90.93
PF12777	344	MT: Microtubule-binding stalk of dynein motor; Int	90.82
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	90.81
KOG0963	629	consensus Transcription factor/CCAAT displacement	90.77
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	90.76
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	90.7
PF10205	102	KLRAQ: Predicted coiled-coil domain-containing pro	90.58
PF14662	193	CCDC155: Coiled-coil region of CCDC155	90.43
KOG4398	359	consensus Predicted coiled-coil protein [General f	90.4
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	90.37
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	90.36
COG4026	290	Uncharacterized protein containing TOPRIM domain,	90.31
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	90.27
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	90.24
PF09798	654	LCD1: DNA damage checkpoint protein; InterPro: IPR	90.17
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	90.06
PF10205	102	KLRAQ: Predicted coiled-coil domain-containing pro	90.03
KOG1962	216	consensus B-cell receptor-associated protein and r	89.96
PF11544	76	Spc42p: Spindle pole body component Spc42p; InterP	89.92
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	89.88
COG4942	420	Membrane-bound metallopeptidase [Cell division and	89.82
KOG1103	561	consensus Predicted coiled-coil protein [Function	89.62
PRK12704	520	phosphodiesterase; Provisional	89.6
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	89.45
PRK02119	73	hypothetical protein; Provisional	89.45
COG5185	622	HEC1 Protein involved in chromosome segregation, i	89.42
PF04201	162	TPD52: Tumour protein D52 family; InterPro: IPR007	89.3
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	89.25
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	89.14
PF14362	301	DUF4407: Domain of unknown function (DUF4407)	89.13
PF10779	71	XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemoly	89.13
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	89.13
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	89.1
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	89.1
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	88.98
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	88.92
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	88.89
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	88.8
PRK09039	343	hypothetical protein; Validated	88.7
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	88.67
KOG4673	961	consensus Transcription factor TMF, TATA element m	88.6
PF11068	131	YlqD: YlqD protein; InterPro: IPR021297 This bacte	88.54
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	88.52
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	88.45
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	88.42
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	88.4
KOG2129	552	consensus Uncharacterized conserved protein H4 [Fu	88.35
PRK04406	75	hypothetical protein; Provisional	88.34
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	88.18
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	88.13
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	88.1
COG2433	652	Uncharacterized conserved protein [Function unknow	88.1
PF14817	632	HAUS5: HAUS augmin-like complex subunit 5	88.07
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	88.05
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	88.03
KOG0288	459	consensus WD40 repeat protein TipD [General functi	87.98
PF11594	106	Med28: Mediator complex subunit 28; InterPro: IPR0	87.9
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	87.87
KOG2991	330	consensus Splicing regulator [RNA processing and m	87.87
PRK02793	72	phi X174 lysis protein; Provisional	87.71
KOG4673	961	consensus Transcription factor TMF, TATA element m	87.68
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	87.66
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	87.64
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	87.59
PF09755	310	DUF2046: Uncharacterized conserved protein H4 (DUF	87.51
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	87.5
PF02601	319	Exonuc_VII_L: Exonuclease VII, large subunit; Inte	87.42
PRK04863	1486	mukB cell division protein MukB; Provisional	87.41
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	87.4
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	87.35
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	87.3
PF05384	159	DegS: Sensor protein DegS; InterPro: IPR008595 Thi	87.25
KOG0244	913	consensus Kinesin-like protein [Cytoskeleton]	87.2
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	87.07
PF10158	131	LOH1CR12: Tumour suppressor protein; InterPro: IPR	87.04
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	87.03
PF13747	89	DUF4164: Domain of unknown function (DUF4164)	86.94
PRK00106	535	hypothetical protein; Provisional	86.9
PF13874	141	Nup54: Nucleoporin complex subunit 54; PDB: 3T97_B	86.89
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	86.63
KOG0962	1294	consensus DNA repair protein RAD50, ABC-type ATPas	86.62
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	86.55
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	86.51
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	86.5
KOG4687	389	consensus Uncharacterized coiled-coil protein [Fun	86.25
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	86.15
PF04100	383	Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007	86.06
PF09486	158	HrpB7: Bacterial type III secretion protein (HrpB7	86.03
PF06818	202	Fez1: Fez1; InterPro: IPR009638 This family repres	86.0
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	85.89
PRK10803	263	tol-pal system protein YbgF; Provisional	85.89
KOG1962	216	consensus B-cell receptor-associated protein and r	85.77
TIGR02559	158	HrpB7 type III secretion protein HrpB7. This famil	85.74
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	85.68
PF08647	96	BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR01395	85.58
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	85.58
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	85.53
PF06120	301	Phage_HK97_TLTM: Tail length tape measure protein;	85.53
PRK12705	508	hypothetical protein; Provisional	85.48
PRK00295	68	hypothetical protein; Provisional	85.3
TIGR00293	126	prefoldin, archaeal alpha subunit/eukaryotic subun	85.18
PF12240	205	Angiomotin_C: Angiomotin C terminal; InterPro: IPR	85.14
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	85.13
PF08700	87	Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT te	85.02
TIGR01010	362	BexC_CtrB_KpsE polysaccharide export inner-membran	84.94
PF02994	370	Transposase_22: L1 transposable element; InterPro:	84.84
KOG3119	269	consensus Basic region leucine zipper transcriptio	84.83
PF05622	713	HOOK: HOOK protein; InterPro: IPR008636 This famil	84.75
KOG0996	1293	consensus Structural maintenance of chromosome pro	84.71
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	84.64
PF05781	538	MRVI1: MRVI1 protein; InterPro: IPR008677 This fam	84.5
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	84.46
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	84.43
KOG0999	772	consensus Microtubule-associated protein Bicaudal-	84.34
PF09728	309	Taxilin: Myosin-like coiled-coil protein; InterPro	84.2
PRK04778	569	septation ring formation regulator EzrA; Provision	84.15
PF05278	269	PEARLI-4: Arabidopsis phospholipase-like protein (	84.12
PRK01156	895	chromosome segregation protein; Provisional	84.09
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	84.05
PRK01156	895	chromosome segregation protein; Provisional	84.04
PRK04863	1486	mukB cell division protein MukB; Provisional	83.97
PF09787	511	Golgin_A5: Golgin subfamily A member 5; InterPro:	83.92
PRK00888	105	ftsB cell division protein FtsB; Reviewed	83.82
PRK00286	438	xseA exodeoxyribonuclease VII large subunit; Revie	83.81
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	83.79
PRK10803	263	tol-pal system protein YbgF; Provisional	83.77
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	83.74
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	83.74
PF14932	256	HAUS-augmin3: HAUS augmin-like complex subunit 3	83.72
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	83.63
PF00038	312	Filament: Intermediate filament protein; InterPro:	83.62
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	83.53
KOG1899	861	consensus LAR transmembrane tyrosine phosphatase-i	83.46
PRK13169	110	DNA replication intiation control protein YabA; Re	83.36
PRK12704	520	phosphodiesterase; Provisional	83.19
KOG0971	1243	consensus Microtubule-associated protein dynactin	83.06
KOG0933	1174	consensus Structural maintenance of chromosome pro	82.98
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	82.98
KOG4552	272	consensus Vitamin-D-receptor interacting protein c	82.95
PRK00736	68	hypothetical protein; Provisional	82.86
TIGR00237	432	xseA exodeoxyribonuclease VII, large subunit. This	82.71
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	82.62
smart00338	65	BRLZ basic region leucin zipper.	82.58
PF02841	297	GBP_C: Guanylate-binding protein, C-terminal domai	82.41
PRK04778	569	septation ring formation regulator EzrA; Provision	82.36
PF04136	157	Sec34: Sec34-like family ; InterPro: IPR007265 Sec	82.24
PRK04325	74	hypothetical protein; Provisional	82.17
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	82.17
PF14282	106	FlxA: FlxA-like protein	82.09
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	82.0
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	81.93
COG1842	225	PspA Phage shock protein A (IM30), suppresses sigm	81.88
PF06246	255	Isy1: Isy1-like splicing family; InterPro: IPR0093	81.86
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	81.76
PRK00846	77	hypothetical protein; Provisional	81.73
PRK10869	553	recombination and repair protein; Provisional	81.71
PF13747	89	DUF4164: Domain of unknown function (DUF4164)	81.71
PF01576	859	Myosin_tail_1: Myosin tail; InterPro: IPR002928 Mu	81.65
TIGR02231	525	conserved hypothetical protein. This family consis	81.47
PF02388	406	FemAB: FemAB family; InterPro: IPR003447 The femAB	81.3
KOG0249	916	consensus LAR-interacting protein and related prot	81.18
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	81.11
smart00502	127	BBC B-Box C-terminal domain. Coiled coil region C-	81.0
smart00338	65	BRLZ basic region leucin zipper.	80.79
PF13863	126	DUF4200: Domain of unknown function (DUF4200)	80.48
PF10046	99	BLOC1_2: Biogenesis of lysosome-related organelles	80.32
COG1570	440	XseA Exonuclease VII, large subunit [DNA replicati	80.19
PF06657	79	Cep57_MT_bd: Centrosome microtubule-binding domain	80.19
PF08898	53	DUF1843: Domain of unknown function (DUF1843); Int	80.19
PF11740	120	KfrA_N: Plasmid replication region DNA-binding N-t	80.18
PRK00409	782	recombination and DNA strand exchange inhibitor pr	80.17
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	80.12
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	80.09
PF05010	207	TACC: Transforming acidic coiled-coil-containing p	80.08
TIGR03495	135	phage_LysB phage lysis regulatory protein, LysB fa	80.06

>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=96.87  E-value=0.025  Score=49.58  Aligned_cols=82  Identities=26%  Similarity=0.434  Sum_probs=28.3

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      ++.||..+..++..|+.++.++...|.+|+..+..|+..+.   ..|+.....+..|..|..+|--+...|...+.+|+.
T Consensus        93 l~~~L~~~~~~l~~l~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~  172 (194)
T PF08614_consen   93 LAQQLVELNDELQELEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLEE  172 (194)
T ss_dssp             ---------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555555555555555555555554444   333444444444444444444444444444444444


Q ss_pred             HHHHH
Q 024140          118 FRKTL  122 (272)
Q Consensus       118 FKk~L  122 (272)
                      =-+.|
T Consensus       173 En~~L  177 (194)
T PF08614_consen  173 ENREL  177 (194)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            33333

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=96.86  E-value=0.028  Score=47.88  Aligned_cols=78  Identities=21%  Similarity=0.321  Sum_probs=53.3

Q ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           35 KITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        35 kIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      |+=.-++-.|+..+|..+..|-+...+|+..|..|+.|+..||..|- ++...+.+......+.+....++..|+|-|.
T Consensus         6 k~E~d~a~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld-~~~~~l~~~k~~lee~~~~~~~~E~l~rriq   83 (143)
T PF12718_consen    6 KLEADNAQDRAEELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELD-KLEEQLKEAKEKLEESEKRKSNAEQLNRRIQ   83 (143)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhHHHHHHhHHHHHhhHH
Confidence            34455677899999999999999999999999999999999999986 3333333333333333333333333444333

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>PRK11637 AmiB activator; Provisional

Probab=96.84  E-value=0.019  Score=55.62  Aligned_cols=109  Identities=17%  Similarity=0.254  Sum_probs=53.6

Q ss_pred             CCCChhHHHhcCCCCchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH--
Q 024140           11 TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAEL-------QSQIESIYSSLS--   81 (272)
Q Consensus        11 dF~lp~eil~vLP~DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~L-------q~r~s~le~~l~--   81 (272)
                      .|.+-.-|+.+|       |-++-  ..++++.-...++.++..+++++.++...|.++       ++++..++.+|.  
T Consensus        17 ~~~~~~~~~~~l-------l~~~~--~~~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~   87 (428)
T PRK11637         17 RFAIRPILYASV-------LSAGV--LLCAFSAHASDNRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQA   87 (428)
T ss_pred             hhhhhhHHHHHH-------HHHHH--HHhhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567766666665       22111  222222222344444444444444444444444       444444444443  


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 024140           82 -DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus        82 -~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (272)
                       .+|....++..++.++.+.|...++.+..++.+++.--+.+|..+..
T Consensus        88 ~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~rlra~Y~  135 (428)
T PRK11637         88 SRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAAQLDAAFR  135 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             45555555556666666666666666666666555444444444443

>PRK10884 SH3 domain-containing protein; Provisional

Probab=96.73  E-value=0.024  Score=51.17  Aligned_cols=69  Identities=26%  Similarity=0.381  Sum_probs=43.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      -...|+-+||.|+..|+++|++-+...   .++...+    +.++..+.+...+|.+||+.|...+.++..++..|
T Consensus        90 ~~~~rlp~le~el~~l~~~l~~~~~~~---~~~~~~l----~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l  158 (206)
T PRK10884         90 SLRTRVPDLENQVKTLTDKLNNIDNTW---NQRTAEM----QQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAA  158 (206)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHhHH---HHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356788899999999999998865442   2222222    23333555555556666666666666666655444

>PF06637 PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to mammals

Probab=96.62  E-value=0.03  Score=55.46  Aligned_cols=64  Identities=22%  Similarity=0.305  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS-------------------------DKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-------------------------~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      ++.||..+.+..++..+||.+-..+|..|+                         -.-..+++|++.|.+|+|+|+..+.
T Consensus       287 ar~Lr~~I~~VarENs~LqrQKle~e~~l~a~qeakek~~KEAqareaklqaec~rQ~qlaLEEKaaLrkerd~L~keLe  366 (442)
T PF06637_consen  287 ARSLRAGIERVARENSDLQRQKLEAEQGLQASQEAKEKAGKEAQAREAKLQAECARQTQLALEEKAALRKERDSLAKELE  366 (442)
T ss_pred             HHHHhhhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455555555555555555555555554443                         2233578888999999999999988


Q ss_pred             HHhhhHHHH
Q 024140          107 KLQRDVSKL  115 (272)
Q Consensus       107 kL~rDvaKL  115 (272)
                      ...|+++.|
T Consensus       367 ekkreleql  375 (442)
T PF06637_consen  367 EKKRELEQL  375 (442)
T ss_pred             HHHHHHHHH
Confidence            888887763

PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms []. The function of this family is unknown.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=96.59  E-value=0.034  Score=57.63  Aligned_cols=84  Identities=29%  Similarity=0.406  Sum_probs=74.5

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~------~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      -+++-.+|.+||.|+..|+..+.|.++.|..|+.++..+...+.      -.+...+.++.+|.++...=...|..|.+.
T Consensus       424 i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~e~~~~ve~L~~~  503 (652)
T COG2433         424 IKKLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERK  503 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46888999999999999999999999999999999999988877      445567788899999999999999999999


Q ss_pred             HHHHHHHHHH
Q 024140          112 VSKLEVFRKT  121 (272)
Q Consensus       112 vaKLE~FKk~  121 (272)
                      ++.|+.+++-
T Consensus       504 l~~l~k~~~l  513 (652)
T COG2433         504 LAELRKMRKL  513 (652)
T ss_pred             HHHHHHHHhh
Confidence            9999988773

>PRK11637 AmiB activator; Provisional

Probab=96.53  E-value=0.052  Score=52.60  Aligned_cols=68  Identities=9%  Similarity=0.180  Sum_probs=28.8

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      .++..++.++..|..+|.+-...|.+++.++..++.++.    ...+++.+++++.+.+...++++.|.+.+
T Consensus        68 ~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~----~l~~eI~~~q~~l~~~~~~l~~rlra~Y~  135 (428)
T PRK11637         68 QQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQID----ELNASIAKLEQQQAAQERLLAAQLDAAFR  135 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444444444444444444443332    44444444444444444444444444443

>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=96.42  E-value=0.034  Score=48.74  Aligned_cols=72  Identities=18%  Similarity=0.364  Sum_probs=48.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT-VRKLQRDVSKL  115 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~T-vKkL~rDvaKL  115 (272)
                      .+...+..|+.++..|...|.||+..|..|++-+..|.-++.    .+.++..+|++||+.|... +++-++|..+|
T Consensus       120 ~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~----~~e~k~~~l~~En~~Lv~Rwm~~k~~eAe~m  192 (194)
T PF08614_consen  120 ELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLN----MLEEKLRKLEEENRELVERWMQRKAQEAERM  192 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344455555556666666666666666666666666666554    8899999999999999876 34455555544

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.

>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures

Probab=96.36  E-value=0.05  Score=41.86  Aligned_cols=65  Identities=28%  Similarity=0.435  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           54 ALRSQLAEKDSRIAELQSQIESIYSS---LSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        54 ~LR~~L~EKd~~i~~Lq~r~s~le~~---l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      .|-..|+|||..|+.|.+.-..|-..   +..-++.....+..+.++.+.|...+.++..++..|+.+
T Consensus         2 sl~~~l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~   69 (74)
T PF12329_consen    2 SLEKKLAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEER   69 (74)
T ss_pred             hHHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46778999999999999655555433   334444445555555555555555555555555555443

The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.

>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch

Probab=96.16  E-value=0.11  Score=43.56  Aligned_cols=30  Identities=20%  Similarity=0.297  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +.+|+.+++++++.+..++.+...++..+.
T Consensus        75 ~~rL~~~~~~~ere~~~~~~~~~~l~~~~~  104 (151)
T PF11559_consen   75 VERLKEQLEELERELASAEEKERQLQKQLK  104 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555555555555555555555555544

pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.

>PRK09039 hypothetical protein; Validated

Probab=96.14  E-value=0.097  Score=50.19  Aligned_cols=88  Identities=17%  Similarity=0.233  Sum_probs=68.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-HHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRD-VSKL  115 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rD-vaKL  115 (272)
                      ....|+..|+.+...++....|....|.-|+.++..|..+|.   +.|..+.++....+...+.|...+.++-.+ +..|
T Consensus       113 ~~~~~~~~l~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~~~~~l  192 (343)
T PRK09039        113 AAEGRAGELAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQRVQEL  192 (343)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677777788888888888888888888888888888877   666677777777777777777777666544 8889


Q ss_pred             HHHHHHHHhhcc
Q 024140          116 EVFRKTLVQSLK  127 (272)
Q Consensus       116 E~FKk~LmqSLq  127 (272)
                      +.||..+..-|.
T Consensus       193 ~~~~~~~~~~l~  204 (343)
T PRK09039        193 NRYRSEFFGRLR  204 (343)
T ss_pred             HHhHHHHHHHHH
Confidence            999999977775

>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]

Probab=95.97  E-value=0.41  Score=41.31  Aligned_cols=96  Identities=26%  Similarity=0.376  Sum_probs=70.1

Q ss_pred             hHHHHHHHH-----HHHHHHhhhhhHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           29 QLDVARKIT-----SIAISTRVSDLESEHSALRSQLA-------EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSK   96 (272)
Q Consensus        29 QLdlarkIt-----s~A~atRVs~LE~E~~~LR~~L~-------EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~   96 (272)
                      ||+|.-+.-     +--+..||-+||+|+......+.       .+.+.|..|+.++..+...+    .....+...|.+
T Consensus         5 ~l~v~~kLK~~~~e~dsle~~v~~LEreLe~~q~~~e~~~~daEn~k~eie~L~~el~~lt~el----~~L~~EL~~l~s   80 (140)
T PF10473_consen    5 FLHVEEKLKESESEKDSLEDHVESLERELEMSQENKECLILDAENSKAEIETLEEELEELTSEL----NQLELELDTLRS   80 (140)
T ss_pred             HHHHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH
Confidence            455544433     45577889999998776655433       34455666666666666555    488899999999


Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 024140           97 ENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus        97 E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      ||..|.....+.+..|.-||...-.+..-|+.
T Consensus        81 Ek~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~  112 (140)
T PF10473_consen   81 EKENLDKELQKKQEKVSELESLNSSLENLLQE  112 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            99999999999999999999987766655554

There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=95.67  E-value=0.19  Score=46.68  Aligned_cols=35  Identities=20%  Similarity=0.355  Sum_probs=16.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ++++|..+++..+.+++..+.+|+.++..++..++
T Consensus        35 k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~   69 (239)
T COG1579          35 KAKAELEALNKALEALEIELEDLENQVSQLESEIQ   69 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=95.66  E-value=0.34  Score=45.14  Aligned_cols=83  Identities=22%  Similarity=0.401  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHhhhhhHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH---HHH-------HHHHHHHHHHHHHH
Q 024140           32 VARKITSIAISTRVSDLESEHSALRSQLAE---KDSRIAELQSQIESIYSSLS---DKL-------GQAQADKERLSKEN   98 (272)
Q Consensus        32 larkIts~A~atRVs~LE~E~~~LR~~L~E---Kd~~i~~Lq~r~s~le~~l~---~rL-------~~a~ee~~kL~~E~   98 (272)
                      ++.+|.--.|..-|+++|.|+..+|.++..   |-..+.+ ++.+++|+.+++   .|+       ..+.++..+|+++.
T Consensus        48 ~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~-~~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i  126 (239)
T COG1579          48 EALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKD-ERELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEI  126 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566677888899999999999888762   2211111 223344444443   333       35555566666666


Q ss_pred             HHHHHHHHHHhhhHHHH
Q 024140           99 EALTNTVRKLQRDVSKL  115 (272)
Q Consensus        99 ~~La~TvKkL~rDvaKL  115 (272)
                      ..|...+.++.+++.-+
T Consensus       127 ~~l~~~~~~~e~~~~e~  143 (239)
T COG1579         127 EDLKERLERLEKNLAEA  143 (239)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            66655555555555443

>PHA02562 46 endonuclease subunit; Provisional

Probab=95.51  E-value=0.34  Score=47.44  Aligned_cols=97  Identities=10%  Similarity=0.224  Sum_probs=60.1

Q ss_pred             HhcCCCCchhhHHHHHHHH--------HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           19 LQVLPSDPFEQLDVARKIT--------SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQAD   90 (272)
Q Consensus        19 l~vLP~DP~EQLdlarkIt--------s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee   90 (272)
                      ...++..|.+-..+..+|.        ....+.++..++.++..|+.++.+....+..++..+..++..+...+....++
T Consensus       142 ~~f~~~~~~er~~il~~l~~~~~~~~~~~~~k~~~~e~~~~i~~l~~~i~~l~~~i~~~~~~i~~~~~~~~~~i~~l~~e  221 (562)
T PHA02562        142 VPFMQLSAPARRKLVEDLLDISVLSEMDKLNKDKIRELNQQIQTLDMKIDHIQQQIKTYNKNIEEQRKKNGENIARKQNK  221 (562)
T ss_pred             hhHhcCChHhHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555        34457777788888888888888888888888777777776655444444445


Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           91 KERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        91 ~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ..+|.++...|...+.+|..++..|
T Consensus       222 ~~~l~~~~~~l~~~l~~l~~~i~~l  246 (562)
T PHA02562        222 YDELVEEAKTIKAEIEELTDELLNL  246 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555555544444444444333

>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch

Probab=95.49  E-value=0.21  Score=41.85  Aligned_cols=68  Identities=22%  Similarity=0.404  Sum_probs=54.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      ..|+.++.+|+..+..-...+..|+++++.++.++.    .+..+...|.++...+..++|.+..+|.||.+
T Consensus        55 e~l~~~~~~l~~d~~~l~~~~~rL~~~~~~~ere~~----~~~~~~~~l~~~~~~~~~~~k~~kee~~klk~  122 (151)
T PF11559_consen   55 EDLSDKLRRLRSDIERLQNDVERLKEQLEELERELA----SAEEKERQLQKQLKSLEAKLKQEKEELQKLKN  122 (151)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345556667777777777777888888888887776    78888888999999999999999999999864

pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.

>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking

Probab=95.47  E-value=0.41  Score=42.70  Aligned_cols=86  Identities=23%  Similarity=0.364  Sum_probs=43.7

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH----
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSK----  114 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK----  114 (272)
                      +..+..++..+..||..+.+..+.|.+.++++..+..++.   ..|....+...++.+....+.+.++.+.+.+.+    
T Consensus        62 ~~~~~~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  141 (302)
T PF10186_consen   62 KREIEELRERLERLRERIERLRKRIEQKRERLEELRESLEQRRSRLSASQDLVESRQEQLEELQNELEERKQRLSQLQSQ  141 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555566666666666666666666666665555   333322333334444444444444444444443    


Q ss_pred             HHHHHHHHHhhcc
Q 024140          115 LEVFRKTLVQSLK  127 (272)
Q Consensus       115 LE~FKk~LmqSLq  127 (272)
                      |..=++.+++.|.
T Consensus       142 l~~~r~~l~~~l~  154 (302)
T PF10186_consen  142 LARRRRQLIQELS  154 (302)
T ss_pred             HHHHHHHHHHHHH
Confidence            4444555665544

In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy

>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function

Probab=95.33  E-value=0.85  Score=41.08  Aligned_cols=89  Identities=17%  Similarity=0.196  Sum_probs=72.7

Q ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           30 LDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        30 LdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      |+|.-+-..+||......||+.+..|...|.+..+.|.++..+=-..+.+...+|+...++-..|...|-.+...+..|.
T Consensus       123 LeLl~~~g~naW~~~n~~Le~~~~~le~~l~~~k~~ie~vN~~RK~~Q~~~~~~L~~Le~~W~~~v~kn~eie~a~~~Le  202 (221)
T PF05700_consen  123 LELLSKYGENAWLIHNEQLEAMLKRLEKELAKLKKEIEEVNRERKRRQEEAGEELRYLEQRWKELVSKNLEIEVACEELE  202 (221)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67777888999999999999999999999999999999997655555555557777888888888888888888888888


Q ss_pred             hhHHHHHHH
Q 024140          110 RDVSKLEVF  118 (272)
Q Consensus       110 rDvaKLE~F  118 (272)
                      ++|..|+.=
T Consensus       203 ~ei~~l~~~  211 (221)
T PF05700_consen  203 QEIEQLKRK  211 (221)
T ss_pred             HHHHHHHHH
Confidence            777777543

The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].

>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion

Probab=95.22  E-value=0.62  Score=39.94  Aligned_cols=79  Identities=18%  Similarity=0.360  Sum_probs=42.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      ....+...|+.|+..+...+.+...++..+++....+...+.   +++....+...++.+|-..|.+-++.+.+.+..++
T Consensus        85 ~~~~~l~~l~~el~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~  164 (191)
T PF04156_consen   85 ELQQQLQQLQEELDQLQERIQELESELEKLKEDLQELRELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELR  164 (191)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555556666666666666666666555555554443333   55666666666666666666543333334444443


Q ss_pred             HH
Q 024140          117 VF  118 (272)
Q Consensus       117 ~F  118 (272)
                      ..
T Consensus       165 ~~  166 (191)
T PF04156_consen  165 SQ  166 (191)
T ss_pred             HH
Confidence            33

The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].

>PRK03918 chromosome segregation protein; Provisional

Probab=95.19  E-value=0.67  Score=48.04  Aligned_cols=94  Identities=24%  Similarity=0.305  Sum_probs=41.4

Q ss_pred             cCCCCchhhHHHHHHHHHHHHHHhhhhhHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHH
Q 024140           21 VLPSDPFEQLDVARKITSIAISTRVSDLESEH----------SALRSQLAEKDSRIAELQSQIESIYSSLS------DKL   84 (272)
Q Consensus        21 vLP~DP~EQLdlarkIts~A~atRVs~LE~E~----------~~LR~~L~EKd~~i~~Lq~r~s~le~~l~------~rL   84 (272)
                      ++-.|-|+++.-..+-....+..++..|+..+          ..|+.++.+....+..++.++..++.++.      ..|
T Consensus       154 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~i~~~l~~l~~~~~~l~~ei~~l~~e~~~l~~~~~~~~~~l~~l  233 (880)
T PRK03918        154 ILGLDDYENAYKNLGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKEL  233 (880)
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555554444444444555555544443          23333333444444444444444444443      233


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           85 GQAQADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        85 ~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      ....++...|.++...|....+.|..++.+
T Consensus       234 ~~~~~~~~~l~~~~~~l~~~~~~l~~~i~~  263 (880)
T PRK03918        234 EELKEEIEELEKELESLEGSKRKLEEKIRE  263 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444433333

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=95.05  E-value=0.5  Score=48.36  Aligned_cols=44  Identities=16%  Similarity=0.305  Sum_probs=34.6

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAE--KDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~E--Kd~~i~~Lq~r~s~le~~l~   81 (272)
                      ..++..++..||.|+..|.++|..  .+..|..|++++..++..+.
T Consensus       393 ~~~~~~~~~~~e~el~~l~~~l~~~~~~e~i~~l~e~l~~l~~~l~  438 (650)
T TIGR03185       393 KSQLLKELRELEEELAEVDKKISTIPSEEQIAQLLEELGEAQNELF  438 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHH
Confidence            567788899999999999999974  44677777777777777665

This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.

>PF03148 Tektin: Tektin family; InterPro: IPR000435 Tektin heteropolymers form unique protofilaments of flagellar microtubules []

Probab=95.01  E-value=0.99  Score=43.86  Aligned_cols=98  Identities=21%  Similarity=0.303  Sum_probs=79.1

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH----------------
Q 024140           28 EQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQ----------------   88 (272)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~----------------   88 (272)
                      ..|.-...-|..||..||...+.--..|-.++.+-..+|++++.-+..|+.++.   +-|+.|.                
T Consensus       236 ~dl~~Q~~~vn~al~~Ri~et~~ak~~Le~ql~~~~~ei~~~e~~i~~L~~ai~~k~~~lkvaqTRL~~R~~RP~vElcr  315 (384)
T PF03148_consen  236 NDLRAQADAVNAALRKRIHETQEAKNELEWQLKKTLQEIAEMEKNIEDLEKAIRDKEGPLKVAQTRLENRTQRPNVELCR  315 (384)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhHhcCCchHHHH
Confidence            445555666789999999998888888888888888889999999999988888   3333322                


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Q 024140           89 -ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS  125 (272)
Q Consensus        89 -ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS  125 (272)
                       .-+..|.+|-..|..++.+|+..+...+..-+.|...
T Consensus       316 D~~q~~L~~Ev~~l~~~i~~L~~~L~~a~~~l~~L~~~  353 (384)
T PF03148_consen  316 DPPQYGLIEEVKELRESIEALQEKLDEAEASLQKLERT  353 (384)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             2237899999999999999999999998888888765

The proteins are predicted to form extended rods composed of 2 alpha- helical segments (~180 residues long) capable of forming coiled coils, interrupted by non-helical linkers []. The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur with a periodicity of ~8nm, coincident with the axial repeat of tubulin dimers in microtubules []. It is proposed that the assembly of tektin heteropolymers produces filaments with repeats of 8, 16, 24, 32, 40, 48 and 96nm, generating the basis for the complex spatial arrangements of axonemal components [].; GO: 0000226 microtubule cytoskeleton organization, 0005874 microtubule

>KOG3990 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.01  E-value=0.1  Score=49.63  Aligned_cols=34  Identities=29%  Similarity=0.413  Sum_probs=31.3

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~   78 (272)
                      +..|+.||++|+..|.+||+.|-+-.++|+.|-.
T Consensus       227 i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKa  260 (305)
T KOG3990|consen  227 IQKLKEEIARLKKLLHQKDQLILEKDKQISNLKA  260 (305)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCc
Confidence            5689999999999999999999999999998865

>PRK02224 chromosome segregation protein; Provisional

Probab=94.87  E-value=0.8  Score=47.74  Aligned_cols=6  Identities=17%  Similarity=0.285  Sum_probs=2.5

Q ss_pred             hhhHHH
Q 024140           27 FEQLDV   32 (272)
Q Consensus        27 ~EQLdl   32 (272)
                      ||+++-
T Consensus       164 ~e~~~~  169 (880)
T PRK02224        164 LEEYRE  169 (880)
T ss_pred             HHHHHH
Confidence            444433

>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function

Probab=94.71  E-value=0.35  Score=46.74  Aligned_cols=74  Identities=20%  Similarity=0.387  Sum_probs=60.2

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHH----------------HHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAE----------------KDSRI---AELQSQIESIYSSLSDKLGQAQADKERLSKEN   98 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~E----------------Kd~~i---~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~   98 (272)
                      ...+..|+..++.++.-||.+++.                |.+.|   +.+++++..|+..|+    ...+|.+.|..||
T Consensus        88 v~~Lrqkl~E~qGD~KlLR~~la~~r~~~~~~~~~~~~~ere~lV~qLEk~~~q~~qLe~d~q----s~lDEkeEl~~ER  163 (319)
T PF09789_consen   88 VEELRQKLNEAQGDIKLLREKLARQRVGDEGIGARHFPHEREDLVEQLEKLREQIEQLERDLQ----SLLDEKEELVTER  163 (319)
T ss_pred             HHHHHHHHHHHhchHHHHHHHHHhhhhhhccccccccchHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            457778888888888888887754                45555   455678888888888    9999999999999


Q ss_pred             HHHHHHHHHHhhhHHHH
Q 024140           99 EALTNTVRKLQRDVSKL  115 (272)
Q Consensus        99 ~~La~TvKkL~rDvaKL  115 (272)
                      |....-|-+||.++..+
T Consensus       164 D~yk~K~~RLN~ELn~~  180 (319)
T PF09789_consen  164 DAYKCKAHRLNHELNYI  180 (319)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999999998764

>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]

Probab=94.63  E-value=0.43  Score=47.93  Aligned_cols=71  Identities=18%  Similarity=0.220  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140           55 LRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus        55 LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      ++.|+.--...-..+..++...|.+|+    ...+|+.+|.+|+-.+..|+|.|.+|+-.+|+.+=.+.+-+.+-
T Consensus        32 ~~aq~~~~~a~~~ai~a~~~~~E~~l~----~Lq~e~~~l~e~~v~~~a~~~~~t~~~~~~en~~~r~~~eir~~  102 (459)
T KOG0288|consen   32 LSAQLVILRAESRAIKAKLQEKELELN----RLQEENTQLNEERVREEATEKTLTVDVLIAENLRIRSLNEIREL  102 (459)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333344444444444443    44455556666666666677777777777776666555555443

>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain

Probab=94.61  E-value=0.84  Score=44.13  Aligned_cols=86  Identities=31%  Similarity=0.457  Sum_probs=51.3

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHh
Q 024140           39 IAISTRVSDLESEHSALRSQLA-EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT--------VRKLQ  109 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~-EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~T--------vKkL~  109 (272)
                      +.+..|+.+|-.|-..|=.+|. |...++.-|+.++..|+.+..    .......+|.+|+-.|.++        |.+|.
T Consensus       109 n~L~rkl~qLr~EK~~lE~~Le~EqE~~V~kL~k~i~~Le~e~~----~~q~~le~Lr~EKVdlEn~LE~EQE~lvN~L~  184 (310)
T PF09755_consen  109 NDLSRKLNQLRQEKVELENQLEQEQEYLVNKLQKKIERLEKEKS----AKQEELERLRREKVDLENTLEQEQEALVNRLW  184 (310)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH----HhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444 344444555555555544332    2233345677777777666        57899


Q ss_pred             hhHHHHHHHHHHHHhhccc
Q 024140          110 RDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus       110 rDvaKLE~FKk~LmqSLq~  128 (272)
                      +.+++|++=||.|=..|..
T Consensus       185 Kqm~~l~~eKr~Lq~~l~~  203 (310)
T PF09755_consen  185 KQMDKLEAEKRRLQEKLEQ  203 (310)
T ss_pred             HHHHHHHHHHHHHHHHHcc
Confidence            9999999999998877754

>PF08647 BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR013956 BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions []

Probab=94.52  E-value=1.2  Score=35.40  Aligned_cols=79  Identities=23%  Similarity=0.296  Sum_probs=58.5

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH-------HHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSK-------LEV  117 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK-------LE~  117 (272)
                      +-+||.+...++..+..|-..+..|++++..|+.+..    .+.++.-.+-+-+++|.+-+|+|+..+.|       |..
T Consensus         5 L~~~~~a~~~~~~~~~~k~~~~~~lE~k~~rl~~Ek~----kadqkyfa~mr~~d~l~~e~k~L~~~~~Ks~~~i~~L~~   80 (96)
T PF08647_consen    5 LVSMEQAFKELSEQADKKVKELTILEQKKLRLEAEKA----KADQKYFAAMRSKDALDNEMKKLNTQLSKSSELIEQLKE   80 (96)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHhHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            4578899999999999999999999999999999887    66666666666666666666666665554       554


Q ss_pred             HHHHHHhhcc
Q 024140          118 FRKTLVQSLK  127 (272)
Q Consensus       118 FKk~LmqSLq  127 (272)
                      .=+.+++.|.
T Consensus        81 ~E~~~~~~l~   90 (96)
T PF08647_consen   81 TEKEFVRKLK   90 (96)
T ss_pred             HHHHHHHHHH
Confidence            4444554443

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.51  E-value=0.53  Score=42.60  Aligned_cols=68  Identities=13%  Similarity=0.220  Sum_probs=42.9

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      -++...+.+|+.+...++++..   +..++|++++..++..+.    ...++|.+|.+|...+.+.+..|+.++.
T Consensus        96 p~le~el~~l~~~l~~~~~~~~---~~~~~l~~~~~~~~~~~~----~L~~~n~~L~~~l~~~~~~~~~l~~~~~  163 (206)
T PRK10884         96 PDLENQVKTLTDKLNNIDNTWN---QRTAEMQQKVAQSDSVIN----GLKEENQKLKNQLIVAQKKVDAANLQLD  163 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHH---HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3677888888888888887654   555666666666665554    4555555555555555555555544433

>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=94.47  E-value=0.86  Score=38.88  Aligned_cols=78  Identities=19%  Similarity=0.326  Sum_probs=49.5

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRI----------AELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNT  104 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i----------~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~T  104 (272)
                      -.++-.|+..||.++..+..+|.+-...+          ..|+.||..||.+|-   .+|+.+.+........-+-+...
T Consensus        37 I~sL~~K~~~lE~eld~~~~~l~~~k~~lee~~~~~~~~E~l~rriq~LEeele~ae~~L~e~~ekl~e~d~~ae~~eRk  116 (143)
T PF12718_consen   37 ITSLQKKNQQLEEELDKLEEQLKEAKEKLEESEKRKSNAEQLNRRIQLLEEELEEAEKKLKETTEKLREADVKAEHFERK  116 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            34677888888888887777766433332          346666666766666   66666666666666666666666


Q ss_pred             HHHHhhhHHHH
Q 024140          105 VRKLQRDVSKL  115 (272)
Q Consensus       105 vKkL~rDvaKL  115 (272)
                      |+.|......+
T Consensus       117 v~~le~~~~~~  127 (143)
T PF12718_consen  117 VKALEQERDQW  127 (143)
T ss_pred             HHHHHhhHHHH
Confidence            66665544433

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].

