Citrus Sinensis ID: 028818

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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---
Protein Sequence
MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPECRSKSSSFFLNSNIKLVLCLSTTFC
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccEEEEEEEccccc
Coil and Loop (DISEMBL)
mlakepgagstfdlpeevlqvlpsdpfeqLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLkddedastgatriakptpneddaavaptgtssvhsqiseggnssfaeerepecrsksssfflnsniKLVLCLSTTFC
Flexible Loop (DISEMBL)
mlakepgagstfdlpeEVLQVLPSDPFEQLDVARKITSIAIstrvsdlesEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLskenealtntvrklqrdvsklevFRKTLvqslkddedastgatriakptpneddaaVAPTGTssvhsqiseggnssfaeeREPECRsksssfflnsniklvlclsttfc
Low Complexity Region (SEG)
MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPECRSKSSSFFLNSNIKLVLCLSTTFC
Disordered region (IsUnstruct)
****************************QLDVARKITSIAI***************************************************************************VF*******************************************************************FFLNSNIKLVLCLSTT**
Disordered Region (DISOPRED)
***************EEVLQVLPSDPFEQLDVARKITSIAIST******************************************************************RDVSKLEVF**************************************************************************KLVLCLSTTFC
Disordered Region (DISEMBL)
*********STFDLPEEVLQVLPSDPFEQLDVARKITSIAIST**********************IAELQSQIESIYSSLSD*************KENEALTNTVRKLQRDVSKLEVFRKTLVQS**********ATRIAKPTP***************************************SSFFLNSNIKLVLCLSTTFC
Disordered Region (DISPRO)
**********TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSL********************************************************SSSFFLNSNIKLVLCLSTTFC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAKEPGAGSTFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRxxxxxxxxxxxxxxxxxxxxxxxxxxxxIESIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVSKLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPECRSKSSSFFLNSNIKLVLCLSTTFC
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	203	2.2.26 [Sep-21-2011]
Q93W28	337	Uncharacterized protein A	yes	no	0.743	0.448	0.641	5e-45

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

 Score =  180 bits (457), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 100/156 (64%), Positives = 121/156 (77%), Gaps = 5/156 (3%)

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 DDEDASTGATR-IAKPTPNEDDAAVAPTGTSSVHSQ 162
           DD D + G T+ IAKPTPN+DD    P+  SS+ SQ
Sbjct: 141 DD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQ 175

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	203
255551573	338	conserved hypothetical protein [Ricinus	0.886	0.532	0.725	5e-61
224107297	346	predicted protein [Populus trichocarpa]	0.857	0.502	0.688	2e-52
297804694	335	hypothetical protein ARALYDRAFT_915246 [	0.763	0.462	0.65	2e-45
359477457	332	PREDICTED: uncharacterized protein LOC10	0.901	0.551	0.568	8e-44
18414476	337	uncharacterized protein [Arabidopsis tha	0.743	0.448	0.641	2e-43
2244910	576	hypothetical protein [Arabidopsis thalia	0.743	0.262	0.621	1e-41
357478537	389	hypothetical protein MTR_4g118510 [Medic	0.655	0.341	0.691	6e-41
357478533	344	hypothetical protein MTR_4g118510 [Medic	0.655	0.386	0.691	8e-41
449473478	284	PREDICTED: uncharacterized LOC101204510	0.857	0.612	0.557	2e-40
356555589	332	PREDICTED: uncharacterized protein LOC10	0.773	0.472	0.553	2e-40

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

 Score =  239 bits (610), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 135/186 (72%), Positives = 155/186 (83%), Gaps = 6/186 (3%)

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

Query: 61  EKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           EKD  IAELQS IES+ +SLS   DKL QA A+KE L KEN +L+N V+KLQRDVSKLEV
Sbjct: 60  EKDHLIAELQSHIESLDASLSDSADKLAQADAEKENLLKENASLSNIVKKLQRDVSKLEV 119