>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]

Probab=94.42  E-value=0.74  Score=47.44  Aligned_cols=80  Identities=18%  Similarity=0.342  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHH------HhhhhhHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHH---HHHHHHHHHHHHH
Q 024140           31 DVARKITSIAIS------TRVSDLESEHSALRSQLAEKDSRI-------AELQSQIESIYSSLS---DKLGQAQADKERL   94 (272)
Q Consensus        31 dlarkIts~A~a------tRVs~LE~E~~~LR~~L~EKd~~i-------~~Lq~r~s~le~~l~---~rL~~a~ee~~kL   94 (272)
                      .=||++..-+-+      --+.+|+.|+..||.++.++....       .+...+++.+++++.   .+.+..+++...|
T Consensus        95 ~~ar~~l~e~~~~ra~~e~ei~kl~~e~~elr~~~~~~~k~~~~~re~~~~~~~~l~~leAe~~~~krr~~~le~e~~~L  174 (546)
T KOG0977|consen   95 ATARKLLDETARERAKLEIEITKLREELKELRKKLEKAEKERRGAREKLDDYLSRLSELEAEINTLKRRIKALEDELKRL  174 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            345666655433      346778888888888888885443       455667777887777   7788888888888


Q ss_pred             HHHHHHHHHHHHHHhh
Q 024140           95 SKENEALTNTVRKLQR  110 (272)
Q Consensus        95 ~~E~~~La~TvKkL~r  110 (272)
                      .+|+..|-..+..+..
T Consensus       175 k~en~rl~~~l~~~r~  190 (546)
T KOG0977|consen  175 KAENSRLREELARARK  190 (546)
T ss_pred             HHHhhhhHHHHHHHHH
Confidence            8888877776666554

>PHA02562 46 endonuclease subunit; Provisional

Probab=94.42  E-value=0.52  Score=46.24  Aligned_cols=35  Identities=14%  Similarity=0.264  Sum_probs=13.7

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIY   77 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le   77 (272)
                      .|+..|+.++..+|..+.++-+.+..|+.++..|+
T Consensus       337 ~~i~el~~~i~~~~~~i~~~~~~~~~l~~ei~~l~  371 (562)
T PHA02562        337 KKLLELKNKISTNKQSLITLVDKAKKVKAAIEELQ  371 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333443333333334444444433

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=94.35  E-value=0.68  Score=35.43  Aligned_cols=60  Identities=25%  Similarity=0.340  Sum_probs=38.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQ--SQIESIYSSLS-DKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq--~r~s~le~~l~-~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      +||+++..||..|.-=.+++...+  .+.-..|+.-. .+|..+-+++.+|..|++.|....+
T Consensus         2 ~Lea~~~~Lr~rLd~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~   64 (69)
T PF14197_consen    2 KLEAEIATLRNRLDSLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELE   64 (69)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            688999999988854444333222  22222233222 6777888888888888888876633

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=94.33  E-value=0.79  Score=43.58  Aligned_cols=78  Identities=19%  Similarity=0.319  Sum_probs=43.6

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKL  108 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----------~rL~~a~ee~~kL~~E~~~La~TvKkL  108 (272)
                      .++...+..||.|...|.+.|.+=+..-.+|.+.+..|+.++.          .......-+...+++|+++|.+++.-.
T Consensus        46 ~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q~~~~  125 (314)
T PF04111_consen   46 EELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQYEYA  125 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566666666666666666655555555555555555543          111122223344556666666666666


Q ss_pred             hhhHHHHH
Q 024140          109 QRDVSKLE  116 (272)
Q Consensus       109 ~rDvaKLE  116 (272)
                      ..++.+|+
T Consensus       126 ~~~L~~L~  133 (314)
T PF04111_consen  126 SNQLDRLR  133 (314)
T ss_dssp             HHHHHCHH
T ss_pred             HHHHHHHH
Confidence            66666664

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. 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 [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=94.26  E-value=0.47  Score=49.89  Aligned_cols=41  Identities=32%  Similarity=0.463  Sum_probs=35.5

Q ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           36 ITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI   76 (272)
Q Consensus        36 Its~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~l   76 (272)
                      -...+...|+..||.|+.+||..|..|++.+..|++.+..|
T Consensus       538 e~~e~~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~l  578 (697)
T PF09726_consen  538 ECAESCRQRRRQLESELKKLRRELKQKEEQIRELESELQEL  578 (697)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34557899999999999999999999999999999877433

; GO: 0016021 integral to membrane

>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins

Probab=94.18  E-value=0.51  Score=43.82  Aligned_cols=84  Identities=23%  Similarity=0.328  Sum_probs=61.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------------------------------------
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS--------------------------------------------   81 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~--------------------------------------------   81 (272)
                      ..|+.++..|.+++.|-.+.|..||+-+..++....                                            
T Consensus         2 ~~lq~~l~~l~~~~~~~~~L~~kLE~DL~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~g~~sp~ss~~~~~~~~siL   81 (248)
T PF08172_consen    2 EELQKELSELEAKLEEQKELNAKLENDLAKVQASSSASRSFNDGASMASGATRQIPNSGRSGSLSPTSSIIGGGGDSSIL   81 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccCCCCcccccccchhhccCccccCCCCCCccCCCCCCcccHH
Confidence            578999999999999999999999999998885411                                            


Q ss_pred             ----HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH------HHHHHhhcccc
Q 024140           82 ----DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF------RKTLVQSLKDD  129 (272)
Q Consensus        82 ----~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F------Kk~LmqSLq~d  129 (272)
                          ..=-.-.++|.+|.+|...+.+++.+|.++|++|++=      |---|||.+..
T Consensus        82 pIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqSY~~~  139 (248)
T PF08172_consen   82 PIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQSYNNK  139 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCccc
Confidence                0001224677888888888888888888888887542      33456776643

These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane

>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells

Probab=94.02  E-value=1.4  Score=39.77  Aligned_cols=54  Identities=22%  Similarity=0.355  Sum_probs=33.7

Q ss_pred             hhHHHHHHHHHH------HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           28 EQLDVARKITSI------AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        28 EQLdlarkIts~------A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      .||.-|..+..-      .+..|+.-+|.++.+.-.++..-...|.+|+.++..+...|.
T Consensus        99 ~~l~ea~~~~ee~e~k~~E~~rkl~~~E~~Le~aEeR~e~~E~ki~eLE~el~~~~~~lk  158 (237)
T PF00261_consen   99 QQLKEAKRRAEEAERKYEEVERKLKVLEQELERAEERAEAAESKIKELEEELKSVGNNLK  158 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHHHHH
Confidence            456666666633      345666667777776666666666666666666666655554

In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....

>PF13851 GAS: Growth-arrest specific micro-tubule binding

Probab=93.96  E-value=2.5  Score=37.84  Aligned_cols=79  Identities=18%  Similarity=0.291  Sum_probs=54.6

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~------~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      .......|..+..|..+|+.-|..-...+.+|+.++...+..-.      .|+....++...|.-|...|...+.+|.++
T Consensus        43 e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y~kdK~~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~E  122 (201)
T PF13851_consen   43 EERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNYEKDKQSLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQE  122 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455567777777777777777777777777777776665433      677777777777777777777777777776


Q ss_pred             HHHHH
Q 024140          112 VSKLE  116 (272)
Q Consensus       112 vaKLE  116 (272)
                      -.-|.
T Consensus       123 rdeL~  127 (201)
T PF13851_consen  123 RDELY  127 (201)
T ss_pred             HHHHH
Confidence            65554

>KOG2685 consensus Cystoskeletal protein Tektin [Cytoskeleton]

Probab=93.95  E-value=2.3  Score=42.71  Aligned_cols=100  Identities=24%  Similarity=0.317  Sum_probs=80.3

Q ss_pred             chhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHH----------
Q 024140           26 PFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-----DKLGQAQAD----------   90 (272)
Q Consensus        26 P~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-----~rL~~a~ee----------   90 (272)
                      .-.||..=.-.+..||..|+...+.=..+|.-+|+.+.++|++.+..|..++.+|.     -|+.+.+.+          
T Consensus       261 tan~lr~Q~~~ve~af~~ri~etqdar~kL~~ql~k~leEi~~~e~~I~~le~airdK~~pLKVAqTRle~Rt~RPnvEL  340 (421)
T KOG2685|consen  261 TANDLRTQADAVELAFKKRIRETQDARNKLEWQLAKTLEEIADAENNIEALERAIRDKEGPLKVAQTRLENRTYRPNVEL  340 (421)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccccHHHHHHHHHHcccCCchHH
Confidence            34566666667789999999999999999999999999999999999999999998     334443333          


Q ss_pred             -----HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Q 024140           91 -----KERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS  125 (272)
Q Consensus        91 -----~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS  125 (272)
                           +-.|..|--.|-.||..|.-.|++=|.-++.|...
T Consensus       341 CrD~AQ~~L~~EV~~l~~t~~~L~~kL~eA~~~l~~L~~~  380 (421)
T KOG2685|consen  341 CRDQAQYRLVDEVHELDDTVAALKEKLDEAEDSLKLLVNH  380 (421)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 35788888888888888888888777666666543

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=93.90  E-value=2.4  Score=36.44  Aligned_cols=52  Identities=17%  Similarity=0.330  Sum_probs=24.8

Q ss_pred             CchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           25 DPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        25 DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      .-||||    +|-...|..++..=..|+.+||.....--+.+...++++..+...+
T Consensus        42 iDFeqL----kien~~l~~kIeERn~eL~~Lk~~~~~~v~~L~h~keKl~~~~~~~   93 (177)
T PF13870_consen   42 IDFEQL----KIENQQLNEKIEERNKELLKLKKKIGKTVQILTHVKEKLHFLSEEL   93 (177)
T ss_pred             HHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346776    3444455555544445555555444444444444444444333333

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=93.90  E-value=1  Score=47.30  Aligned_cols=26  Identities=23%  Similarity=0.363  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           89 ADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        89 ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      ++...|.++.+.|...+..+...+.+
T Consensus       896 ~~~~~l~~~~~~l~~~~~~~~~~~~~  921 (1164)
T TIGR02169       896 AQLRELERKIEELEAQIEKKRKRLSE  921 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333

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.

>PF11180 DUF2968: Protein of unknown function (DUF2968); InterPro: IPR021350 This family of proteins has no known function

Probab=93.81  E-value=1.2  Score=40.58  Aligned_cols=75  Identities=27%  Similarity=0.403  Sum_probs=57.6

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      -|--+||++..-+...+++-+.....|+.-+.-...+=+   .+-..+.++...|..|+..+-.++.+|+|.|.-|+.
T Consensus       105 irR~~LeAQka~~eR~ia~~~~ra~~LqaDl~~~~~Q~~~va~~Q~q~r~ea~aL~~e~~aaqaQL~~lQ~qv~~Lq~  182 (192)
T PF11180_consen  105 IRRAQLEAQKAQLERLIAESEARANRLQADLQIARQQQQQVAARQQQARQEAQALEAERRAAQAQLRQLQRQVRQLQR  182 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455677777777777777777777777655543333222   788889999999999999999999999999998874

>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

Probab=93.81  E-value=1.4  Score=41.57  Aligned_cols=84  Identities=27%  Similarity=0.410  Sum_probs=52.9

Q ss_pred             hHHHHHHHHHHHHHH-------hhh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           29 QLDVARKITSIAIST-------RVS---DLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKEN   98 (272)
Q Consensus        29 QLdlarkIts~A~at-------RVs---~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~   98 (272)
                      -++|.||=.-+|+..       ||-   .|-.....+|.+|.|-.....+|.+++..||..+-    ..+++...|..||
T Consensus       104 D~elvrkEl~nAlvRAGLktL~~v~~~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~e----e~~erlk~le~E~  179 (290)
T COG4026         104 DVELVRKELKNALVRAGLKTLQRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYE----EVQERLKRLEVEN  179 (290)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            357788877777642       221   33344566677777666667777777777777765    5555555566666


Q ss_pred             HHHHHHHHHHhhhHHHHH
Q 024140           99 EALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        99 ~~La~TvKkL~rDvaKLE  116 (272)
                      +.|..-.|+|-..|.+|+
T Consensus       180 s~LeE~~~~l~~ev~~L~  197 (290)
T COG4026         180 SRLEEMLKKLPGEVYDLK  197 (290)
T ss_pred             HHHHHHHHhchhHHHHHH
Confidence            666666666665555553

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=93.79  E-value=1.5  Score=49.21  Aligned_cols=111  Identities=20%  Similarity=0.258  Sum_probs=73.5

Q ss_pred             ChhHHHh-cCCCCchhhHHHHHHHHH---------------HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           14 LPEEVLQ-VLPSDPFEQLDVARKITS---------------IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIY   77 (272)
Q Consensus        14 lp~eil~-vLP~DP~EQLdlarkIts---------------~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le   77 (272)
                      |.++||. +||.+|.+=.+|+-+|..               .+=..|+..|++|+.+-|.....-.....+.++-+...+
T Consensus      1497 vA~~vL~l~lp~tpeqi~~L~~~I~e~v~sL~nVd~IL~~T~~di~ra~~L~s~A~~a~~~A~~v~~~ae~V~eaL~~Ad 1576 (1758)
T KOG0994|consen 1497 VAEEVLALELPLTPEQIQQLTGEIQERVASLPNVDAILSRTKGDIARAENLQSEAERARSRAEDVKGQAEDVVEALEEAD 1576 (1758)
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHHHHHHHhcccHHHHHHhhhhhHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            4556664 799999998888888862               233568999999999888877655555555555555555


Q ss_pred             HHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH----HHHHHHHh
Q 024140           78 SSLS----------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE----VFRKTLVQ  124 (272)
Q Consensus        78 ~~l~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE----~FKk~Lmq  124 (272)
                      .++.          .-+..+.+...|.++|-..-...+..-+..|.+||    .+|...||
T Consensus      1577 ~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~~eL~~~~e~lk~~~~q 1637 (1758)
T KOG0994|consen 1577 VAQGEAQDAIQGADRDIRLAQQLLAKVQEETAAAEKLATSATQQLGELETRMEELKHKAAQ 1637 (1758)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5544          34455666667777777666666665566665554    45555554

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=93.73  E-value=1.3  Score=51.61  Aligned_cols=91  Identities=24%  Similarity=0.354  Sum_probs=80.2

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-----------DKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-----------~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      ..+++..+.+|+.|+..||.++.|=...+++|+.+++.+..+++           .++....+.+.+|++.-..+...+.
T Consensus      1317 k~~l~~~l~~l~~e~~~l~e~leee~e~~~~l~r~lsk~~~e~~~~~~k~e~~~~~~~eelee~kk~l~~~lq~~qe~~e 1396 (1930)
T KOG0161|consen 1317 KSALENALRQLEHELDLLREQLEEEQEAKNELERKLSKANAELAQWKKKFEEEVLQRLEELEELKKKLQQRLQELEEQIE 1396 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            67889999999999999999999999999999999998888777           3356777778888888899999999


Q ss_pred             HHhhhHHHHHHHHHHHHhhccc
Q 024140          107 KLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus       107 kL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      -++.-.++||.-|..|+|-|.+
T Consensus      1397 ~~~~~~~~Lek~k~~l~~el~d 1418 (1930)
T KOG0161|consen 1397 AANAKNASLEKAKNRLQQELED 1418 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHH
Confidence            9999999999999999887654

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=93.53  E-value=0.67  Score=41.56  Aligned_cols=61  Identities=30%  Similarity=0.431  Sum_probs=38.4

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-------~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      ..|..++..+..+|.+++..|.+|+.++.-....+.       .|...+..++..|..|...|-+.+|
T Consensus       121 eeL~~kL~~~~~~l~~~~~ki~~Lek~leL~~k~~~rql~~e~kK~~~~~~~~~~l~~ei~~L~~klk  188 (194)
T PF15619_consen  121 EELQRKLSQLEQKLQEKEKKIQELEKQLELENKSFRRQLASEKKKHKEAQEEVKSLQEEIQRLNQKLK  188 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566777788888888888888888888877776666       3333444444444444444444433

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=93.45  E-value=1.7  Score=41.18  Aligned_cols=13  Identities=31%  Similarity=0.473  Sum_probs=5.0

Q ss_pred             hhhhHHHHHHHHH
Q 024140           45 VSDLESEHSALRS   57 (272)
Q Consensus        45 Vs~LE~E~~~LR~   57 (272)
                      -..|+.|+..||+
T Consensus       186 ~~~L~~e~~~Lk~  198 (325)
T PF08317_consen  186 KAELEEELENLKQ  198 (325)
T ss_pred             HHHHHHHHHHHHH
Confidence            3334444333333

>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

Probab=93.32  E-value=0.92  Score=45.46  Aligned_cols=67  Identities=21%  Similarity=0.388  Sum_probs=35.3

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      .|..+...|++.+...+.+....-..|++.+..+|.++.   ..|.+...+..++.+..+.+...+.+|.
T Consensus        38 ~~l~q~q~ei~~~~~~i~~~~~~~~kL~~~lk~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~l~~l~  107 (420)
T COG4942          38 KQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNARLNALE  107 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHH
Confidence            555666666666666666665555555555555555444   3333444444444444444444444443

>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences

Probab=93.18  E-value=1.1  Score=38.25  Aligned_cols=61  Identities=28%  Similarity=0.432  Sum_probs=27.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      .|..|+..|+.++.+-...+..|+..+..|...+.  ..++.+.+.+|.+|+..|...+..|.
T Consensus        76 ~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t--~~el~~~i~~l~~e~~~l~~kL~~l~  136 (169)
T PF07106_consen   76 ELDAEIKELREELAELKKEVKSLEAELASLSSEPT--NEELREEIEELEEEIEELEEKLEKLR  136 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555544555555544444444432  12333344444444444444444443

TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].

>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking

Probab=93.15  E-value=4.5  Score=36.10  Aligned_cols=41  Identities=27%  Similarity=0.445  Sum_probs=23.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ....|+..|..++..+|..+.++.+.+.++++.+......|
T Consensus        67 ~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l~~~~~~l  107 (302)
T PF10186_consen   67 ELRERLERLRERIERLRKRIEQKRERLEELRESLEQRRSRL  107 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555666666666666666666666555555555444443

In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy

>PF15070 GOLGA2L5: Putative golgin subfamily A member 2-like protein 5

Probab=93.12  E-value=2.7  Score=43.84  Aligned_cols=79  Identities=23%  Similarity=0.326  Sum_probs=45.9

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHH
Q 024140           37 TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------------DKLGQAQADKERLSKENEALTNT  104 (272)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~------------~rL~~a~ee~~kL~~E~~~La~T  104 (272)
                      .+.-|..|+..|-.++..|+.....=-.+|.+|+..+..|..++.            ..-....++...|.+|+..|...
T Consensus        23 e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eLk~q~~~~~~~~~pa~pse~E~~Lq~E~~~L~kElE~L~~q  102 (617)
T PF15070_consen   23 ESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSELKNQMAEPPPPEPPAGPSEVEQQLQAEAEHLRKELESLEEQ  102 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCccccccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344466777777777777766666555666666666666665554            11123344455566666666666


Q ss_pred             HHHHhhhHHHH
Q 024140          105 VRKLQRDVSKL  115 (272)
Q Consensus       105 vKkL~rDvaKL  115 (272)
                      ++...++...|
T Consensus       103 lqaqv~~ne~L  113 (617)
T PF15070_consen  103 LQAQVENNEQL  113 (617)
T ss_pred             HHHHHHHHHHH
Confidence            55554444443

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=93.11  E-value=1.8  Score=44.00  Aligned_cols=97  Identities=12%  Similarity=0.182  Sum_probs=53.5

Q ss_pred             hhhHHHHHHHHHHHHHHhhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHH
Q 024140           27 FEQLDVARKITSIAISTRVSDLES-EHSALRSQLAEKDSRIAELQSQIESIYSSLS-----------------DKLGQAQ   88 (272)
Q Consensus        27 ~EQLdlarkIts~A~atRVs~LE~-E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-----------------~rL~~a~   88 (272)
                      ..||+--|+--.    .+++++|. ++...|+.+.+|-....+|+...+.++.+-+                 ..|+...
T Consensus       327 ~sqleSqr~y~e----~~~~e~~qsqlen~k~~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~  402 (493)
T KOG0804|consen  327 TSQLESQRKYYE----QIMSEYEQSQLENQKQYYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKEER  402 (493)
T ss_pred             hhhhhHHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            367777666544    67777776 7888887777666665554444443333322                 2233444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        89 ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      |++..|.+..+...+++|+++....+.-.=|..-++-||
T Consensus       403 E~n~~l~knq~vw~~kl~~~~e~~~~~~~s~d~~I~dLq  441 (493)
T KOG0804|consen  403 EENKKLIKNQDVWRGKLKELEEREKEALGSKDEKITDLQ  441 (493)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555555556666666666555444333333333333

>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT)

Probab=93.10  E-value=2.4  Score=43.89  Aligned_cols=63  Identities=17%  Similarity=0.290  Sum_probs=34.0

Q ss_pred             hHHHhcCCCCchhhHHHH--HHH------HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           16 EEVLQVLPSDPFEQLDVA--RKI------TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (272)
Q Consensus        16 ~eil~vLP~DP~EQLdla--rkI------ts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~   78 (272)
                      .++|-|.|..-+.|..|-  .|=      ....+...+..|+.++.+|...|.........|+.+...+..
T Consensus       129 ~DmLvV~~ka~~lQ~qlE~~qkE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e~L~~~~kel~~  199 (546)
T PF07888_consen  129 SDMLVVTTKAQLLQNQLEECQKEKEELLKENEQLEEEVEQLREEVERLEAELEQEEEEMEQLKQQQKELTE  199 (546)
T ss_pred             cceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            366777777555443332  221      134555566666666666666666555555555555444433

This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []

Probab=92.94  E-value=2.3  Score=35.80  Aligned_cols=20  Identities=25%  Similarity=0.448  Sum_probs=9.5

Q ss_pred             HHHHhhhHHHHHHHHHHHHh
Q 024140          105 VRKLQRDVSKLEVFRKTLVQ  124 (272)
Q Consensus       105 vKkL~rDvaKLE~FKk~Lmq  124 (272)
                      |-.|.-||.-|+.+=|..++
T Consensus        98 veEL~~Dv~DlK~myr~Qi~  117 (120)
T PF12325_consen   98 VEELRADVQDLKEMYREQID  117 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            34445555555544444443

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=92.92  E-value=4.1  Score=37.32  Aligned_cols=72  Identities=21%  Similarity=0.277  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           51 EHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        51 E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      |+..+|.++..-...+..|+.+...|+..+.       ..+......+..|..|...|-..+....++...|-..|-.|
T Consensus       217 E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~~~~~~~~~~~i~~le~el~~l~~~~~~~~~ey~~Ll~~K~~L  295 (312)
T PF00038_consen  217 ELKELRRQIQSLQAELESLRAKNASLERQLRELEQRLDEEREEYQAEIAELEEELAELREEMARQLREYQELLDVKLAL  295 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            3444555555544444444444444444443       33444455556666666666666666666666666666554

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

>PRK03918 chromosome segregation protein; Provisional

Probab=92.91  E-value=1.9  Score=44.83  Aligned_cols=6  Identities=33%  Similarity=0.761  Sum_probs=2.1

Q ss_pred             HHHHHH
Q 024140           68 ELQSQI   73 (272)
Q Consensus        68 ~Lq~r~   73 (272)
                      +|++++
T Consensus       644 ~l~~~~  649 (880)
T PRK03918        644 ELRKEL  649 (880)
T ss_pred             HHHHHH
Confidence            333333

>smart00787 Spc7 Spc7 kinetochore protein

Probab=92.91  E-value=1.8  Score=41.42  Aligned_cols=30  Identities=13%  Similarity=0.118  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ...||.+|++-+..|...+.++..++.+|+
T Consensus       206 L~~lk~~l~~~~~ei~~~~~~l~e~~~~l~  235 (312)
T smart00787      206 LDRAKEKLKKLLQEIMIKVKKLEELEEELQ  235 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444455555555555554444

This domain is found in cell division proteins which are required for kinetochore-spindle association.

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=92.90  E-value=1.3  Score=42.51  Aligned_cols=42  Identities=24%  Similarity=0.358  Sum_probs=35.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      .+.+++..+|.+...|+....++.-.+.+|+.++..++..+.
T Consensus       258 ~l~~~l~~le~~l~~l~~~y~~~hP~v~~l~~~i~~l~~~l~  299 (444)
T TIGR03017       258 NLKTDIARAESKLAELSQRLGPNHPQYKRAQAEINSLKSQLN  299 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHH
Confidence            567888888999999888888888888888888888888775

Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.

>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids []

Probab=92.87  E-value=1.9  Score=33.40  Aligned_cols=35  Identities=20%  Similarity=0.402  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           82 DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      ..+....++++.|....+.|...|..|+..|.+|.
T Consensus        35 ~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~rLs   69 (70)
T PF04899_consen   35 HMFEQTSQENAALSEQVNNLSQQVQRLSEQLERLS   69 (70)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34458888888999999999999999999998874

>PF05266 DUF724: Protein of unknown function (DUF724); InterPro: IPR007930 This family contains several uncharacterised proteins found exclusively in Arabidopsis thaliana

Probab=92.82  E-value=2.5  Score=37.85  Aligned_cols=66  Identities=26%  Similarity=0.369  Sum_probs=40.2

Q ss_pred             hhHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           47 DLESEHSALRSQLAEK-------DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EK-------d~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      ++-.+..+|..++.++       +.+|.+|+.++..|+.+.+    .....++...+|...|..-+.+++.++...|
T Consensus       107 ~~~e~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~~~~~----~~~~~ke~~~~ei~~lks~~~~l~~~~~~~e  179 (190)
T PF05266_consen  107 KLLEERKKLEKKIEEKEAELKELESEIKELEMKILELQRQAA----KLKEKKEAKDKEISRLKSEAEALKEEIENAE  179 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444556666666665       7777777777777776654    3333333444666666666666666666654

>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription

Probab=92.72  E-value=6.6  Score=34.59  Aligned_cols=101  Identities=21%  Similarity=0.268  Sum_probs=56.6

Q ss_pred             CCchhhHHHHHHHHHHHHH---HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Q 024140           24 SDPFEQLDVARKITSIAIS---TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----DKLGQAQADKERLSK   96 (272)
Q Consensus        24 ~DP~EQLdlarkIts~A~a---tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----~rL~~a~ee~~kL~~   96 (272)
                      .||..-|+.+++=...+|.   .-|...-+....|..++.+-.+.+.++++++.   .+|.    +.-+.+..++..+..
T Consensus        22 EDP~~~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~A~---~Al~~g~edLAr~al~~k~~~e~   98 (221)
T PF04012_consen   22 EDPEKMLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQAE---LALAAGREDLAREALQRKADLEE   98 (221)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHcCCHHHHHHHHHHHHHHHH
Confidence            3777777777665533332   23333344444555555555555555555443   3344    444566677777777


Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           97 ENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        97 E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      +...|..++..+...|.+|+..-+.|-..|.
T Consensus        99 ~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~  129 (221)
T PF04012_consen   99 QAERLEQQLDQAEAQVEKLKEQLEELEAKLE  129 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777766666666666666655555444443

The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].

>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=92.70  E-value=1.7  Score=40.10  Aligned_cols=41  Identities=12%  Similarity=0.115  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-ccccccC
Q 024140           92 ERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS-LKDDEDA  132 (272)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS-Lq~d~~~  132 (272)
                      .++..|++...+.+.+|..++.+|+.+=-.+..+ |+.+...
T Consensus        70 kqa~~er~~~~~~i~r~~eey~~Lk~~in~~R~e~lgl~~Lp  111 (230)
T PF10146_consen   70 KQAESERNKRQEKIQRLYEEYKPLKDEINELRKEYLGLEPLP  111 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            3445677777788888888888888887777777 7666553

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.

>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association []

Probab=92.67  E-value=3  Score=39.52  Aligned_cols=89  Identities=18%  Similarity=0.336  Sum_probs=48.4

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------H-------HHHHHHHHHHHHHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS--------------D-------KLGQAQADKERLSKENE   99 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~--------------~-------rL~~a~ee~~kL~~E~~   99 (272)
                      +..++..|+.+...|...+..=+..+.+|.++...|+.++.              .       .|.....+++.+.++..
T Consensus       154 L~~~~~~L~~D~~~L~~~~~~l~~~~~~l~~~~~~L~~e~~~Lk~~~~e~~~~D~~eL~~lr~eL~~~~~~i~~~k~~l~  233 (325)
T PF08317_consen  154 LEENLELLQEDYAKLDKQLEQLDELLPKLRERKAELEEELENLKQLVEEIESCDQEELEALRQELAEQKEEIEAKKKELA  233 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445555555555655555555555555555555555443              2       22223333333344444


Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140          100 ALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      .|...+..|+.++..++.-|..+..-|++-
T Consensus       234 el~~el~~l~~~i~~~~~~k~~l~~eI~e~  263 (325)
T PF08317_consen  234 ELQEELEELEEKIEELEEQKQELLAEIAEA  263 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666767676666666553

>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]

Probab=92.63  E-value=0.65  Score=51.89  Aligned_cols=79  Identities=25%  Similarity=0.326  Sum_probs=51.0

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHH----------HHHHHHHHH-------HHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLA----------EKDSRIAEL-------QSQIESIYSSLS---DKLGQAQADKERLSKE   97 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~----------EKd~~i~~L-------q~r~s~le~~l~---~rL~~a~ee~~kL~~E   97 (272)
                      --||.+++..||..+...|..|.          +-+..+++|       .+++..+|..|.   .-+..+..+.+-|++|
T Consensus      1196 ~gay~s~f~~me~kl~~ir~il~~~svs~~~i~~l~~~~~~lr~~l~~~~e~L~~~E~~Lsdi~~~~~~a~~~LesLq~~ 1275 (1758)
T KOG0994|consen 1196 LGAYASRFLDMEEKLEEIRAILSAPSVSAEDIAQLASATESLRRQLQALTEDLPQEEETLSDITNSLPLAGKDLESLQRE 1275 (1758)
T ss_pred             chhhHhHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhccchhhhhHHHHHHH
Confidence            45889999999988888887772          122222222       233333333332   2233444566788999


Q ss_pred             HHHHHHHHHHHhhhHHHHH
Q 024140           98 NEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        98 ~~~La~TvKkL~rDvaKLE  116 (272)
                      .+.|.+++|.|...+.||+
T Consensus      1276 ~~~l~~~~keL~e~~~~ik 1294 (1758)
T KOG0994|consen 1276 FNGLLTTYKELREQLEKIK 1294 (1758)
T ss_pred             HHHHHHHHHHHHHHHHHhh
Confidence            9999999999998888875

>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []

Probab=92.61  E-value=5.2  Score=33.63  Aligned_cols=74  Identities=24%  Similarity=0.386  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhhHHHHHHHHHHHHhhccc
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEAL---TNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~L---a~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      +.+|-..|.-++-++..|+.++..|+.+=.    .+.++..+|.++++.+   ...+.+|.+++..|+.==.++++=|++
T Consensus        18 ve~L~s~lr~~E~E~~~l~~el~~l~~~r~----~l~~Eiv~l~~~~e~~~~~~~~~~~L~~el~~l~~ry~t~LellGE   93 (120)
T PF12325_consen   18 VERLQSQLRRLEGELASLQEELARLEAERD----ELREEIVKLMEENEELRALKKEVEELEQELEELQQRYQTLLELLGE   93 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            345555555566666667777776666544    6667777777777544   455666666666666655556655554


Q ss_pred             c
Q 024140          129 D  129 (272)
Q Consensus       129 d  129 (272)
                      -
T Consensus        94 K   94 (120)
T PF12325_consen   94 K   94 (120)
T ss_pred             h
Confidence            3

The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].

>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=92.60  E-value=0.99  Score=41.21  Aligned_cols=80  Identities=13%  Similarity=0.172  Sum_probs=59.7

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      -+.+++...||+++.+++++.+.+.+.|+-.+       .-.    ....++++.|.++.++|....+-|.-+|+|++-=
T Consensus        77 ~~~ks~~qeLe~~L~~~~qk~~tl~e~~en~K-------~~~----e~tEer~~el~kklnslkk~~e~lr~el~k~~e~  145 (203)
T KOG3433|consen   77 CDRKSVLQELESQLATGSQKKATLGESIENRK-------AGR----EETEERTDELTKKLNSLKKILESLRWELAKIQET  145 (203)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHhHHHHHHHHHH-------hhh----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            46788899999999999999888877665443       111    2455666799999999999999999999998765


Q ss_pred             HHHHHhhcccc
Q 024140          119 RKTLVQSLKDD  129 (272)
Q Consensus       119 Kk~LmqSLq~d  129 (272)
                      +-++..-+..+
T Consensus       146 dpqv~~k~~~~  156 (203)
T KOG3433|consen  146 DPQVFEKKVHL  156 (203)
T ss_pred             CHHHHHHHHHH
Confidence            55554444443

>PF13851 GAS: Growth-arrest specific micro-tubule binding

Probab=92.58  E-value=2.6  Score=37.78  Aligned_cols=86  Identities=21%  Similarity=0.291  Sum_probs=61.4

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHH--HHHHHH-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 024140           39 IAISTRVSDLESEHSALRSQLA--EKDSRI-AELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~--EKd~~i-~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (272)
                      .-+.-=+.+++.|+..|+.+|.  +||... ..++.|+..++..|.   ---....++..+|.+||+.|-.+....-.||
T Consensus        58 ~~L~epL~~a~~e~~eL~k~L~~y~kdK~~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~~~i~ev  137 (201)
T PF13851_consen   58 KRLSEPLKKAEEEVEELRKQLKNYEKDKQSLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYRKFESAIQEV  137 (201)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3345556788999999999998  566543 344555555555554   2223677888999999999999998888888


Q ss_pred             HHHHHHHHHHHh
Q 024140          113 SKLEVFRKTLVQ  124 (272)
Q Consensus       113 aKLE~FKk~Lmq  124 (272)
                      ..==.||-.|++
T Consensus       138 qQk~~~kn~lLE  149 (201)
T PF13851_consen  138 QQKTGLKNLLLE  149 (201)
T ss_pred             HHHHHHHHHHHH
Confidence            876677666653

>PF05911 DUF869: Plant protein of unknown function (DUF869); InterPro: IPR008587 This family consists of a number of sequences found in plants

Probab=92.55  E-value=1.7  Score=46.57  Aligned_cols=91  Identities=20%  Similarity=0.315  Sum_probs=61.5

Q ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH------------HHHHH
Q 024140           35 KITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERL------------SKENE   99 (272)
Q Consensus        35 kIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL------------~~E~~   99 (272)
                      |++.-||++- -+-|+|+..||++|..--..-..+++||+.||.+|.   -.|+.+.+|+++.            .+.+.
T Consensus        10 kvaeeav~gw-ekae~e~~~lk~~l~~~~~~~~~~e~r~~hld~aLkec~~qlr~~ree~eq~i~~~~~~~s~e~e~~~~   88 (769)
T PF05911_consen   10 KVAEEAVSGW-EKAEAEAASLKQQLEAATQQKLALEDRVSHLDGALKECMRQLRQVREEQEQKIHEAVAKKSKEWEKIKS   88 (769)
T ss_pred             HHHHHHHhhH-HHHHHHHHHHHHHHHHHHHHhHHHHHHhhhhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHhHHHHHHHH
Confidence            5666677654 367899999999999888888899999999999998   6777777776443            23344


Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 024140          100 ALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (272)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (272)
                      .|...+-.+++.++++.+=-.+|-.+|
T Consensus        89 ~le~~l~e~~~~l~~~~~e~~~l~~~l  115 (769)
T PF05911_consen   89 ELEAKLAELSKRLAESAAENSALSKAL  115 (769)
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence            555555555555555444333333333

The function of this family is unknown.

>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast)

Probab=92.53  E-value=2.2  Score=37.88  Aligned_cols=30  Identities=23%  Similarity=0.436  Sum_probs=17.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQSQIESI   76 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~l   76 (272)
                      .++.++..|..++.+....|.+|++++..+
T Consensus        66 ~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~   95 (188)
T PF03962_consen   66 KRQNKLEKLQKEIEELEKKIEELEEKIEEA   95 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555666666666666666666665554

The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].

>PRK02224 chromosome segregation protein; Provisional

Probab=92.53  E-value=2.6  Score=44.07  Aligned_cols=14  Identities=14%  Similarity=0.375  Sum_probs=6.7

Q ss_pred             CCchhhHHHHHHHH
Q 024140           24 SDPFEQLDVARKIT   37 (272)
Q Consensus        24 ~DP~EQLdlarkIt   37 (272)
                      .+|-+-.++-.+|.
T Consensus       146 ~~p~~R~~ii~~l~  159 (880)
T PRK02224        146 ATPSDRQDMIDDLL  159 (880)
T ss_pred             CCHHHHHHHHHHHh
Confidence            34444444444444

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=92.53  E-value=1.2  Score=45.22  Aligned_cols=71  Identities=21%  Similarity=0.297  Sum_probs=38.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHhh
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLG----QAQADKERLSKENEALTNTVRKLQR  110 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~----~a~ee~~kL~~E~~~La~TvKkL~r  110 (272)
                      -|..+|.+|+.|+..|..+=..=.+++..|++|-..++..++.+|.    +..+++.+|++|+..|...+-.|++
T Consensus        63 Tlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~  137 (472)
T TIGR03752        63 TLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQR  137 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455666666666666555544445566777777777777763332    2333444444444444444444433

Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.

>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]

Probab=92.32  E-value=2.4  Score=45.58  Aligned_cols=73  Identities=22%  Similarity=0.292  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIE-----------SIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s-----------~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      +.+|+.++.|+...++.+..|..           +.+.-|+   ..+-+++|+++.|..|-+.+.+++-.++++-.||-+
T Consensus       165 ~~kl~~~~qe~naeL~rarqreemneeh~~rlsdtvdErlqlhlkermaAle~kn~L~~e~~s~kk~l~~~~~~k~rl~~  244 (916)
T KOG0249|consen  165 TRKLEEQLEELNAELQRARQREKMNEEHNKRLSDTVDERLQLHLKERMAALEDKNRLEQELESVKKQLEEMRHDKDKLRT  244 (916)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            55666666666666666555443           1222233   456688999999999999999999999999888888


Q ss_pred             HHHHHHh
Q 024140          118 FRKTLVQ  124 (272)
Q Consensus       118 FKk~Lmq  124 (272)
                      |+-.|.+
T Consensus       245 d~E~Lr~  251 (916)
T KOG0249|consen  245 DIEDLRG  251 (916)
T ss_pred             hHHHHHH
Confidence            8766654

>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans

Probab=92.30  E-value=3.7  Score=36.01  Aligned_cols=93  Identities=16%  Similarity=0.204  Sum_probs=61.0

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           28 EQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRK  107 (272)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKk  107 (272)
                      |-||.+..-.. +....+-.|..+...|..+...+.+.-...+.++..+|..+...-+.....+..|+.++..|...+|.
T Consensus        36 E~Le~~~~~n~-~~~~e~~~L~~d~e~L~~q~~~ek~~r~~~e~~l~~~Ed~~~~e~k~L~~~v~~Le~e~r~L~~~~~~  114 (158)
T PF09744_consen   36 ELLESLASRNQ-EHEVELELLREDNEQLETQYEREKELRKQAEEELLELEDQWRQERKDLQSQVEQLEEENRQLELKLKN  114 (158)
T ss_pred             HHHHHHHHhhh-hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            66665544333 44555556666666666666555555556666777777777756667777788888888888888877


Q ss_pred             HhhhHHHHHHHHHH
Q 024140          108 LQRDVSKLEVFRKT  121 (272)
Q Consensus       108 L~rDvaKLE~FKk~  121 (272)
                      +.-.+.+|+.=...
T Consensus       115 ~~~q~~rlee~e~~  128 (158)
T PF09744_consen  115 LSDQSSRLEEREAE  128 (158)
T ss_pred             hhhhccccchhHHH
Confidence            77777777643333

Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.

>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion

Probab=92.23  E-value=5  Score=34.39  Aligned_cols=38  Identities=26%  Similarity=0.469  Sum_probs=14.5

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      .++..++.++..++....+-.......++++..++..+
T Consensus       102 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~  139 (191)
T PF04156_consen  102 ERIQELESELEKLKEDLQELRELLKSVEERLDSLDESI  139 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            33333344443333333333333333333333333333

The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].

>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]

Probab=92.18  E-value=2  Score=44.68  Aligned_cols=41  Identities=20%  Similarity=0.423  Sum_probs=21.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ++.+|...+|..+..|...+.+|+.+|..|+.....|-..+
T Consensus       284 ~~~~k~~~~~~~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~I  324 (581)
T KOG0995|consen  284 QMKSKKQHMEKKLEMLKSEIEEKEEEIEKLQKENDELKKQI  324 (581)
T ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555555555555555554443

>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT)

Probab=92.14  E-value=2.6  Score=43.61  Aligned_cols=39  Identities=13%  Similarity=0.337  Sum_probs=16.3

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      .++...+.|...|.+....=......|++++..|+.+|.
T Consensus       143 ~qlE~~qkE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~  181 (546)
T PF07888_consen  143 NQLEECQKEKEELLKENEQLEEEVEQLREEVERLEAELE  181 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444333433333333333444444444444443

This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].

>smart00787 Spc7 Spc7 kinetochore protein

Probab=92.06  E-value=3.2  Score=39.72  Aligned_cols=77  Identities=16%  Similarity=0.270  Sum_probs=35.1

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDS----RIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~----~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      +..|...|+.|+..||+.-.|.+.    ....+++++..+..++           ....++-..+..++..|+.++..++
T Consensus       177 l~~~~~~L~~e~~~L~~~~~e~~~~d~~eL~~lk~~l~~~~~ei-----------~~~~~~l~e~~~~l~~l~~~I~~~~  245 (312)
T smart00787      177 LRDRKDALEEELRQLKQLEDELEDCDPTELDRAKEKLKKLLQEI-----------MIKVKKLEELEEELQELESKIEDLT  245 (312)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHhCCHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555555555544322    4444444444444433           3344444444444444444444444


Q ss_pred             HHHHHHHhhccc
Q 024140          117 VFRKTLVQSLKD  128 (272)
Q Consensus       117 ~FKk~LmqSLq~  128 (272)
                      .-|..+...|++
T Consensus       246 ~~k~e~~~~I~~  257 (312)
T smart00787      246 NKKSELNTEIAE  257 (312)
T ss_pred             HHHHHHHHHHHH
Confidence            444444444443

This domain is found in cell division proteins which are required for kinetochore-spindle association.

>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length

Probab=91.97  E-value=1.8  Score=37.53  Aligned_cols=33  Identities=30%  Similarity=0.519  Sum_probs=30.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQ   72 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r   72 (272)
                      +...++..++.|...|+.+|.+.+..|.+|+..
T Consensus        17 ~~K~~~~~~~~e~~~~k~ql~~~d~~i~~Lk~~   49 (155)
T PF06810_consen   17 APKAKVDKVKEERDNLKTQLKEADKQIKDLKKS   49 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999874

The function of this family is unknown.; GO: 0005198 structural molecule activity

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=91.81  E-value=4.8  Score=41.38  Aligned_cols=68  Identities=22%  Similarity=0.259  Sum_probs=42.7

Q ss_pred             ChhHHHhcCCCCchhhHHHHHHH---------HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           14 LPEEVLQVLPSDPFEQLDVARKI---------TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        14 lp~eil~vLP~DP~EQLdlarkI---------ts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      |-+.|-.+|==+.+++|.-=-.+         ....+..++..||.++..+..++.+..+.+..++.++..++..+.
T Consensus       171 l~~Ai~~LlGl~~~~~L~~dl~~~~~~~~~~~~~~~~~~~~~~le~el~~l~~~~e~l~~~i~~l~~ele~a~~~l~  247 (650)
T TIGR03185       171 LKEAIEVLLGLDLIDRLAGDLTNVLRRRKKSELPSSILSEIEALEAELKEQSEKYEDLAQEIAHLRNELEEAQRSLE  247 (650)
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555566666677776421111         133555677778888777777777777777777666666666554

This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.

>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family

Probab=91.72  E-value=6.9  Score=36.48  Aligned_cols=43  Identities=19%  Similarity=0.305  Sum_probs=24.8

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ...+..++..|+.++..++.++..-.+.+..++.++..++..+
T Consensus       139 ~~~~~~~~~~l~~~i~~~~~~i~~~~~~l~~~~~~l~~~~~~~  181 (423)
T TIGR01843       139 KSTLRAQLELILAQIKQLEAELAGLQAQLQALRQQLEVISEEL  181 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445666666666666666666655555555555555444444

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.

>KOG4010 consensus Coiled-coil protein TPD52 [General function prediction only]

Probab=91.71  E-value=0.31  Score=44.49  Aligned_cols=35  Identities=31%  Similarity=0.473  Sum_probs=32.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIE   74 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s   74 (272)
                      -|.+.+.++|.||..||+-|+-|++|..||..|+-
T Consensus        48 elr~EL~kvEeEI~TLrqVLaAKerH~~ELKRKLG   82 (208)
T KOG4010|consen   48 ELRTELAKVEEEIVTLRQVLAAKERHAAELKRKLG   82 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            68889999999999999999999999999998764

>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes

Probab=91.68  E-value=0.94  Score=47.74  Aligned_cols=56  Identities=32%  Similarity=0.452  Sum_probs=39.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYS---SLSDKLGQAQADKERLSKENEALT  102 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~---~l~~rL~~a~ee~~kL~~E~~~La  102 (272)
                      +||+|+.+||..|.-....-.||+.+++.|+.   .+..-|.+..++|+.|+.....|.
T Consensus       422 rLE~dvkkLraeLq~~Rq~E~ELRsqis~l~~~Er~lk~eL~qlr~ene~Lq~Kl~~L~  480 (697)
T PF09726_consen  422 RLEADVKKLRAELQSSRQSEQELRSQISSLTNNERSLKSELSQLRQENEQLQNKLQNLV  480 (697)
T ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            79999999999999888888999988766654   333445566666666655444443

; GO: 0016021 integral to membrane

>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway

Probab=91.62  E-value=4.7  Score=30.50  Aligned_cols=84  Identities=21%  Similarity=0.342  Sum_probs=56.0

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKD-----SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd-----~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (272)
                      -..+..++..|+.+...+...+....     ..+...+.-+..|+..+    .....+...+.++...+-..+....+++
T Consensus        14 ~~~~~~~l~~L~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~l~~~i----~~~~~~~~~~~~~~~~~r~~l~~a~~~~   89 (123)
T PF02050_consen   14 LQEAEEQLEQLQQERQEYQEQLSESQQGVSVAQLRNYQRYISALEQAI----QQQQQELERLEQEVEQAREELQEARRER   89 (123)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHT-----SGGGHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556677777777777777666666     55555555555555444    4777788888888888888889999999


Q ss_pred             HHHHHHHHHHHhh
Q 024140          113 SKLEVFRKTLVQS  125 (272)
Q Consensus       113 aKLE~FKk~LmqS  125 (272)
                      .+||.++-.-...
T Consensus        90 k~~e~L~e~~~~~  102 (123)
T PF02050_consen   90 KKLEKLKERRREE  102 (123)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9998887654443

Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.

>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure

Probab=91.55  E-value=0.98  Score=35.76  Aligned_cols=40  Identities=28%  Similarity=0.457  Sum_probs=32.4

Q ss_pred             HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           72 QIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        72 r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      ++-.|+..|.   +|.....+++.||..||.-|..-|..|.+.
T Consensus        24 ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~~   66 (80)
T PF10224_consen   24 EILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMSS   66 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4445555555   788899999999999999999999988654

The exact function is unknown.

>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily

Probab=91.47  E-value=2.1  Score=41.82  Aligned_cols=41  Identities=20%  Similarity=0.343  Sum_probs=28.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      .+..++..||.|+..|+....++.-.+.+|++++..++..+
T Consensus       251 ~l~~~l~~l~~~l~~l~~~y~~~hP~v~~l~~qi~~l~~~l  291 (498)
T TIGR03007       251 ELDGRIEALEKQLDALRLRYTDKHPDVIATKREIAQLEEQK  291 (498)
T ss_pred             chHHHHHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHH
Confidence            44566777777777777777666666666666666666654

Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene.

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation

Probab=91.45  E-value=3.6  Score=31.78  Aligned_cols=57  Identities=19%  Similarity=0.251  Sum_probs=24.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKL  108 (272)
Q Consensus        48 LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL  108 (272)
                      ||..|..+=..++-=...|.+|+++...|..+-.    ...++|.+|..|+......++.|
T Consensus         9 LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~----~L~~en~~L~~e~~~~~~rl~~L   65 (72)
T PF06005_consen    9 LEEKIQQAVETIALLQMENEELKEKNNELKEENE----ELKEENEQLKQERNAWQERLRSL   65 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333334444444444433322    44455555555555555555444

It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.

>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.34  E-value=8.2  Score=35.68  Aligned_cols=20  Identities=20%  Similarity=0.433  Sum_probs=9.1

Q ss_pred             HHHHHHHHH---HHHHHHHHHHH
Q 024140           61 EKDSRIAEL---QSQIESIYSSL   80 (272)
Q Consensus        61 EKd~~i~~L---q~r~s~le~~l   80 (272)
                      ||.+|..+|   ..-++.||..+
T Consensus        47 Er~~h~eeLrqI~~DIn~lE~iI   69 (230)
T PF10146_consen   47 ERMAHVEELRQINQDINTLENII   69 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444   33444444444

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=91.34  E-value=2.6  Score=49.23  Aligned_cols=89  Identities=20%  Similarity=0.363  Sum_probs=72.7

Q ss_pred             hhHHHHHHHHH-----HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 024140           28 EQLDVARKITS-----IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENE   99 (272)
Q Consensus        28 EQLdlarkIts-----~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~   99 (272)
                      |.++++-+|..     -++...=.+||.+|..|...|+|......-..+|+..+...+.   .-|..-.+.+.+|...|.
T Consensus      1696 e~~E~~e~i~~~~~~~s~l~~~KrklE~~i~~l~~elee~~~~~~~~~Er~kka~~~a~~~~~el~~Eq~~~~~le~~k~ 1775 (1930)
T KOG0161|consen 1696 ELEELAERVNELNAQNSSLTAEKRKLEAEIAQLQSELEEEQSELRAAEERAKKAQADAAKLAEELRKEQETSQKLERLKK 1775 (1930)
T ss_pred             HHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            44455555553     4566677789999999999999999999999999998888776   788888999999999999


Q ss_pred             HHHHHHHHHhhhHHHHH
Q 024140          100 ALTNTVRKLQRDVSKLE  116 (272)
Q Consensus       100 ~La~TvKkL~rDvaKLE  116 (272)
                      +|..+||.|.-.+..+|
T Consensus      1776 ~LE~~~kdLq~rL~e~E 1792 (1930)
T KOG0161|consen 1776 SLERQVKDLQLRLDEAE 1792 (1930)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999998876555544

>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=91.21  E-value=8.4  Score=34.94  Aligned_cols=40  Identities=15%  Similarity=0.292  Sum_probs=19.1

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      -.|+.++..|...|.+.+..-.+.+..|+.+...++..+.
T Consensus        41 Q~~id~~~~e~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~   80 (251)
T PF11932_consen   41 QKRIDQWDDEKQELLAEYRQLEREIENLEVYNEQLERQVA   80 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555555554444444444444444444444433

However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.

>TIGR02231 conserved hypothetical protein

Probab=91.18  E-value=2.4  Score=42.27  Aligned_cols=78  Identities=18%  Similarity=0.276  Sum_probs=51.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL---------------------SDKLGQAQADKERLSKEN   98 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l---------------------~~rL~~a~ee~~kL~~E~   98 (272)
                      +...+|..|+.++..|+.++++-+..+..++.++.-|+.--                     .+-+....++..+|..+.
T Consensus        68 ~~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (525)
T TIGR02231        68 PDPERLAELRKQIRELEAELRDLEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTED  147 (525)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34457777888888888877777777777777665555432                     022223344566777777


Q ss_pred             HHHHHHHHHHhhhHHHHHH
Q 024140           99 EALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        99 ~~La~TvKkL~rDvaKLE~  117 (272)
                      ..|...+++|++.+++|+.
T Consensus       148 ~~~~~~~~~~~~~l~~l~~  166 (525)
T TIGR02231       148 REAERRIRELEKQLSELQN  166 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            7777777777777777744

This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=91.17  E-value=5.6  Score=34.23  Aligned_cols=80  Identities=21%  Similarity=0.351  Sum_probs=62.4

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      -+|.-|...|..++.||...+..|+.++..-=..|.   .+|.....++..+..+.......+.++..++.+++.=+..+
T Consensus        45 eqLkien~~l~~kIeERn~eL~~Lk~~~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~  124 (177)
T PF13870_consen   45 EQLKIENQQLNEKIEERNKELLKLKKKIGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKL  124 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356778889999999999999999988876555555   88888888888888888888888888888877776554444


Q ss_pred             Hhh
Q 024140          123 VQS  125 (272)
Q Consensus       123 mqS  125 (272)
                      -..
T Consensus       125 ~~~  127 (177)
T PF13870_consen  125 RKQ  127 (177)
T ss_pred             HHH
Confidence            433

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=91.16  E-value=1.8  Score=44.75  Aligned_cols=30  Identities=13%  Similarity=0.246  Sum_probs=21.5

Q ss_pred             HHHHHHHhhhHHHHHHHHHHHHhhcccccc
Q 024140          102 TNTVRKLQRDVSKLEVFRKTLVQSLKDDED  131 (272)
Q Consensus       102 a~TvKkL~rDvaKLE~FKk~LmqSLq~d~~  131 (272)
                      ......|+|++.-.+..=..|++.+++-.-
T Consensus       375 ~~e~~~L~Re~~~~~~~Y~~ll~r~~e~~~  404 (754)
T TIGR01005       375 QVDLDALQRDAAAKRQLYESYLTNYRQAAS  404 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555667778887777777778887776544

The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.

>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function

Probab=91.15  E-value=8.8  Score=34.81  Aligned_cols=53  Identities=13%  Similarity=0.126  Sum_probs=26.7

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           28 EQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      .+++-+.+.....+..+. ....++..+-++-.+-.+.|..|++++..|+....
T Consensus        21 ~~~~~~~~~~~~~~~~~~-~sQ~~id~~~~e~~~L~~e~~~l~~e~e~L~~~~~   73 (251)
T PF11932_consen   21 ATLDQAQQVQQQWVQAAQ-QSQKRIDQWDDEKQELLAEYRQLEREIENLEVYNE   73 (251)
T ss_pred             ccHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555555544444442 23335555555555555555555555555555443

However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=91.13  E-value=2.4  Score=44.82  Aligned_cols=65  Identities=18%  Similarity=0.263  Sum_probs=38.4

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      ..++..||..|..+...-.++|.+-.+.+..|+++...|.    +|+.++.+.+++|.+.-+.+.+.+.
T Consensus       560 r~ei~~rv~~Lk~~~e~Ql~~L~~l~e~~~~l~~~ae~La----eR~e~a~d~Qe~L~~R~~~vl~~l~  624 (717)
T PF10168_consen  560 REEIQRRVKLLKQQKEQQLKELQELQEERKSLRESAEKLA----ERYEEAKDKQEKLMKRVDRVLQLLN  624 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4566667766666666655555555555555555544444    5556666666666665555544443

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

>PF13863 DUF4200: Domain of unknown function (DUF4200)

Probab=91.07  E-value=6.9  Score=31.40  Aligned_cols=35  Identities=23%  Similarity=0.433  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      ..++.+|..+...|..-+.+|...|.++..|+.-|
T Consensus        80 ~~ei~~l~~~l~~l~~~~~k~e~~l~~~~~Y~~fL  114 (126)
T PF13863_consen   80 EAEIKKLKAELEELKSEISKLEEKLEEYKKYEEFL  114 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444333

>PRK10361 DNA recombination protein RmuC; Provisional

Probab=91.05  E-value=8.5  Score=39.26  Aligned_cols=74  Identities=24%  Similarity=0.394  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHhhh---------HHHH
Q 024140           53 SALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTV--------RKLQRD---------VSKL  115 (272)
Q Consensus        53 ~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~Tv--------KkL~rD---------vaKL  115 (272)
                      ..+++.+.+-.....+|+.++.........++....+-..+|..+-.+|++.+        ...|+.         =.+|
T Consensus        70 ~~~~~~~~~~~~~~~~l~~~le~~~~~~~ek~~~l~~~~~~L~~~F~~LA~~ile~k~~~f~~~~~~~l~~ll~Pl~e~l  149 (475)
T PRK10361         70 RSLQSINTSLEADLREVTTRMEAAQQHADDKIRQMINSEQRLSEQFENLANRIFEHSNRRVDEQNRQSLNSLLSPLREQL  149 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            33333333333333333333333333333566666666667777777777643        112221         1357


Q ss_pred             HHHHHHHHhhc
Q 024140          116 EVFRKTLVQSL  126 (272)
Q Consensus       116 E~FKk~LmqSL  126 (272)
                      +.|++.|-+.-
T Consensus       150 ~~f~~~v~~~~  160 (475)
T PRK10361        150 DGFRRQVQDSF  160 (475)
T ss_pred             HHHHHHHHHHH
Confidence            78888776543

>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp

Probab=90.95  E-value=3.4  Score=39.93  Aligned_cols=90  Identities=24%  Similarity=0.356  Sum_probs=52.1

Q ss_pred             chhhHHHHHHHHHHHHHH---hhhhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----
Q 024140           26 PFEQLDVARKITSIAIST---RVSDLESEHSALRSQLAEK-DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKE----   97 (272)
Q Consensus        26 P~EQLdlarkIts~A~at---RVs~LE~E~~~LR~~L~EK-d~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E----   97 (272)
                      |..|=+|++|=...-++-   |+..=|.||..||.||+-. +.-|+|=   --..|++|.  ||+|+.|+.+|..-    
T Consensus        62 PLQQKEV~iRHLkakLkes~~~l~dRetEI~eLksQL~RMrEDWIEEE---CHRVEAQLA--LKEARkEIkQLkQvieTm  136 (305)
T PF15290_consen   62 PLQQKEVCIRHLKAKLKESENRLHDRETEIDELKSQLARMREDWIEEE---CHRVEAQLA--LKEARKEIKQLKQVIETM  136 (305)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence            567888888765444443   3333355666666666632 2233222   222345553  78999999888764    


Q ss_pred             HHHHHHHHH-------HHhhhHHHHHHHHH
Q 024140           98 NEALTNTVR-------KLQRDVSKLEVFRK  120 (272)
Q Consensus        98 ~~~La~TvK-------kL~rDvaKLE~FKk  120 (272)
                      |++|+..=|       ..|-+--|||+|=+
T Consensus       137 rssL~ekDkGiQKYFvDINiQN~KLEsLLq  166 (305)
T PF15290_consen  137 RSSLAEKDKGIQKYFVDINIQNKKLESLLQ  166 (305)
T ss_pred             HhhhchhhhhHHHHHhhhhhhHhHHHHHHH
Confidence            455555433       34445678998844

>PF00769 ERM: Ezrin/radixin/moesin family; InterPro: IPR011259 The ERM family consists of three closely-related proteins, ezrin, radixin and moesin []

Probab=90.93  E-value=3.9  Score=37.71  Aligned_cols=78  Identities=22%  Similarity=0.400  Sum_probs=46.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKER-------LSKENEALTNTVRKLQ  109 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~k-------L~~E~~~La~TvKkL~  109 (272)
                      -|--|+..+|.|....+..|.+..+.|..|+++...++.+-.   .+...+.+++.+       ..+|+..|+.-+..+.
T Consensus         9 Ele~rL~q~eee~~~a~~~L~e~e~~a~~Leek~k~aeeea~~Le~k~~eaee~~~rL~~~~~~~~eEk~~Le~e~~e~~   88 (246)
T PF00769_consen    9 ELEERLRQMEEEMRRAQEALEESEETAEELEEKLKQAEEEAEELEQKRQEAEEEKQRLEEEAEMQEEEKEQLEQELREAE   88 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356788888999988888888888888888777766555433   333334444433       3456666666666666


Q ss_pred             hhHHHHHH
Q 024140          110 RDVSKLEV  117 (272)
Q Consensus       110 rDvaKLE~  117 (272)
                      ..+++|+.
T Consensus        89 ~~i~~l~e   96 (246)
T PF00769_consen   89 AEIARLEE   96 (246)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66666544

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

>PF12777 MT: Microtubule-binding stalk of dynein motor; InterPro: IPR024743 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=90.82  E-value=1.4  Score=41.94  Aligned_cols=57  Identities=28%  Similarity=0.442  Sum_probs=41.8

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~  103 (272)
                      .++..+|.++...+.+|.++...+.+|++++..|+.++.    .+..++.+|+.+......
T Consensus       221 ~~l~~a~~~l~~~~~~L~~~~~~l~~l~~~l~~l~~~~~----~~~~e~~~l~~~~~~~~~  277 (344)
T PF12777_consen  221 QKLEEAEAELEEAEEQLAEKQAELAELEEKLAALQKEYE----EAQKEKQELEEEIEETER  277 (344)
T ss_dssp             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHh
Confidence            567777888888888888888888888888888887776    556666666655544433

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [].; PDB: 3VKH_A 3VKG_A 3ERR_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 2RR7_A.

>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]

Probab=90.81  E-value=4.4  Score=42.24  Aligned_cols=93  Identities=16%  Similarity=0.299  Sum_probs=58.4

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH---------
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVR---------  106 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvK---------  106 (272)
                      ++..+|...|+...++|+..+..=..-+.++..+-..++..|.   .-+....+++++|+++++.|-+.|.         
T Consensus       255 ek~~~~~eslre~~~~L~~D~nK~~~y~~~~~~k~~~~~~~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~Ie~Q~iS~~dv  334 (581)
T KOG0995|consen  255 EKDPGKEESLREKKARLQDDVNKFQAYVSQMKSKKQHMEKKLEMLKSEIEEKEEEIEKLQKENDELKKQIELQGISGEDV  334 (581)
T ss_pred             hcCcchHHHHHHHHHHHHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHH
Confidence            3445555556555555555554444444444444444444443   3345888999999999999988875         


Q ss_pred             --------HHhhhHHHHHHHHHHHHhhcccccc
Q 024140          107 --------KLQRDVSKLEVFRKTLVQSLKDDED  131 (272)
Q Consensus       107 --------kL~rDvaKLE~FKk~LmqSLq~d~~  131 (272)
                              +|.|+|.+++.=+-.|++.+-+-+.
T Consensus       335 e~mn~Er~~l~r~l~~i~~~~d~l~k~vw~~~l  367 (581)
T KOG0995|consen  335 ERMNLERNKLKRELNKIQSELDRLSKEVWELKL  367 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence                    4667777776666667776665554

>KOG0963 consensus Transcription factor/CCAAT displacement protein CDP1 [Transcription]

Probab=90.77  E-value=2.7  Score=44.12  Aligned_cols=98  Identities=22%  Similarity=0.260  Sum_probs=59.7

Q ss_pred             hHHHHHHHHHHHH--------HHhhhhhHHHHHHHHHHHHHH------H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           29 QLDVARKITSIAI--------STRVSDLESEHSALRSQLAEK------D--SRIAELQSQIESIYSSLSDKLGQAQADKE   92 (272)
Q Consensus        29 QLdlarkIts~A~--------atRVs~LE~E~~~LR~~L~EK------d--~~i~~Lq~r~s~le~~l~~rL~~a~ee~~   92 (272)
                      +.+++.|+.-.-+        -+|+-.||.|++.||.+++.-      +  ..|+.+...+...|..++--.........
T Consensus       227 dee~~~k~aev~lim~eLe~aq~ri~~lE~e~e~L~~ql~~~N~~~~~~~~~~i~~~~~~L~~kd~~i~~L~~di~~~~~  306 (629)
T KOG0963|consen  227 DEEVAAKAAEVSLIMTELEDAQQRIVFLEREVEQLREQLAKANSSKKLAKIDDIDALGSVLNQKDSEIAQLSNDIERLEA  306 (629)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCchHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            3456666653222        258888999999999988631      1  23445555555555555433334445556


Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 024140           93 RLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (272)
Q Consensus        93 kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (272)
                      -|++|+....++|.+|++.+.....-...|-.-|
T Consensus       307 S~~~e~e~~~~qI~~le~~l~~~~~~leel~~kL  340 (629)
T KOG0963|consen  307 SLVEEREKHKAQISALEKELKAKISELEELKEKL  340 (629)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6778888888888888887766444444443333

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=90.76  E-value=2.8  Score=46.40  Aligned_cols=35  Identities=31%  Similarity=0.419  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 024140           92 ERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (272)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (272)
                      ..+..++...++-.+-|++.|.|||..-..|-..+
T Consensus       390 ~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~  424 (1074)
T KOG0250|consen  390 NELGSELEERENKLEQLKKEVEKLEEQINSLREEL  424 (1074)
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44556666667777777778888877544444433

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=90.70  E-value=5.5  Score=43.81  Aligned_cols=40  Identities=20%  Similarity=0.368  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Q 024140           85 GQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ  124 (272)
Q Consensus        85 ~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lmq  124 (272)
                      .....+...|.+....+.+.++.+.+++.++..-...+.+
T Consensus       442 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (1163)
T COG1196         442 EELNEELEELEEQLEELRDRLKELERELAELQEELQRLEK  481 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555566666666666666666666554444443

>PF10205 KLRAQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019343 This entry represents a N-terminal 100 residues long domain, which contains a conserved KLRAQ motif

Probab=90.58  E-value=4.9  Score=33.34  Aligned_cols=61  Identities=30%  Similarity=0.350  Sum_probs=31.1

Q ss_pred             hHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           48 LESEHSALRSQLA-EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        48 LE~E~~~LR~~L~-EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      |=.|-.+||.+.. =|..+| +=|.+...|...|.    ...+..-++..|+++|.-.=..|.+-|+
T Consensus         3 la~eYsKLraQ~~vLKKaVi-eEQ~k~~~L~e~Lk----~ke~~LRk~eqE~dSL~FrN~QL~kRV~   64 (102)
T PF10205_consen    3 LAQEYSKLRAQNQVLKKAVI-EEQAKNAELKEQLK----EKEQALRKLEQENDSLTFRNQQLTKRVE   64 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456666666666 333333 33455565655554    4444444555555555444444444443

This domain is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain a C-terminal TTKRSYEDQ motif domain (IPR019348 from INTERPRO). The function of these proteins is not known.

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=90.43  E-value=3.8  Score=37.40  Aligned_cols=64  Identities=17%  Similarity=0.248  Sum_probs=37.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      ..|+.|++.||.-+.+=++....|..+...+|.+-+   +++....++|.+|..|.+-|....+-|+
T Consensus        63 K~l~eEledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL~  129 (193)
T PF14662_consen   63 KALEEELEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKELA  129 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHH
Confidence            345566666666666656666666666666666555   5555556666666666655555555553

>KOG4398 consensus Predicted coiled-coil protein [General function prediction only]

Probab=90.40  E-value=1.8  Score=42.03  Aligned_cols=84  Identities=19%  Similarity=0.243  Sum_probs=62.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH----HHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV----SKL  115 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv----aKL  115 (272)
                      ..+.|+.+||.-|..=   -.|....++.|.+..+.++.-+ .|+..-.|+.+||+.-|.-|-+-|+|+.-||    .||
T Consensus         2 ~~k~~~~~~~~~i~k~---nee~~~~~~~~~k~~e~~qkl~-sr~~~~~ekke~i~r~n~k~~d~v~~~~~~~~~~~erl   77 (359)
T KOG4398|consen    2 SCKMRIEQLKQTICKG---NEEMEKNSEGLLKTKEKNQKLY-SRAQRHQEKKEKIQRHNRKLGDLVEKKTIDLRSHYERL   77 (359)
T ss_pred             chhHHHHHHHHHHhcC---cHHHHHhHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhhhhcchHHHHHHHHHHHHHHHH
Confidence            3566776666655543   3355566667766666555433 6888999999999999999999999988774    799


Q ss_pred             HHHHHHHHhhcc
Q 024140          116 EVFRKTLVQSLK  127 (272)
Q Consensus       116 E~FKk~LmqSLq  127 (272)
                      ++++++-++-|-
T Consensus        78 ~~lr~shi~el~   89 (359)
T KOG4398|consen   78 ANLRRSHILELT   89 (359)
T ss_pred             HHHHHHHHHHHH
Confidence            999999877653

>PF05911 DUF869: Plant protein of unknown function (DUF869); InterPro: IPR008587 This family consists of a number of sequences found in plants

Probab=90.37  E-value=2.9  Score=44.76  Aligned_cols=60  Identities=28%  Similarity=0.387  Sum_probs=44.1

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEAL  101 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~L  101 (272)
                      ..++..+.+|...|...|.+|++.|.+|.+.-+..|..+.   .||..+.-+|.-|.=|--.|
T Consensus        98 ~~~l~~~~~e~~~l~~~l~~~~~~i~~l~~~~~~~e~~~~~l~~~l~~~eken~~Lkye~~~~  160 (769)
T PF05911_consen   98 SKRLAESAAENSALSKALQEKEKLIAELSEEKSQAEAEIEDLMARLESTEKENSSLKYELHVL  160 (769)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455566667777788889999999999999999998776   66666666666555544444

The function of this family is unknown.

>PF09730 BicD: Microtubule-associated protein Bicaudal-D; InterPro: IPR018477 BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER) []

Probab=90.36  E-value=3.9  Score=43.54  Aligned_cols=91  Identities=20%  Similarity=0.275  Sum_probs=61.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHH----------HHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQI-------ESIYSSLS----------DKLGQAQADKERLSKENEALT  102 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~-------s~le~~l~----------~rL~~a~ee~~kL~~E~~~La  102 (272)
                      .|..||..||.|+..+|..+......+..|...+       ..+|.+..          -|=...++|...|.+||=+|.
T Consensus        31 ~~~~~i~~l~~elk~~~~~~~~~~~e~~rl~~~~~~~~~~~~~~e~~~~~lr~e~ke~K~rE~rll~dyselEeENislQ  110 (717)
T PF09730_consen   31 YLQQRILELENELKQLRQELSNVQAENERLSQLNQELRKECEDLELERKRLREEIKEYKFREARLLQDYSELEEENISLQ  110 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            5788999999999999999886555554443333       33333322          222344677788999999999


Q ss_pred             HHHHHHhhhHHHHHHHHHHHHhhcccccc
Q 024140          103 NTVRKLQRDVSKLEVFRKTLVQSLKDDED  131 (272)
Q Consensus       103 ~TvKkL~rDvaKLE~FKk~LmqSLq~d~~  131 (272)
                      .+|-.|...=--+|.|| +=+..|.||.+
T Consensus       111 Kqvs~Lk~sQvefE~~K-hei~rl~Ee~~  138 (717)
T PF09730_consen  111 KQVSVLKQSQVEFEGLK-HEIKRLEEEIE  138 (717)
T ss_pred             HHHHHHHHhHHHHHHHH-HHHHHHHHHHH
Confidence            88888877777777774 33455555543

Glycogen synthase kinase-3beta (GSK-3beta) is required for the binding of BICD to dynein but not to dynactin, acting to maintain the anchoring of microtubules to the centromere []. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells [].; GO: 0006810 transport, 0005794 Golgi apparatus

>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

Probab=90.31  E-value=2.2  Score=40.34  Aligned_cols=76  Identities=18%  Similarity=0.222  Sum_probs=50.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFR  119 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FK  119 (272)
                      -++.+...+-.|-..|+..|.+++....++|+|+..|+.+..    +..++..+|-.|-..|......|.-.|.-+|.|.
T Consensus       139 e~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s----~LeE~~~~l~~ev~~L~~r~~ELe~~~El~e~~~  214 (290)
T COG4026         139 ELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENS----RLEEMLKKLPGEVYDLKKRWDELEPGVELPEEEL  214 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHhchhHHHHHHHHHHHhcccccchHHHH
Confidence            456667777777888888888888888888888777777665    4445555555555555555555555555555553

>TIGR00606 rad50 rad50

Probab=90.27  E-value=3.2  Score=46.05  Aligned_cols=76  Identities=4%  Similarity=0.220  Sum_probs=37.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           40 AISTRVSDLESEHSALRSQLAEK--DSRIAELQSQIESIYSSLS--------DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EK--d~~i~~Lq~r~s~le~~l~--------~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      ++...+..++.+...|+..|.-+  ...+.+++.++..|+.++.        .-+....++.+.|..++..|..++++|.
T Consensus      1002 ~l~kel~~~~~~kr~l~dnL~~~~~~~~l~el~~eI~~l~~~~~~~~~~~~~~e~~~l~~~~~~l~~~~a~l~g~~k~le 1081 (1311)
T TIGR00606      1002 LMRQDIDTQKIQERWLQDNLTLRKRENELKEVEEELKQHLKEMGQMQVLQMKQEHQKLEENIDLIKRNHVLALGRQKGYE 1081 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444445555444  5555556666666665554        2233344444445444444445555555


Q ss_pred             hhHHHH
Q 024140          110 RDVSKL  115 (272)
Q Consensus       110 rDvaKL  115 (272)
                      .+|+.|
T Consensus      1082 ~qi~~l 1087 (1311)
T TIGR00606      1082 KEIKHF 1087 (1311)
T ss_pred             HHHHHH
Confidence            544443

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

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=90.24  E-value=4.5  Score=44.47  Aligned_cols=24  Identities=29%  Similarity=0.509  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           92 ERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      .+|.++-+.|...+.++..++.++
T Consensus       887 ~~l~~~l~~~~~~~~~~~~~~~~~  910 (1163)
T COG1196         887 EELEEELRELESELAELKEEIEKL  910 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333

>PF09798 LCD1: DNA damage checkpoint protein; InterPro: IPR018622 This is a family of proteins which regulate checkpoint kinases

Probab=90.17  E-value=1.4  Score=46.42  Aligned_cols=56  Identities=29%  Similarity=0.477  Sum_probs=42.9

Q ss_pred             HHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024140           55 LRSQLA----EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQR  110 (272)
Q Consensus        55 LR~~L~----EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~r  110 (272)
                      ||+||.    ||++++..+.+++..+.......|.....+.++|++||.-|.+-+|.+..
T Consensus         2 LRdkL~~Lq~ek~~E~~~l~~~~~~lk~~~~~el~~Lk~~vqkLEDEKKFL~nE~r~~s~   61 (654)
T PF09798_consen    2 LRDKLELLQQEKQKERQALKSSVEELKESHEEELNKLKSEVQKLEDEKKFLNNELRSLSS   61 (654)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            455554    88888888888888888777666777777778888888888887777654

In Schizosaccharomyces pombe (Fission yeast) this protein is called Rad26 and in Saccharomyces cerevisiae (Baker's yeast) it is called LCD1 [].

>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family

Probab=90.06  E-value=16  Score=34.03  Aligned_cols=42  Identities=21%  Similarity=0.380  Sum_probs=22.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      .+..+...+++++..|+.++..-...|..++.++..++.++.
T Consensus       134 ~~~~~~~~~~~~~~~l~~~i~~~~~~i~~~~~~l~~~~~~l~  175 (423)
T TIGR01843       134 LFESRKSTLRAQLELILAQIKQLEAELAGLQAQLQALRQQLE  175 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555555555555555555555554

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.

>PF10205 KLRAQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019343 This entry represents a N-terminal 100 residues long domain, which contains a conserved KLRAQ motif

Probab=90.03  E-value=4.9  Score=33.36  Aligned_cols=74  Identities=23%  Similarity=0.372  Sum_probs=63.4

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      ||+=-++|-+.+.-||.-+-|=.....+|++.+-.-|.+|.    ...+|+.-|.=.|+.|...|-.|+-++...+..
T Consensus         3 la~eYsKLraQ~~vLKKaVieEQ~k~~~L~e~Lk~ke~~LR----k~eqE~dSL~FrN~QL~kRV~~LQ~El~~~~~~   76 (102)
T PF10205_consen    3 LAQEYSKLRAQNQVLKKAVIEEQAKNAELKEQLKEKEQALR----KLEQENDSLTFRNQQLTKRVEVLQEELEESEQK   76 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            34556788889999999999888889999999999998776    899999999999999999999999998855443

This domain is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain a C-terminal TTKRSYEDQ motif domain (IPR019348 from INTERPRO). The function of these proteins is not known.

>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]

Probab=89.96  E-value=1.7  Score=40.16  Aligned_cols=71  Identities=24%  Similarity=0.392  Sum_probs=44.5

Q ss_pred             HHHhhhhhHH------HHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           41 ISTRVSDLES------EHSALRSQLAE---KDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        41 ~atRVs~LE~------E~~~LR~~L~E---Kd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      +-.+...+++      +...||.++..   ..+.+..+.+....|+.+++    ....+.+++++.+++|..++..++++
T Consensus       119 ll~~l~~l~~~~~~~~~~~~lk~~~~~~~~~~~~~~~~~~~~~kL~~el~----~~~~~Le~~~~~~~al~Kq~e~~~~E  194 (216)
T KOG1962|consen  119 LLRELATLRANEKAMKENEALKKQLENSSKLEEENDKLKADLEKLETELE----KKQKKLEKAQKKVDALKKQSEGLQDE  194 (216)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHhhhcccchhhhHHHHHhhHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHcccH
Confidence            4445555555      66666666653   23445555555555555544    66666677777777777788887777


Q ss_pred             HHHH
Q 024140          112 VSKL  115 (272)
Q Consensus       112 vaKL  115 (272)
                      .++|
T Consensus       195 ydrL  198 (216)
T KOG1962|consen  195 YDRL  198 (216)
T ss_pred             HHHH
Confidence            7776

>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S

Probab=89.92  E-value=4.5  Score=32.07  Aligned_cols=52  Identities=19%  Similarity=0.271  Sum_probs=39.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (272)
Q Consensus        48 LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~  103 (272)
                      |=.+-..|+.+|.+|+++|..|..-+.+|...|+    .-.+-+.+|+.+...+..
T Consensus         3 Li~qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLi----KYt~LnkkLq~~~~~~~~   54 (76)
T PF11544_consen    3 LIKQNKELKKKLNDKQEEIDRLNILVGSLRGKLI----KYTELNKKLQDQLLNLQR   54 (76)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHh
Confidence            4456789999999999999988877777776555    677777777777776654

cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=89.88  E-value=2.7  Score=32.15  Aligned_cols=55  Identities=24%  Similarity=0.415  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH----HHHHHH
Q 024140           63 DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL----EVFRKT  121 (272)
Q Consensus        63 d~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL----E~FKk~  121 (272)
                      +..|..|+.++..+++.+.    ....++..|..||+..+..+-....+..+|    |++|+.
T Consensus         4 ea~~~~Lr~rLd~~~rk~~----~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~e   62 (69)
T PF14197_consen    4 EAEIATLRNRLDSLTRKNS----VHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKE   62 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5678899999998887776    778889999999999888888777776665    445554

>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

Probab=89.82  E-value=5.3  Score=40.22  Aligned_cols=61  Identities=16%  Similarity=0.310  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           51 EHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        51 E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ++...+.+++++...|.+-+++...|+.+|.    ..+.++.++..+....++++++++++++-+
T Consensus        39 ~l~q~q~ei~~~~~~i~~~~~~~~kL~~~lk----~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~   99 (420)
T COG4942          39 QLKQIQKEIAALEKKIREQQDQRAKLEKQLK----SLETEIASLEAQLIETADDLKKLRKQIADL   99 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhHHHHHHhhHHHH
Confidence            3444455555555555555555555554443    444444444444444444444444444433

>KOG1103 consensus Predicted coiled-coil protein [Function unknown]

Probab=89.62  E-value=11  Score=38.08  Aligned_cols=76  Identities=22%  Similarity=0.311  Sum_probs=47.9

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH---
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKL---  115 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL---  115 (272)
                      .+|++++|.|+..-|..-..-+.   ..++.++.++-+.-   ++|..-...+.-|.+|+.+|-.+||.|..|...|   
T Consensus       219 ksr~~k~eee~aaERerglqtea---qvek~i~EfdiEre~LRAel~ree~r~K~lKeEmeSLkeiVkdlEA~hQh~~pN  295 (561)
T KOG1103|consen  219 KSRTKKGEEEAAAERERGLQTEA---QVEKLIEEFDIEREFLRAELEREEKRQKMLKEEMESLKEIVKDLEADHQHLRPN  295 (561)
T ss_pred             ccccCCChHHHHHHHhhccchHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhcCcc
Confidence            36777787777665553332222   22233333332221   5555666677778899999999999999998876   


Q ss_pred             HHHHH
Q 024140          116 EVFRK  120 (272)
Q Consensus       116 E~FKk  120 (272)
                      |.+|+
T Consensus       296 eqLk~  300 (561)
T KOG1103|consen  296 EQLKG  300 (561)
T ss_pred             ccccC
Confidence            45665

>PRK12704 phosphodiesterase; Provisional

Probab=89.60  E-value=11  Score=38.56  Aligned_cols=13  Identities=8%  Similarity=0.388  Sum_probs=7.5

Q ss_pred             HHHHHHHhhcccc
Q 024140          117 VFRKTLVQSLKDD  129 (272)
Q Consensus       117 ~FKk~LmqSLq~d  129 (272)
                      ..|+.||..+.++
T Consensus       154 ea~~~l~~~~~~~  166 (520)
T PRK12704        154 EAKEILLEKVEEE  166 (520)
T ss_pred             HHHHHHHHHHHHH
Confidence            3466666666554

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=89.45  E-value=8.2  Score=42.30  Aligned_cols=42  Identities=29%  Similarity=0.460  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH-----------HHHHHHHHHhh
Q 024140           84 LGQAQADKERLSKENEALTNTVRKLQRDVSK-----------LEVFRKTLVQS  125 (272)
Q Consensus        84 L~~a~ee~~kL~~E~~~La~TvKkL~rDvaK-----------LE~FKk~LmqS  125 (272)
                      |..+.+.+.++.++|.+|..+|.++.|....           ||.||+.|...
T Consensus       454 le~~~~s~~~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~l  506 (980)
T KOG0980|consen  454 LESAEQSIDDVEEENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELALL  506 (980)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            3344555566677777777777766665443           55666655443

>PRK02119 hypothetical protein; Provisional

Probab=89.45  E-value=2.4  Score=32.62  Aligned_cols=15  Identities=13%  Similarity=0.284  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHHHH
Q 024140           66 IAELQSQIESIYSSL   80 (272)
Q Consensus        66 i~~Lq~r~s~le~~l   80 (272)
                      +..+++|+..||..+
T Consensus         4 ~~~~e~Ri~~LE~rl   18 (73)
T PRK02119          4 QQNLENRIAELEMKI   18 (73)
T ss_pred             hHHHHHHHHHHHHHH
Confidence            344555555555443

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

Probab=89.42  E-value=4.4  Score=41.86  Aligned_cols=63  Identities=24%  Similarity=0.429  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 024140           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (272)
Q Consensus        50 ~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (272)
                      .-+.+|+..+.+|+.+|..|+++...|-.++.      .....-.+|.++|.+|.+-.--..-+|.+.|
T Consensus       330 g~l~kl~~eie~kEeei~~L~~~~d~L~~q~~kq~Is~e~fe~mn~Ere~L~reL~~i~~~~~~L~k~V  398 (622)
T COG5185         330 GKLEKLKSEIELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLTKSV  398 (622)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHH
Confidence            34778888889999999999999999988887      5666677777788877776666666666554

>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma

Probab=89.30  E-value=6.1  Score=35.19  Aligned_cols=34  Identities=29%  Similarity=0.494  Sum_probs=30.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQI   73 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~   73 (272)
                      .|..-+.++|.||..||+-|+-|.++.++|+.|+
T Consensus        33 eLr~EL~KvEeEI~TLrqvL~aKer~~~eLKrkL   66 (162)
T PF04201_consen   33 ELRSELAKVEEEIQTLRQVLAAKERHCAELKRKL   66 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            3555678899999999999999999999999885

Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=89.25  E-value=12  Score=38.22  Aligned_cols=12  Identities=8%  Similarity=0.476  Sum_probs=7.2

Q ss_pred             HHHHHHhhcccc
Q 024140          118 FRKTLVQSLKDD  129 (272)
Q Consensus       118 FKk~LmqSLq~d  129 (272)
                      .|..||..+.++
T Consensus       149 ak~~l~~~~~~~  160 (514)
T TIGR03319       149 AKEILLEEVEEE  160 (514)
T ss_pred             HHHHHHHHHHHH
Confidence            466666666554

>TIGR00606 rad50 rad50

Probab=89.14  E-value=7.6  Score=43.25  Aligned_cols=43  Identities=12%  Similarity=0.184  Sum_probs=28.0