Query: 118 FRKTLVQSLKDDEDASTGATR-IAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEERE 176
           FRKTL++SL+DDE++S+GA   IAKPTP EDDA++ P+ TSS+ SQ SE GN SFAE+RE
Sbjct: 120 FRKTLMKSLQDDEESSSGAIPIIAKPTPTEDDASMLPSRTSSMRSQFSEMGN-SFAEDRE 178

Query: 177 PECRSK 182
            +  S+
Sbjct: 179 IDASSR 184

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 =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 124/180 (68%), Positives = 147/180 (81%), Gaps = 6/180 (3%)

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

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  187 bits (476), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 104/160 (65%), Positives = 125/160 (78%), Gaps = 5/160 (3%)

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-IAKPTPNEDDAAVAPTGTSSVHSQISEG 166
           DD D + G T+ IAKPTPN+DD    P+  SS+ SQ SE 
Sbjct: 140 DD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQASEA 178

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 =  182 bits (461), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 116/204 (56%), Positives = 141/204 (69%), Gaps = 21/204 (10%)

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

Query: 61  EKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV 117
           +KD+ +A+L  QIES+  +LS   DKL  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 GGNSSFAEEREPEC-RSKSSSFFL 188
            GN SFAE+RE +  R+  S  FL
Sbjct: 177 IGN-SFAEDRETDASRAGISHGFL 199

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 =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 100/156 (64%), Positives = 121/156 (77%), Gaps = 5/156 (3%)

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 DDEDASTGATR-IAKPTPNEDDAAVAPTGTSSVHSQ 162
           DD D + G T+ IAKPTPN+DD    P+  SS+ SQ
Sbjct: 141 DD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQ 175

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2244910|emb|CAB10332.1| hypothetical protein [Arabidopsis thaliana] gi|7268301|emb|CAB78596.1| hypothetical protein [Arabidopsis thaliana]

 Score =  175 bits (443), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 100/161 (62%), Positives = 121/161 (75%), Gaps = 10/161 (6%)

Query: 11  TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQ 70
           +FDLP+E+LQVLPSDPFEQLDVARKITSIA+STRVS LESE S LR  LAEK+    ELQ
Sbjct: 257 SFDLPDELLQVLPSDPFEQLDVARKITSIALSTRVSALESESSDLRELLAEKEKEFEELQ 316

Query: 71  SQIESIYSSLSD---KLGQAQADK-----ERLSKENEALTNTVRKLQRDVSKLEVFRKTL 122
           S +ES+ +SLSD   KL  A  +K     E L +EN +L+NTV++LQRDVSKLE FRKTL
Sbjct: 317 SHVESLEASLSDAFHKLSLADGEKVRPDPENLIRENASLSNTVKRLQRDVSKLEGFRKTL 376

Query: 123 VQSLKDDEDASTGATR-IAKPTPNEDDAAVAPTGTSSVHSQ 162
           + SL+DD D + G T+ IAKPTPN+DD    P+  SS+ SQ
Sbjct: 377 MMSLQDD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQ 416

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 =  172 bits (436), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 94/136 (69%), Positives = 108/136 (79%), Gaps = 3/136 (2%)

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 140
           SL++DED S GA  I 
Sbjct: 126 SLQEDEDNSGGAPDIV 141

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 =  172 bits (436), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 94/136 (69%), Positives = 108/136 (79%), Gaps = 3/136 (2%)

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 140
           SL++DED S GA  I 
Sbjct: 126 SLQEDEDNSGGAPDIV 141

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 106/190 (55%), Positives = 136/190 (71%), Gaps = 16/190 (8%)

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 GNSSFAEERE 176
            N S  EE E
Sbjct: 180 VN-SVKEEHE 188

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 98/177 (55%), Positives = 123/177 (69%), Gaps = 20/177 (11%)