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ..|..++..|..++..++..+.+.+..|..|+.++..++..+.
T Consensus       884 ~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  926 (1311)
T TIGR00606       884 QQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQEKE  926 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            4455566666666666666666666666666666666666664

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

>PF14362 DUF4407: Domain of unknown function (DUF4407)

Probab=89.13  E-value=18  Score=33.36  Aligned_cols=83  Identities=14%  Similarity=0.257  Sum_probs=44.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-----------HHHHHHHHHHHHHHHHHHHHHH----HHHH
Q 024140           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----D-----------KLGQAQADKERLSKENEALTNT----VRKL  108 (272)
Q Consensus        48 LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----~-----------rL~~a~ee~~kL~~E~~~La~T----vKkL  108 (272)
                      +..++..+..+++..+..+.++++++..+...++    +           +-+.+.+....++.|.+.|.++    +..|
T Consensus       133 ~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~E~~g~~~tg~~G~Gp~~~~~~~~~~~~~~~l~~l~~~~~~~~~~l  212 (301)
T PF14362_consen  133 FDAQIARLDAEIAALQAEIDQLEKEIDRAQQEAQCEIFGTGGTGVPGKGPRYKEKRAQLDAAQAELDTLQAQIDAAIAAL  212 (301)
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            3445666666666666666666666666665555    1           2344444444444444444444    4444


Q ss_pred             h----hhHHHHHHHHHHHHhhccccc
Q 024140          109 Q----RDVSKLEVFRKTLVQSLKDDE  130 (272)
Q Consensus       109 ~----rDvaKLE~FKk~LmqSLq~d~  130 (272)
                      +    ...+.|...++......+.++
T Consensus       213 ~~~~~~~~~~l~~~~~~~~a~~~~~~  238 (301)
T PF14362_consen  213 DAQIAARKARLDEARQAKVAEFQAII  238 (301)
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHhHhh
Confidence            4    555566666666555544443

>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes []

Probab=89.13  E-value=2.1  Score=32.26  Aligned_cols=48  Identities=15%  Similarity=0.374  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           67 AELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        67 ~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      .++++|+..+|..    +....++..+|..-...+...++.++.++.+|+.=
T Consensus         2 ~~i~e~l~~ie~~----l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~n   49 (71)
T PF10779_consen    2 QDIKEKLNRIETK----LDNHEERIDKLEKRDAANEKDIKNLNKQLEKIKSN   49 (71)
T ss_pred             HHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555533    33555556666666666666677788888777653

>PF15070 GOLGA2L5: Putative golgin subfamily A member 2-like protein 5

Probab=89.13  E-value=4.8  Score=42.02  Aligned_cols=75  Identities=25%  Similarity=0.390  Sum_probs=45.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKD----------------SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd----------------~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~  103 (272)
                      ....||..||..+..|+.++++..                +.+..|++++..|+..|+    .-..++..|..-+.....
T Consensus        47 ~~~~~V~eLE~sL~eLk~q~~~~~~~~~pa~pse~E~~Lq~E~~~L~kElE~L~~qlq----aqv~~ne~Ls~L~~EqEe  122 (617)
T PF15070_consen   47 HDISRVQELERSLSELKNQMAEPPPPEPPAGPSEVEQQLQAEAEHLRKELESLEEQLQ----AQVENNEQLSRLNQEQEE  122 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHhhcccCCccccccchHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Confidence            466889999999999998887332                233456666666665554    444455555544444444


Q ss_pred             HHHHHhhhHHHHHHH
Q 024140          104 TVRKLQRDVSKLEVF  118 (272)
Q Consensus       104 TvKkL~rDvaKLE~F  118 (272)
                      .+..|.+.|..++..
T Consensus       123 rL~ELE~~le~~~e~  137 (617)
T PF15070_consen  123 RLAELEEELERLQEQ  137 (617)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            555555555554443

>KOG4674 consensus Uncharacterized conserved coiled-coil protein [Function unknown]

Probab=89.10  E-value=3  Score=48.45  Aligned_cols=47  Identities=30%  Similarity=0.497  Sum_probs=35.6

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKE   92 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~   92 (272)
                      .+|.+||++|+..|.+|+++|++|..++..+...++.+|.....++.
T Consensus      1310 ~kL~~ei~~Lk~el~~ke~~~~el~~~~~~~q~~~k~qld~l~~e~~ 1356 (1822)
T KOG4674|consen 1310 EKLKSEISRLKEELEEKENLIAELKKELNRLQEKIKKQLDELNNEKA 1356 (1822)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677899999999999999999999998888655544444443333

>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins

Probab=89.10  E-value=2  Score=34.87  Aligned_cols=59  Identities=19%  Similarity=0.365  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           51 EHSALRSQLAEKDSRIAELQSQIESI--YSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        51 E~~~LR~~L~EKd~~i~~Lq~r~s~l--e~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      ++..|.+.+.+.++.+..|+.++..|  ...+.    ...-+..++..+-+.|..+++-++|.+.
T Consensus        36 ~~~~l~~~~~~~~~Rl~~lE~~l~~LPt~~dv~----~L~l~l~el~G~~~~l~~~l~~v~~~~~   96 (106)
T PF10805_consen   36 DIEKLEERLDEHDRRLQALETKLEHLPTRDDVH----DLQLELAELRGELKELSARLQGVSHQLD   96 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHH----HHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            44445544444444444444443333  22222    3333444444444555555555544444

The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=88.98  E-value=7.5  Score=37.30  Aligned_cols=86  Identities=17%  Similarity=0.185  Sum_probs=48.5

Q ss_pred             hhhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           44 RVSDLESEHSALRSQLA-EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~-EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      +|-.|+.++..|+.++. |....+..++..+..+...+. .|....++..+-..+-.........|.||+.--+..=..|
T Consensus       283 ~v~~l~~~i~~l~~~l~~e~~~~~~~~~~~~~~~~~~~~-~l~~~l~~~~~~~~~l~~~~~~~~~L~r~~~~~~~~y~~l  361 (444)
T TIGR03017       283 QYKRAQAEINSLKSQLNAEIKKVTSSVGTNSRILKQREA-ELREALENQKAKVLELNRQRDEMSVLQRDVENAQRAYDAA  361 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46677777888888776 334444444444443333332 2222222222112223333456778899998888888888


Q ss_pred             Hhhccccc
Q 024140          123 VQSLKDDE  130 (272)
Q Consensus       123 mqSLq~d~  130 (272)
                      ++.+++-.
T Consensus       362 l~r~~e~~  369 (444)
T TIGR03017       362 MQRYTQTR  369 (444)
T ss_pred             HHHHHHHH
Confidence            88876654

Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.

>PF10174 Cast: RIM-binding protein of the cytomatrix active zone; InterPro: IPR019323 This entry represents a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion []

Probab=88.92  E-value=6.8  Score=42.11  Aligned_cols=71  Identities=32%  Similarity=0.392  Sum_probs=39.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      |.-.+-..|-+++..||..|.+|...+...+.++..++.++.          +.+.....+...|++..++|..+++.=.
T Consensus       333 ~ke~~~~~Lqsdve~Lr~rle~k~~~l~kk~~~~~~~qeE~~~~~~Ei~~l~d~~d~~e~ki~~Lq~kie~Lee~l~ekd  412 (775)
T PF10174_consen  333 AKEQEAEMLQSDVEALRFRLEEKNSQLEKKQAQIEKLQEEKSRLQGEIEDLRDMLDKKERKINVLQKKIENLEEQLREKD  412 (775)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334445556666666666666666666665555555555543          3444444455555555555555554433


Q ss_pred             h
Q 024140          110 R  110 (272)
Q Consensus       110 r  110 (272)
                      +
T Consensus       413 ~  413 (775)
T PF10174_consen  413 R  413 (775)
T ss_pred             H
Confidence            3

Located at the C terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [].

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=88.89  E-value=3.4  Score=36.84  Aligned_cols=21  Identities=43%  Similarity=0.615  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHhhhHHHH
Q 024140           95 SKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        95 ~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ...|+.|.+-+.||..|+.+|
T Consensus        94 ~~~N~~L~~dl~klt~~~~~l  114 (182)
T PF15035_consen   94 RKANEALQEDLQKLTQDWERL  114 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            455555666666666666553

>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily

Probab=88.80  E-value=6  Score=38.71  Aligned_cols=87  Identities=17%  Similarity=0.203  Sum_probs=53.8

Q ss_pred             HhhhhhHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH---HHH
Q 024140           43 TRVSDLESEHSALRSQLAEK--------------DSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENE---ALT  102 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EK--------------d~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~---~La  102 (272)
                      -+|-.|..+++.|+.++.+-              +....+|+.++..++.++.   .++....++.+++..+-.   .+.
T Consensus       275 P~v~~l~~qi~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~  354 (498)
T TIGR03007       275 PDVIATKREIAQLEEQKEEEGSAKNGGPERGEIANPVYQQLQIELAEAEAEIASLEARVAELTARIERLESLLRTIPEVE  354 (498)
T ss_pred             hHHHHHHHHHHHHHHHHHhhccccccCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHH
Confidence            35667777788887776542              1123445555555555554   344444444444444433   355


Q ss_pred             HHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140          103 NTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus       103 ~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      .....|+||+.-.+..=..|++.+++-
T Consensus       355 ~el~~L~Re~~~~~~~Y~~l~~r~eea  381 (498)
T TIGR03007       355 AELTQLNRDYEVNKSNYEQLLTRRESA  381 (498)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            677789999988888878888877664

Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene.

>PRK09039 hypothetical protein; Validated

Probab=88.70  E-value=15  Score=35.38  Aligned_cols=6  Identities=0%  Similarity=0.174  Sum_probs=2.9

Q ss_pred             cccccc
Q 024140          188 FVLASQ  193 (272)
Q Consensus       188 ~~~t~~  193 (272)
                      +.+..|
T Consensus       265 I~I~GH  270 (343)
T PRK09039        265 LRVDGH  270 (343)
T ss_pred             EEEEEe
Confidence            344555

>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []

Probab=88.67  E-value=2  Score=32.07  Aligned_cols=38  Identities=26%  Similarity=0.474  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           66 IAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRK  107 (272)
Q Consensus        66 i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKk  107 (272)
                      |.+|+.++..++..+.    ....++.+|.++.+.+..+||+
T Consensus         2 i~elEn~~~~~~~~i~----tvk~en~~i~~~ve~i~envk~   39 (55)
T PF05377_consen    2 IDELENELPRIESSIN----TVKKENEEISESVEKIEENVKD   39 (55)
T ss_pred             HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555443    3344444444444444444433

In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].

>KOG4673 consensus Transcription factor TMF, TATA element modulatory factor [Transcription]

Probab=88.60  E-value=3.6  Score=44.17  Aligned_cols=42  Identities=31%  Similarity=0.414  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH
Q 024140           55 LRSQLAEKDSRIAELQSQIESIYSS------LSDKLGQAQADKERLSK   96 (272)
Q Consensus        55 LR~~L~EKd~~i~~Lq~r~s~le~~------l~~rL~~a~ee~~kL~~   96 (272)
                      +|+.|+|||+.|..|...-..|-..      ++-||+....++..|.+
T Consensus       444 ~~DeLaEkdE~I~~lm~EGEkLSK~ql~qs~iIkKLRAk~ke~etl~~  491 (961)
T KOG4673|consen  444 LKDELAEKDEIINQLMAEGEKLSKKQLAQSAIIKKLRAKIKEAETLEE  491 (961)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhhhhHHHH
Confidence            3456777888887777654444221      11455555444444433

>PF11068 YlqD: YlqD protein; InterPro: IPR021297 This bacterial family of proteins has no known function

Probab=88.54  E-value=4.8  Score=34.34  Aligned_cols=63  Identities=22%  Similarity=0.339  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 024140           62 KDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENE-----ALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus        62 Kd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~-----~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      |+..+.+|++++..+|.+|+    +..-+..++.+|..     .+.+--...+.+.++++.+|+.|.+-|+.
T Consensus        18 K~~l~~~l~~~i~~~d~el~----QLefq~kr~~~e~~~~~~~~~~~i~~q~~~e~~~r~e~k~~l~~ql~q   85 (131)
T PF11068_consen   18 KEELLQELQEQIQQLDQELQ----QLEFQGKRMIKEIKKQNAQQIQSIQQQFEQEKQERLEQKNQLLQQLEQ   85 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67777888888888888887    55555555555553     44444466667777777777777665543

; PDB: 4DCI_C.

>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function

Probab=88.52  E-value=5.1  Score=41.70  Aligned_cols=41  Identities=22%  Similarity=0.420  Sum_probs=16.6

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +..++..++.|+..|+..+.+-..++.+.+.....++.++.
T Consensus       340 l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~  380 (594)
T PF05667_consen  340 LESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELK  380 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444333444444444444444443

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=88.45  E-value=7.2  Score=35.03  Aligned_cols=79  Identities=19%  Similarity=0.329  Sum_probs=50.5

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---H---HHHHH-----HHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---D---KLGQA-----QADKERLSKENEALTNTVR  106 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~---rL~~a-----~ee~~kL~~E~~~La~TvK  106 (272)
                      ...+..-+.....||+.||.+|-.....+.+++.++-..+.+|.   +   +|...     +.+..+|+.+-+.+...+.
T Consensus        56 e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r~~~~klk~~~~el~k~~~~l~~L~~L~~dknL~eReeL~~kL~~~~~~l~  135 (194)
T PF15619_consen   56 EAELPQLLQRHNEEVRVLRERLRKSQEQERELERKLKDKDEELLKTKDELKHLKKLSEDKNLAEREELQRKLSQLEQKLQ  135 (194)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchhHHHHHHHHHHHHHHHH
Confidence            45566778888899999999998888888888888888888776   2   22221     1233455555555555444


Q ss_pred             HHhhhHHHHH
Q 024140          107 KLQRDVSKLE  116 (272)
Q Consensus       107 kL~rDvaKLE  116 (272)
                      .-.+.+..|+
T Consensus       136 ~~~~ki~~Le  145 (194)
T PF15619_consen  136 EKEKKIQELE  145 (194)
T ss_pred             HHHHHHHHHH
Confidence            4444444443

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=88.42  E-value=4.9  Score=41.61  Aligned_cols=37  Identities=14%  Similarity=0.339  Sum_probs=16.1

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      +...||.++..|+....++.-.+.+|+.++..|+.++
T Consensus       296 ~l~~l~~~~~~l~~~y~~~hP~v~~l~~qi~~l~~~i  332 (754)
T TIGR01005       296 RQAELRATIADLSTTMLANHPRVVAAKSSLADLDAQI  332 (754)
T ss_pred             HHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444444444444444443

The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.

>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells

Probab=88.40  E-value=11  Score=35.91  Aligned_cols=40  Identities=23%  Similarity=0.307  Sum_probs=24.0

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ..-+..++.|+..|.+.-.+..+++.+|++....++.++.
T Consensus        42 ~~~~~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~   81 (314)
T PF04111_consen   42 EEDIEELEEELEKLEQEEEELLQELEELEKEREELDQELE   81 (314)
T ss_dssp             HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445556666666666666666666666666666666655

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. 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 [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.

>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]

Probab=88.35  E-value=14  Score=37.80  Aligned_cols=85  Identities=29%  Similarity=0.406  Sum_probs=57.1

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHH------------------------HHHHHHHHHHHHHHHHHHHH-------HHHH
Q 024140           37 TSIAISTRVSDLESEHSALRSQLAE------------------------KDSRIAELQSQIESIYSSLS-------DKLG   85 (272)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~L~E------------------------Kd~~i~~Lq~r~s~le~~l~-------~rL~   85 (272)
                      ..+-+-.||.+||.|-+-|-.||.+                        --.||.-|+..|..|-..|.       .+|.
T Consensus       202 lvN~LwKrmdkLe~ekr~Lq~KlDqpvs~p~~prdia~~~~~~gD~a~~~~~hi~~l~~EveRlrt~l~~Aqk~~~ek~~  281 (552)
T KOG2129|consen  202 LVNSLWKRMDKLEQEKRYLQKKLDQPVSTPSLPRDIAKIPDVHGDEAAAEKLHIDKLQAEVERLRTYLSRAQKSYQEKLM  281 (552)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcccCCCchhhhhcCccccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3677888999999999988888742                        12345555555555544444       5555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ  124 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lmq  124 (272)
                      +-.+|.....+||..|   -+||.+.|.|=|++-|+|-.
T Consensus       282 qy~~Ee~~~reen~rl---QrkL~~e~erRealcr~lsE  317 (552)
T KOG2129|consen  282 QYRAEEVDHREENERL---QRKLINELERREALCRMLSE  317 (552)
T ss_pred             HHHHHHhhHHHHHHHH---HHHHHHHHHHHHHHHHHhhh
Confidence            5555555555555554   47899999999999888854

>PRK04406 hypothetical protein; Provisional

Probab=88.34  E-value=3.6  Score=31.93  Aligned_cols=16  Identities=25%  Similarity=0.501  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHHHH
Q 024140           66 IAELQSQIESIYSSLS   81 (272)
Q Consensus        66 i~~Lq~r~s~le~~l~   81 (272)
                      |..|++|+..||..+.
T Consensus         6 ~~~le~Ri~~LE~~lA   21 (75)
T PRK04406          6 IEQLEERINDLECQLA   21 (75)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4456666666665443

>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function

Probab=88.18  E-value=3.4  Score=31.16  Aligned_cols=25  Identities=24%  Similarity=0.409  Sum_probs=8.9

Q ss_pred             HHHHHhhhHHHHHHHHHHHHhhccc
Q 024140          104 TVRKLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus       104 TvKkL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      +|.+.++++.+|+.--+.|..-|.+
T Consensus        26 ~v~~Qq~~I~~L~~~l~~L~~rl~~   50 (69)
T PF04102_consen   26 VVTEQQRQIDRLQRQLRLLRERLRE   50 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHT---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444433444444433

It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.

>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8

Probab=88.13  E-value=2  Score=37.35  Aligned_cols=68  Identities=21%  Similarity=0.312  Sum_probs=35.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAE-LQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~-Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      .+..++..+|.+++.++.+.......... +.+....++.++.    ...++..+..+|.+.|..+++.|+++
T Consensus       122 ~li~~l~~~~~~~~~~~kq~~~~~~~~~~~~~~~~~~~~~ei~----~lk~el~~~~~~~~~LkkQ~~~l~~e  190 (192)
T PF05529_consen  122 SLIKELIKLEEKLEALKKQAESASEAAEKLLKEENKKLSEEIE----KLKKELEKKEKEIEALKKQSEGLQKE  190 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            55556666666666666655433322222 2222233333332    44555555666777777777777664

Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane

>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins

Probab=88.10  E-value=4.9  Score=32.64  Aligned_cols=28  Identities=18%  Similarity=0.273  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      .++..+|..+-..+...++.|+..|.-+
T Consensus        64 ~~dv~~L~l~l~el~G~~~~l~~~l~~v   91 (106)
T PF10805_consen   64 RDDVHDLQLELAELRGELKELSARLQGV   91 (106)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            3444444444444444444444444433

The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=88.10  E-value=8.7  Score=40.56  Aligned_cols=85  Identities=22%  Similarity=0.379  Sum_probs=47.0

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH----HHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS----KLE  116 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva----KLE  116 (272)
                      +-.++..||.-+.+|+....+=++.|.+|++.+..|+..|. +++.-........+|-..+...+.+|++.|.    +.|
T Consensus       420 ~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~-~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~e~~~~ve  498 (652)
T COG2433         420 YEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELE-RFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVE  498 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566666666666666666666666666666666666663 4444444444444555555555555555443    345


Q ss_pred             HHHHHHHhhc
Q 024140          117 VFRKTLVQSL  126 (272)
Q Consensus       117 ~FKk~LmqSL  126 (272)
                      -||+.|-+-.
T Consensus       499 ~L~~~l~~l~  508 (652)
T COG2433         499 ELERKLAELR  508 (652)
T ss_pred             HHHHHHHHHH
Confidence            5555554433

>PF14817 HAUS5: HAUS augmin-like complex subunit 5

Probab=88.07  E-value=8.7  Score=40.41  Aligned_cols=77  Identities=23%  Similarity=0.372  Sum_probs=55.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH-------HHHHHHHHHHHHHHhhhHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERL-------SKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL-------~~E~~~La~TvKkL~rDva  113 (272)
                      |-..|+.||++||..+.+.|..|..++..+..-|.++.   +++.....++.=|       ..+...|..-.++|+..|.
T Consensus        80 ~r~~L~~everLraei~~l~~~I~~~e~e~~~~e~~~~q~~~~~~~~~~k~~LL~Ay~q~c~~~~~~l~e~~~rl~~~~~  159 (632)
T PF14817_consen   80 RRRELEKEVERLRAEIQELDKEIESREREVSRQEASREQMLDKISDSRHKQLLLEAYSQQCEEQRRILREYTKRLQGQVE  159 (632)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66789999999999999999999999999999888887   5555555554333       3455555666666666666


Q ss_pred             HHHHHHH
Q 024140          114 KLEVFRK  120 (272)
Q Consensus       114 KLE~FKk  120 (272)
                      .|+...|
T Consensus       160 ~~q~~~R  166 (632)
T PF14817_consen  160 QLQDIQR  166 (632)
T ss_pred             HHHHHHh
Confidence            6555443

>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs

Probab=88.05  E-value=4.5  Score=42.87  Aligned_cols=51  Identities=20%  Similarity=0.347  Sum_probs=27.4

Q ss_pred             HHHHHHH-HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Q 024140           53 SALRSQL-AEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTN  103 (272)
Q Consensus        53 ~~LR~~L-~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~  103 (272)
                      ..||.+- ..-+..-.+|++|+..|..+..   .+|.++.++..+|+..-..|+.
T Consensus       546 ~vlreeYi~~~~~ar~ei~~rv~~Lk~~~e~Ql~~L~~l~e~~~~l~~~ae~Lae  600 (717)
T PF10168_consen  546 KVLREEYIEKQDLAREEIQRRVKLLKQQKEQQLKELQELQEERKSLRESAEKLAE  600 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5566663 3344446777888777776665   3444444444444433333333

It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].

>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure

Probab=88.03  E-value=8.2  Score=29.17  Aligned_cols=56  Identities=30%  Similarity=0.395  Sum_probs=36.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      +.||+||+.       |...-.+|. ++-.....+..||..+...|..|..|.+.|...+..|.
T Consensus         4 saL~~Eira-------kQ~~~eEL~-kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r   59 (61)
T PF08826_consen    4 SALEAEIRA-------KQAIQEELT-KVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEELR   59 (61)
T ss_dssp             HHHHHHHHH-------HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHH-------HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            457777653       444444553 34444444448888999888888888777777766654

It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.

>KOG0288 consensus WD40 repeat protein TipD [General function prediction only]

Probab=87.98  E-value=9.1  Score=38.86  Aligned_cols=36  Identities=22%  Similarity=0.311  Sum_probs=24.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      -.|++|.+.++.++.+|+.++.+||+....|-.++.
T Consensus        37 ~~~~a~~~ai~a~~~~~E~~l~~Lq~e~~~l~e~~v   72 (459)
T KOG0288|consen   37 VILRAESRAIKAKLQEKELELNRLQEENTQLNEERV   72 (459)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356777777777777777777777776666655544

>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]

Probab=87.90  E-value=4.1  Score=34.07  Aligned_cols=52  Identities=27%  Similarity=0.379  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHHHhh--------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           30 LDVARKITSIAISTRV--------SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        30 LdlarkIts~A~atRV--------s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ||+||+.=++-+-.|.        .-|+.|+..||..|+-|++.+..+.+++...+.-|.
T Consensus        14 lD~aRq~e~~FlqKr~~LS~~kpe~~lkEEi~eLK~ElqRKe~Ll~Kh~~kI~~w~~lL~   73 (106)
T PF11594_consen   14 LDVARQMEAFFLQKRFELSAYKPEQVLKEEINELKEELQRKEQLLQKHYEKIDYWEKLLS   73 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999988887775        368899999999999999999999999988876654

It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.87  E-value=4.6  Score=38.37  Aligned_cols=28  Identities=29%  Similarity=0.526  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ...+..+.+|++.+-.-+|+|+.+++.|
T Consensus        65 ~~k~~~~~~~i~~~~~eik~l~~eI~~~   92 (265)
T COG3883          65 QSKIDELQKEIDQSKAEIKKLQKEIAEL   92 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334444444444444444444333

>KOG2991 consensus Splicing regulator [RNA processing and modification]

Probab=87.87  E-value=3.2  Score=40.02  Aligned_cols=71  Identities=27%  Similarity=0.367  Sum_probs=55.9

Q ss_pred             HHHHHHHHhhhhhHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           36 ITSIAISTRVSDLESEH-------SALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTV  105 (272)
Q Consensus        36 Its~A~atRVs~LE~E~-------~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~Tv  105 (272)
                      |.-+|--.|+.+||.|+       +.||.+-.|=+.+|.+|-+-|+.....+.   .+|++.++++..|.+++..+...|
T Consensus       229 lG~q~s~Gria~Le~eLAmQKs~seElkssq~eL~dfm~eLdedVEgmqsTiliLQq~Lketr~~Iq~l~k~~~q~sqav  308 (330)
T KOG2991|consen  229 LGHQASEGRIAELEIELAMQKSQSEELKSSQEELYDFMEELDEDVEGMQSTILILQQKLKETRKEIQRLKKGLEQVSQAV  308 (330)
T ss_pred             HHhhhhcccHHHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44567778999999885       57888888888888888888887776655   888888888888888887776665


Q ss_pred             H
Q 024140          106 R  106 (272)
Q Consensus       106 K  106 (272)
                      +
T Consensus       309 ~  309 (330)
T KOG2991|consen  309 G  309 (330)
T ss_pred             c
Confidence            4

>PRK02793 phi X174 lysis protein; Provisional

Probab=87.71  E-value=3.7  Score=31.49  Aligned_cols=10  Identities=20%  Similarity=0.454  Sum_probs=4.5

Q ss_pred             HHHHHHHHHH
Q 024140           69 LQSQIESIYS   78 (272)
Q Consensus        69 Lq~r~s~le~   78 (272)
                      +++|+..||.
T Consensus         6 ~e~Ri~~LE~   15 (72)
T PRK02793          6 LEARLAELES   15 (72)
T ss_pred             HHHHHHHHHH
Confidence            4444444443

>KOG4673 consensus Transcription factor TMF, TATA element modulatory factor [Transcription]

Probab=87.68  E-value=5.1  Score=43.09  Aligned_cols=37  Identities=32%  Similarity=0.401  Sum_probs=27.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      .|..|++|..+|++.|+.|.+.-..+++-|..+.+++
T Consensus       496 ~i~~L~sE~~~lk~il~~Kee~Ek~~~E~I~k~~ae~  532 (961)
T KOG4673|consen  496 LITKLQSEENKLKSILRDKEETEKLLQETIEKHQAEL  532 (961)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence            6889999999999999988876655555555444443

>PF10174 Cast: RIM-binding protein of the cytomatrix active zone; InterPro: IPR019323 This entry represents a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion []

Probab=87.66  E-value=6.8  Score=42.09  Aligned_cols=64  Identities=27%  Similarity=0.390  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHH
Q 024140           33 ARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALT  102 (272)
Q Consensus        33 arkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----------~rL~~a~ee~~kL~~E~~~La  102 (272)
                      +.+....+.+.|+       .+++.+|..|+..|..|+.++..++.+..          .-|..+.++++.|+.+++.|-
T Consensus       277 ~~~s~~~~mK~k~-------d~~~~eL~rk~~E~~~~qt~l~~~~~~~~d~r~hi~~lkesl~~ke~~~~~Lqsdve~Lr  349 (775)
T PF10174_consen  277 VYKSHSLAMKSKM-------DRLKLELSRKKSELEALQTRLETLEEQDSDMRQHIEVLKESLRAKEQEAEMLQSDVEALR  349 (775)
T ss_pred             HHHhhHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            3555566666663       44444444555444444444444444333          222344444455555554443


Q ss_pred             H
Q 024140          103 N  103 (272)
Q Consensus       103 ~  103 (272)
                      .
T Consensus       350 ~  350 (775)
T PF10174_consen  350 F  350 (775)
T ss_pred             H
Confidence            3

Located at the C terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). These proteins also contain four coiled-coil domains [].

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=87.64  E-value=2.3  Score=43.26  Aligned_cols=21  Identities=29%  Similarity=0.289  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 024140           59 LAEKDSRIAELQSQIESIYSS   79 (272)
Q Consensus        59 L~EKd~~i~~Lq~r~s~le~~   79 (272)
                      |+|-.....+||+++..|..+
T Consensus        71 LteqQ~kasELEKqLaaLrqE   91 (475)
T PRK13729         71 TTEMQVTAAQMQKQYEEIRRE   91 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            334444444555554444433

>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]

Probab=87.59  E-value=10  Score=32.80  Aligned_cols=70  Identities=24%  Similarity=0.350  Sum_probs=36.1

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      .+....|+.|+..||..-.+=+......+.||+.||....   ..|..+.++..++.   ..+...|-.|..++..
T Consensus        65 t~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~~E~ek~q~~---e~~~~~ve~L~~ql~~  137 (140)
T PF10473_consen   65 TSELNQLELELDTLRSEKENLDKELQKKQEKVSELESLNSSLENLLQEKEQEKVQLK---EESKSAVEMLQKQLKE  137 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhh
Confidence            4444556666666664333333334445555777776555   44445556544443   3344555555555443

There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding

>PF09755 DUF2046: Uncharacterized conserved protein H4 (DUF2046); InterPro: IPR019152 This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain

Probab=87.51  E-value=20  Score=34.85  Aligned_cols=86  Identities=27%  Similarity=0.436  Sum_probs=53.6

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHHHHHHHH-------HHHHH
Q 024140           37 TSIAISTRVSDLESEHSALRSQLAE-----------------------KDSRIAELQSQIESIYSSLS-------DKLGQ   86 (272)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~L~E-----------------------Kd~~i~~Lq~r~s~le~~l~-------~rL~~   86 (272)
                      .-+=+-.||.+|++|-+.|..+|..                       ...||..|..-|..|-.+|.       .++.+
T Consensus       179 lvN~L~Kqm~~l~~eKr~Lq~~l~~~~s~~~s~~d~~~~~~~~Dt~e~~~shI~~Lr~EV~RLR~qL~~sq~e~~~k~~~  258 (310)
T PF09755_consen  179 LVNRLWKQMDKLEAEKRRLQEKLEQPVSAPPSPRDTVNVSEENDTAERLSSHIRSLRQEVSRLRQQLAASQQEHSEKMAQ  258 (310)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHccccCCCCCcchHHhhcccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444556666666666666666542                       12334444444444433333       56666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Q 024140           87 AQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS  125 (272)
Q Consensus        87 a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS  125 (272)
                      ..++-..+..||..|.   ++|.++|++-|++=|+|--|
T Consensus       259 ~~~eek~ireEN~rLq---r~L~~E~erreal~R~lses  294 (310)
T PF09755_consen  259 YLQEEKEIREENRRLQ---RKLQREVERREALCRHLSES  294 (310)
T ss_pred             HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
Confidence            6666677777777776   57899999999999888543

>TIGR00634 recN DNA repair protein RecN

Probab=87.50  E-value=4  Score=41.26  Aligned_cols=47  Identities=26%  Similarity=0.293  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH-----HHHHHHHHhhcccc
Q 024140           83 KLGQAQADKERLSKENEALTNTVRKLQRDVSKL-----EVFRKTLVQSLKDD  129 (272)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL-----E~FKk~LmqSLq~d  129 (272)
                      .|....++.++|.++.+.+...+.++...+.+.     +.|.+.+..-|++=
T Consensus       340 ~l~~~~~~le~L~~el~~l~~~l~~~a~~Ls~~R~~~a~~l~~~v~~~l~~L  391 (563)
T TIGR00634       340 QLDDSDESLEALEEEVDKLEEELDKAAVALSLIRRKAAERLAKRVEQELKAL  391 (563)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            334444566777778888888888888888777     77777777777653

All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.

>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3

Probab=87.42  E-value=17  Score=33.70  Aligned_cols=54  Identities=17%  Similarity=0.294  Sum_probs=38.3

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHH
Q 024140           28 EQLDVARKITSIAISTRVSDLESEHSALRSQLAEKD-----SRIAELQSQIESIYSSLS   81 (272)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd-----~~i~~Lq~r~s~le~~l~   81 (272)
                      ++|+-...-...++..++...+.++..|...+..+.     +.+...+.++..+...|.
T Consensus       150 ~~l~~~~~~l~~~~~~~l~~~~~~L~~l~~~l~~~~~~~p~~~l~~~~~~Ld~l~~rL~  208 (319)
T PF02601_consen  150 QRLDELRQRLNRAMRNRLQRKRQRLNQLAKRLQLQSRRLPERKLEQQQQRLDELKQRLK  208 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            556666666677788888888888888888777655     456777777766666665

1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity

>PRK04863 mukB cell division protein MukB; Provisional

Probab=87.41  E-value=15  Score=42.20  Aligned_cols=28  Identities=14%  Similarity=0.090  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           91 KERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        91 ~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      ..++..+.+.+...+..++..++.|+.-
T Consensus       399 Laelqqel~elQ~el~q~qq~i~~Le~~  426 (1486)
T PRK04863        399 LADYQQALDVQQTRAIQYQQAVQALERA  426 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444444444

>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization

Probab=87.40  E-value=3.6  Score=30.00  Aligned_cols=20  Identities=30%  Similarity=0.400  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 024140           61 EKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        61 EKd~~i~~Lq~r~s~le~~l   80 (272)
                      -|...|.+|+.++..|+.+.
T Consensus        23 RKk~~~~~Le~~~~~L~~en   42 (64)
T PF00170_consen   23 RKKQYIEELEEKVEELESEN   42 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHHH
Confidence            45666777777766665444

; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....

>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication

Probab=87.35  E-value=5  Score=33.10  Aligned_cols=41  Identities=24%  Similarity=0.440  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024140           66 IAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQR  110 (272)
Q Consensus        66 i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~r  110 (272)
                      |.+|-+.+..|-..+    ....+||+.|.-||..|-..+.++..
T Consensus        17 l~~l~~~~~~LK~~~----~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen   17 LGQLLEELEELKKQL----QELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            333344444444333    37888999999999988888777665

SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.

>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility

Probab=87.30  E-value=5.4  Score=35.43  Aligned_cols=24  Identities=13%  Similarity=0.235  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           94 LSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        94 L~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      ++.++....+.|..|.+.-..|++
T Consensus       161 ~~~~~k~~~~ei~~lk~~~~ql~~  184 (189)
T PF10211_consen  161 RQEEEKKHQEEIDFLKKQNQQLKA  184 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455555555555555543

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 [].

>PF05384 DegS: Sensor protein DegS; InterPro: IPR008595 This is a group of Bacillus DegS proteins

Probab=87.25  E-value=15  Score=32.31  Aligned_cols=79  Identities=19%  Similarity=0.339  Sum_probs=57.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRI-----AELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i-----~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      -+...|-+||......|..|+|=.+..     .++++=|..+.. +|-+|....++-.+|...+|.|...++.|..-|.+
T Consensus        45 ~~I~evD~Le~~er~aR~rL~eVS~~f~~ysE~dik~AYe~A~~-lQ~~L~~~re~E~qLr~rRD~LErrl~~l~~tier  123 (159)
T PF05384_consen   45 EVIEEVDKLEKRERQARQRLAEVSRNFDRYSEEDIKEAYEEAHE-LQVRLAMLREREKQLRERRDELERRLRNLEETIER  123 (159)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456678888888888888888655444     233333333221 22566688888899999999999999999999998


Q ss_pred             HHHHH
Q 024140          115 LEVFR  119 (272)
Q Consensus       115 LE~FK  119 (272)
                      -|.+=
T Consensus       124 AE~l~  128 (159)
T PF05384_consen  124 AENLV  128 (159)
T ss_pred             HHHHH
Confidence            87763

The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon []. The entry also contains one sequence Q8R9D3 from SWISSPROT from Thermoanaerobacter tengcongensis which is described as a sensory transduction histidine kinase.; GO: 0016301 kinase activity, 0007165 signal transduction

>KOG0244 consensus Kinesin-like protein [Cytoskeleton]

Probab=87.20  E-value=3.3  Score=45.18  Aligned_cols=96  Identities=21%  Similarity=0.250  Sum_probs=77.3

Q ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           36 ITSIAISTRVSDLESEHSALRSQLAEKDSRI----AELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        36 Its~A~atRVs~LE~E~~~LR~~L~EKd~~i----~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      +-..-+--+++.||.|..+||..|..-....    .+-..++..||.++ +.|+..+..+.+|.+-+..-..+++||...
T Consensus       509 ~~~~~le~e~~~le~E~~~l~~el~~~~~~~~kl~eer~qklk~le~q~-s~lkk~l~~~~~l~~~~~~~~~~~~kl~~e  587 (913)
T KOG0244|consen  509 SDSGTLEAEKSPLESERSRLRNELNVFNRLAAKLGEERVQKLKSLETQI-SLLKKKLSSQRKLIKPKPKSEGIRAKLLQE  587 (913)
T ss_pred             hhhhhHHHHhcccccccHHHHHHHHhhhHHHHHhhhHHHHHHHHHHHHH-HHHHHhhHHHHHHhccchhhHHHHHHHHHH
Confidence            3345566677788888889998888655533    33345666677766 688889999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccccccC
Q 024140          112 VSKLEVFRKTLVQSLKDDEDA  132 (272)
Q Consensus       112 vaKLE~FKk~LmqSLq~d~~~  132 (272)
                      +-.+|.-|.+||+-..+|.+.
T Consensus       588 i~~~k~~kv~l~~~~~~d~ek  608 (913)
T KOG0244|consen  588 IHIAKGQKVQLLRVMKEDAEK  608 (913)
T ss_pred             HHHHHHHHHHHHHHHhhhHHH
Confidence            999999999999999888764

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation

Probab=87.07  E-value=11  Score=29.05  Aligned_cols=28  Identities=25%  Similarity=0.443  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ..++..|.++|..|...-..|.+...+|
T Consensus        24 q~e~eeLke~n~~L~~e~~~L~~en~~L   51 (72)
T PF06005_consen   24 QMENEELKEKNNELKEENEELKEENEQL   51 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            3333344444333333333333333333

It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.

>PF10158 LOH1CR12: Tumour suppressor protein; InterPro: IPR018780 This entry represents a region of 130 amino acids that is the most conserved part of some hypothetical proteins involved in loss of heterozygosity, and thus, tumour suppression []

Probab=87.04  E-value=8.5  Score=32.80  Aligned_cols=81  Identities=26%  Similarity=0.386  Sum_probs=49.0

Q ss_pred             HHHhcCCCCchhhHHH---------HHHHH--HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           17 EVLQVLPSDPFEQLDV---------ARKIT--SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLG   85 (272)
Q Consensus        17 eil~vLP~DP~EQLdl---------arkIt--s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~   85 (272)
                      |++.-|-..|+-.|-.         |--|+  .++|..|+.+.|.++.++-.++.|+...+...-+.++.++     .|.
T Consensus        19 ~~leklds~~~l~Lc~R~Q~HL~~cA~~Va~~Q~~L~~riKevd~~~~~l~~~~~erqk~~~k~ae~L~kv~-----els   93 (131)
T PF10158_consen   19 EVLEKLDSRPVLRLCSRYQEHLNQCAEAVAFDQNALAKRIKEVDQEIAKLLQQMVERQKRFAKFAEQLEKVN-----ELS   93 (131)
T ss_pred             HHHHccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHH
Confidence            5777777677665432         11222  7888888999999999998888888776665554444332     223


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 024140           86 QAQADKERLSKENEALT  102 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La  102 (272)
                      ..+.++..|.++.-.+.
T Consensus        94 ~~L~~~~~lL~~~v~~i  110 (131)
T PF10158_consen   94 QQLSRCQSLLNQTVPSI  110 (131)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            44444444444433333

The exact function of these proteins is not known.

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=87.03  E-value=8.5  Score=37.73  Aligned_cols=26  Identities=15%  Similarity=0.245  Sum_probs=16.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAEL   69 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~L   69 (272)
                      .+..|+.++..|+.++++....+.++
T Consensus       237 ~~~~~~~~i~~l~~~i~~~~~~~~~~  262 (457)
T TIGR01000       237 ILATIQQQIDQLQKSIASYQVQKAGL  262 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            56666666666666666666666655

This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.

>PF13747 DUF4164: Domain of unknown function (DUF4164)

Probab=86.94  E-value=7.7  Score=30.87  Aligned_cols=25  Identities=28%  Similarity=0.465  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           82 DKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      .+|-.+..++++|..-+..+...++
T Consensus        53 ~eLD~~~ar~~~Le~~~~Evs~rL~   77 (89)
T PF13747_consen   53 QELDQAEARANRLEEANREVSRRLD   77 (89)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            3333555555555555555444444

>PRK00106 hypothetical protein; Provisional

Probab=86.90  E-value=20  Score=37.11  Aligned_cols=14  Identities=7%  Similarity=0.133  Sum_probs=8.4

Q ss_pred             HHHHHHHhhccccc
Q 024140          117 VFRKTLVQSLKDDE  130 (272)
Q Consensus       117 ~FKk~LmqSLq~d~  130 (272)
                      -.|..||..+.++-
T Consensus       169 eak~~l~~~~~~~~  182 (535)
T PRK00106        169 EAREIILAETENKL  182 (535)
T ss_pred             HHHHHHHHHHHHHH
Confidence            35666676666553

>PF13874 Nup54: Nucleoporin complex subunit 54; PDB: 3T97_B

Probab=86.89  E-value=5  Score=33.86  Aligned_cols=33  Identities=30%  Similarity=0.383  Sum_probs=12.8

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQ   70 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq   70 (272)
                      =..+..|+...+.++..++..|.+=...+.+|+
T Consensus        32 F~dL~~R~~~Q~~~~~~~~~~l~~i~~~l~~L~   64 (141)
T PF13874_consen   32 FEDLKKRVEAQEEEIAQHRERLKEINDKLEELQ   64 (141)
T ss_dssp             --------------HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345667777777777777777776666666663

>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast)

Probab=86.63  E-value=5  Score=35.67  Aligned_cols=30  Identities=20%  Similarity=0.366  Sum_probs=16.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAEL   69 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~L   69 (272)
                      +...++.+|+.++..++.++.+-...|.++
T Consensus        66 ~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~   95 (188)
T PF03962_consen   66 KRQNKLEKLQKEIEELEKKIEELEEKIEEA   95 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555555555444

The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].

>KOG0962 consensus DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]

Probab=86.62  E-value=7.2  Score=44.10  Aligned_cols=81  Identities=21%  Similarity=0.350  Sum_probs=55.5

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH----
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS----  113 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva----  113 (272)
                      =+.+..++..+|.|+..|+-|+.+-+  ++..++++..|+..+.    ...-+.+.+..+...+.+.|+++.++|.    
T Consensus      1010 ~~~l~~q~~e~~re~~~ld~Qi~~~~--~~~~~ee~~~L~~~~~----~l~se~~~~lg~~ke~e~~i~~~k~eL~~~~~ 1083 (1294)
T KOG0962|consen 1010 LRNLERKLKELERELSELDKQILEAD--IKSVKEERVKLEEERE----KLSSEKNLLLGEMKQYESQIKKLKQELREKDF 1083 (1294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhH--HHHHHHHHHHHHHHHH----HhhhHhhHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            35566677777777777777776655  5566666666665554    5555667777778888888888888887    


Q ss_pred             --HHHHHHHHHHh
Q 024140          114 --KLEVFRKTLVQ  124 (272)
Q Consensus       114 --KLE~FKk~Lmq  124 (272)
                        ..++|.++++.
T Consensus      1084 kd~~~nyr~~~ie 1096 (1294)
T KOG0962|consen 1084 KDAEKNYRKALIE 1096 (1294)
T ss_pred             ccHHHHHHHHHHH
Confidence              46677666654

>TIGR00634 recN DNA repair protein RecN

Probab=86.55  E-value=2.3  Score=42.97  Aligned_cols=57  Identities=18%  Similarity=0.202  Sum_probs=42.8

Q ss_pred             CchhhHHHHHHHHH-HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           25 DPFEQLDVARKITS-IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        25 DP~EQLdlarkIts-~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +|.+|+++--.+.. ..+..++..+..+...++++|.+......++++++..|+.++.
T Consensus       142 ~~~~~~~lLD~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~~~~~~~eld~L~~ql~  199 (563)
T TIGR00634       142 RPDEQRQLLDTFAGANEKVKAYRELYQAWLKARQQLKDRQQKEQELAQRLDFLQFQLE  199 (563)
T ss_pred             CHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            88899888777764 3577788888888888888887777777777777776666655

All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.51  E-value=8  Score=36.78  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 024140           86 QAQADKERLSKENEALTNTVRK  107 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKk  107 (272)
                      +..++..+|++|.+.|.++++.
T Consensus        77 ~~~~eik~l~~eI~~~~~~I~~   98 (265)
T COG3883          77 QSKAEIKKLQKEIAELKENIVE   98 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444443

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=86.50  E-value=5.2  Score=44.37  Aligned_cols=68  Identities=19%  Similarity=0.352  Sum_probs=52.2

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      ..+++.-+.-||.-|+.||++|.||.....+|+..+..++.++.    ..++++..+..|......-.++|.
T Consensus       172 ~~hL~velAdle~kir~LrqElEEK~enll~lr~eLddleae~~----klrqe~~e~l~ea~ra~~yrdeld  239 (1195)
T KOG4643|consen  172 NLHLEVELADLEKKIRTLRQELEEKFENLLRLRNELDDLEAEIS----KLRQEIEEFLDEAHRADRYRDELD  239 (1195)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhhhhhhhHHH
Confidence            56778888899999999999999999999999999999888775    566666666665554444444333

>KOG4687 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=86.25  E-value=3.3  Score=40.34  Aligned_cols=31  Identities=19%  Similarity=0.295  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           97 ENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        97 E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      |+..|+.-+.+-.++--||-+=+..|++.+.
T Consensus        84 erqdLaa~i~etkeeNlkLrTd~eaL~dq~a  114 (389)
T KOG4687|consen   84 ERQDLAADIEETKEENLKLRTDREALLDQKA  114 (389)
T ss_pred             hhhHHHHHHHHHHHHhHhhhHHHHHHHHHHH
Confidence            4455555555555555555555555554433

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=86.15  E-value=9.7  Score=36.37  Aligned_cols=81  Identities=21%  Similarity=0.286  Sum_probs=52.1

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----hhHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRI---AELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ----RDVSK  114 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i---~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~----rDvaK  114 (272)
                      ..|+.-|--|-.-+|.||-.+-+.-   .--++|.+.+|.++.    ...|||.+|+.||+.|-..-+.|.    .-+..
T Consensus        58 r~RL~HLS~EEK~~RrKLKNRVAAQtaRDrKKaRm~eme~~i~----dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~  133 (292)
T KOG4005|consen   58 RRRLDHLSWEEKVQRRKLKNRVAAQTARDRKKARMEEMEYEIK----DLTEENEILQNENDSLRAINESLLAKNHELDSE  133 (292)
T ss_pred             HHhhcccCHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Confidence            4566666666666666664332111   112345666665554    888899999999999887766663    44677


Q ss_pred             HHHHHHHHHhhc
Q 024140          115 LEVFRKTLVQSL  126 (272)
Q Consensus       115 LE~FKk~LmqSL  126 (272)
                      ||-++..||.+=
T Consensus       134 le~~~~~l~~~~  145 (292)
T KOG4005|consen  134 LELLRQELAELK  145 (292)
T ss_pred             HHHHHHHHHhhH
Confidence            888888887663

>PF04100 Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007234 Vps53 complexes with Vps52 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events []

Probab=86.06  E-value=8.5  Score=37.62  Aligned_cols=43  Identities=19%  Similarity=0.375  Sum_probs=22.6

Q ss_pred             CCCCChhHHHhcCCCCc-hhhHHHHHHHHHHHHHHhhhhhHHHHHHHH
Q 024140           10 STFDLPEEVLQVLPSDP-FEQLDVARKITSIAISTRVSDLESEHSALR   56 (272)
Q Consensus        10 ~dF~lp~eil~vLP~DP-~EQLdlarkIts~A~atRVs~LE~E~~~LR   56 (272)
                      +||+.=+-|=..+|+.- ..+||--+    ..+..++..|+.||..+-
T Consensus         2 ~dfdpv~~in~lfp~e~SL~~ld~~i----~~l~~~i~~ld~eI~~~v   45 (383)
T PF04100_consen    2 PDFDPVDYINELFPDEQSLSNLDELI----AKLRKEIRELDEEIKELV   45 (383)
T ss_pred             CCCCHHHHHHHhCCChHHHHhHHHHH----HHHHHHHHHHHHHHHHHH
Confidence            36777777777777632 13333332    344445555555555433

>PF09486 HrpB7: Bacterial type III secretion protein (HrpB7); InterPro: IPR013392 This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia

Probab=86.03  E-value=11  Score=33.28  Aligned_cols=46  Identities=24%  Similarity=0.255  Sum_probs=40.6

Q ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           36 ITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        36 Its~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +----+.-|+..+|.+...|++.|..|...|...+..|..++..+.
T Consensus        79 ~~r~~l~~~~~~~e~~~a~l~~~l~~~~~~ia~~~raIarn~a~id  124 (158)
T PF09486_consen   79 RYRDVLEERVRAAEAELAALRQALRAAEDEIAATRRAIARNDARID  124 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Confidence            3344567899999999999999999999999999999999998887

>PF06818 Fez1: Fez1; InterPro: IPR009638 This family represents the eukaryotic Fez1 protein

Probab=86.00  E-value=6.9  Score=35.89  Aligned_cols=67  Identities=28%  Similarity=0.395  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        50 ~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      +||-.||.+|.+-...+...+.++..|..++.   .-|.....+......|...|-..|-+|..+++.|.
T Consensus        31 ~Eiv~Lr~ql~e~~~~l~~~~~~~~~l~~~~~~K~~ELE~ce~ELqr~~~Ea~lLrekl~~le~El~~Lr  100 (202)
T PF06818_consen   31 SEIVSLRAQLRELRAELRNKESQIQELQDSLRTKQLELEVCENELQRKKNEAELLREKLGQLEAELAELR  100 (202)
T ss_pred             hHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhHhHHHhHHHHHHHhCHHHHhhhhhhhhHHHHHHHH
Confidence            45555555555555555555555555555554   33446666767777777777777878777777764

Fez1 contains a leucine-zipper region with similarity to the DNA-binding domain of the cAMP-responsive activating-transcription factor 5 []. There is evidence that Fez1 inhibits cancer cell growth through regulation of mitosis, and that its alterations result in abnormal cell growth []. Note that some family members contain more than one copy of this region.; GO: 0005737 cytoplasm, 0016020 membrane

>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures

Probab=85.89  E-value=5.5  Score=30.64  Aligned_cols=35  Identities=34%  Similarity=0.505  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           84 LGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        84 L~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      +.+..++..+|.+..-.+.++||||...+..+|.-
T Consensus        14 Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~   48 (74)
T PF12329_consen   14 IAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQ   48 (74)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            34777888888888888888888888887777643

The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=85.89  E-value=6.5  Score=36.41  Aligned_cols=63  Identities=11%  Similarity=0.169  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        49 E~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      |..+.+|-+.+.-..+.+.+|+.|+..|+.++.    ..+-.++.++-+.+.|...-|.|..||..+
T Consensus        39 ~~r~~~le~~~~~~~~~~~~l~~ql~~lq~ev~----~LrG~~E~~~~~l~~~~~rq~~~y~dld~r  101 (263)
T PRK10803         39 EDRVTQLERISNAHSQLLTQLQQQLSDNQSDID----SLRGQIQENQYQLNQVVERQKQIYLQIDSL  101 (263)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH----HHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444455555566667777776666665    555555666667777777777777777764

>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]

Probab=85.77  E-value=7.1  Score=36.16  Aligned_cols=56  Identities=18%  Similarity=0.370  Sum_probs=31.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTV  105 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~Tv  105 (272)
                      ..+.++...|+.++.+|+.....+++++..|.-+..    ...+|...|.+|++.|.++|
T Consensus       154 ~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e----~~~~EydrLlee~~~Lq~~i  209 (216)
T KOG1962|consen  154 DKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSE----GLQDEYDRLLEEYSKLQEQI  209 (216)
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HcccHHHHHHHHHHHHHHHH
Confidence            444455555555555555555555555555555444    55555555555555555544

>TIGR02559 HrpB7 type III secretion protein HrpB7

Probab=85.74  E-value=13  Score=33.01  Aligned_cols=63  Identities=17%  Similarity=0.254  Sum_probs=52.5

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEA  100 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~------~rL~~a~ee~~kL~~E~~~  100 (272)
                      --.+.-++..+|.++..|++-|..|...|+..+..|..++..+.      ++|..+.|.......|-+.
T Consensus        81 r~vl~~~~~~aE~~~aaa~~al~~~~~~laa~~r~iaRn~a~id~c~eR~~~l~ra~ea~~edA~dEEa  149 (158)
T TIGR02559        81 RDVLEAHLGAAEQAEAAARAALQALAAALAAKKREIARLDAQIDVCRERAERLRRAGEAAREEALEEEA  149 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHH
Confidence            34457789999999999999999999999999999999999988      7777777777666555443

This family of genes is found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)

Probab=85.68  E-value=13  Score=30.84  Aligned_cols=30  Identities=33%  Similarity=0.431  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +..||.++.+-...|.+|+..+..+...|.
T Consensus        61 L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~   90 (132)
T PF07926_consen   61 LQQLREELQELQQEINELKAEAESAKAELE   90 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555544555555544444444443

These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore

>PF08647 BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR013956 BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions []

Probab=85.58  E-value=13  Score=29.58  Aligned_cols=49  Identities=16%  Similarity=0.215  Sum_probs=26.5

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLS   95 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~   95 (272)
                      ..||..+.+|-...+.-|+.+.++......|+.++. +|......+..+.
T Consensus        27 ~~lE~k~~rl~~Ek~kadqkyfa~mr~~d~l~~e~k-~L~~~~~Ks~~~i   75 (96)
T PF08647_consen   27 TILEQKKLRLEAEKAKADQKYFAAMRSKDALDNEMK-KLNTQLSKSSELI   75 (96)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH-HHHHHHHHhHHHH
Confidence            345555555555556566666666666666666654 3334333433333

>PF04849 HAP1_N: HAP1 N-terminal conserved region; InterPro: IPR006933 This family is defined by an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues

Probab=85.58  E-value=18  Score=35.12  Aligned_cols=86  Identities=19%  Similarity=0.333  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHH---HHHHHHHHHHHHHH
Q 024140           30 LDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI-----------YSSLS---DKLGQAQADKERLS   95 (272)
Q Consensus        30 LdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~l-----------e~~l~---~rL~~a~ee~~kL~   95 (272)
                      +.+-..|...++..|+..||.|-..||.....=......++++-..|           -.++.   .=|....+++...+
T Consensus       154 ~~~~~~~~le~Lq~Klk~LEeEN~~LR~Ea~~L~~et~~~EekEqqLv~dcv~QL~~An~qia~LseELa~k~Ee~~rQQ  233 (306)
T PF04849_consen  154 LSSQKCIQLEALQEKLKSLEEENEQLRSEASQLKTETDTYEEKEQQLVLDCVKQLSEANQQIASLSEELARKTEENRRQQ  233 (306)
T ss_pred             cccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHH
Confidence            33445577789999999999999999987664443333333332222           11111   23335555666666


Q ss_pred             HHHHHHHHHHHHHhhhHHHH
Q 024140           96 KENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        96 ~E~~~La~TvKkL~rDvaKL  115 (272)
                      +|...|..+|-.|++.+..+
T Consensus       234 EEIt~LlsqivdlQ~r~k~~  253 (306)
T PF04849_consen  234 EEITSLLSQIVDLQQRCKQL  253 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            66666666666666555444

HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntingtons disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34 [].

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=85.53  E-value=20  Score=35.14  Aligned_cols=39  Identities=18%  Similarity=0.287  Sum_probs=26.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~   78 (272)
                      .+.+|...+++++..+.+++...+..+..++.....++.
T Consensus       162 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  200 (457)
T TIGR01000       162 KSQTQNEAAEKTKAQLDQQISKTDQKLQDYQALKNAISN  200 (457)
T ss_pred             hhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            455667777777777777777777777777666664444

This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.

>PF06120 Phage_HK97_TLTM: Tail length tape measure protein; InterPro: IPR009302 This entry consists of the tail length tape measure protein from Bacteriophage HK97 and related sequences from Escherichia coli (strain K12)

Probab=85.53  E-value=20  Score=34.60  Aligned_cols=75  Identities=19%  Similarity=0.269  Sum_probs=40.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHH----HHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLS--------------DKLG----QAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        48 LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~--------------~rL~----~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      |-+.+++++..|.+-.+.|.+|+++|..|+.++.              ..+.    ...+-..+|.+=.+.|+..-.+|+
T Consensus        72 l~~~~~k~~~si~~q~~~i~~l~~~i~~l~~~i~~y~~~~~~~~~~~~~~~~n~~~~~~~~t~~la~~t~~L~~~~~~l~  151 (301)
T PF06120_consen   72 LRANIAKAEESIAAQKRAIEDLQKKIDSLKDQIKNYQQQLAEKGITENGYIINHLMSQADATRKLAEATRELAVAQERLE  151 (301)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455666666666666666666666666665552              1221    112223344444444666666777


Q ss_pred             hhHHHHHHHHHHH
Q 024140          110 RDVSKLEVFRKTL  122 (272)
Q Consensus       110 rDvaKLE~FKk~L  122 (272)
                      +.+.|+...-++|
T Consensus       152 q~~~k~~~~q~~l  164 (301)
T PF06120_consen  152 QMQSKASETQATL  164 (301)
T ss_pred             HHHHHHHHHHHHH
Confidence            7777666654433

>PRK12705 hypothetical protein; Provisional

Probab=85.48  E-value=13  Score=38.27  Aligned_cols=14  Identities=29%  Similarity=0.389  Sum_probs=10.1

Q ss_pred             HHHHHHhhcccccc
Q 024140          118 FRKTLVQSLKDDED  131 (272)
Q Consensus       118 FKk~LmqSLq~d~~  131 (272)
                      .|+.||..+.++-.
T Consensus       143 ak~~l~~~~~~~~~  156 (508)
T PRK12705        143 ARKLLLKLLDAELE  156 (508)
T ss_pred             HHHHHHHHHHHHHH
Confidence            58888888876643

>PRK00295 hypothetical protein; Provisional

Probab=85.30  E-value=7.4  Score=29.53  Aligned_cols=40  Identities=15%  Similarity=0.070  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           66 IAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        66 i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      |.+||.|++-.|..+.    ...+...+.+++.+.|...++.|.
T Consensus         7 i~~LE~kla~qE~tie----~Ln~~v~~Qq~~I~~L~~ql~~L~   46 (68)
T PRK00295          7 VTELESRQAFQDDTIQ----ALNDVLVEQQRVIERLQLQMAALI   46 (68)
T ss_pred             HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555554444332    444444444445455554444443

>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5

Probab=85.18  E-value=18  Score=29.16  Aligned_cols=42  Identities=29%  Similarity=0.322  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      ...+-..-|.+..+.|...+++|+.++.+|..--.++++-|+
T Consensus        83 ~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~~l~  124 (126)
T TIGR00293        83 DAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQEAQ  124 (126)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345556677788888888999999999888877777766554

This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.

>PF12240 Angiomotin_C: Angiomotin C terminal; InterPro: IPR024646 This domain represents the C-terminal region of angiomotin

Probab=85.14  E-value=30  Score=32.03  Aligned_cols=80  Identities=18%  Similarity=0.298  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--H----------------HHH---------------HHHHHHHHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS--D----------------KLG---------------QAQADKERLSKEN   98 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~--~----------------rL~---------------~a~ee~~kL~~E~   98 (272)
                      +..|+++|.||++.|-.|+.-+...|..+-  .                |..               ..+|+...-....
T Consensus        59 ~~~L~~~LrEkEErILaLEad~~kWEqkYLEEs~mrq~a~dAaa~aa~~rdttiI~~s~~~s~~~s~r~~eel~~a~~K~  138 (205)
T PF12240_consen   59 ASNLKELLREKEERILALEADMTKWEQKYLEESAMRQFAMDAAATAAAQRDTTIINHSPSESYNSSLREEEELHMANRKC  138 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhcCCCCCCCccccchHHHHHhhhhH
Confidence            445788899999999999988888776654  1                111               0122222223344


Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhhcccccc
Q 024140           99 EALTNTVRKLQRDVSKLEVFRKTLVQSLKDDED  131 (272)
Q Consensus        99 ~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d~~  131 (272)
                      -.|.+.||.|+..|..=++.=|.|=|..+.|..
T Consensus       139 qemE~RIK~LhaqI~EKDAmIkVLQqrs~~~~~  171 (205)
T PF12240_consen  139 QEMENRIKALHAQIAEKDAMIKVLQQRSRKDPG  171 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCC
Confidence            567889999999999988888888888777764

Angiomotin regulates the action of angiogenesis-inhibitor angiostatin []. The C-terminal region of angiomotin appears to be involved in directing the protein chemotactically [].

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=85.13  E-value=12  Score=42.11  Aligned_cols=42  Identities=21%  Similarity=0.354  Sum_probs=38.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +=..|+..|+.+|..|+.++++.++.+..|+.++..|+.++.
T Consensus       739 ~R~~ri~el~~~IaeL~~~i~~l~~~l~~l~~r~~~L~~e~~  780 (1353)
T TIGR02680       739 ARLRRIAELDARLAAVDDELAELARELRALGARQRALADELA  780 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345689999999999999999999999999999999998877

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.

>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi

Probab=85.02  E-value=14  Score=27.70  Aligned_cols=61  Identities=21%  Similarity=0.324  Sum_probs=38.9

Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           51 EHSALRSQLA-EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        51 E~~~LR~~L~-EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ++..+..+|. +++..-.+||.-|-.=-..|    -.+-+++.+|.++-..|.+.+..|+..+.+|
T Consensus        23 ~i~~~~~~L~~~i~~~~~eLr~~V~~nY~~f----I~as~~I~~m~~~~~~l~~~l~~l~~~~~~l   84 (87)
T PF08700_consen   23 EIRQLENKLRQEIEEKDEELRKLVYENYRDF----IEASDEISSMENDLSELRNLLSELQQSIQSL   84 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3333333333 33344444554444444444    4888888899999889999998888888776

Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].

>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family

Probab=84.94  E-value=6.9  Score=36.95  Aligned_cols=80  Identities=23%  Similarity=0.313  Sum_probs=44.2

Q ss_pred             HhhhhhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHhhh
Q 024140           43 TRVSDLESEHSALRSQLAE-------KDSRIAELQSQIESIYSSLSDKLGQAQADKERLSK----ENEALTNTVRKLQRD  111 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~E-------Kd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~----E~~~La~TvKkL~rD  111 (272)
                      .-++.|+.++..++.+|++       ..-.+..|+.++..|+.++.       +++.++..    ....+......|.||
T Consensus       214 ~~i~~L~~~l~~~~~~l~~l~~~~~~~~P~v~~l~~~i~~l~~~i~-------~e~~~i~~~~~~~l~~~~~~~~~L~re  286 (362)
T TIGR01010       214 SLISTLEGELIRVQAQLAQLRSITPEQNPQVPSLQARIKSLRKQID-------EQRNQLSGGLGDSLNEQTADYQRLVLQ  286 (362)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCCchHHHHHHHHHHHHHHH-------HHHHHhhcCCCccHHHHHHHHHHHHHH
Confidence            3344555555555444443       33445667777777777665       11122211    234445567788888


Q ss_pred             HHHHHHHHHHHHhhcccc
Q 024140          112 VSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus       112 vaKLE~FKk~LmqSLq~d  129 (272)
                      +.--+..=..+++.+++-
T Consensus       287 ~~~a~~~y~~~l~r~~~a  304 (362)
T TIGR01010       287 NELAQQQLKAALTSLQQT  304 (362)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            877666666666666544

This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.

>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition

Probab=84.84  E-value=2.1  Score=41.53  Aligned_cols=68  Identities=19%  Similarity=0.404  Sum_probs=11.8

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKL  108 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL  108 (272)
                      +..++..|..|+..++....|.-..|..+..+...++..|..|+..+.+++..|.+.-..+.++++.+
T Consensus       103 l~~~~~elkkEie~IKk~q~e~~~~i~~~~~~~~~~~~~l~~Ri~e~Eeris~lEd~~~~i~~~~~~~  170 (370)
T PF02994_consen  103 LKKRIKELKKEIENIKKNQSEMKLEIENLKKKLENIDESLNSRIDELEERISELEDRIEEIEQAIKEL  170 (370)
T ss_dssp             ---------------H-------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhHHHHH
Confidence            45667778888888887666655555555444443333333344444444444444443333333333

Some of these have been shown to exhibit reverse transcriptase (RT) activity [] although the function of many are, as yet, unknown. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 2LDY_A 3SOO_A 2YKQ_A 2YKO_C 2YKP_B 2W7A_B 2JRB_A.

>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]

Probab=84.83  E-value=2.6  Score=39.38  Aligned_cols=86  Identities=22%  Similarity=0.239  Sum_probs=57.2

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYS-SLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~-~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      .++..+-.....++.-...|+....+.++|-+..=+ ...   -+..+...+...|.+||+.|...|..|.+++++|..+
T Consensus       172 ~~~~~~~~K~~~~~~~~~~~~~~y~err~rNN~A~~kSR~~~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~  251 (269)
T KOG3119|consen  172 LKPQSTARKKSKLSSPVEKKDPEYKERRRRNNEAVRKSRDKRKQKEDEMAHRVAELEKENEALRTQVEQLKKELATLRRL  251 (269)
T ss_pred             cCCccchhhhccCCCchhcCCHHHHHHHHhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333444445555667777777666553211 111   3344566677889999999999999999999999999


Q ss_pred             HHHHHhhccc
Q 024140          119 RKTLVQSLKD  128 (272)
Q Consensus       119 Kk~LmqSLq~  128 (272)
                      +.+.++-..+
T Consensus       252 ~~~~~~~~~~  261 (269)
T KOG3119|consen  252 FLQLPKPGGA  261 (269)
T ss_pred             HHhhccccCC
Confidence            8887766443

>PF05622 HOOK: HOOK protein; InterPro: IPR008636 This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms

Probab=84.75  E-value=0.29  Score=50.76  Aligned_cols=41  Identities=20%  Similarity=0.319  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 024140           83 KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLV  123 (272)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lm  123 (272)
                      +++...++|..|.+.+..|...+++.+.--.+|+.+|+++.
T Consensus       333 qvk~Lee~N~~l~e~~~~LEeel~~~~~~~~qle~~k~qi~  373 (713)
T PF05622_consen  333 QVKELEEDNAVLLETKAMLEEELKKARALKSQLEEYKKQIQ  373 (713)
T ss_dssp             -----------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            33344444444555555555555554444445555555443

The different members of the Homo sapiens gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three Homo sapiens HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerisation and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes [], whereas both HOOK1 and HOOK2 are localised to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head [].; GO: 0008017 microtubule binding, 0000226 microtubule cytoskeleton organization, 0005737 cytoplasm; PDB: 1WIX_A.

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=84.71  E-value=10  Score=42.79  Aligned_cols=81  Identities=22%  Similarity=0.261  Sum_probs=46.8

Q ss_pred             cCCCCchhhHHHHHHH-----HHHHHHHhhhhhHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHH
Q 024140           21 VLPSDPFEQLDVARKI-----TSIAISTRVSDLESEHSALRSQL--------------AEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        21 vLP~DP~EQLdlarkI-----ts~A~atRVs~LE~E~~~LR~~L--------------~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      |.+-+|.+==.+.++.     ..+++..++..||..+..||...              ..=...|+.|+.++..+|.++.
T Consensus       772 ~t~~s~~~v~~le~~l~~~~~~~~~~~~~~~~~ee~~~~lr~~~~~l~~~l~~~~~~~k~~~~~~~~l~~~i~~~E~~~~  851 (1293)
T KOG0996|consen  772 VTGVSKESVEKLERALSKMSDKARQHQEQLHELEERVRKLRERIPELENRLEKLTASVKRLAELIEYLESQIAELEAAVL  851 (1293)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            5555555433333332     23444555555555555554433              3334466777777778887765


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHH
Q 024140           82 ------DKLGQAQADKERLSKENEAL  101 (272)
Q Consensus        82 ------~rL~~a~ee~~kL~~E~~~L  101 (272)
                            .+|+...+-+.+|.+|.+.|
T Consensus       852 k~~~d~~~l~~~~~~ie~l~kE~e~~  877 (1293)
T KOG0996|consen  852 KKVVDKKRLKELEEQIEELKKEVEEL  877 (1293)
T ss_pred             hccCcHHHHHHHHHHHHHHHHHHHHH
Confidence                  66776666677777777777

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)

Probab=84.64  E-value=23  Score=29.78  Aligned_cols=41  Identities=15%  Similarity=0.264  Sum_probs=19.0

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~   78 (272)
                      .+.+..|+..||.++...+-.-.|=...-.+|+..+..|..
T Consensus        11 ~~el~n~La~Le~slE~~K~S~~eL~kqkd~L~~~l~~L~~   51 (107)
T PF09304_consen   11 QNELQNRLASLERSLEDEKTSQGELAKQKDQLRNALQSLQA   51 (107)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHH
Confidence            45566677777777666654433222222234444444433

The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.

>PF05781 MRVI1: MRVI1 protein; InterPro: IPR008677 This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB)

Probab=84.50  E-value=23  Score=36.83  Aligned_cols=98  Identities=22%  Similarity=0.339  Sum_probs=54.0

Q ss_pred             chhhHHHHHHHHHHHHHHhhhh-----------hHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHH
Q 024140           26 PFEQLDVARKITSIAISTRVSD-----------LESEHSALRSQLAEK----------DSRIAELQSQIESIYSSLSDKL   84 (272)
Q Consensus        26 P~EQLdlarkIts~A~atRVs~-----------LE~E~~~LR~~L~EK----------d~~i~~Lq~r~s~le~~l~~rL   84 (272)
                      -|-||-||+|.=..-|..||..           |+.||..++..|..=          .+.|..|++.+.-|.... .|+
T Consensus       196 ~F~~lsL~f~~D~~TLe~R~~~~eR~RdlaEeNl~kEi~~~~~~l~~l~~lc~~d~e~~e~~~kl~~~l~~l~~~~-~rv  274 (538)
T PF05781_consen  196 EFLRLSLGFKCDRFTLEKRLKLEERSRDLAEENLKKEIENCLKLLESLAPLCWEDNESREIIQKLQKSLDVLHQCA-TRV  274 (538)
T ss_pred             HHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchhhHHHHHHHHHHHHHHHHHHHHH-HHH
Confidence            3779999999999999999864           444555555544311          122233333333332222 222


Q ss_pred             H-------HHHHHHHHHHHHHHHHHHHHHHHhh----hHHHHHHHHHHHHhh
Q 024140           85 G-------QAQADKERLSKENEALTNTVRKLQR----DVSKLEVFRKTLVQS  125 (272)
Q Consensus        85 ~-------~a~ee~~kL~~E~~~La~TvKkL~r----DvaKLE~FKk~LmqS  125 (272)
                      .       .+.|| .++.+--....+-|..|.|    +-+.|+-|||.|+|.
T Consensus       275 ss~AE~lGAv~QE-~R~SkAvevM~qhvenLkr~~~kehaeL~E~k~~l~qn  325 (538)
T PF05781_consen  275 SSRAEMLGAVHQE-SRVSKAVEVMIQHVENLKRMYEKEHAELEELKKLLLQN  325 (538)
T ss_pred             HHHHHHhcchHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            2       22222 2244444455555666655    455689999988764

The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene []. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP []. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins [].

>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin

Probab=84.46  E-value=16  Score=34.81  Aligned_cols=67  Identities=15%  Similarity=0.287  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        49 E~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      |-+.+..|.+..-+.-.|.++++.+...-.+++..+....+.+..|..+..+|...++|-..++.+.
T Consensus       143 E~~lr~~R~~a~~r~~e~~~iE~~l~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~  209 (267)
T PF10234_consen  143 EVELREERQRALARPLELNEIEKALKEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERN  209 (267)
T ss_pred             hHhHHHHHHHHHcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5556666777666666777777666666555557777888889999999999999998877776653

Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].

>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8

Probab=84.43  E-value=10  Score=32.94  Aligned_cols=69  Identities=20%  Similarity=0.330  Sum_probs=37.9

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRK  120 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk  120 (272)
                      +--|+-.|-.++..+++++.+.........+....+          ..++..++.+|...|...+++...|+.   ++|+
T Consensus       116 ~I~r~~~li~~l~~~~~~~~~~~kq~~~~~~~~~~~----------~~~~~~~~~~ei~~lk~el~~~~~~~~---~Lkk  182 (192)
T PF05529_consen  116 VIRRVHSLIKELIKLEEKLEALKKQAESASEAAEKL----------LKEENKKLSEEIEKLKKELEKKEKEIE---ALKK  182 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhh----------hhhhhhhhHHHHHHHHHHHHHHHHHHH---HHHH
Confidence            456777777777776666654444443332222211          335556666666666666666555544   4455


Q ss_pred             HH
Q 024140          121 TL  122 (272)
Q Consensus       121 ~L  122 (272)
                      +.
T Consensus       183 Q~  184 (192)
T PF05529_consen  183 QS  184 (192)
T ss_pred             HH
Confidence            43

Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane

>KOG0999 consensus Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.34  E-value=9.9  Score=40.15  Aligned_cols=37  Identities=19%  Similarity=0.277  Sum_probs=30.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI   76 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~l   76 (272)
                      -|-.||-.||.|...||+.|+++..+..-|...++.+
T Consensus       104 ~yl~kI~eleneLKq~r~el~~~q~E~erl~~~~sd~  140 (772)
T KOG0999|consen  104 YYLQKILELENELKQLRQELTNVQEENERLEKVHSDL  140 (772)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3678999999999999999999998887777666544

>PF09728 Taxilin: Myosin-like coiled-coil protein; InterPro: IPR019132 Taxilin contains an extraordinarily long coiled-coil domain in its C-terminal half and is ubiquitously expressed

Probab=84.20  E-value=40  Score=32.24  Aligned_cols=79  Identities=23%  Similarity=0.378  Sum_probs=56.9

Q ss_pred             hhhhhHHHHHHHHHHHH---HHHHH------------------HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 024140           44 RVSDLESEHSALRSQLA---EKDSR------------------IAELQSQIESIYSSLS---DKLGQAQADKERLSKENE   99 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~---EKd~~------------------i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~   99 (272)
                      +|..|-.+-..||.+|.   +|-..                  |..+-+++-.||.+-.   .|-..+..-..++..|+.
T Consensus       203 ~~~~~~~~E~~Lr~QL~~Y~~Kf~efq~tL~kSNe~F~tfk~Emekm~Kk~kklEKE~~~~k~k~e~~n~~l~~m~eer~  282 (309)
T PF09728_consen  203 QVQTLKETEKELREQLNLYSEKFEEFQDTLNKSNEVFETFKKEMEKMSKKIKKLEKENQTWKSKWEKSNKALIEMAEERQ  282 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            66666667777777776   44322                  2334445555555544   566666777788999999


Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHH
Q 024140          100 ALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      .+...+.++.+.+.+||++-|+|
T Consensus       283 ~~~~~~~~~~~k~~kLe~LcRaL  305 (309)
T PF09728_consen  283 KLEKELEKLKKKIEKLEKLCRAL  305 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998876

It is a novel binding partner of several syntaxin family members and is possibly involved in Ca(2+)-dependent exocytosis in neuroendocrine cells []. Gamma-taxilin, described as leucine zipper protein Factor Inhibiting ATF4-mediated Transcription (FIAT), localises to the nucleus in osteoblasts and dimerises with ATF4 to form inactive dimers, thus inhibiting ATF4-mediated transcription [].

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=84.15  E-value=14  Score=37.56  Aligned_cols=49  Identities=22%  Similarity=0.424  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH----------HHHHhhhHHHHHHHHHHHHhhccccc
Q 024140           82 DKLGQAQADKERLSKENEALTNT----------VRKLQRDVSKLEVFRKTLVQSLKDDE  130 (272)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~T----------vKkL~rDvaKLE~FKk~LmqSLq~d~  130 (272)
                      ..|.++.+.+..|..|-+.|...          ++++..++..|+.=-+.+...+.+..
T Consensus       317 ~~l~~~~e~~~~l~~Ei~~l~~sY~l~~~e~~~~~~lekeL~~Le~~~~~~~~~i~~~~  375 (569)
T PRK04778        317 DFLEHAKEQNKELKEEIDRVKQSYTLNESELESVRQLEKQLESLEKQYDEITERIAEQE  375 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            56678888888999999988888          88888888888776666666655443

>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4

Probab=84.12  E-value=17  Score=34.71  Aligned_cols=66  Identities=17%  Similarity=0.338  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        50 ~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      .|....+.+|..+..++..+++.+...|.++.   .|+.+..++..+|..|...|..+|..+.--|.|+
T Consensus       193 ~eke~~~r~l~~~~~ELe~~~EeL~~~Eke~~e~~~~i~e~~~rl~~l~~~~~~l~k~~~~~~sKV~kf  261 (269)
T PF05278_consen  193 EEKEEKDRKLELKKEELEELEEELKQKEKEVKEIKERITEMKGRLGELEMESTRLSKTIKSIKSKVEKF  261 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33344444444444444444444444554444   5555556666666666666666666665444443

>PRK01156 chromosome segregation protein; Provisional

Probab=84.09  E-value=19  Score=38.11  Aligned_cols=14  Identities=29%  Similarity=0.375  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHHH
Q 024140           91 KERLSKENEALTNT  104 (272)
Q Consensus        91 ~~kL~~E~~~La~T  104 (272)
                      ...|..+...|..+
T Consensus       697 ~~~l~~~i~~l~~~  710 (895)
T PRK01156        697 RARLESTIEILRTR  710 (895)
T ss_pred             HHHHHHHHHHHHhh
Confidence            33333333444333

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=84.05  E-value=11  Score=41.90  Aligned_cols=77  Identities=19%  Similarity=0.295  Sum_probs=42.2

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------------DKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-------------~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      .++|++....|+.|+.+++.+...+-+|+..|+..+.             ..|+..-+..+.|.+.++.|...-++|..=
T Consensus       504 lsrl~a~~~elkeQ~kt~~~qye~~~~k~eeLe~~l~~lE~ENa~LlkqI~~Lk~t~qn~~~LEq~~n~lE~~~~elkk~  583 (1195)
T KOG4643|consen  504 LSRLHALKNELKEQYKTCDIQYELLSNKLEELEELLGNLEEENAHLLKQIQSLKTTSQNGALLEQNNNDLELIHNELKKY  583 (1195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHH
Confidence            3556666666666666666555544444444444333             344444455555666666555555555555


Q ss_pred             HHHHHHHHHH
Q 024140          112 VSKLEVFRKT  121 (272)
Q Consensus       112 vaKLE~FKk~  121 (272)
                      +.+|++++++
T Consensus       584 idaL~alrrh  593 (1195)
T KOG4643|consen  584 IDALNALRRH  593 (1195)
T ss_pred             HHHHHHHHHH
Confidence            5666665554

>PRK01156 chromosome segregation protein; Provisional

Probab=84.04  E-value=15  Score=38.77  Aligned_cols=18  Identities=17%  Similarity=0.508  Sum_probs=7.4

Q ss_pred             HHHhhhHHHHHHHHHHHH
Q 024140          106 RKLQRDVSKLEVFRKTLV  123 (272)
Q Consensus       106 KkL~rDvaKLE~FKk~Lm  123 (272)
                      +++..-+..|+.|++.|.
T Consensus       729 ~~~~~~~~~l~~~r~~l~  746 (895)
T PRK01156        729 KKIKKAIGDLKRLREAFD  746 (895)
T ss_pred             HHHHHHHHHHHHHHHHhh
Confidence            333334444444444333

>PRK04863 mukB cell division protein MukB; Provisional

Probab=83.97  E-value=29  Score=39.98  Aligned_cols=76  Identities=21%  Similarity=0.319  Sum_probs=37.9

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDS------RIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~------~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      ..+..|+..||.++..+++.+..+.+      .+..+...+..|+..+.   .++..+.++..++.++...+...++.|.
T Consensus       317 ~ELe~rL~kLEkQaEkA~kyleL~ee~lr~q~ei~~l~~~LeELee~Lee~eeeLeeleeeleeleeEleelEeeLeeLq  396 (1486)
T PRK04863        317 AELNEAESDLEQDYQAASDHLNLVQTALRQQEKIERYQADLEELEERLEEQNEVVEEADEQQEENEARAEAAEEEVDELK  396 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56677777777777776666554332      22333333334443333   4444444444444444444444444444


Q ss_pred             hhHHH
Q 024140          110 RDVSK  114 (272)
Q Consensus       110 rDvaK  114 (272)
                      ..++.
T Consensus       397 eqLae  401 (1486)
T PRK04863        397 SQLAD  401 (1486)
T ss_pred             HHHHH
Confidence            44433

>PF09787 Golgin_A5: Golgin subfamily A member 5; InterPro: IPR019177 This entry represents a family of proteins involved in maintaining Golgi structure

Probab=83.92  E-value=4.5  Score=40.69  Aligned_cols=71  Identities=30%  Similarity=0.412  Sum_probs=57.7

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKD--SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd--~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (272)
                      ...+..|+..-|.|+..||.+|..|.  ..-.||+.|+..|...|+    +.....+.|..||++|.-+..+|.+.+
T Consensus       357 ~s~~~~k~~~ke~E~q~lr~~l~~~~~~s~~~elE~rl~~lt~~Li----~KQ~~lE~l~~ek~al~lqlErl~~~l  429 (511)
T PF09787_consen  357 KSPLQLKLKEKESEIQKLRNQLSARASSSSWNELESRLTQLTESLI----QKQTQLESLGSEKNALRLQLERLETQL  429 (511)
T ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHhccCCcHhHHHHHhhccHHHH----HHHHHHHHHHhhhhhccccHHHHHHHH
Confidence            55677888888999999999999877  334689999998887777    778888899999999988877776554

They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterised: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1 [].