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 FRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEE 174
           FRKTL++SL++DED S G                 P   + +HSQ S    S F ++
Sbjct: 120 FRKTLMKSLREDEDTSEG----------------TPDTAAKLHSQASFTSTSQFGDD 160

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	203
TAIR|locus:505006472	337	AT4G15545 "AT4G15545" [Arabido	0.866	0.522	0.582	3.1e-44
TAIR|locus:2205230	310	AT1G56080 "AT1G56080" [Arabido	0.763	0.5	0.385	3.6e-25
TAIR|locus:2017933	325	AT1G16520 "AT1G16520" [Arabido	0.729	0.455	0.424	4.2e-24
MGI|MGI:96687	487	Krt12 "keratin 12" [Mus muscul	0.748	0.312	0.254	1.7e-05
ZFIN|ZDB-GENE-081104-2	1926	tpra "translocated promoter re	0.665	0.070	0.244	2.3e-05
DICTYBASE|DDB_G0292068	1096	frpA "fimbrin-related protein"	0.487	0.090	0.333	2.9e-05
RGD|1304805	456	Krt12 "keratin 12" [Rattus nor	0.743	0.331	0.253	3.7e-05
UNIPROTKB|Q6IFW5	456	Krt12 "Keratin, type I cytoske	0.743	0.331	0.253	3.7e-05
DICTYBASE|DDB_G0286985	1024	zipA "zipper-like domain-conta	0.517	0.102	0.336	8.3e-05
MGI|MGI:1914738	691	Calcoco1 "calcium binding and	0.753	0.221	0.257	0.00036

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

 Score = 466 (169.1 bits), Expect = 3.1e-44, P = 3.1e-44
 Identities = 106/182 (58%), Positives = 130/182 (71%)

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-AKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPECRSKS 183
             SL+DD D + G T+I AKPTPN+DD    P+  SS+ SQ +       A + E +    S
Sbjct:   138 SLQDD-DQNAGTTQIIAKPTPNDDDTPFQPSRHSSIQSQQASEAIEPAATDNENDAPKPS 196

Query:   184 SS 185
              S
Sbjct:   197 LS 198

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

 Score = 286 (105.7 bits), Expect = 3.6e-25, P = 3.6e-25
 Identities = 62/161 (38%), Positives = 101/161 (62%)

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 SLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISE 165
             SL DD  + T    +      +D+ +    G+ S +  +SE
Sbjct:   124 SLNDDNPSQTETADVRMVPRGKDENS---NGSYSNNEGLSE 161

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

 Score = 276 (102.2 bits), Expect = 4.2e-24, P = 4.2e-24
 Identities = 65/153 (42%), Positives = 94/153 (61%)

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 DEDASTGATRIAKPTPNEDDAAVAPTGTSSVHS 161
             +    T    I   T ++  +     G  + HS
Sbjct:   128 ESGPQTEPVDIR--TCDQPGSYPGKDGRINAHS 158

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005886 "plasma membrane" evidence=IDA

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

 Score = 124 (48.7 bits), Expect = 1.7e-05, P = 1.7e-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

ZFIN|ZDB-GENE-081104-2 tpra "translocated promoter region a (to activated MET oncogene)" [Danio rerio (taxid:7955)]

 Score = 129 (50.5 bits), Expect = 2.3e-05, P = 2.3e-05
 Identities = 35/143 (24%), Positives = 72/143 (50%)

Query:    44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN 103
             R+  L  E   L++++A   + I   QSQ+++    L D LG+   +++ L KE EA T 
Sbjct:   925 RIQQLTEETGKLKNEVARSQASITTAQSQVQN----LQDSLGKVTTERDSLKKELEAKTL 980

Query:   104 TVRKLQRDVSKLE-VFR--KTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVH 160
              +++  + +++++ + R  KT  + LK+  D    A   +KP   ++D   +     ++ 
Sbjct:   981 DIQEKVKTITQVKKIGRRYKTQYEELKEQHDKMV-AEAASKPAQEQEDRQASVQEIQNLK 1039