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=83.82  E-value=5.5  Score=32.45  Aligned_cols=44  Identities=16%  Similarity=0.218  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      +..+++.+|+.+|+.|...|+.|+.|-+-+|..=|.=+.=..++
T Consensus        38 ~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe~AR~~Lg~vk~g   81 (105)
T PRK00888         38 AQQQTNAKLKARNDQLFAEIDDLKGGQEAIEERARNELGMVKPG   81 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHHHcCCCCCC
Confidence            56667778888888888888888877667776666555444443

>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed

Probab=83.81  E-value=27  Score=34.13  Aligned_cols=53  Identities=15%  Similarity=0.260  Sum_probs=30.5

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Q 024140           28 EQLDVARKITSIAISTRVSDLESEHSALRSQLA--EKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~--EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ++||-..+-...++..++..-+..+..|+..|.  .-...+..++.++..+...|
T Consensus       267 q~Ld~l~~rL~~a~~~~L~~~~~~L~~L~~rL~~~~P~~~l~~~~q~L~~l~~rL  321 (438)
T PRK00286        267 QRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRL  321 (438)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHH
Confidence            355555555677777788777777777776663  22333444444444444433

>KOG0250 consensus DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair]

Probab=83.79  E-value=14  Score=41.14  Aligned_cols=69  Identities=22%  Similarity=0.368  Sum_probs=27.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----DKLGQAQADKERLSKENEALTNTVRKL  108 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----~rL~~a~ee~~kL~~E~~~La~TvKkL  108 (272)
                      ++..+|..++.+++.--..+.++...+..|+++|..++.++.    ..+.+..++.+.|.+|...|...+..|
T Consensus       348 ~~~re~~~~~~~~~~~~n~i~~~k~~~d~l~k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~evek~e~~~~~L  420 (1074)
T KOG0250|consen  348 DLRREVNDLKEEIREIENSIRKLKKEVDRLEKQIADLEKQTNNELGSELEERENKLEQLKKEVEKLEEQINSL  420 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455444433333333333333333444444443331    333344444444444444444433333

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=83.77  E-value=5.3  Score=37.01  Aligned_cols=61  Identities=20%  Similarity=0.322  Sum_probs=26.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEA  100 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~  100 (272)
                      +.-.||..||..+..-.+.+.|-...|.+||..|..|-.++.   -.|.+..+++..|-.+.|.
T Consensus        37 ~~~~r~~~le~~~~~~~~~~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~  100 (263)
T PRK10803         37 SVEDRVTQLERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDS  100 (263)
T ss_pred             chHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344566666655554333333444444444444443333333   2222444444444444443

>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []

Probab=83.74  E-value=6.5  Score=28.75  Aligned_cols=35  Identities=31%  Similarity=0.485  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRK  120 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk  120 (272)
                      ....++++|.+|++.|...++.|..|-+.+|.+=|
T Consensus        28 ~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR   62 (80)
T PF04977_consen   28 ELQKEIEELKKENEELKEEIERLKNDPDYIEKVAR   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            44455567777777777777777667777777655

These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle

>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function

Probab=83.74  E-value=6.7  Score=38.12  Aligned_cols=73  Identities=21%  Similarity=0.267  Sum_probs=47.3

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      ..-+...|..|+..||++|.|=.--|.-|+++++....... .-.+...++.++|..+-..+-.+..-|.+||.
T Consensus        77 sre~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~la~~r~~~~~~~~~~~~~ere~lV~qLEk~~~q~~qLe~d~q  150 (319)
T PF09789_consen   77 SREQNKKLKEEVEELRQKLNEAQGDIKLLREKLARQRVGDEGIGARHFPHEREDLVEQLEKLREQIEQLERDLQ  150 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccccccccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677899999999999999999999999999887766554 11111114444444444444444444444443

>PF14932 HAUS-augmin3: HAUS augmin-like complex subunit 3

Probab=83.72  E-value=21  Score=32.95  Aligned_cols=38  Identities=24%  Similarity=0.167  Sum_probs=25.4

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ..|..||.|+..|+.....+...+..|+.....+...+
T Consensus        68 ~~le~Le~el~~l~~~~~~~~~~~~~lq~~~~~~~~~~  105 (256)
T PF14932_consen   68 EDLEALEEELEALQEYKELYEQLRNKLQQLDSSLSQEL  105 (256)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667888888887777777777777765555444443

>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function

Probab=83.63  E-value=8.6  Score=28.99  Aligned_cols=47  Identities=17%  Similarity=0.272  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           65 RIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        65 ~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      .|.+||.|++-+|..+.    ...+...+.+++.+.|...++.|...|..+
T Consensus         5 Ri~~LE~~la~qe~~ie----~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~   51 (69)
T PF04102_consen    5 RIEELEIKLAFQEDTIE----ELNDVVTEQQRQIDRLQRQLRLLRERLREL   51 (69)
T ss_dssp             HHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHT----
T ss_pred             HHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444444443333332    444455555555555555555555444433

It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.

>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope

Probab=83.62  E-value=36  Score=31.24  Aligned_cols=84  Identities=19%  Similarity=0.322  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH-HHHHHHHHHHHHHHHH
Q 024140           32 VARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQ-ADKERLSKENEALTNT  104 (272)
Q Consensus        32 larkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~------~rL~~a~-ee~~kL~~E~~~La~T  104 (272)
                      -.+.-+-..|..++..|...+..-...+..-...+.+++.++..|+..|.      +.|.... +-...+..++..+...
T Consensus       184 ~~~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~~~~~~~~~~~  263 (312)
T PF00038_consen  184 KNREELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELEQRLDEEREEYQAE  263 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHHHHHHHHHHHHHh
Confidence            33334456677777777776666555555555556666666666655554      1121111 1123445555555555


Q ss_pred             HHHHhhhHHHH
Q 024140          105 VRKLQRDVSKL  115 (272)
Q Consensus       105 vKkL~rDvaKL  115 (272)
                      |..|...+++|
T Consensus       264 i~~le~el~~l  274 (312)
T PF00038_consen  264 IAELEEELAEL  274 (312)
T ss_dssp             HHHHHHHHHHH
T ss_pred             hhccchhHHHH
Confidence            55555555554

They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=83.53  E-value=13  Score=33.08  Aligned_cols=34  Identities=32%  Similarity=0.407  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHH-------HHHHHHHhhhHHHH
Q 024140           82 DKLGQAQADKERLSKENEAL-------TNTVRKLQRDVSKL  115 (272)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~L-------a~TvKkL~rDvaKL  115 (272)
                      .||.+-.+++..|..-|.-|       -.+-..|..|+.||
T Consensus        67 ~rLeEEqqR~~~L~qvN~lLReQLEq~~~~N~~L~~dl~kl  107 (182)
T PF15035_consen   67 IRLEEEQQRSEELAQVNALLREQLEQARKANEALQEDLQKL  107 (182)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46666666666666666666       34555666666665

>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]

Probab=83.46  E-value=39  Score=36.42  Aligned_cols=79  Identities=18%  Similarity=0.235  Sum_probs=55.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHH---HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI---YSS---LS-DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~l---e~~---l~-~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (272)
                      +|-++...--.|++.||++++||+..+.-|++++..-   +..   ++ .+|+.+.|..+.-.++++....-.+.+....
T Consensus       228 qye~klkstk~e~a~L~Eq~~eK~~e~~rl~~~lv~~~~~d~e~~~~rd~~lk~a~eslm~ane~kdr~ie~lr~~ln~y  307 (861)
T KOG1899|consen  228 QYETKLKSTKGEMAPLREQRSEKNDEEMRLLRTLVQRLMADGEHKSLRDNTLKNALESLMRANEQKDRFIESLRNYLNNY  307 (861)
T ss_pred             HHHhhcccccchhhhHHHHHhhhhhHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHhhchhhhhHHHHHHHHhhhh
Confidence            3334444444568999999999999999988776531   222   22 6888888888888888888777777776666


Q ss_pred             HHHHHH
Q 024140          113 SKLEVF  118 (272)
Q Consensus       113 aKLE~F  118 (272)
                      .|....
T Consensus       308 ~k~~~i  313 (861)
T KOG1899|consen  308 DKNAQI  313 (861)
T ss_pred             hhhhhh
Confidence            555444

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=83.36  E-value=9.4  Score=31.83  Aligned_cols=38  Identities=18%  Similarity=0.326  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           67 AELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKL  108 (272)
Q Consensus        67 ~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL  108 (272)
                      ..|-+.+..|...++    ...+||+.|.-||+.|-..+.++
T Consensus        18 ~~l~~el~~LK~~~~----el~EEN~~L~iEN~~Lr~~l~~~   55 (110)
T PRK13169         18 GVLLKELGALKKQLA----ELLEENTALRLENDKLRERLEEL   55 (110)
T ss_pred             HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHh
Confidence            333344444444333    77888999999998887777655

>PRK12704 phosphodiesterase; Provisional

Probab=83.19  E-value=39  Score=34.61  Aligned_cols=36  Identities=25%  Similarity=0.406  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           92 ERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      .+|.+....|...-+.|.+--..++.++....+-|.
T Consensus       110 ~eL~~re~~Le~re~eLe~~~~~~~~~~~~~~~~l~  145 (520)
T PRK12704        110 EELEKKEKELEQKQQELEKKEEELEELIEEQLQELE  145 (520)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333443333344444444444443

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=83.06  E-value=5.6  Score=43.92  Aligned_cols=31  Identities=26%  Similarity=0.533  Sum_probs=18.7

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIE   74 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s   74 (272)
                      -++.|+...+.|..++.+-+..|.+|+++|.
T Consensus       411 E~~eL~r~kE~Lsr~~d~aEs~iadlkEQVD  441 (1243)
T KOG0971|consen  411 ELEELRRQKERLSRELDQAESTIADLKEQVD  441 (1243)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555556666666666666666666654

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=82.98  E-value=9.7  Score=42.39  Aligned_cols=39  Identities=21%  Similarity=0.231  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           84 LGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        84 L~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      +.....++.+...|+....-.+++|..+|.|++.=++..
T Consensus       887 i~~~~~~~e~~~~e~~~~~l~~kkle~e~~~~~~e~~~~  925 (1174)
T KOG0933|consen  887 ISGLLTSQEKCLSEKSDGELERKKLEHEVTKLESEKANA  925 (1174)
T ss_pred             HhhhhhHHHHHHHHhhcccchHHHHHhHHHHhhhhHHHH
Confidence            334455667888888999999999999999998766554

>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences

Probab=82.98  E-value=7.8  Score=33.09  Aligned_cols=65  Identities=28%  Similarity=0.373  Sum_probs=34.9

Q ss_pred             HHHhcCCCCchhhHHHHHHHH---HHHHHHhhhhhHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHH
Q 024140           17 EVLQVLPSDPFEQLDVARKIT---SIAISTRVSDLESEHSALRSQLA--EKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        17 eil~vLP~DP~EQLdlarkIt---s~A~atRVs~LE~E~~~LR~~L~--EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +.+.+++.+-...||--+.-.   -..+...+..|++|+..|+..+.  |-...|.+|++.+..|+..|.
T Consensus        64 ~~~~~~s~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~  133 (169)
T PF07106_consen   64 DELEVPSPEELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLE  133 (169)
T ss_pred             cccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444445555442221   24556666666666666666663  555566666666666665443

TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].

>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]

Probab=82.95  E-value=9.7  Score=35.86  Aligned_cols=37  Identities=22%  Similarity=0.279  Sum_probs=25.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      -.+.|.+++.|+..+..+|+.|..||+.+-..|..|.
T Consensus        69 q~k~e~~m~~Lea~VEkrD~~IQqLqk~LK~aE~iLt  105 (272)
T KOG4552|consen   69 QQKREQLMRTLEAHVEKRDEVIQQLQKNLKSAEVILT  105 (272)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            3455666777777777777777777777777776665

>PRK00736 hypothetical protein; Provisional

Probab=82.86  E-value=9.6  Score=28.91  Aligned_cols=41  Identities=15%  Similarity=0.229  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           65 RIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        65 ~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      .|.+||.|+.-.|..+.    ...+...+.+++.+.|...++.|.
T Consensus         6 Ri~~LE~klafqe~tie----~Ln~~v~~Qq~~i~~L~~ql~~L~   46 (68)
T PRK00736          6 RLTELEIRVAEQEKTIE----ELSDQLAEQWKTVEQMRKKLDALT   46 (68)
T ss_pred             HHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35555555555554433    334444444444444444444443

>TIGR00237 xseA exodeoxyribonuclease VII, large subunit

Probab=82.71  E-value=31  Score=34.22  Aligned_cols=52  Identities=19%  Similarity=0.133  Sum_probs=30.5

Q ss_pred             hHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Q 024140           29 QLDVARKITSIAISTRVSDLESEHSALRSQLA--EKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        29 QLdlarkIts~A~atRVs~LE~E~~~LR~~L~--EKd~~i~~Lq~r~s~le~~l   80 (272)
                      +|+-...-...|+..++...+.++..|+..|.  .-...+...+.++..+...|
T Consensus       263 rLd~l~~RL~~am~~~L~~~r~rL~~L~~RL~~~~P~~~L~~~~qrLd~L~~RL  316 (432)
T TIGR00237       263 RLDGFNVRLHRAFDTLLHQKKARLEQLVASLQRQHPQNKLALQQLQFEKLEKRK  316 (432)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHH
Confidence            45555555677888888888888887777654  22233444444444444333

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.

>PF05266 DUF724: Protein of unknown function (DUF724); InterPro: IPR007930 This family contains several uncharacterised proteins found exclusively in Arabidopsis thaliana

Probab=82.62  E-value=22  Score=31.98  Aligned_cols=24  Identities=21%  Similarity=0.202  Sum_probs=12.2

Q ss_pred             ChhHHHhcCCCCchhhHHHHHHHH
Q 024140           14 LPEEVLQVLPSDPFEQLDVARKIT   37 (272)
Q Consensus        14 lp~eil~vLP~DP~EQLdlarkIt   37 (272)
                      |-++|...==+||-..|+.=.+..
T Consensus        55 l~e~v~~l~idd~~~~f~~~~~tl   78 (190)
T PF05266_consen   55 LAEKVKKLQIDDSRSSFESLMKTL   78 (190)
T ss_pred             HHHHHHHcccCCcHHHHHHHHHHH
Confidence            344454444556666555544443

>smart00338 BRLZ basic region leucin zipper

Probab=82.58  E-value=11  Score=27.37  Aligned_cols=28  Identities=36%  Similarity=0.617  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           89 ADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        89 ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      .+...|..||..|...|..|..++..|+
T Consensus        33 ~~~~~L~~en~~L~~~~~~l~~e~~~lk   60 (65)
T smart00338       33 RKVEQLEAENERLKKEIERLRRELEKLK   60 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555555555554

>PF02841 GBP_C: Guanylate-binding protein, C-terminal domain; InterPro: IPR003191 Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma

Probab=82.41  E-value=17  Score=33.87  Aligned_cols=72  Identities=19%  Similarity=0.285  Sum_probs=39.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKT  121 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~  121 (272)
                      .++.-+-.+-++|.+++..|.+.+.|...++.++..--....+....|..+..++...++.|.   .||+.-|+.
T Consensus       187 ~~~~~ilq~d~~L~~~ek~~~~~~~k~e~~e~e~~~l~e~~~~~~~~le~~~~~~ee~~~~L~---ekme~e~~~  258 (297)
T PF02841_consen  187 SMENSILQADQQLTEKEKEIEEEQAKAEAAEKEKEKLEEKQKEQEQMLEQQERSYEEHIKQLK---EKMEEEREQ  258 (297)
T ss_dssp             HHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH
Confidence            445555666667777777777777777777766651112223334445555555555555554   344444443

GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) []. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function (IPR015894 from INTERPRO), and an alpha-helical finger-like C-terminal domain. Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1DG3_A 2D4H_A 2B8W_B 2B92_A 2BC9_A 1F5N_A.

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=82.36  E-value=17  Score=37.12  Aligned_cols=11  Identities=27%  Similarity=0.389  Sum_probs=5.3

Q ss_pred             HHHHHHHHHhh
Q 024140          115 LEVFRKTLVQS  125 (272)
Q Consensus       115 LE~FKk~LmqS  125 (272)
                      |..+||.|+.+
T Consensus       427 L~~ikr~l~k~  437 (569)
T PRK04778        427 LHEIKRYLEKS  437 (569)
T ss_pred             HHHHHHHHHHc
Confidence            34455555544

>PF04136 Sec34: Sec34-like family ; InterPro: IPR007265 Sec34 and Sec35 form a sub-complex in a seven-protein complex that includes Dor1

Probab=82.24  E-value=32  Score=29.71  Aligned_cols=81  Identities=20%  Similarity=0.259  Sum_probs=59.6

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKT  121 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~  121 (272)
                      ...+..+..++..|-.++.+=...+.+|++++...+    .+-....+.+++|.+|...|...+..+...|.-.+.+ ..
T Consensus         6 ~~~L~~~~~~~~~ll~~~~~~~~~l~~l~~~~~~Vs----~kT~~l~~~ce~Ll~eq~~L~~~ae~I~~~L~yF~~L-d~   80 (157)
T PF04136_consen    6 LDYLQQYREECDQLLDQTDEILDQLDELQEQYNSVS----EKTNSLHEACEQLLEEQTRLEELAEEISEKLQYFEEL-DP   80 (157)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHhhH-HH
Confidence            344555556666666666666666666666665555    4455788899999999999999999999999888877 56


Q ss_pred             HHhhcc
Q 024140          122 LVQSLK  127 (272)
Q Consensus       122 LmqSLq  127 (272)
                      +++.|+
T Consensus        81 itr~Ln   86 (157)
T PF04136_consen   81 ITRRLN   86 (157)
T ss_pred             HHHHHc
Confidence            777775

This complex is thought to be important for tethering vesicles to the Golgi [].; GO: 0006886 intracellular protein transport, 0005801 cis-Golgi network, 0016020 membrane

>PRK04325 hypothetical protein; Provisional

Probab=82.17  E-value=7.4  Score=29.96  Aligned_cols=12  Identities=33%  Similarity=0.285  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHHH
Q 024140           66 IAELQSQIESIY   77 (272)
Q Consensus        66 i~~Lq~r~s~le   77 (272)
                      |.+||.|++-.|
T Consensus        11 i~~LE~klAfQE   22 (74)
T PRK04325         11 ITELEIQLAFQE   22 (74)
T ss_pred             HHHHHHHHHHHH
Confidence            344444443333

>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription

Probab=82.17  E-value=28  Score=30.65  Aligned_cols=105  Identities=17%  Similarity=0.225  Sum_probs=49.3

Q ss_pred             hhHHHhcCCCCchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHH
Q 024140           15 PEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRI------------AELQSQIESIYSSLSD   82 (272)
Q Consensus        15 p~eil~vLP~DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i------------~~Lq~r~s~le~~l~~   82 (272)
                      |..+|--.=.|--++|.=+++-+..+++.+. .||.++..+...+.+-....            .+.-.+...++.    
T Consensus        24 P~~~l~q~ird~e~~l~~a~~~~a~~~a~~~-~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~e~----   98 (221)
T PF04012_consen   24 PEKMLEQAIRDMEEQLRKARQALARVMANQK-RLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADLEE----   98 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH----
Confidence            5555555555666677666666655544432 45555555555554333222            111112222222    


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Q 024140           83 KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ  124 (272)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lmq  124 (272)
                      .+....+....+...-+.|...+++|...+..|+.=+..|+-
T Consensus        99 ~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l~a  140 (221)
T PF04012_consen   99 QAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREELKA  140 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            222333334444444445555555555555555554444443

The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].

>PF14282 FlxA: FlxA-like protein

Probab=82.09  E-value=8.2  Score=31.34  Aligned_cols=59  Identities=27%  Similarity=0.424  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           63 DSRIAELQSQIESIYSSLSDKLGQA-QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        63 d~~i~~Lq~r~s~le~~l~~rL~~a-~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      +..|+.|++++..|+..|. .|... .-....-.+....|...+.-|...++.|..=+..-
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~-~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~~   77 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQ-ELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAEQ   77 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5566666666666666654 22221 10122223445556666666666666665544433

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=82.00  E-value=44  Score=34.14  Aligned_cols=35  Identities=26%  Similarity=0.363  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 024140           92 ERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (272)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (272)
                      .+|.+....|...-+.|..-..+++.+.....+-|
T Consensus       104 ~~Le~ke~~L~~re~eLee~~~e~~~~~~~~~~~l  138 (514)
T TIGR03319       104 ENLEKKEKELSNKEKNLDEKEEELEELIAEQREEL  138 (514)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333334444444444444444444444444333

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)

Probab=81.93  E-value=11  Score=31.67  Aligned_cols=14  Identities=43%  Similarity=0.572  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHHH
Q 024140           68 ELQSQIESIYSSLS   81 (272)
Q Consensus        68 ~Lq~r~s~le~~l~   81 (272)
                      +|+.++..|+..|.
T Consensus        13 el~n~La~Le~slE   26 (107)
T PF09304_consen   13 ELQNRLASLERSLE   26 (107)
T ss_dssp             -HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            44455555555443

The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.

>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]

Probab=81.88  E-value=43  Score=30.90  Aligned_cols=14  Identities=29%  Similarity=0.294  Sum_probs=9.4

Q ss_pred             CCchhhHHHHHHHH
Q 024140           24 SDPFEQLDVARKIT   37 (272)
Q Consensus        24 ~DP~EQLdlarkIt   37 (272)
                      .||..+|+-+++=.
T Consensus        23 EDp~~~l~Q~ird~   36 (225)
T COG1842          23 EDPEKMLEQAIRDM   36 (225)
T ss_pred             cCHHHHHHHHHHHH
Confidence            47887777776543

>PF06246 Isy1: Isy1-like splicing family; InterPro: IPR009360 Isy1 protein is important in the optimisation of splicing []

Probab=81.86  E-value=6.1  Score=37.14  Aligned_cols=58  Identities=12%  Similarity=0.172  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS--DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~--~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      |..|++-.-=+-..|.|+-.+|+.+...--  -+++..+++++||.+|+..-...|+.|.
T Consensus        39 v~~l~~ae~WR~~ii~EIs~kv~~Iqd~~L~E~~IRdLNDeINkL~rEK~~WE~rI~~LG   98 (255)
T PF06246_consen   39 VKSLPEAEKWRRQIIKEISRKVTRIQDPSLGEFQIRDLNDEINKLIREKRHWERRIKELG   98 (255)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHH--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            344444444455667777777777665433  7889999999999999999999999987

; PDB: 1X4T_A.

>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []

Probab=81.76  E-value=7.6  Score=28.39  Aligned_cols=29  Identities=28%  Similarity=0.404  Sum_probs=12.3

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIE   74 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s   74 (272)
                      ..+..|+..|+.++++-...+.+|++++.
T Consensus        20 ~~~~~ei~~l~~~i~~l~~e~~~L~~ei~   48 (80)
T PF04977_consen   20 YQLNQEIAELQKEIEELKKENEELKEEIE   48 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444443333

These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle

>PRK00846 hypothetical protein; Provisional

Probab=81.73  E-value=9.7  Score=30.04  Aligned_cols=10  Identities=10%  Similarity=0.368  Sum_probs=4.3

Q ss_pred             HHHHHHHHHH
Q 024140           69 LQSQIESIYS   78 (272)
Q Consensus        69 Lq~r~s~le~   78 (272)
                      |++|+..||.
T Consensus        11 le~Ri~~LE~   20 (77)
T PRK00846         11 LEARLVELET   20 (77)
T ss_pred             HHHHHHHHHH
Confidence            3344444443

>PRK10869 recombination and repair protein; Provisional

Probab=81.71  E-value=12  Score=38.26  Aligned_cols=55  Identities=9%  Similarity=0.033  Sum_probs=30.7

Q ss_pred             CCchhhHHHHHHHHH-HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           24 SDPFEQLDVARKITS-IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (272)
Q Consensus        24 ~DP~EQLdlarkIts-~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~   78 (272)
                      -+|..||++--.+.. ..+...+..+-.+...++.+|.+......+.++++.-|+.
T Consensus       137 l~~~~~~~lLD~~~~~~~~~~~~~~~y~~~~~~~~~l~~l~~~~~~~~~~~d~l~f  192 (553)
T PRK10869        137 LKPEHQKTLLDAYANETSLLQEMRAAYQLWHQSCRDLAQHQQQSQERAARKQLLQY  192 (553)
T ss_pred             cCHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            489999998777664 4455555555555555555554444444334334333333

>PF13747 DUF4164: Domain of unknown function (DUF4164)

Probab=81.71  E-value=25  Score=28.02  Aligned_cols=39  Identities=13%  Similarity=0.293  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Q 024140           87 AQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS  125 (272)
Q Consensus        87 a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS  125 (272)
                      ..++..+|..+++.|++.+.+......+||.--+-+-+-
T Consensus        37 ~e~ei~~l~~dr~rLa~eLD~~~ar~~~Le~~~~Evs~r   75 (89)
T PF13747_consen   37 LEEEIQRLDADRSRLAQELDQAEARANRLEEANREVSRR   75 (89)
T ss_pred             HHHHHHHHHhhHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555555444455555544444433

>PF01576 Myosin_tail_1: Myosin tail; InterPro: IPR002928 Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril

Probab=81.65  E-value=0.45  Score=50.80  Aligned_cols=91  Identities=26%  Similarity=0.411  Sum_probs=0.0

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-----------DKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-----------~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      -.++..++..||.|+..||.++.|-.....+|+.+++.+..+|.           .+.....+-..+|..+-..|...+.
T Consensus       259 k~~L~~~l~~le~e~~~L~eqleeE~e~k~~l~~qlsk~~~El~~~k~K~e~e~~~~~EelEeaKKkL~~~L~el~e~le  338 (859)
T PF01576_consen  259 KQALEKQLRQLEHELEQLREQLEEEEEAKSELERQLSKLNAELEQWKKKYEEEAEQRTEELEEAKKKLERKLQELQEQLE  338 (859)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45788899999999999999999999999999999999998887           2333445566788888888888999


Q ss_pred             HHhhhHHHHHHHHHHHHhhccc
Q 024140          107 KLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus       107 kL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      .++..+++||.-|+.|..=+.|
T Consensus       339 ~~~~~~~~LeK~k~rL~~EleD  360 (859)
T PF01576_consen  339 EANAKVSSLEKTKKRLQGELED  360 (859)
T ss_dssp             ----------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999988887655443

Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains [], 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family []. Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy []. The 3-D structure of the head portion of myosin has been determined [] and a model for actin-myosin complex has been constructed []. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament []. The coiled-coil region provides the structural backbone of the thick filament [].; GO: 0003774 motor activity, 0016459 myosin complex; PDB: 2LNK_C 3ZWH_Q.

>TIGR02231 conserved hypothetical protein

Probab=81.47  E-value=22  Score=35.57  Aligned_cols=37  Identities=11%  Similarity=0.202  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           82 DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      .++.++..+..+|..+...|...+.+|.+++++|..-
T Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~  174 (525)
T TIGR02231       138 SEIERLLTEDREAERRIRELEKQLSELQNELNALLTG  174 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence            5666666777777777777777777777777777654

This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.

>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []

Probab=81.30  E-value=10  Score=37.01  Aligned_cols=54  Identities=15%  Similarity=0.302  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 024140           65 RIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFR  119 (272)
Q Consensus        65 ~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FK  119 (272)
                      -+..|++++..++..+ ++|...++++.|..+.+..|.+++.++.+.++.++.|.
T Consensus       243 ~~~~l~~~~~~~~~~i-~~l~~~l~~~~k~~~k~~~~~~q~~~~~k~~~~~~~~~  296 (406)
T PF02388_consen  243 YLESLQEKLEKLEKEI-EKLEEKLEKNPKKKNKLKELEEQLASLEKRIEEAEELI  296 (406)
T ss_dssp             HHHHHHHHHHHHHHHH-HHHHHHHHH-THHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHhCcchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456666666666655 35555555666777778888888888888888887773

These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.

>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]

Probab=81.18  E-value=22  Score=38.68  Aligned_cols=24  Identities=21%  Similarity=0.227  Sum_probs=11.2

Q ss_pred             HHHHHHHhhhHHHHHHHHHHHHhh
Q 024140          102 TNTVRKLQRDVSKLEVFRKTLVQS  125 (272)
Q Consensus       102 a~TvKkL~rDvaKLE~FKk~LmqS  125 (272)
                      .++..+-|+=...|+.|||+|.+.
T Consensus       212 maAle~kn~L~~e~~s~kk~l~~~  235 (916)
T KOG0249|consen  212 MAALEDKNRLEQELESVKKQLEEM  235 (916)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444455555555443

>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]

Probab=81.11  E-value=18  Score=39.89  Aligned_cols=51  Identities=22%  Similarity=0.260  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           61 EKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        61 EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      ++++.+.+|.+++..+.++..   .|.....+...+|..|...|.-.+++|.+.
T Consensus       463 ~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~l~~e~~~lq~~  516 (980)
T KOG0980|consen  463 DVEEENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELALLLIELEELQRT  516 (980)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444445555554444443   222233333333344444444444444443

>smart00502 BBC B-Box C-terminal domain

Probab=81.00  E-value=23  Score=27.22  Aligned_cols=17  Identities=24%  Similarity=0.335  Sum_probs=6.9

Q ss_pred             HHHHHHHHhhhHHHHHH
Q 024140          101 LTNTVRKLQRDVSKLEV  117 (272)
Q Consensus       101 La~TvKkL~rDvaKLE~  117 (272)
                      |....+.|+.++++|..
T Consensus        77 l~~q~~~l~~~l~~l~~   93 (127)
T smart00502       77 LEQQLESLTQKQEKLSH   93 (127)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33334444444444433

Coiled coil region C-terminal to (some) B-Box domains

>smart00338 BRLZ basic region leucin zipper

Probab=80.79  E-value=8.2  Score=28.15  Aligned_cols=39  Identities=28%  Similarity=0.440  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           61 EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (272)
Q Consensus        61 EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~  103 (272)
                      .|..+|.+|+.++..|+.+..    ....+...|..|+..|.+
T Consensus        23 rKk~~~~~Le~~~~~L~~en~----~L~~~~~~l~~e~~~lk~   61 (65)
T smart00338       23 RKKAEIEELERKVEQLEAENE----RLKKEIERLRRELEKLKS   61 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Confidence            456778888888877776554    444444445555544443

>PF13863 DUF4200: Domain of unknown function (DUF4200)

Probab=80.48  E-value=28  Score=27.88  Aligned_cols=61  Identities=21%  Similarity=0.271  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           67 AELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        67 ~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      ..|++.+..++.-|.   .+...|.....+=.+.+.....-+++|..++..|...+..+..-|+
T Consensus        42 ~~l~~~~~~f~~flken~~k~~rA~k~a~~e~k~~~~k~~ei~~l~~~l~~l~~~~~k~e~~l~  105 (126)
T PF13863_consen   42 QELEEDVIKFDKFLKENEAKRERAEKRAEEEKKKKEEKEAEIKKLKAELEELKSEISKLEEKLE  105 (126)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            556666666666666   7778888888888888888888888888888888888777766554

>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system []

Probab=80.32  E-value=28  Score=27.79  Aligned_cols=32  Identities=22%  Similarity=0.313  Sum_probs=16.3

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQ   70 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq   70 (272)
                      .+.+.|..+|...+..|+..+.+.+....+|+
T Consensus        31 ~~~~~kY~~~~~~~~~l~~~~~~l~~k~~~l~   62 (99)
T PF10046_consen   31 KATSLKYKKMKDIAAGLEKNLEDLNQKYEELQ   62 (99)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455565555555555555544444443333

>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]

Probab=80.19  E-value=39  Score=34.37  Aligned_cols=72  Identities=18%  Similarity=0.300  Sum_probs=51.0

Q ss_pred             CCCCChhHHHhc---CCCCc-----------hhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH--HHHHHHHHHHHHH
Q 024140           10 STFDLPEEVLQV---LPSDP-----------FEQLDVARKITSIAISTRVSDLESEHSALRSQLA--EKDSRIAELQSQI   73 (272)
Q Consensus        10 ~dF~lp~eil~v---LP~DP-----------~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~--EKd~~i~~Lq~r~   73 (272)
                      .||-|.|-|.-+   -|+..           -+||+-.++...+|+..++.+-+..+..|+..+.  .-++.+..-+.++
T Consensus       236 tD~tL~DfVAD~RApTPTaAAE~~vP~~~el~~~l~~~~~rL~~~~~~~l~~~~~~l~~l~~~l~~~~p~~~l~~~~q~l  315 (440)
T COG1570         236 TDFTLADFVADLRAPTPTAAAELVVPDSAELLQQLDQLQRRLHRALRRLLDQKKQRLEHLARRLQFRSPERLLSEQQQRL  315 (440)
T ss_pred             CCccHHHhhhhccCCCchHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence            478887766543   23322           3466777777889999999998988888888887  6667777777777


Q ss_pred             HHHHHHHH
Q 024140           74 ESIYSSLS   81 (272)
Q Consensus        74 s~le~~l~   81 (272)
                      ..++..|.
T Consensus       316 d~~~~rL~  323 (440)
T COG1570         316 DELAIRLR  323 (440)
T ss_pred             HHHHHHHH
Confidence            66665555

>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein)

Probab=80.19  E-value=11  Score=29.45  Aligned_cols=65  Identities=26%  Similarity=0.314  Sum_probs=40.3

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      .-|++.-+-.||.|++.|+-.+.+       |++++..++.+.. .+=+....+...|.++-..=+++|.+|.
T Consensus        12 ~~~Ls~vl~~LqDE~~hm~~e~~~-------L~~~~~~~d~s~~~~~R~~L~~~l~~lv~~mE~K~dQI~~L~   77 (79)
T PF06657_consen   12 GEALSEVLKALQDEFGHMKMEHQE-------LQDEYKQMDPSLGRRKRRDLEQELEELVKRMEAKADQIYKLY   77 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHhcccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            357788888999999999887765       4445555555544 2223344455556666665566665553

It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].

>PF08898 DUF1843: Domain of unknown function (DUF1843); InterPro: IPR014994 This domain is found in functionally uncharacterised proteins

Probab=80.19  E-value=6  Score=29.46  Aligned_cols=36  Identities=22%  Similarity=0.364  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           82 DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      ++++.....-++-..+...|...+.+|+.+++|||.
T Consensus        17 a~MK~l~~~aeq~L~~~~~i~~al~~Lk~EIaklE~   52 (53)
T PF08898_consen   17 AQMKALAAQAEQQLAEAGDIAAALEKLKAEIAKLEA   52 (53)
T ss_pred             HHHHHHHHHHHHHHccchHHHHHHHHHHHHHHHHhc
Confidence            677777777788888999999999999999999985

It can be found independently or at the C terminus of the protein.

>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions

Probab=80.18  E-value=16  Score=29.02  Aligned_cols=63  Identities=24%  Similarity=0.364  Sum_probs=42.3

Q ss_pred             CCCChhHHHhcCCCCchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           11 TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        11 dF~lp~eil~vLP~DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ..+||++|...+       .++...+...|...-...|+.+...+...+.+-+....++..++..++.++
T Consensus        56 ~~~lP~~l~~~~-------~~~~~~~~~~a~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~e~  118 (120)
T PF11740_consen   56 APDLPEALQDAL-------AELMARLWEAAQEEAEEELEAARAELEQERAAAEAELAEAEAQAEELEAEL  118 (120)
T ss_pred             ccCCChhHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345555554422       356666777777777777777777777777777777777777777776654

These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=80.17  E-value=37  Score=36.39  Aligned_cols=50  Identities=18%  Similarity=0.283  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           31 DVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        31 dlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +-|+++....- .++.+|=.++...|.++.++.+.++.+++++..+..+|.
T Consensus       505 ~~A~~~~~~~~-~~~~~li~~l~~~~~~~e~~~~~~~~~~~e~~~~~~~l~  554 (782)
T PRK00409        505 EEAKKLIGEDK-EKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELE  554 (782)
T ss_pred             HHHHHHHhhhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555543211 144444444444444444444444444444444443333

>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins

Probab=80.12  E-value=25  Score=27.03  Aligned_cols=64  Identities=22%  Similarity=0.311  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      +.+|++-+.+=.+.+..|++++..+-.+..   .......++.+.-.+.-+.+...|+.+..-|..|
T Consensus        21 l~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~~k~~~v~~~~~~v~~~g~~v~~l   87 (90)
T PF06103_consen   21 LKKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHNTNELLEDVNEKLEKVDPVFEAVADLGESVSEL   87 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            344555555555566666666555555544   3333444444444444555555555555555444

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=80.09  E-value=38  Score=38.39  Aligned_cols=67  Identities=16%  Similarity=0.221  Sum_probs=32.1

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL-------SDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l-------~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      .++..++.++...++.+.+-...+..++.++..++..+       ..+|.++.++...+.+|...+...+..+.
T Consensus       882 ~~le~ae~~l~~~~~e~~~~~~e~~~a~~~l~~l~e~l~~~~eel~a~L~e~r~rL~~l~~el~~~~~~~~~a~  955 (1353)
T TIGR02680       882 ARAARAESDAREAAEDAAEARAEAEEASLRLRTLEESVGAMVDEIRARLAETRAALASGGRELPRLAEALATAE  955 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444333       35555666666666655555554443333

Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.

>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules

Probab=80.08  E-value=48  Score=30.35  Aligned_cols=65  Identities=18%  Similarity=0.306  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        49 E~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      |.|+..|+.+..++...+.++..=+..+|..+.       -.-.....+..++..|++.+..-+..+.+.++
T Consensus        22 E~e~~~l~~k~~e~~~~~~~m~~i~~e~Ek~i~~~i~e~~~~~~~~~~~i~~~~~erdq~~~dL~s~E~sfs   93 (207)
T PF05010_consen   22 EEEEQELKKKYEELHKENQEMRKIMEEYEKTIAQMIEEKQKQKELSEAEIQKLLKERDQAYADLNSLEKSFS   93 (207)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHHHHhhHHHHHHHHHHHHhhHH
Confidence            345555555555555554444444444444333       22223344555666666666665555554443

The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].