Query:   161 SQISEGGNSSFAEEREPECRSKS 183
             S +S+  N +   E + +C  K+
Sbjct:  1040 SSLSQTQNRTSELETQLDCIQKT 1062

GO:0005643 "nuclear pore" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

DICTYBASE|DDB_G0292068 frpA "fimbrin-related protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 126 (49.4 bits), Expect = 2.9e-05, P = 2.9e-05
 Identities = 36/108 (33%), Positives = 56/108 (51%)

Query:    28 EQLDVARKITSIAISTRVSDLESEHSALRSQLAEK----DSRIAELQSQIESIYSSLSDK 83
             E LD+  K     IS R++  E E ++ + QL EK    + +I + + ++ESI S   D 
Sbjct:   839 EDLDIKEK----RISERLAKTEKETTS-KKQLVEKKEKENQKIQQEKQKLESILSQAKDM 893

Query:    84 LGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDED 131
             +G  + DK++  KE E + N  + L   V      +K+L QS KD ED
Sbjct:   894 IGDIKKDKDQTIKEREIIQNKHKTLMETVGSTTKTKKSLEQSKKDLED 941

GO:0003779 "actin binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

RGD|1304805 Krt12 "keratin 12" [Rattus norvegicus (taxid:10116)]

 Score = 121 (47.7 bits), Expect = 3.7e-05, P = 3.7e-05
 Identities = 40/158 (25%), Positives = 74/158 (46%)

Query:    22 LPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS 81
             L S   E  D+ R + ++ I  + S L  + S+L   LAE +       SQ++ +  SL 
Sbjct:   300 LQSSKSEVTDLKRMVQNLEIELQ-SQLAMK-SSLEGSLAETEGGYCCQLSQMQQLIGSLE 357

Query:    82 DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDE-DASTGATRIA 140
             ++L Q +AD ER +++++ L     +L+ ++   E +R+ L    + D  D S   T ++
Sbjct:   358 EQLQQLRADAERQNEDHQRLLGVKARLEMEI---ETYRRLLEGDTQGDGFDESLSLT-VS 413

Query:   141 KPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPE 178
             KP     D++  P  T  + + + E  N      +  E
Sbjct:   414 KPQAPSVDSSKDPNKTRKIKTVVQEIVNGEVVSSQVQE 451

GO:0003674 "molecular_function" evidence=ND

GO:0005198 "structural molecule activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005882 "intermediate filament" evidence=IEA

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q6IFW5 Krt12 "Keratin, type I cytoskeletal 12" [Rattus norvegicus (taxid:10116)]

 Score = 121 (47.7 bits), Expect = 3.7e-05, P = 3.7e-05
 Identities = 40/158 (25%), Positives = 74/158 (46%)

Query:    22 LPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS 81
             L S   E  D+ R + ++ I  + S L  + S+L   LAE +       SQ++ +  SL 
Sbjct:   300 LQSSKSEVTDLKRMVQNLEIELQ-SQLAMK-SSLEGSLAETEGGYCCQLSQMQQLIGSLE 357

Query:    82 DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDE-DASTGATRIA 140
             ++L Q +AD ER +++++ L     +L+ ++   E +R+ L    + D  D S   T ++
Sbjct:   358 EQLQQLRADAERQNEDHQRLLGVKARLEMEI---ETYRRLLEGDTQGDGFDESLSLT-VS 413

Query:   141 KPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEEREPE 178
             KP     D++  P  T  + + + E  N      +  E
Sbjct:   414 KPQAPSVDSSKDPNKTRKIKTVVQEIVNGEVVSSQVQE 451

GO:0005198 "structural molecule activity" evidence=IEA

GO:0005882 "intermediate filament" evidence=IEA

DICTYBASE|DDB_G0286985 zipA "zipper-like domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 122 (48.0 bits), Expect = 8.3e-05, P = 8.3e-05
 Identities = 37/110 (33%), Positives = 60/110 (54%)