>TIGR03495 phage_LysB phage lysis regulatory protein, LysB family

Probab=80.06  E-value=23  Score=30.54  Aligned_cols=30  Identities=17%  Similarity=0.220  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           51 EHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        51 E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      +...||..+......+...+..+..+..+|
T Consensus        20 ~~~~l~~~~~~a~~~~~~~~~~l~~~~~qL   49 (135)
T TIGR03495        20 RLRNARADLERANRVLKAQQAELASKANQL   49 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence            334455555555555555544444444444

Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	272
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 50.6 bits (120), Expect = 2e-07
 Identities = 42/332 (12%), Positives = 89/332 (26%), Gaps = 104/332 (31%)

Query: 12  FDLPE------EVLQVLPSDPF-EQLDV--ARKITSIAISTRVSD--LESEHSALRSQ-- 58
           F+  E      ++L V   D F +  D    + +    +S    D  + S+ +   +   
Sbjct: 9   FETGEHQYQYKDILSVF-EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL 67

Query: 59  ---LAEKDSRIAE------LQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ 109
              L  K   + +      L+   + + S +  +  Q         ++ + L N  +   
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF- 126

Query: 110 RDVSKLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEG--- 166
              +K  V R      L+        A    +P  N     V       +      G   
Sbjct: 127 ---AKYNVSRLQPYLKLRQ-------ALLELRPAKN-----VL------ID-----GVLG 160

Query: 167 -GNSSFAEE----REPESSRPG----ISRG---------------FVLASQTSTPRLTPP 202
            G +  A +     + +         ++                         T R    
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220

Query: 203 GSPPSLSASVSP------TKTPKP--------VSPRRHSISFS-------TSRGMFDDRS 241
            +      S+           P          V   +   +F+       T+R     + 
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR----FKQ 276

Query: 242 --SILSSVHSSHSSISSSESGSQTGKLENFLL 271
               LS+  ++H S+          ++++ LL
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 50.2 bits (119), Expect = 3e-07
 Identities = 28/183 (15%), Positives = 58/183 (31%), Gaps = 52/183 (28%)

Query: 1   MLAKEPGAGSTFDLPEEVLQVLP----------------SDPFEQLDVARKITSIAISTR 44
           +L K        DLP EVL   P                 D ++ ++  +  T I  S  
Sbjct: 306 LLLKYLDC-RPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS-- 362

Query: 45  VSDLES-EHSALRSQLA--EKDSRI---------AELQSQ-IESIYSSLSDK-LGQAQAD 90
           ++ LE  E+  +  +L+     + I          ++    +  + + L    L + Q  
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422

Query: 91  KERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK-----DDEDASTGATRIAKPTPN 145
           +  +S     + +   +L+  +       +++V         D +D            P 
Sbjct: 423 ESTIS-----IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDD---------LIPPY 468

Query: 146 EDD 148
            D 
Sbjct: 469 LDQ 471

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.1 bits (98), Expect = 1e-04
 Identities = 28/135 (20%), Positives = 47/135 (34%), Gaps = 33/135 (24%)

Query: 15  PEEVLQVLPSDPFEQLD---VARKITSIAISTRVSDLESEHSALRSQLAEK--------- 62
           PE VL++L      Q+D    +R   S  I  R+  +++E   LR  L  K         
Sbjct: 195 PETVLEML-QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE---LRRLLKSKPYENCLLVL 250

Query: 63  ----DSRIAE---LQSQI--ESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS 113
               +++      L  +I   + +  ++D L  A      L   +  LT        D  
Sbjct: 251 LNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT-------PDEV 303

Query: 114 KLEVFRKTLVQSLKD 128
              +  K L    +D
Sbjct: 304 -KSLLLKYLDCRPQD 317

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	272
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	97.04
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	97.03
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	96.86
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	96.67
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	96.46
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	96.41
3bas_A	89	Myosin heavy chain, striated muscle/general contro	96.06
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	96.04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	95.88
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	95.68
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	95.41
3a7o_A	75	Autophagy protein 16; coiled-coil, coiled coil, cy	95.27
2b9c_A	147	Striated-muscle alpha tropomyosin; alpha-helix, co	95.23
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	95.19
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	94.97
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	94.88
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	94.86
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	94.66
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	94.35
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	94.23
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	94.13
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	94.12
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	94.04
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	93.95
3jsv_C	94	NF-kappa-B essential modulator; ubiquitin, coiled-	93.66
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	93.65
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	93.62
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	93.51
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	93.47
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	93.46
2q6q_A	74	Spindle POLE BODY component SPC42; SPC42P, budding	93.35
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	93.34
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	93.01
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	93.0
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	92.82
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	92.68
4emc_A	190	Monopolin complex subunit CSM1; RWD domain, kineto	92.64
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	92.59
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	92.52
4fm3_A	98	Uncharacterized hypothetical protein; PF14346 fami	91.65
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	91.64
1cii_A	602	Colicin IA; bacteriocin, ION channel formation, tr	91.62
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	91.6
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	91.41
2xnx_M	146	M protein, M1-BC1; cell adhesion, virulence factor	91.18
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	91.11
2akf_A	32	Coronin-1A; coiled coil, protein binding; 1.20A {S	90.8
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	90.67
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	90.66
1x4t_A	92	Hypothetical protein LOC57905; structural genomics	90.52
1gk4_A	84	Vimentin; intermediate filament, dimer, parallel c	90.47
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	90.44
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	90.41
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	90.29
2e7s_A	135	RAB guanine nucleotide exchange factor SEC2; coile	89.8
3etw_A	119	Adhesin A; antiparallel helix-loop-helix, leucine	89.32
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	88.95
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	88.82
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	88.7
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	88.7
1x79_B	112	RAB GTPase binding effector protein 1; rabaptin5,	88.7
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	88.65
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	88.6
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	88.33
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	88.19
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	87.7
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	87.55
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	87.53
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	87.34
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	87.14
2no2_A	107	HIP-I, huntingtin-interacting protein 1; clathrin	86.91
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	86.87
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	86.72
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	86.68
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	86.54
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	86.53
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	86.53
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	86.49
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	85.94
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	85.88
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	85.79
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	85.71
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	85.66
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	85.36
3mov_A	95	Lamin-B1; LMNB1, B-type lamins, intermediate filam	85.29
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	84.99
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	84.84
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	84.45
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	83.76
1d7m_A	101	Cortexillin I; coiled-coil, coiled-coil trigger si	83.45
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	83.2
3bas_A	89	Myosin heavy chain, striated muscle/general contro	83.03
4dci_A	150	Uncharacterized protein; PSI-biology, midwest cent	82.93
3he4_A	56	Synzip6; heterodimeric coiled-coil, de novo protei	82.79
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	82.42
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	82.3
3htk_A	60	Structural maintenance of chromosomes protein 5; S	81.93
2lw1_A	89	ABC transporter ATP-binding protein UUP; ABC REG s	81.75
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	81.73
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	81.46
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	81.37
4dyl_A	406	Tyrosine-protein kinase FES/FPS; structural genomi	80.73
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	80.6
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	80.57
1yf2_A	425	Type I restriction-modification enzyme, S subunit;	80.54
3k29_A	169	Putative uncharacterized protein; YSCO, type III s	80.43
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	80.1

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=97.04  E-value=0.0088  Score=49.73  Aligned_cols=71  Identities=14%  Similarity=0.207  Sum_probs=58.6

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024140           37 TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (272)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (272)
                      ++.=|+.-.-++..++..|++++.+++..|++|...+..++..+    ..+.+++.+|.+|++.|...+++|...
T Consensus        62 aALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~----e~~~~e~~~l~~~~~~l~~~~~~le~~  132 (138)
T 3hnw_A           62 MYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKA----ESSAKEIKELKSEINKYQKNIVKLETE  132 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556777778888999999999999999999998888777555    488888888888888888888888643

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A

Probab=97.03  E-value=0.017  Score=47.09  Aligned_cols=42  Identities=12%  Similarity=0.173  Sum_probs=22.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +|..+|..|+.++..+..++.+-...+..++.++..++..+.
T Consensus         3 ~~~~~~~~l~~~~~~~~~~~~~l~~~l~~l~~~~~~~~~~~~   44 (284)
T 1c1g_A            3 AIKKKMQMLKLDKENALDRADEAEADKKAAEDRSKQLEDELV   44 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455555555555555555555555555555555554444443

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=96.86  E-value=0.024  Score=44.55  Aligned_cols=77  Identities=16%  Similarity=0.212  Sum_probs=63.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      .+.-|+..+|.++..+.+....++..|..|+.|+..+|..|-   .+|..+.+....-.+-...-...|..|||-|.-||
T Consensus        20 ~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~ee~L~ea~~kLee~ek~~~~aE~ev~~L~RriqllE   99 (101)
T 3u1c_A           20 NALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQVLEELHKSEDSLLFAEENAAKAESEVASLNRRIQLVE   99 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            456688888999999999999999999999999999999987   66776666666555556666678999999888776

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

Probab=96.67  E-value=0.017  Score=61.07  Aligned_cols=80  Identities=18%  Similarity=0.318  Sum_probs=38.4

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRK  120 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk  120 (272)
                      ...+|..||.|+..|++++.+-..+..+|++++..+...|+.++....+++.+|.++.+.|...+.+.+.+.+  |.+|.
T Consensus       982 ~~~~v~~L~~e~~~l~~~~~~~~ke~~~lee~~~~~~~~L~~kv~~L~~e~~~L~qq~~~l~~~~~~~~~~~~--~~~~~ 1059 (1080)
T 2dfs_A          982 ATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKEIT--ETMEK 1059 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH
Confidence            3345555555555555555555555555555555555544444444444444444444444444444433222  23555


Q ss_pred             HH
Q 024140          121 TL  122 (272)
Q Consensus       121 ~L  122 (272)
                      .+
T Consensus      1060 ~~ 1061 (1080)
T 2dfs_A         1060 KL 1061 (1080)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=96.46  E-value=0.043  Score=42.86  Aligned_cols=77  Identities=16%  Similarity=0.238  Sum_probs=62.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      .+.-|+..+|.++..+.+....++..|..|+.|+..++..+-   .+|..+.+....-.+....-...|..|||-+.-||
T Consensus        20 ~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~e~l~~a~~kLe~~ek~~~~AE~evasLnRriqllE   99 (101)
T 3u59_A           20 NAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVKEAQEKLEQAEKKATDAEAEVASLNRRIQLVE   99 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            455678888899999999999999999999999999999886   66776666666666666666778999999887664

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=96.41  E-value=0.046  Score=46.70  Aligned_cols=75  Identities=19%  Similarity=0.215  Sum_probs=56.8

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhHHHH
Q 024140           37 TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT-VRKLQRDVSKL  115 (272)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~T-vKkL~rDvaKL  115 (272)
                      +-..+..-...|+.+|..|...+.+|...+..|++-+..|..++.    .+.++..+|++||+.|... +++-+++-.+|
T Consensus        69 ~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n----~lE~kl~kLq~EN~~LV~RWM~rk~qEAe~M  144 (152)
T 3a7p_A           69 TLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENN----VLQQKLSDLKKEHSQLVARWLKKTEKETEAM  144 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344556666777777777778888888888888888888877765    8899999999999988765 55666666554

>3bas_A Myosin heavy chain, striated muscle/general control protein GCN4 chimera; alpha-helical coiled coil, disorder, salt links; 2.30A {Argopecten irradians} SCOP: h.1.26.1 PDB: 1nkn_A 3bat_A

Probab=96.06  E-value=0.085  Score=40.53  Aligned_cols=70  Identities=20%  Similarity=0.269  Sum_probs=60.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      -+..++.|+..|+..+..-.....+|+.++..|..+..   ..|..+.+.+.+|.+.+..|...++.|+..|.
T Consensus        15 Em~~~eeel~~lke~l~k~e~~rkele~~~~~l~~ek~~L~~ql~eaEe~~~~L~~~K~eLE~~l~el~~rl~   87 (89)
T 3bas_A           15 EMKEQLKQMDKMKEDLAKTERIKKELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSKNYHLENEVARLKKLVG   87 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            45578999999999999888899999999988887765   44889999999999999999999999987653

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=96.04  E-value=0.072  Score=43.41  Aligned_cols=64  Identities=19%  Similarity=0.345  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           49 ESEHSALRSQLAEKDS---RIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        49 E~E~~~LR~~L~EKd~---~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      ..+|..|++.++.++.   .|.-|+.++.-....+.    .=+.+-++|+.|+..|...+..|++++.+|+
T Consensus        44 q~~idelk~ei~q~~~~lE~I~vLkaQv~IY~~DF~----aERadREkl~~eKe~L~~ql~~Lq~q~~~l~  110 (110)
T 2v4h_A           44 QELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQ----AERHAREKLVEKKEYLQEQLEQLQREFNKLK  110 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc----cchhhHHHHHhHHHHHHHHHHHHHHHHHhcC
Confidence            3566777777766666   55555555555544443    5556678999999999999999999998874

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

Probab=95.88  E-value=0.0074  Score=63.85  Aligned_cols=71  Identities=23%  Similarity=0.299  Sum_probs=19.6

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ..+||.++..|..+|.++.+...+|++++..++..+.   .+|+..+++.+++.+|+..+.+.|+.|..++++|
T Consensus       923 ~~~LE~kl~eLq~rL~~~e~~n~~L~~~~~~~~~~~~~e~~~L~~~l~~le~~~~e~~~~~~~v~~L~~e~~~l  996 (1080)
T 2dfs_A          923 HIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKL  996 (1080)
T ss_dssp             ----------------------------CHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4677777777777777766666666666554444443   3444444444444444444444444444444433

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=95.68  E-value=0.084  Score=45.67  Aligned_cols=79  Identities=20%  Similarity=0.397  Sum_probs=45.7

Q ss_pred             hhHHHHHHHHHHHH-HH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH---
Q 024140           47 DLESEHSALRSQLA-EK------DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE---  116 (272)
Q Consensus        47 ~LE~E~~~LR~~L~-EK------d~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE---  116 (272)
                      .||.|+..|..+|. ||      .+.|.+|+.|+..|+.+|.    ...+...++..||..|..-|-.|.+.-+-||   
T Consensus        66 ~Leke~~~LQa~L~qEr~~r~q~se~~~elq~ri~~L~~El~----~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~~eid~  141 (168)
T 3o0z_A           66 QTDKDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQEEVK----HLKHNLEKVEGERKEAQDMLNHSEKEKNNLEIDL  141 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence            45566666666666 55      3566888888888888876    3334444445555555555555555555554   


Q ss_pred             HHH-HHHHhhcccc
Q 024140          117 VFR-KTLVQSLKDD  129 (272)
Q Consensus       117 ~FK-k~LmqSLq~d  129 (272)
                      +|| |+|=++++-+
T Consensus       142 ~~eLKalQ~~~eqE  155 (168)
T 3o0z_A          142 NYKLKSLQQRLEQE  155 (168)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            344 4444444443

>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil (dimeric, parallel), familial hypertrophic cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo sapiens} SCOP: h.1.26.1 PDB: 2fxm_A

Probab=95.41  E-value=0.39  Score=38.84  Aligned_cols=69  Identities=20%  Similarity=0.400  Sum_probs=31.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIES-------IYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~-------le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      ..++.++..|+.+|..-.....+|+.+...       |..+|+   +.+..+.+.+.+|...+..|...++-|+.++..
T Consensus        16 ~~~~eel~~lke~l~k~e~~r~ele~~~~~l~~Ek~~L~~qL~~E~~~l~e~EE~~~~L~~~k~eLe~~l~el~~rlee   94 (129)
T 2fxo_A           16 ASMKEEFTRLKEALEKSEARRKELEEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNKRLED   94 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555555555554333333333333222       222222   444555555555555555555555555544443

>3a7o_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.50A {Saccharomyces cerevisiae}

Probab=95.27  E-value=0.12  Score=39.49  Aligned_cols=61  Identities=18%  Similarity=0.192  Sum_probs=43.6

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      -+.|+.-+..||..|.+||.+|..|++.+.---.    -.....+|..-|.=||+-|.+.+.+|.
T Consensus        13 ~~~~~~~l~~Lr~eL~~Ke~eI~~L~e~i~lk~k----d~ErLNDEiislNIENNlL~~rl~~l~   73 (75)
T 3a7o_A           13 DDALLNTLAILQKELKSKEQEIRRLKEVIALKNK----NTERLNDELISGTIENNVLQQKLSDLK   73 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc----cHHHhhHHHHHhHHHHHHHHHHHHHHh
Confidence            3456667899999999999999999977652222    223567788888888888877766654

>2b9c_A Striated-muscle alpha tropomyosin; alpha-helix, coiled coil, alanine, axial stagger, radius, SIDE-chain packing, crystal packing; 2.30A {Rattus norvegicus} SCOP: h.1.5.1

Probab=95.23  E-value=0.35  Score=40.49  Aligned_cols=76  Identities=16%  Similarity=0.223  Sum_probs=69.5

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      +++.--|+..||.++...+....+.|+...+...|+.-++..|.   .|+..+...+..|..|...+.+.+|.|...-.
T Consensus        47 ~~~deEr~~~lE~qLkeak~~aeeadrKyeE~~RKl~~~E~dLeraeeRae~aE~k~~eLEeeL~~~~~nlKsLE~~ee  125 (147)
T 2b9c_A           47 AQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEDKVE  125 (147)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             hcccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHH
Confidence            66778899999999999999999999999999999999999998   89999999999999999999999999875543

>3cvf_A Homer-3, homer protein homolog 3; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, phosphoprotein, polymorphism; 2.90A {Homo sapiens}

Probab=95.19  E-value=0.11  Score=40.01  Aligned_cols=56  Identities=25%  Similarity=0.395  Sum_probs=40.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTV  105 (272)
Q Consensus        46 s~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~Tv  105 (272)
                      ..||+|...+-++|.+-.....+|++||..|+..|.    .+..+...+..|-..|..+.
T Consensus         2 ~~l~~e~e~~~~klq~~E~rN~~Le~~v~~le~~Le----~s~~~q~~~~~Elk~l~e~L   57 (79)
T 3cvf_A            2 SHMAAEREETQQKVQDLETRNAELEHQLRAMERSLE----EARAERERARAEVGRAAQLL   57 (79)
T ss_dssp             --------CTTHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
Confidence            368899999999999999999999999999998877    77777777777766666553

>2efr_A General control protein GCN4 and tropomyosin 1 Al; destabilizing cluster, hydrophobic core, contractIle protein; 1.80A {Saccharomyces cerevisiae} PDB: 2efs_A 2d3e_A

Probab=94.97  E-value=0.61  Score=39.64  Aligned_cols=80  Identities=21%  Similarity=0.260  Sum_probs=60.2

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      ...+..|...+|.+|..|..+|.|-+.....-+..|..|+..+.   ++|......+..+..|-+..-+.+..+.-++-.
T Consensus        65 eekasqrEd~yEeqIk~L~~kLKEAE~RAE~AERsv~kLEk~id~lEd~L~~~Kek~~~i~~eLd~tl~el~~~~~~~~~  144 (155)
T 2efr_A           65 AEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEEMKQLEDKVEELLSKNYH  144 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHH
Confidence            55667899999999999999999998888888888888887776   667777777777777777655555555555444


Q ss_pred             HHH
Q 024140          115 LEV  117 (272)
Q Consensus       115 LE~  117 (272)
                      |++
T Consensus       145 ~~~  147 (155)
T 2efr_A          145 LEN  147 (155)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=94.88  E-value=0.17  Score=48.11  Aligned_cols=41  Identities=15%  Similarity=0.101  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140           89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus        89 ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      ++.++|.+.-+.-..+++.|.+++++++.=.|+|++-+++.
T Consensus       544 ~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~~~  584 (597)
T 3oja_B          544 QENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKNRN  584 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC--
T ss_pred             hhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            44444444444444577777777777766667777766654

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=94.86  E-value=0.46  Score=41.63  Aligned_cols=41  Identities=27%  Similarity=0.368  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      ..+..+|.+++..|...+++|...-.-||+=.|.+.-||.|
T Consensus        94 q~el~~l~~~~~~l~~~ireLEq~NDdlEr~~R~~~~SleD  134 (189)
T 2v71_A           94 EDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIMSLED  134 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhHHH
Confidence            34444555555555555555555555566666666655544

>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil (dimeric, parallel), familial hypertrophic cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo sapiens} SCOP: h.1.26.1 PDB: 2fxm_A

Probab=94.66  E-value=0.66  Score=37.46  Aligned_cols=76  Identities=18%  Similarity=0.353  Sum_probs=46.5

Q ss_pred             HHHhhhhhHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024140           41 ISTRVSDLESEHSALRSQLA-------EKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQR  110 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~-------EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~r  110 (272)
                      +-.+...|+.|...|..+|.       +++.....|..+-..|+..|.   .||..-.+.+..|..++..|...+..|..
T Consensus        39 le~~~~~l~~Ek~~L~~qL~~E~~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~  118 (129)
T 2fxo_A           39 LEEKMVSLLQEKNDLQLQVQAEQDNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKR  118 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455666777777666655       344444444444455555555   66666666667777777777777777766


Q ss_pred             hHHHHH
Q 024140          111 DVSKLE  116 (272)
Q Consensus       111 DvaKLE  116 (272)
                      |+.-||
T Consensus       119 ~led~e  124 (129)
T 2fxo_A          119 DIDDLE  124 (129)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666655

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=94.35  E-value=0.34  Score=45.97  Aligned_cols=22  Identities=27%  Similarity=0.335  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHH
Q 024140           92 ERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDva  113 (272)
                      .+|.+|+..|...+++-.+.+.
T Consensus       540 ~~~~~~~~~le~~~~~~~~~~~  561 (597)
T 3oja_B          540 EDLEQENIALEKQLDNKRAKQA  561 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhhHHHHHHHhhhhhHHH
Confidence            3333455555544444444443

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=94.23  E-value=0.033  Score=50.89  Aligned_cols=69  Identities=17%  Similarity=0.303  Sum_probs=26.9

Q ss_pred             HHhhhhhHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           42 STRVSDLESEHSALRSQLAEK---DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EK---d~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      +..|..|+.|+..||.+|.+-   .+.... ++|+..|+.++.    .....|.+|..+...|...+.+|..+|.+|
T Consensus        23 ~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~-~~~l~eL~~ql~----~L~arNe~L~~~Lk~ar~El~~LkeElerL   94 (251)
T 3m9b_A           23 AAELEQLRREAAVLREQLENAVGSHAPTRS-ARDIHQLEARID----SLAARNSKLMETLKEARQQLLALREEVDRL   94 (251)
T ss_dssp             -----------------------------C-CHHHHHHHHHHH----HHTTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhhhhcccCcccchh-hhHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            566677888888888888654   444333 455555555544    555566667777777777777777776665

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=94.13  E-value=0.18  Score=38.27  Aligned_cols=46  Identities=20%  Similarity=0.184  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEAL  101 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~L  101 (272)
                      +..|+..|.+|++.|...++++..||..|+    +.++++.+|+.|-|.+
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~----ekd~eI~~LqseLDKf   66 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELD----QKDELIQMLQNELDKY   66 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHh
Confidence            556666666666666666666666665554    5555555555554443

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=94.12  E-value=0.33  Score=39.61  Aligned_cols=53  Identities=26%  Similarity=0.293  Sum_probs=34.9

Q ss_pred             hHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Q 024140           48 LESEHSALRSQ----LAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEA  100 (272)
Q Consensus        48 LE~E~~~LR~~----L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~  100 (272)
                      |-.|+.+||..    ..|-.+.|.+|+.||+.|+.+|.   .-...|..+|..|..|...
T Consensus        20 Lkreie~lk~ele~l~~E~q~~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~   79 (120)
T 3i00_A           20 LYREISGLKAQLENMKTESQRVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDE   79 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444    45889999999999999999998   2233445555555555444

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=94.04  E-value=0.34  Score=51.23  Aligned_cols=75  Identities=11%  Similarity=0.235  Sum_probs=45.1

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      ++..|+.++..|+.+|..-+..+.+|++++..|+.++.          ..+..+.++..+|..++..|...++.|..++.
T Consensus       858 El~~L~~eL~el~~~L~~le~~l~ele~~l~~Le~e~~~l~~~L~~e~~~l~~~e~~l~~l~~~~~~Le~~l~ele~ele  937 (1184)
T 1i84_S          858 EMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIE  937 (1184)
T ss_dssp             HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456666777777666666666666666666555444          34444555666666666666666666666655


Q ss_pred             HHHHH
Q 024140          114 KLEVF  118 (272)
Q Consensus       114 KLE~F  118 (272)
                      .++.-
T Consensus       938 e~ee~  942 (1184)
T 1i84_S          938 EEEER  942 (1184)
T ss_dssp             HHHHC
T ss_pred             HHHHH
Confidence            54443

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=93.95  E-value=1.1  Score=36.24  Aligned_cols=61  Identities=11%  Similarity=0.213  Sum_probs=39.0

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKD----SRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENE   99 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd----~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~   99 (272)
                      ..+..++..|+.|+..+|.++..-.    ..|..||+.+..|-..-.   .+|+...+.|..|.....
T Consensus         6 rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R   73 (111)
T 2v66_B            6 RDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKR   73 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHH
Confidence            3577888999999999998887543    345666666665554433   555555555555555443

>3jsv_C NF-kappa-B essential modulator; ubiquitin, coiled-coil, cellular signaling, cytoplasm, isopeptide bond, nucleus, phosphoprotein, UBL conjugation; 2.70A {Mus musculus} PDB: 3f89_A 2zvo_B 2zvn_B

Probab=93.66  E-value=0.73  Score=36.58  Aligned_cols=66  Identities=20%  Similarity=0.351  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           48 LESEHSALRSQLAEKD---SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        48 LE~E~~~LR~~L~EKd---~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      ...+|..|++.++.+.   ..|.-|+.++.-....+.    .=+.+-++|..|+..|...+..|.+++.+|..
T Consensus        21 kq~~id~lke~~~q~~~~~E~i~vLk~Qv~IY~~DF~----aERadREkl~~eKe~L~~ql~~lq~q~~~L~~   89 (94)
T 3jsv_C           21 KQELIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQ----AERHAREKLVEKKEYLQEQLEQLQREFNKLKV   89 (94)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHTTSHHHHHHHHHHHTTC----
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            4567788888777666   666777777777766665    55667789999999999999999999999854

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=93.65  E-value=1.3  Score=38.95  Aligned_cols=82  Identities=9%  Similarity=0.127  Sum_probs=51.6

Q ss_pred             CchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           25 DPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT  104 (272)
Q Consensus        25 DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~T  104 (272)
                      ++-|-=+|-..|.  .+..|+..||.++..+..++.++...+.+++.++..++..|...-....+....+.+|...|...
T Consensus        88 ~~kE~~aL~kEie--~~~~~i~~lE~eile~~e~ie~~~~~l~~~~~~l~~~~~~l~~~~~~~~~~~~e~~~e~~~l~~~  165 (256)
T 3na7_A           88 SERELRSLNIEED--IAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLALELESLVENEVKNIKETQQIIFKK  165 (256)
T ss_dssp             SSSHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444445556666  45578888888888888888888888888888888888777633333333444444444444433


Q ss_pred             HHHH
Q 024140          105 VRKL  108 (272)
Q Consensus       105 vKkL  108 (272)
                      -..|
T Consensus       166 r~~l  169 (256)
T 3na7_A          166 KEDL  169 (256)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            3333

>1ic2_A Tropomyosin alpha chain, skeletal muscle; alpha-helical coiled coil, alanine, symmetry, axial stagger, BEND, contractIle protein; 2.00A {Gallus gallus} SCOP: h.1.5.1

Probab=93.62  E-value=1.4  Score=32.99  Aligned_cols=42  Identities=10%  Similarity=0.158  Sum_probs=22.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ||..|+..|+.|......++.+-...+.+.+.+...++..+.
T Consensus         3 ~ikkKm~~lk~e~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~   44 (81)
T 1ic2_A            3 AIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDELV   44 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            456666666666655555555555555555544444444443

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=93.51  E-value=0.86  Score=37.69  Aligned_cols=54  Identities=28%  Similarity=0.311  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           64 SRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        64 ~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      +.+..|+.++..++.++.   ..|..+..++..+.+|+..|...+..|.+.+.+||+
T Consensus        75 ~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~  131 (138)
T 3hnw_A           75 KMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLET  131 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444   555688899999999999999999999999999985

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=93.47  E-value=1.5  Score=34.05  Aligned_cols=71  Identities=13%  Similarity=0.241  Sum_probs=46.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      .|--||-.||.+-..|..++.+-..      ...+.+...+..-+..+......+..||..|...+..|..++..|+
T Consensus        20 syIdKVR~LEqqN~~Le~~i~~l~~------~~~~~~~~~ye~~i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~~~k   90 (93)
T 3s4r_A           20 NLIDKVRFLEQQNKILLAELEQLKG------QGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMRLR   90 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh------ccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999998888766643221      1223333333345556667777777888888888888777776553

>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1

Probab=93.46  E-value=1.5  Score=33.59  Aligned_cols=32  Identities=22%  Similarity=0.514  Sum_probs=14.9

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESI   76 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~l   76 (272)
                      ...++.++..|+....+-...|.+|++.+..+
T Consensus        12 ~~~~~~~l~~L~~~~~~l~~~i~~l~~~l~~l   43 (112)
T 1l8d_A           12 KTTIEEERNEITQRIGELKNKIGDLKTAIEEL   43 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444444444444444444444444444444

>2q6q_A Spindle POLE BODY component SPC42; SPC42P, budding yeast, cell cycle; 1.97A {Saccharomyces cerevisiae}

Probab=93.35  E-value=0.72  Score=35.04  Aligned_cols=59  Identities=25%  Similarity=0.352  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           51 EHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        51 E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      +-..|-.+|.+|+++|..|..=+.+|-    +||-.-.+-+.||+.+...+..-+..|++|+.
T Consensus         4 QNKeL~~kl~~Kq~EI~rLnvlvgslR----~KLiKYtelnKKLe~~~~~~q~s~~~l~k~~~   62 (74)
T 2q6q_A            4 QNKELNFKLREKQNEIFELKKIAETLR----SKLEKYVDITKKLEDQNLNLQIKISDLEKKLS   62 (74)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcc
Confidence            346788999999999988875555444    66668899999999999999999988888764

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=93.34  E-value=1.6  Score=35.11  Aligned_cols=27  Identities=19%  Similarity=0.295  Sum_probs=14.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRI   66 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i   66 (272)
                      -+...|+.|+.|+..|+.+-+-=...|
T Consensus        40 elrr~iq~L~~el~~l~~~~~~LE~~l   66 (129)
T 3tnu_B           40 EMNRMIQRLRAEIDNVKKQCANLQNAI   66 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            344556666666666655444333333

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=93.01  E-value=0.56  Score=55.07  Aligned_cols=86  Identities=19%  Similarity=0.281  Sum_probs=60.0

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHHHHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-----------------DKLGQAQADKERLSKENEALTNT  104 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-----------------~rL~~a~ee~~kL~~E~~~La~T  104 (272)
                      ..++.++|.+....+++|.++.+.+++|++++..|+.++.                 .||..|..=...|..|+..=..+
T Consensus      2013 r~~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA~~Li~gL~~Ek~RW~~~ 2092 (3245)
T 3vkg_A         2013 REEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQ 2092 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccHHHH
Confidence            3567777777777778888888888877777777776654                 44455555556778888877777


Q ss_pred             HHHHhhhHHHH------------------HHHHHHHHhhcc
Q 024140          105 VRKLQRDVSKL------------------EVFRKTLVQSLK  127 (272)
Q Consensus       105 vKkL~rDvaKL------------------E~FKk~LmqSLq  127 (272)
                      ++.|..+...|                  +.||+.|++...
T Consensus      2093 ~~~l~~~~~~L~GD~LLaaafisY~G~f~~~~R~~l~~~W~ 2133 (3245)
T 3vkg_A         2093 SENFNTQMSTVVGDVVLASAFLAYIGFFDQNFRTDLMRKWM 2133 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTGGGSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            77777666554                  457777766543

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=93.00  E-value=1.7  Score=38.32  Aligned_cols=28  Identities=14%  Similarity=0.220  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 024140           99 EALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (272)
Q Consensus        99 ~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (272)
                      ..+...+..+..+++.|..=+..|...|
T Consensus       146 ~~~~~~~~e~~~e~~~l~~~r~~l~~~i  173 (256)
T 3na7_A          146 SLVENEVKNIKETQQIIFKKKEDLVEKT  173 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3334444444455555554444555544

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=92.82  E-value=3.8  Score=37.99  Aligned_cols=63  Identities=16%  Similarity=0.282  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           55 LRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        55 LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      |+++|.|=..-..+++.+.+.....+.....-.+.+..+-++....|.+.|++||..+..+++
T Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  464 (471)
T 3mq9_A          402 LQQELTEAQKGFQDVEAQAATANHTVMALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASA  464 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444555555444333322111111222233334556677778888777766554

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A

Probab=92.68  E-value=0.85  Score=48.28  Aligned_cols=11  Identities=27%  Similarity=0.356  Sum_probs=4.0

Q ss_pred             hhHHHHHHHHH
Q 024140           47 DLESEHSALRS   57 (272)
Q Consensus        47 ~LE~E~~~LR~   57 (272)
                      .|+.+...|+.
T Consensus       889 ~Le~e~~~l~~  899 (1184)
T 1i84_S          889 QLCEEKNLLQE  899 (1184)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

>4emc_A Monopolin complex subunit CSM1; RWD domain, kinetochore-binding, kinetoch replication-replication complex; 3.05A {Saccharomyces cerevisiae} PDB: 3n7n_A 3n4x_A

Probab=92.64  E-value=0.37  Score=42.44  Aligned_cols=37  Identities=32%  Similarity=0.487  Sum_probs=33.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      |++|-.|...|+++|..|+.+|..|++++.+++.+..
T Consensus        22 V~~L~~En~~L~~ql~~k~~ei~~L~~ql~sl~~~~~   58 (190)
T 4emc_A           22 VANLVNENFVLSEKLDTKATEIKQLQKQIDSLNAQVK   58 (190)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            6789999999999999999999999999999987764

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=92.59  E-value=1.9  Score=37.75  Aligned_cols=67  Identities=12%  Similarity=0.221  Sum_probs=32.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSR----IAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVR  106 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~----i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvK  106 (272)
                      .+..++..|..|+..+|.++..=...    |..||+.+..|.....   .+|+...+.|..|......+..++.
T Consensus        60 ~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ireLEq~NDdlEr~~R~~~~Sle  133 (189)
T 2v71_A           60 DLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIMSLE  133 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhHH
Confidence            34455555555555555555432222    5555555555544443   4444555555555555444444443

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=92.52  E-value=1.5  Score=35.42  Aligned_cols=21  Identities=24%  Similarity=0.203  Sum_probs=12.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLA   60 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~   60 (272)
                      -+...|+.|+.|+..|+.+-+
T Consensus        42 elrr~iq~L~~el~~l~~~~~   62 (131)
T 3tnu_A           42 ELRRTMQNLEIELQSQLSMKA   62 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhHH
Confidence            344566677777666665444

>4fm3_A Uncharacterized hypothetical protein; PF14346 family protein, DUF4398, structural genomics, joint for structural genomics, JCSG; HET: PG4; 2.47A {Pseudomonas aeruginosa}

Probab=91.65  E-value=2  Score=34.18  Aligned_cols=87  Identities=13%  Similarity=0.246  Sum_probs=64.1

Q ss_pred             chhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           26 PFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAEL---QSQIESIYSSLSDKLGQAQADKERLSKENEALT  102 (272)
Q Consensus        26 P~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~L---q~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La  102 (272)
                      |.|||.++..-+..|....+.....|...-+.+|..-..-+.+=   +.|.-.=+.++-++|..+.-...|=++..+.|.
T Consensus         5 P~eql~~te~Ai~~A~~aga~~~apEl~~A~dKl~~A~~Am~~~~y~~Ar~lAEqAe~DArLAeAka~~~Ka~~~~~el~   84 (98)
T 4fm3_A            5 PLEQMRLTEQALEQAKAVGATDDVAELKLAQDKYAAAQIAMTAESYKKARLLAEQAELDARLAESKVLTQKSKDQLGELD   84 (98)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCTTSHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHCCcccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999989888888888655555321   112211222333778888888888888888888


Q ss_pred             HHHHHHhhhH
Q 024140          103 NTVRKLQRDV  112 (272)
Q Consensus       103 ~TvKkL~rDv  112 (272)
                      ..|..|..++
T Consensus        85 ~~I~~LrqEl   94 (98)
T 4fm3_A           85 KSLKRLRKQL   94 (98)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            8777776655

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=91.64  E-value=0.58  Score=35.49  Aligned_cols=37  Identities=19%  Similarity=0.287  Sum_probs=29.1

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      |-.|+..+..-.++|..||..|.+|++++...|..++
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~   57 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELDQKDELIQ   57 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6777777777777788888888888888888887775

>1cii_A Colicin IA; bacteriocin, ION channel formation, transmembrane protein; 3.00A {Escherichia coli} SCOP: f.1.1.1 h.4.3.1

Probab=91.62  E-value=1.8  Score=43.16  Aligned_cols=64  Identities=23%  Similarity=0.385  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        50 ~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      +|-.+||+.+.++...|..++.-++++...+.   ...+.|.+..+.+.+|+..+.+.+-.++..++
T Consensus       349 ae~~~lrQRlddArNEItsaeSaInslqaqvSa~t~e~k~A~d~l~a~~kek~~~~n~~a~~~~KiA  415 (602)
T 1cii_A          349 AEWDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEKENIRNQLSGINQKIA  415 (602)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHH
Confidence            57889999999999999999999998888888   67788999999999999999888877776654

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=91.60  E-value=3.6  Score=33.30  Aligned_cols=80  Identities=19%  Similarity=0.269  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus        50 ~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      ...+.|+.+..-=...+.+++.|+.....+.........++..+|..+++.|..-++.|...-.-||.=.|...-||.|=
T Consensus         3 k~~rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R~t~~SLeD~   82 (111)
T 2v66_B            3 QRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSLEDF   82 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHhhHHHH
Confidence            33455555555555556666666666555444445566677788888888888888888888888888888888887663

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1

Probab=91.41  E-value=0.4  Score=35.86  Aligned_cols=45  Identities=24%  Similarity=0.412  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           60 AEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        60 ~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      .-|+.+|.+|+.+|..|+....           .|..||..|-..|..|..++..|
T Consensus        25 eRK~~~i~~LE~~v~~le~~~~-----------~l~~en~~Lr~~i~~L~~El~~l   69 (70)
T 1gd2_E           25 KRKEDHLKALETQVVTLKELHS-----------STTLENDQLRQKVRQLEEELRIL   69 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHTTHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHc
Confidence            3588999999999887776443           46677777777777777665543

>2xnx_M M protein, M1-BC1; cell adhesion, virulence factor, streptococcal toxic shock S; 3.30A {Streptococcus pyogenes}

Probab=91.18  E-value=0.16  Score=43.20  Aligned_cols=37  Identities=22%  Similarity=0.337  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      ....+..||..|+..+...-+.|.||+.-...-||+|
T Consensus        98 ~LeAE~aKLeEekQIseASRqgLrRDLeASReAKKql  134 (146)
T 2xnx_M           98 QLTIEKAKLEEEKQISDASRQSLRRDLDASREAKKQV  134 (146)
T ss_dssp             HHHHHHHHHGGGTTTC---------------------
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555566655555555543

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=91.11  E-value=2.9  Score=35.61  Aligned_cols=30  Identities=23%  Similarity=0.279  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKL  115 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (272)
                      ...+|..-|+=+.+.|...+++|..+-.+|
T Consensus       100 ~l~DEl~aLqlq~n~lE~kl~kLq~EN~~L  129 (152)
T 3a7p_A          100 RLNAALISGTIENNVLQQKLSDLKKEHSQL  129 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455556666666666666666666655443

>2akf_A Coronin-1A; coiled coil, protein binding; 1.20A {Synthetic}

Probab=90.80  E-value=0.29  Score=31.71  Aligned_cols=30  Identities=23%  Similarity=0.422  Sum_probs=21.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      |++||.|++.|.       ..+.+||+|+..||..+|
T Consensus         1 isrlee~~r~l~-------~ivq~lq~r~drle~tvq   30 (32)
T 2akf_A            1 VSRLEEDVRNLN-------AIVQKLQERLDRLEETVQ   30 (32)
T ss_dssp             CCHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHH-------HHHHHHHHHHHHHHHHHh
Confidence            467888877775       455678888888877665

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=90.67  E-value=5.2  Score=31.77  Aligned_cols=71  Identities=15%  Similarity=0.240  Sum_probs=44.3

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        43 tRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      .+++..+.|+.+|+..|.+-...-.+.+.+...++.+|-    +-..+|+.+...-..++..+...+.+|...|.
T Consensus        19 ~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTasLFeEAN~MVa~ar~e~~~~e~kn~~L~~qL~   93 (97)
T 2eqb_B           19 RELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLR   93 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            556667788888888888666666666666666666655    33455555555555555555555555555443

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=90.66  E-value=4.5  Score=32.51  Aligned_cols=74  Identities=20%  Similarity=0.183  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 024140           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKT  121 (272)
Q Consensus        49 E~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~  121 (272)
                      ..|+..||..+..-...|..|+.+...||..|.       ..+..+...+..|..|...+-..+....++...|=+.|-.
T Consensus        37 k~Ei~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~em~~ql~EYq~Ll~vKl~  116 (131)
T 3tnu_A           37 KSEISELRRTMQNLEIELQSQLSMKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEYKILLDVKTR  116 (131)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555565555555555555555555555554       3344444455555555555555555556666656555544


Q ss_pred             H
Q 024140          122 L  122 (272)
Q Consensus       122 L  122 (272)
                      |
T Consensus       117 L  117 (131)
T 3tnu_A          117 L  117 (131)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1x4t_A Hypothetical protein LOC57905; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.2.15.1

Probab=90.52  E-value=0.31  Score=38.61  Aligned_cols=48  Identities=13%  Similarity=0.227  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           62 KDSRIAELQSQIESIYSSLS--DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        62 Kd~~i~~Lq~r~s~le~~l~--~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      +.+.|.|+-++|+.++..--  -+++..+|+++||.+|+..-...++.|.
T Consensus        30 R~qvikEIs~Kv~~Iqn~~L~E~~IRdLNDEINkL~rEK~~WE~rI~eLG   79 (92)
T 1x4t_A           30 RRQIIGEISKKVAQIQNAGLGEFRIRDLNDEINKLLREKGHWEVRIKELG   79 (92)
T ss_dssp             HHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            34566777777776654433  7888999999999999999999998875

>1gk4_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, stutter; 2.3A {Homo sapiens} SCOP: h.1.20.1

Probab=90.47  E-value=4.4  Score=30.50  Aligned_cols=67  Identities=18%  Similarity=0.267  Sum_probs=48.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      ++.+....||..+..+.....   ..+.+++.++..+|.+|+    .+.++.+....|-..|.+.=-+|.-+++
T Consensus         5 ~l~~~~~sLE~~l~e~e~~~~---~~~~~~q~~i~~lE~eL~----~~r~e~~~q~~EYq~LlnvK~~Ld~EIa   71 (84)
T 1gk4_A            5 ALKGTNESLERQMREMEENFA---VEAANYQDTIGRLQDEIQ----NMKEEMARHLREYQDLLNVKMALDIEIA   71 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            345566677777776666653   346788888999998887    7777777777888888776666665554

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=90.44  E-value=3.9  Score=31.57  Aligned_cols=63  Identities=13%  Similarity=0.224  Sum_probs=30.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      +||+-|..+=+.++-=...|.+|+++-..|..+.+   +.-....++|++|..|..+-...+.+|-
T Consensus        10 qLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~LL   75 (81)
T 2jee_A           10 KLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQALL   75 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444333333333333344444444444444443   1122355667777777777666666654