Query:    28 EQLDVARKITSIAISTRVSDLESEHSALRS---QLAEKDSRIAELQSQIESIYSSLSDKL 84
             EQL      T   +S+    L S+ S L+S   QL+ KDS+I  ++S ++S+   LS K 
Sbjct:   630 EQLSSQSSNTDSELSSVKDQLLSKDSELKSKDEQLSNKDSQIKSIESDLQSVKDQLSSKD 689

Query:    85 GQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDAST 134
              + Q+ K++LS ++E L+N   +++   S L+  +  L  S KD E  ST
Sbjct:   690 QELQSTKDQLSSKDEQLSNKDTQIKSIESDLQSVKDQL--SSKDQELQST 737

GO:0005615 "extracellular space" evidence=IDA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0044351 "macropinocytosis" evidence=RCA

MGI|MGI:1914738 Calcoco1 "calcium binding and coiled coil domain 1" [Mus musculus (taxid:10090)]

 Score = 115 (45.5 bits), Expect = 0.00036, P = 0.00036
 Identities = 42/163 (25%), Positives = 81/163 (49%)

Query:    18 VLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLA-EKDSRIAELQSQIESI 76
             +LQ + ++  + L ++ +I  + +   V +  ++    +++LA EKDS + +L S+ +  
Sbjct:   415 LLQSMEAEKDKILKLSAEI--LRLEKTVQEERTQSHVFKTELAREKDSSLVQL-SESKRE 471

Query:    77 YSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDEDASTGA 136
              + L   L   Q +KE+L  E + L   +RKL+  + K+    K    +  +DE+A+ G 
Sbjct:   472 LTELRSALRVLQKEKEQLQTEKQELLEYMRKLEARLEKV-ADEKWTEDAATEDEEATAGL 530

Query:   137 TRIAKPTPNEDDAAVAPTGTSSVHSQISEGGNSSFAEE--REP 177
             +  A  T +ED++   P         + E GN+S +    REP
Sbjct:   531 SCPASLTDSEDES---PEDMRLPSYGLCESGNTSSSPPGPREP 570

GO:0000790 "nuclear chromatin" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0003712 "transcription cofactor activity" evidence=ISO

GO:0003713 "transcription coactivator activity" evidence=ISO;IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IC

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0007165 "signal transduction" evidence=IDA

GO:0008013 "beta-catenin binding" evidence=ISO

GO:0008022 "protein C-terminus binding" evidence=ISO

GO:0016055 "Wnt receptor signaling pathway" evidence=IEA

GO:0030374 "ligand-dependent nuclear receptor transcription coactivator activity" evidence=ISO

GO:0030518 "intracellular steroid hormone receptor signaling pathway" evidence=IDA

GO:0043565 "sequence-specific DNA binding" evidence=ISO

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISO

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

GO:0070016 "armadillo repeat domain binding" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	203
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	1e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	2e-04
pfam03962	188	pfam03962, Mnd1, Mnd1 family	6e-04
pfam04156	186	pfam04156, IncA, IncA protein	0.003

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

 Score = 41.1 bits (97), Expect = 1e-04
 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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 40.9 bits (96), Expect = 2e-04
 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|202833 pfam03962, Mnd1, Mnd1 family

 Score = 38.8 bits (91), Expect = 6e-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|217933 pfam04156, IncA, IncA protein