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=90.41  E-value=5  Score=32.12  Aligned_cols=75  Identities=15%  Similarity=0.209  Sum_probs=45.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 024140           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRK  120 (272)
Q Consensus        48 LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~-------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk  120 (272)
                      -..|+..||..+..-...|..|+.+...||..|.       ..+..+...+..|..|...+-..+....++...|=+.|-
T Consensus        34 ~k~Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EYq~LlnvKl  113 (129)
T 3tnu_B           34 TKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQELMNTKL  113 (129)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456666777666666666666666666666665       334444555555666666665666666666666666665


Q ss_pred             HH
Q 024140          121 TL  122 (272)
Q Consensus       121 ~L  122 (272)
                      .|
T Consensus       114 ~L  115 (129)
T 3tnu_B          114 AL  115 (129)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>1l8d_A DNA double-strand break repair RAD50 ATPase; zinc finger, DNA repair, recombination, HOOK motif, replication; HET: DNA CIT; 2.20A {Pyrococcus furiosus} SCOP: h.4.12.1

Probab=90.29  E-value=3.9  Score=31.27  Aligned_cols=38  Identities=21%  Similarity=0.444  Sum_probs=26.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        44 RVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      .+..++.++..++.+|.+-...+.+++.++..++..+.
T Consensus         4 ~~~~~~~~~~~~~~~l~~L~~~~~~l~~~i~~l~~~l~   41 (112)
T 1l8d_A            4 LLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIE   41 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566677777777777777777777777777776665

>2e7s_A RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 3.00A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.80  E-value=1.7  Score=36.45  Aligned_cols=46  Identities=17%  Similarity=0.329  Sum_probs=30.2

Q ss_pred             CchhhHHHHHHHHHHHHHHhhhhhHH---HHHHHHHHHHHHHHHHHHHHH
Q 024140           25 DPFEQLDVARKITSIAISTRVSDLES---EHSALRSQLAEKDSRIAELQS   71 (272)
Q Consensus        25 DP~EQLdlarkIts~A~atRVs~LE~---E~~~LR~~L~EKd~~i~~Lq~   71 (272)
                      |=.++|.++|++.+. ...|+.+||.   +...|...+..++..+..|+.
T Consensus         5 ~LEd~L~~~r~~l~~-~~~~~~~le~l~~~l~~l~~~l~~~~~e~~~L~~   53 (135)
T 2e7s_A            5 SLEEQLNKSLKTIAS-QKAAIENYNQLKEDYNTLKRELSDRDDEVKRLRE   53 (135)
T ss_dssp             -CCSTTTHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHTTTHHHHHHTHHH
T ss_pred             hHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            445788888886643 3677777776   555555566667777766665

>3etw_A Adhesin A; antiparallel helix-loop-helix, leucine chain, cell adhesin, cell adhesion; 2.00A {Fusobacterium nucleatum} PDB: 3ety_A 3etx_A 3etz_A 2gl2_A

Probab=89.32  E-value=7.9  Score=31.66  Aligned_cols=28  Identities=11%  Similarity=0.204  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 024140           92 ERLSKENEALTNTVRKLQRDVSKLEVFR  119 (272)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKLE~FK  119 (272)
                      .++.+.+..|...+|+...=|.-+|.+|
T Consensus        78 k~Y~~~~keLd~~ik~qekiIdnFE~ik  105 (119)
T 3etw_A           78 SKYEDALKKLEAEMEQQKAVISDFEKIQ  105 (119)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5666677777777777777666666654

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=88.95  E-value=0.57  Score=44.40  Aligned_cols=39  Identities=15%  Similarity=0.371  Sum_probs=24.4

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        42 atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ++++..|+.|+..|+++..+.++.|++++.++..++..|
T Consensus         2 ~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~   40 (403)
T 4etp_A            2 ASKIAALKEKIAALKEKIAALKEKIKDTELGMKELNEIL   40 (403)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355667777777777777777777777766655555433

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=88.82  E-value=4.7  Score=30.44  Aligned_cols=46  Identities=17%  Similarity=0.311  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           55 LRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT  104 (272)
Q Consensus        55 LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~T  104 (272)
                      +-++|.+-.....+|++||..|+..|.    .+..++..+..|-..|..+
T Consensus         5 ~~~kLq~~E~~N~~Le~~v~~le~~Le----~s~~~q~~~~~Elk~~~e~   50 (72)
T 3cve_A            5 SHMKLQEVEIRNKDLEGQLSEMEQRLE----KSQSEQDAFRSNLKTLLEI   50 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHH
Confidence            445666666777788888888887665    6666666666665555544

>1go4_E MAD1 (mitotic arrest deficient)-like 1; mitotic spindle checkpoint, cell cycle, mitosis, nuclear Pro; 2.05A {Homo sapiens} SCOP: h.1.22.1

Probab=88.70  E-value=2.1  Score=34.10  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=13.2

Q ss_pred             HHHHHhhhhhHHHHHHHHHHH
Q 024140           39 IAISTRVSDLESEHSALRSQL   59 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L   59 (272)
                      ..+..+|..||.|..+||+..
T Consensus        15 ~~lr~ei~~Le~E~~rLr~~~   35 (100)
T 1go4_E           15 DTLRLKVEELEGERSRLEEEK   35 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            345566677777777776543

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B*

Probab=88.70  E-value=6.7  Score=38.42  Aligned_cols=73  Identities=11%  Similarity=0.145  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           54 ALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADK--ERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        54 ~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~--~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      .|+..+.+++..+.+++..+......|... ....++.  .+....-..|...+..|+..|.+||..-.+++..+.
T Consensus       125 ~Iq~slk~~Q~Qi~en~n~~~~~~~~~e~~-~~~i~~~~~~~~~~~i~~L~~~~~~l~~ki~~l~~~~~~~~~~~~  199 (464)
T 1m1j_B          125 MIDNKLVKTQKQRKDNDIILSEYNTEMELH-YNYIKDNLDNNIPSSLRVLRAVIDSLHKKIQKLENAIATQTDYCR  199 (464)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhhcccccccchhhHHHHHHHHHHHH-HHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            355566666666666666666655555411 1111111  123444556777788888888888888777776554

>1x79_B RAB GTPase binding effector protein 1; rabaptin5, GGA protein, GAT domain, intracellular trafficking, protein transport; 2.41A {Homo sapiens} SCOP: h.1.27.2

Probab=88.70  E-value=2.1  Score=34.78  Aligned_cols=16  Identities=25%  Similarity=0.202  Sum_probs=8.1

Q ss_pred             hhhhHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLA   60 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~   60 (272)
                      +.+|..+.+.|+.+|.
T Consensus         8 ~~~lq~~~~ql~~qL~   23 (112)
T 1x79_B            8 VKKLQLMLRQANDQLE   23 (112)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3445555555555544

>1ic2_A Tropomyosin alpha chain, skeletal muscle; alpha-helical coiled coil, alanine, symmetry, axial stagger, BEND, contractIle protein; 2.00A {Gallus gallus} SCOP: h.1.5.1

Probab=88.65  E-value=3  Score=31.14  Aligned_cols=42  Identities=14%  Similarity=0.249  Sum_probs=30.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ....|+..+|.++..........+..|..|+.|+..||..|-
T Consensus        17 ~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld   58 (81)
T 1ic2_A           17 NALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELD   58 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence            345677777777777777777777777777777777777665

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=88.60  E-value=2  Score=43.10  Aligned_cols=60  Identities=23%  Similarity=0.264  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH---------------------HHHHHHHHHHhhc
Q 024140           68 ELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS---------------------KLEVFRKTLVQSL  126 (272)
Q Consensus        68 ~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva---------------------KLE~FKk~LmqSL  126 (272)
                      +|++++..|+..++    .-...+..|++-.+.+...++||.-||+                     --|+.-|+|.|-+
T Consensus       114 ELRRrIqyLKekVd----nQlsnIrvLQsnLedq~~kIQRLEvDIdiqirsCKgsCsr~~~~~vd~~sY~~~QKQLeQv~  189 (562)
T 3ghg_A          114 DLRSRIEVLKRKVI----EKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYEDQQKQLEQVI  189 (562)
T ss_dssp             HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTBSCCCCCCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchheeecchHHHHHHHHHHHHHh
Confidence            45555554444444    2223334455444555555555555543                     2567888998876


Q ss_pred             ccccc
Q 024140          127 KDDED  131 (272)
Q Consensus       127 q~d~~  131 (272)
                      --|-.
T Consensus       190 a~dL~  194 (562)
T 3ghg_A          190 AKDLL  194 (562)
T ss_dssp             TTCCC
T ss_pred             hcccC
Confidence            66544

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D

Probab=88.33  E-value=3.1  Score=29.80  Aligned_cols=34  Identities=29%  Similarity=0.477  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           85 GQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        85 ~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      ....++...|.++|..|...|..|...+..|+.+
T Consensus        26 ~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~~   59 (63)
T 2wt7_A           26 DTLQAETDQLEDEKSALQTEIANLLKEKEKLEFI   59 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444556677778888888888888888877654

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=88.19  E-value=12  Score=32.28  Aligned_cols=81  Identities=19%  Similarity=0.203  Sum_probs=39.9

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKT  121 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~  121 (272)
                      ++.+|.-++.|+.++.-=...-..|++.+..|+.+|.   .-..+..+.+..|+.....|..-++.+.--..|++.=+|+
T Consensus        43 ~~~~E~~~rELq~~~~~L~~~k~~Leke~~~LQa~L~qEr~~r~q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~  122 (168)
T 3o0z_A           43 ISQLESLNRELQERNRILENSKSQTDKDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKE  122 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555555555444444455555555555554   1223334444445555555555555555555555555555


Q ss_pred             HHhh
Q 024140          122 LVQS  125 (272)
Q Consensus       122 LmqS  125 (272)
                      |--.
T Consensus       123 L~Ek  126 (168)
T 3o0z_A          123 AQDM  126 (168)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5433

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=87.70  E-value=8.3  Score=29.94  Aligned_cols=42  Identities=7%  Similarity=0.151  Sum_probs=27.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ||+.++..|..|....-.+..+-...+.+++.+...+|.++.
T Consensus         6 aIKkKm~~lk~e~e~a~drae~~e~~~k~~e~~~~~~E~Ei~   47 (101)
T 3u1c_A            6 AIKKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDDIV   47 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            677788777777666666666555556666666555555554

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=87.55  E-value=5.5  Score=28.11  Aligned_cols=32  Identities=28%  Similarity=0.357  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      ...++...|..||..|...|..|..++..|+.
T Consensus        26 ~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk~   57 (61)
T 1t2k_D           26 SLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQ   57 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455556677778888888888888777753

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=87.53  E-value=8.5  Score=29.85  Aligned_cols=77  Identities=16%  Similarity=0.267  Sum_probs=38.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      |+...+..|+.|-.+|.+.|.+=+..-+.|...+..++.++.          .....-.-....+++|+++|.++..--.
T Consensus         8 ~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~eE~~~w~eyn~~~~ql~e~~dE~~Sl~~q~~~~~   87 (96)
T 3q8t_A            8 QLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVENQMRYAQ   87 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555554333333333333333333332          1112233344667778888887777666


Q ss_pred             hhHHHHH
Q 024140          110 RDVSKLE  116 (272)
Q Consensus       110 rDvaKLE  116 (272)
                      ..+.||.
T Consensus        88 ~qLdkL~   94 (96)
T 3q8t_A           88 MQLDKLK   94 (96)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhh
Confidence            6666663

>3mq7_A Bone marrow stromal antigen 2; HIV, antiviral protein; 2.28A {Homo sapiens} PDB: 3mqc_A 3mqb_A 3mkx_A 3nwh_A 2xg7_A* 2x7a_A

Probab=87.34  E-value=3  Score=34.38  Aligned_cols=33  Identities=15%  Similarity=0.300  Sum_probs=14.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        48 LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      ||.++..-.+-|.+++.....-..-|..|-..|
T Consensus        30 Lq~qLTqAQe~l~~~eaQAaTCNqTV~tL~~SL   62 (121)
T 3mq7_A           30 LQQELTEAQKGFQDVEAQAATANHTVMALMASL   62 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444444

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=87.14  E-value=7  Score=39.24  Aligned_cols=64  Identities=16%  Similarity=0.132  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           55 LRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        55 LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      +.+.|.++.....+++..+.++-.+|..++..+.++.+.-..-..+|.+.|+.+.-++.|||+=
T Consensus        90 ~~E~Lr~rq~q~~dNdNtynE~S~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvD  153 (562)
T 3ghg_A           90 IMEILRGDFSSANNRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVD  153 (562)
T ss_dssp             HHHTTSSHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444445555555544444442222333332222245566666666666666666653

>2no2_A HIP-I, huntingtin-interacting protein 1; clathrin light chain binding, HIP1 coiled-coil domain, endocytosis, clathrin SELF-assembly, cell adhesion; 2.80A {Homo sapiens}

Probab=86.91  E-value=10  Score=30.09  Aligned_cols=39  Identities=21%  Similarity=0.232  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ  124 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lmq  124 (272)
                      ...++...|.+..+.+.+.=.+|+-.++-|+.-|..|+.
T Consensus        65 ~~~~el~~lq~~l~~~~~~~~~l~~~~~~l~~Ek~~L~~  103 (107)
T 2no2_A           65 TSQRELQVLQGSLETSAQSEANWAAEFAELEKERDSLVS  103 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            334444444444444444444455555555555555554

>1x8y_A Lamin A/C; structural protein, intermediate filament protein; 2.20A {Homo sapiens} SCOP: h.1.20.1 PDB: 3v5b_A 3v4w_A 3v4q_A

Probab=86.87  E-value=3.2  Score=31.52  Aligned_cols=66  Identities=11%  Similarity=0.153  Sum_probs=39.0

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        41 ~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      +.+....||..+..+....   ...+.+++..+..+|.+|+    .+..+.+....|-..|.+.=-+|--+++
T Consensus         8 L~~q~~~Le~~l~e~E~~~---~~~l~~~q~~i~~lE~el~----~~r~e~~~ql~EYq~LlnvK~~Le~EIa   73 (86)
T 1x8y_A            8 LQCQLAAKEAKLRDLEDSL---ARERDTSRRLLAEKEREMA----EMRARMQQQLDEYQELLDIKLALDMEIH   73 (86)
T ss_dssp             ----CTTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            3444455665555555544   3355667777777777776    6666666667777777766556655554

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=86.72  E-value=1.3  Score=34.38  Aligned_cols=35  Identities=37%  Similarity=0.530  Sum_probs=20.8

Q ss_pred             HHHHHhhhhhHHH--------------HHHHHHHHHHHHHHHHHHHHHH
Q 024140           39 IAISTRVSDLESE--------------HSALRSQLAEKDSRIAELQSQI   73 (272)
Q Consensus        39 ~A~atRVs~LE~E--------------~~~LR~~L~EKd~~i~~Lq~r~   73 (272)
                      +-+.-||+.||.|              +..|+++|.+||..|.-|+.++
T Consensus        29 ~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l   77 (81)
T 3qh9_A           29 RHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQL   77 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            3455667666644              5566666666666666665544

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=86.68  E-value=6  Score=30.26  Aligned_cols=9  Identities=44%  Similarity=0.671  Sum_probs=4.8

Q ss_pred             HHhhhhhHH
Q 024140           42 STRVSDLES   50 (272)
Q Consensus        42 atRVs~LE~   50 (272)
                      ..||..||.
T Consensus         5 e~rv~~LEr   13 (83)
T 2xdj_A            5 EDRVTQLER   13 (83)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            445555554

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=86.54  E-value=15  Score=34.05  Aligned_cols=18  Identities=11%  Similarity=0.121  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 024140           64 SRIAELQSQIESIYSSLS   81 (272)
Q Consensus        64 ~~i~~Lq~r~s~le~~l~   81 (272)
                      .....||+++..++.-|.
T Consensus       397 ~~~~~~~~~~~~~~~~~~  414 (471)
T 3mq9_A          397 NVTHLLQQELTEAQKGFQ  414 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhhHH
Confidence            333455555555555544

>3s9g_A Protein hexim1; cyclin T-binding domain (TBD), cyclin T1/P-TEFB/7SK snRNA, N transcription; 2.10A {Homo sapiens} PDB: 2gd7_A

Probab=86.53  E-value=3.3  Score=33.32  Aligned_cols=50  Identities=28%  Similarity=0.483  Sum_probs=31.8

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENE   99 (272)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~   99 (272)
                      +-+-.|+++||.|..+||..-.+=...|.+|+..|.           ....+|..|..||.
T Consensus        40 l~LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~eve-----------rL~~ENq~L~~e~~   89 (104)
T 3s9g_A           40 LELEKSLSRMEDENNRLRLESKRLDARVRELELELD-----------RLRAENLQLLTENE   89 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHH-----------HHHHHHHHHHHHHH
Confidence            456678888999999988875555555555554433           34445555655554

>1x8y_A Lamin A/C; structural protein, intermediate filament protein; 2.20A {Homo sapiens} SCOP: h.1.20.1 PDB: 3v5b_A 3v4w_A 3v4q_A

Probab=86.53  E-value=6.5  Score=29.79  Aligned_cols=66  Identities=15%  Similarity=0.246  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        50 ~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      .|+..||.+.+..+..|.+++.++.       ..+.........|..|...+-..+....++...|=+.|-.|
T Consensus         3 ~eie~L~~q~~~Le~~l~e~E~~~~-------~~l~~~q~~i~~lE~el~~~r~e~~~ql~EYq~LlnvK~~L   68 (86)
T 1x8y_A            3 CQLSQLQCQLAAKEAKLRDLEDSLA-------RERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLAL   68 (86)
T ss_dssp             ---------CTTHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4666777776666666666655543       22334445555555565566666666666666666665443

>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine exchange factor, coiled-coil, endocytosis/exocytosis complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=86.49  E-value=14  Score=31.33  Aligned_cols=21  Identities=24%  Similarity=0.485  Sum_probs=10.0

Q ss_pred             HHHHhhhHHHHHHHHHHHHhhcccc
Q 024140          105 VRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus       105 vKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      +..|+..|..|    |++|+.+.+|
T Consensus       131 l~~lq~ql~~L----K~v~~~m~~e  151 (154)
T 2ocy_A          131 LDTLTLQLKNL----KKVMHSLDNE  151 (154)
T ss_dssp             HHHHHHHHHHH----HHTTSCCC--
T ss_pred             HHHHHHHHHHH----HHHHHHhhhc
Confidence            34445555555    5566665554

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=85.94  E-value=3.6  Score=31.88  Aligned_cols=34  Identities=32%  Similarity=0.411  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           85 GQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        85 ~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      ....++...|.+||..|...|..|..+|..|..+
T Consensus        39 ~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~Lr~l   72 (87)
T 1hjb_A           39 LETQHKVLELTAENERLQKKVEQLSRELSTLRNL   72 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455677889999999999999999999888543

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=85.88  E-value=3.7  Score=31.42  Aligned_cols=44  Identities=18%  Similarity=0.319  Sum_probs=29.0

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           37 TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (272)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l   80 (272)
                      .-.-+..++..|..||..||-++.+-...|..|++|-..+-..|
T Consensus        21 ~~~~Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~rQrd~Y~dL   64 (83)
T 2xdj_A           21 LLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQI   64 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556667777777777777777777777777766655544444

>1lwu_C Fibrinogen gamma chain; heterotrimer, protein-peptide complex, blood clotting; HET: NDG MAN NAG BMA GAL; 2.80A {Petromyzon marinus} SCOP: d.171.1.1 h.1.8.1 PDB: 1n73_C*

Probab=85.79  E-value=2.3  Score=39.78  Aligned_cols=42  Identities=17%  Similarity=0.103  Sum_probs=32.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ++..++++|..|+.+|...+...+..|..|++++..++..|+
T Consensus         2 ~~~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~   43 (323)
T 1lwu_C            2 SGQKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVT   43 (323)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHH
Confidence            456788999999999988888888888888888777665544

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=85.71  E-value=2  Score=30.97  Aligned_cols=35  Identities=23%  Similarity=0.337  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           83 KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      +.....++...|.++|+.|...|..|.+++.-|..
T Consensus        24 ~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~   58 (63)
T 1ci6_A           24 EQEALTGECKELEKKNEALKERADSLAKEIQYLKD   58 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455667778888999999999999999888844

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=85.36  E-value=2.2  Score=40.45  Aligned_cols=28  Identities=25%  Similarity=0.364  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           52 HSALRSQLAEKDSRIAELQSQIESIYSS   79 (272)
Q Consensus        52 ~~~LR~~L~EKd~~i~~Lq~r~s~le~~   79 (272)
                      +..|+.++.+-.+.+.+|++++..++.+
T Consensus         5 ~~~~~~~~~~l~~~~~~l~~~~~~~~~~   32 (403)
T 4etp_A            5 IAALKEKIAALKEKIAALKEKIKDTELG   32 (403)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444433

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A

Probab=84.99  E-value=3  Score=29.66  Aligned_cols=35  Identities=20%  Similarity=0.389  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 024140           83 KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (272)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (272)
                      ++....++...|..||+.|...|..|...++.|+.
T Consensus        23 ~~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk~   57 (62)
T 1jnm_A           23 RIARLEEKVKTLKAQNSELASTANMLREQVAQLKQ   57 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445556667778888888888888888877743

>4ghu_A TNF receptor-associated factor 3; alpha/beta, innate immunity, IFN pathway, immune system; 2.20A {Mus musculus} PDB: 2gkw_A 1kzz_A 1l0a_A 1zms_A 1rf3_A

Probab=84.84  E-value=1.2  Score=37.94  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=26.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (272)
Q Consensus        47 ~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~   78 (272)
                      .||..++.|...|..|+..|.+|++|+..+|.
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   35 (198)
T 4ghu_A            4 LLESQLSRHDQMLSVHDIRLADMDLRFQVLET   35 (198)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            67888888888888898888888888776663

>1ik9_A DNA repair protein XRCC4; DNA END joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil; HET: DNA; 2.30A {Homo sapiens} SCOP: b.59.1.1 h.1.11.1 PDB: 3ii6_A* 1fu1_A* 3rwr_A*

Probab=84.45  E-value=18  Score=31.64  Aligned_cols=90  Identities=16%  Similarity=0.288  Sum_probs=51.8

Q ss_pred             CCchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           24 SDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (272)
Q Consensus        24 ~DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~  103 (272)
                      .||++   +-+.+..+++-. +..|+.++..|..+.....+.+.+|.+++..+-             ++|-.-|.+-+..
T Consensus       117 ~d~~e---~i~elfd~~~~~-~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~v-------------~~K~~~E~~L~~K  179 (213)
T 1ik9_A          117 ENPAE---VIRELIAYALDT-IAENQAKNEHLQKENERLLRDWNDVQGRFEKAV-------------SAKEALETDLYKR  179 (213)
T ss_dssp             SCHHH---HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHH
T ss_pred             CChHH---HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHH
Confidence            45554   223334444433 557777777777666665555555554333221             1333456666666


Q ss_pred             HHHHHhhhHHHHHHHHHHHHhhccccc
Q 024140          104 TVRKLQRDVSKLEVFRKTLVQSLKDDE  130 (272)
Q Consensus       104 TvKkL~rDvaKLE~FKk~LmqSLq~d~  130 (272)
                      -|--||--=+|+..+++.|++..|+.+
T Consensus       180 F~~lLNeKK~KIR~lq~~Ll~~~~~~~  206 (213)
T 1ik9_A          180 FILVLNEKKTKIRSLHNKLLNAAQERE  206 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHhh
Confidence            677777777777777777777666543

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=83.76  E-value=13  Score=28.60  Aligned_cols=42  Identities=7%  Similarity=0.141  Sum_probs=24.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      ||+.++..|--|....-.+...-...+.+++.+...++..+.
T Consensus         6 ~iKkKm~~lk~e~e~a~d~ae~~e~~~k~~e~~~~~~E~ei~   47 (101)
T 3u59_A            6 AIKKKMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQ   47 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            677777777666655555555555555555555555555443

>1d7m_A Cortexillin I; coiled-coil, coiled-coil trigger site, alpha helix, dimeriza contractIle protein; 2.70A {Dictyostelium discoideum} SCOP: h.1.10.1

Probab=83.45  E-value=15  Score=29.16  Aligned_cols=42  Identities=24%  Similarity=0.413  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           34 RKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIES   75 (272)
Q Consensus        34 rkIts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~   75 (272)
                      -|...--++.....||+-...||.+-+++..+|.+||.|+..
T Consensus        16 EK~S~eeL~kQk~eL~~~l~~l~~e~~~R~~~i~el~akidd   57 (101)
T 1d7m_A           16 EKVSREQLIKQKDQLNSLLASLESEGAEREKRLRELEAKLDE   57 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455667777889999999999999999999999988764

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=83.20  E-value=5  Score=30.23  Aligned_cols=29  Identities=10%  Similarity=0.150  Sum_probs=13.4

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140          101 LTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus       101 La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      |..+|-+.++++++|+.-=+.|.+-|++-
T Consensus        33 Ln~~v~~Qq~~Id~L~~ql~~L~~rl~~~   61 (78)
T 3efg_A           33 LSEALADARLTGARNAELIRHLLEDLGKV   61 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44445555555555555555555555443

>3bas_A Myosin heavy chain, striated muscle/general control protein GCN4 chimera; alpha-helical coiled coil, disorder, salt links; 2.30A {Argopecten irradians} SCOP: h.1.26.1 PDB: 1nkn_A 3bat_A

Probab=83.03  E-value=13  Score=28.15  Aligned_cols=61  Identities=11%  Similarity=0.204  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 024140           58 QLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (272)
Q Consensus        58 ~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (272)
                      .+..|+..+..|++++...+...    +...+.+.+|..|++.|..++....--+++|..-|..|
T Consensus        15 Em~~~eeel~~lke~l~k~e~~r----kele~~~~~l~~ek~~L~~ql~eaEe~~~~L~~~K~eL   75 (89)
T 3bas_A           15 EMKEQLKQMDKMKEDLAKTERIK----KELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSKNYHL   75 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            34456666777776666665444    47777777888888888777444444445555544444

>4dci_A Uncharacterized protein; PSI-biology, midwest center for structural genomics, MCSG, S genomics, unknown function; 2.82A {Synechococcus SP}

Probab=82.93  E-value=8.4  Score=32.53  Aligned_cols=63  Identities=17%  Similarity=0.258  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 024140           62 KDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEA-------------LTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (272)
Q Consensus        62 Kd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~-------------La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (272)
                      |+....+|++++..+|.+|+    +..-+..++.+|...             +.+--...+...++++..|++|.+-|+.
T Consensus        27 Ke~l~~~l~~~i~q~d~elq----QLefq~kr~~~e~~~q~~~~~~p~~~~qi~~iq~q~~~ek~~r~e~k~~l~~ql~q  102 (150)
T 4dci_A           27 KEEAEREISNGIANADQQLA----QLEQEGQTVVDQVRRQSANPLDPRVQEQVANIQQQVAGKRSELEEQKRNLLQQQAQ  102 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56667777777777777776    333333333333221             1122244555666666677666655543

>3he4_A Synzip6; heterodimeric coiled-coil, de novo protein; 2.46A {Artificial gene}

Probab=82.79  E-value=0.74  Score=32.83  Aligned_cols=28  Identities=29%  Similarity=0.516  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 024140           87 AQADKERLSKENEALTNTVRKLQRDVSK  114 (272)
Q Consensus        87 a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (272)
                      .+.+++.|.+...+|..-+-.|.|||++
T Consensus        29 lendnanlekdianlekdianlerdvar   56 (56)
T 3he4_A           29 LENDNANLEKDIANLEKDIANLERDVAR   56 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HhcccchHHHHHHHHHHHHHHHHHhhcC
Confidence            3456777777777777777777777753

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=82.42  E-value=5  Score=28.34  Aligned_cols=39  Identities=21%  Similarity=0.245  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           61 EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (272)
Q Consensus        61 EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~La~  103 (272)
                      -|...+.+|+.++..|+.+-.    ....++..|..|+..|-+
T Consensus        19 rKk~~~~~Le~~~~~L~~~n~----~L~~~i~~L~~e~~~Lk~   57 (61)
T 1t2k_D           19 KRKVWVQSLEKKAEDLSSLNG----QLQSEVTLLRNEVAQLKQ   57 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Confidence            455677778777777665543    444445555555555443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=82.30  E-value=12  Score=34.73  Aligned_cols=27  Identities=22%  Similarity=0.279  Sum_probs=16.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHH
Q 024140           40 AISTRVSDLESEHSALRSQLAEKDSRI   66 (272)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L~EKd~~i   66 (272)
                      .+..+...||..+..+|....+.+...
T Consensus       364 ~l~~~~~~le~~~~~~~~~~~~~~~~~  390 (487)
T 3oja_A          364 TLEQKKKALDEQVSNGRRAHAELDGTL  390 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhH
Confidence            555556666666666666655555444

>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=81.93  E-value=8.2  Score=26.68  Aligned_cols=48  Identities=15%  Similarity=0.250  Sum_probs=24.5

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSK   96 (272)
Q Consensus        45 Vs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~   96 (272)
                      +.+||..+..+..+..++.+.+..+..++..+...|.    .+.+++.+|..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~----~~~~~I~~~k~   54 (60)
T 3htk_A            7 KKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLN----TIRDEVIKKKN   54 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
Confidence            3445555555555555555555555555555444443    55555555443

>2lw1_A ABC transporter ATP-binding protein UUP; ABC REG subfamily, DNA binding protein; NMR {Escherichia coli}

Probab=81.75  E-value=9.2  Score=28.77  Aligned_cols=16  Identities=13%  Similarity=0.495  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHHHHH
Q 024140           65 RIAELQSQIESIYSSL   80 (272)
Q Consensus        65 ~i~~Lq~r~s~le~~l   80 (272)
                      .|..|+.++..|+..|
T Consensus        30 ~Ie~LE~~i~~le~~l   45 (89)
T 2lw1_A           30 LLEDLEAKLEALQTQV   45 (89)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3334444444444433

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=81.73  E-value=10  Score=29.20  Aligned_cols=31  Identities=19%  Similarity=0.342  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (272)
                      +..++|..|..|+..+.+....|.++..+|.
T Consensus        31 ELKekN~~L~~e~~e~~~~~~~L~~en~qLk   61 (81)
T 2jee_A           31 ELKEKNNSLSQEVQNAQHQREELERENNHLK   61 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            5556666666666666666666666666654

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A

Probab=81.37  E-value=5.2  Score=30.33  Aligned_cols=33  Identities=33%  Similarity=0.468  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 024140           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (272)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (272)
                      ...++...|.+||..|...|..|..+|..|..+
T Consensus        40 e~~~r~~~L~~eN~~L~~~v~~L~~E~~~Lr~l   72 (78)
T 1gu4_A           40 ETQHKVLELTAENERLQKKVEQLSRELSTLRNL   72 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445667788899999999999999999888543

>4dyl_A Tyrosine-protein kinase FES/FPS; structural genomics, structural genomics consortium, BCR, CR associated substrate, transferase; 2.18A {Homo sapiens}

Probab=80.73  E-value=13  Score=34.53  Aligned_cols=90  Identities=11%  Similarity=0.178  Sum_probs=57.6

Q ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 024140           36 ITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS--DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (272)
Q Consensus        36 Its~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~--~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (272)
                      ++--.|..|+++|+.++..++..+..|.+.+..|+..+.....-..  ..+ ...-...-|++    +..+|--|...-+
T Consensus       302 ~~~~~lq~~L~~~~~~l~~~~~~~~~k~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~e----~~~~~~~~~~~~~  376 (406)
T 4dyl_A          302 LTVESVQHTLTSVTDELAVATEMVFRRQEMVTQLQQELRNEEENTHPRERV-QLLGKRQVLQE----ALQGLQVALCSQA  376 (406)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTCGG-GGHHHHHHHHH----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcchHH-HHHhHHhhHHH----HHHHHHHHHhHHH
Confidence            3456788999999999999999999999999999877765432111  010 00011111111    2345566777777


Q ss_pred             HHHHHHHHHHhhccccc
Q 024140          114 KLEVFRKTLVQSLKDDE  130 (272)
Q Consensus       114 KLE~FKk~LmqSLq~d~  130 (272)
                      ||++-|-.|-+.|++-.
T Consensus       377 ~~~~q~~~~~~~~~~~~  393 (406)
T 4dyl_A          377 KLQAQQELLQTKLEHLG  393 (406)
T ss_dssp             HHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHhcC
Confidence            77777777766666543

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=80.60  E-value=7  Score=27.62  Aligned_cols=34  Identities=24%  Similarity=0.348  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           64 SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEAL  101 (272)
Q Consensus        64 ~~i~~Lq~r~s~le~~l~~rL~~a~ee~~kL~~E~~~L  101 (272)
                      +.+..|.+|-..|...|.    .+.+++.+|.+|-+.|
T Consensus        16 ~~l~~L~~rN~rL~~~L~----~AR~el~~Lkeele~L   49 (51)
T 3m91_A           16 ARIDSLAARNSKLMETLK----EARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHh
Confidence            333444444444444443    5666666665555544

>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine exchange factor, coiled-coil, endocytosis/exocytosis complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=80.57  E-value=12  Score=31.84  Aligned_cols=28  Identities=14%  Similarity=0.151  Sum_probs=14.5

Q ss_pred             hhhHHHHHHHHHHHHHHhhhhhHHHHHHH
Q 024140           27 FEQLDVARKITSIAISTRVSDLESEHSAL   55 (272)
Q Consensus        27 ~EQLdlarkIts~A~atRVs~LE~E~~~L   55 (272)
                      ++.|-.+|+... ....|+..||..-..+
T Consensus        19 eD~L~~~R~el~-~~~~ri~~lE~~r~~~   46 (154)
T 2ocy_A           19 EEQLNKSLKTIA-SQKAAIENYNQLKEDY   46 (154)
T ss_dssp             HHHHHHHHHHHH-HHHHHHHTTHHHHHHH
T ss_pred             HHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            345555555544 3345666666543333

>1yf2_A Type I restriction-modification enzyme, S subunit; structura genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii} SCOP: d.287.1.2 d.287.1.2

Probab=80.54  E-value=2.7  Score=36.91  Aligned_cols=39  Identities=13%  Similarity=0.308  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (272)
                      .+||.+..+--+.|-..+..+++.+.+|+.+|+.||+.|
T Consensus       378 l~eQ~~I~~~l~~ld~~i~~~~~~~~~l~~~k~~Ll~~l  416 (425)
T 1yf2_A          378 LEEQKQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELL  416 (425)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666666777788888999999999999986

>3k29_A Putative uncharacterized protein; YSCO, type III secretion apparatus, S genomics, csgid; HET: MSE; 2.00A {Chlamydia trachomatis}

Probab=80.43  E-value=28  Score=30.12  Aligned_cols=60  Identities=20%  Similarity=0.249  Sum_probs=47.5

Q ss_pred             CCCCchhhHHHHHHH----HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024140           22 LPSDPFEQLDVARKI----TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (272)
Q Consensus        22 LP~DP~EQLdlarkI----ts~A~atRVs~LE~E~~~LR~~L~EKd~~i~~Lq~r~s~le~~l~   81 (272)
                      +|.-|.|||=-.++-    +-.+++.+.-.||.|-..|+..-+|+|......+.++..|-..+-
T Consensus         2 m~~yple~~~~~k~~r~e~aek~~~~k~~~le~ek~~l~~~e~~r~k~~~h~~~k~~qlre~~d   65 (169)
T 3k29_A            2 MVRYPLEPVLSIKKDRVDRAEKVVKEKRRLLELEQEKLRERESERDKVKNHYMQKIRQLREQLD   65 (169)
T ss_dssp             CCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            477788886443332    267899999999999999999999999998888888887766554

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=80.10  E-value=37  Score=31.44  Aligned_cols=24  Identities=25%  Similarity=0.354  Sum_probs=13.8

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHH
Q 024140           38 SIAISTRVSDLESEHSALRSQLAE   61 (272)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~L~E   61 (272)
                      ..++-..|.++..+...++..+.+
T Consensus       369 ~~~le~~~~~~~~~~~~~~~~~~~  392 (487)
T 3oja_A          369 KKALDEQVSNGRRAHAELDGTLQQ  392 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhhhhHHH
Confidence            445566666666666555555543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	272
d1yf2a2	205	Bipartite methylase S protein MJ0130 {Methanocaldo	91.82
d1ydxa2	181	Bipartite methylase S protein MG438 {Mycoplasma ge	88.86
d1x4ta1	80	Pre-mRNA-splicing factor ISY1 homolog {Mouse (Mus	86.78
d1ydxa1	193	Bipartite methylase S protein MG438 {Mycoplasma ge	85.45
d1yf2a1	220	Bipartite methylase S protein MJ0130 {Methanocaldo	80.67

>d1yf2a2 d.287.1.2 (A:221-425) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: DNA methylase specificity domain
superfamily: DNA methylase specificity domain
family: Type I restriction modification DNA specificity domain
domain: Bipartite methylase S protein MJ0130
species: Methanocaldococcus jannaschii [TaxId: 2190]

Probab=91.82  E-value=0.15  Score=38.18  Aligned_cols=39  Identities=13%  Similarity=0.308  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (272)
                      .++|.+..+.-+.+-..+.++.+.+.+|+.+|+.|||.|
T Consensus       158 ~~eQ~~I~~~l~~id~~i~~~~~~~~~l~~~k~~Ll~~l  196 (205)
T d1yf2a2         158 LEEQKQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELL  196 (205)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456666677777777888889999999999999999986

>d1ydxa2 d.287.1.2 (A:194-374) Bipartite methylase S protein MG438 {Mycoplasma genitalium [TaxId: 2097]}

class: Alpha and beta proteins (a+b)
fold: DNA methylase specificity domain
superfamily: DNA methylase specificity domain
family: Type I restriction modification DNA specificity domain
domain: Bipartite methylase S protein MG438
species: Mycoplasma genitalium [TaxId: 2097]

Probab=88.86  E-value=0.37  Score=36.13  Aligned_cols=40  Identities=23%  Similarity=0.277  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      .++|.+..+--+.+-..+..+.+.+.+|+.+|+.|||.|=
T Consensus       138 l~eQ~~I~~~l~~~d~~i~~~~~~i~~l~~lk~~Ll~~lF  177 (181)
T d1ydxa2         138 FQLQRKAGKIVFLLDQKLDQYKKELSSLTVIRDTLLKKLF  177 (181)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4666777777778888999999999999999999999863

>d1x4ta1 a.2.15.1 (A:7-86) Pre-mRNA-splicing factor ISY1 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: ISY1 domain-like
family: ISY1 N-terminal domain-like
domain: Pre-mRNA-splicing factor ISY1 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.78  E-value=0.38  Score=35.36  Aligned_cols=55  Identities=13%  Similarity=0.172  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024140           55 LRSQLAEKDSRIAELQSQIESIYSSLS--DKLGQAQADKERLSKENEALTNTVRKLQ  109 (272)
Q Consensus        55 LR~~L~EKd~~i~~Lq~r~s~le~~l~--~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (272)
                      |.+.--=+.+.|.|+-.+++.++..--  .+++...++++||.+|+..-...++.|.
T Consensus        17 l~~aekwR~~iikEI~~kvs~Iqn~~L~e~~IRdLNDeINkL~reK~~WE~rI~eLG   73 (80)
T d1x4ta1          17 LPKAEKWRRQIIGEISKKVAQIQNAGLGEFRIRDLNDEINKLLREKGHWEVRIKELG   73 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            333333445567777777776654332  7888999999999999999999999885

>d1ydxa1 d.287.1.2 (A:1-193) Bipartite methylase S protein MG438 {Mycoplasma genitalium [TaxId: 2097]}

class: Alpha and beta proteins (a+b)
fold: DNA methylase specificity domain
superfamily: DNA methylase specificity domain
family: Type I restriction modification DNA specificity domain
domain: Bipartite methylase S protein MG438
species: Mycoplasma genitalium [TaxId: 2097]

Probab=85.45  E-value=0.75  Score=34.49  Aligned_cols=42  Identities=7%  Similarity=0.121  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (272)
                      .++|.+..+--+.|-..+.++++.+.+|+.+|+.|||.|=-.
T Consensus       143 ~~eQ~~I~~~l~~ld~~i~~~~~~i~~l~~~~~~ll~~lft~  184 (193)
T d1ydxa1         143 KNEQHAIANTLSVFDERLENLASLIEINRKLRDEYAHKLFSL  184 (193)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            455566666666777778888889999999999999987543

>d1yf2a1 d.287.1.2 (A:1-220) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: DNA methylase specificity domain
superfamily: DNA methylase specificity domain
family: Type I restriction modification DNA specificity domain
domain: Bipartite methylase S protein MJ0130
species: Methanocaldococcus jannaschii [TaxId: 2190]

Probab=80.67  E-value=1.4  Score=33.74  Aligned_cols=40  Identities=18%  Similarity=0.379  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 024140           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (272)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (272)
                      .++|.+..+--+.|-+.+..+++.+.+|+.+|+.||+.|=
T Consensus       168 ~~eQ~~I~~~l~~i~~~i~~~~~~i~~L~~~r~~ll~~l~  207 (220)
T d1yf2a1         168 LEEQKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLL  207 (220)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4556666666667777788888889999999999999874