 Score = 36.7 bits (85), Expect = 0.003
 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	203
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	96.82
PRK11637	428	AmiB activator; Provisional	96.64
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	96.61
PRK10884	206	SH3 domain-containing protein; Provisional	96.61
COG2433	652	Uncharacterized conserved protein [Function unknow	96.24
PF06637	442	PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 Th	96.2
PRK11637	428	AmiB activator; Provisional	96.19
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	96.15
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	96.13
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	95.92
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	95.85
PRK09039	343	hypothetical protein; Validated	95.78
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	95.28
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	95.19
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	95.07
PHA02562	562	46 endonuclease subunit; Provisional	95.04
PF10186	302	Atg14: UV radiation resistance protein and autopha	95.04
PF05700	221	BCAS2: Breast carcinoma amplified sequence 2 (BCAS	94.9
PRK03918	880	chromosome segregation protein; Provisional	94.76
PF09755	310	DUF2046: Uncharacterized conserved protein H4 (DUF	94.73
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	94.54
PF03148	384	Tektin: Tektin family; InterPro: IPR000435 Tektin	94.24
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	94.21
PRK02224	880	chromosome segregation protein; Provisional	94.2
PF08647	96	BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR01395	94.16
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	93.94
PHA02562	562	46 endonuclease subunit; Provisional	93.83
KOG3990	305	consensus Uncharacterized conserved protein [Funct	93.7
PRK10884	206	SH3 domain-containing protein; Provisional	93.68
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	93.59
KOG0288	459	consensus WD40 repeat protein TipD [General functi	93.56
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	93.49
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	93.38
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	93.29
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	93.2
PF11180	192	DUF2968: Protein of unknown function (DUF2968); In	93.06
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	93.0
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	93.0
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	92.88
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	92.81
COG4026	290	Uncharacterized protein containing TOPRIM domain,	92.63
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	92.58
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	92.53
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	92.52
PF04899	70	MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 Th	92.45
KOG2685	421	consensus Cystoskeletal protein Tektin [Cytoskelet	92.37
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	92.15
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	92.02
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	91.99
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	91.96
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	91.91
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	91.77
PF00038	312	Filament: Intermediate filament protein; InterPro:	91.73
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	91.71
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	91.58
PRK02224	880	chromosome segregation protein; Provisional	91.57
COG4942	420	Membrane-bound metallopeptidase [Cell division and	91.53
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	91.49
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	91.26
KOG4010	208	consensus Coiled-coil protein TPD52 [General funct	91.16
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	91.15
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	91.15
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	91.09
KOG2129	552	consensus Uncharacterized conserved protein H4 [Fu	91.02
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	90.95
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	90.68
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	90.61
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	90.61
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	90.59
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	90.57
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	90.52
KOG3433	203	consensus Protein involved in meiotic recombinatio	90.51
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	90.44
PF10186	302	Atg14: UV radiation resistance protein and autopha	90.1
PF14362	301	DUF4407: Domain of unknown function (DUF4407)	90.05
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	90.03
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	89.99
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	89.95
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	89.89
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	89.64
PF12777	344	MT: Microtubule-binding stalk of dynein motor; Int	89.62
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	89.57
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	89.57
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	89.54
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	89.52
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	89.37
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	89.31
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	89.23
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	89.19
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	89.18
TIGR02231	525	conserved hypothetical protein. This family consis	89.02
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	89.0
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	88.84
COG5185	622	HEC1 Protein involved in chromosome segregation, i	88.79
PF09798	654	LCD1: DNA damage checkpoint protein; InterPro: IPR	88.59
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	88.55
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	88.41
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	88.39
PRK09039	343	hypothetical protein; Validated	88.07
PF14662	193	CCDC155: Coiled-coil region of CCDC155	87.96
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	87.91
PF00038	312	Filament: Intermediate filament protein; InterPro:	87.9
KOG0963	629	consensus Transcription factor/CCAAT displacement	87.87
KOG1962	216	consensus B-cell receptor-associated protein and r	87.85
PF15290	305	Syntaphilin: Golgi-localised syntaxin-1-binding cl	87.83
PF10205	102	KLRAQ: Predicted coiled-coil domain-containing pro	87.77
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	87.72
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	87.7
PF10205	102	KLRAQ: Predicted coiled-coil domain-containing pro	87.7
COG4026	290	Uncharacterized protein containing TOPRIM domain,	87.69
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	87.67
PF11544	76	Spc42p: Spindle pole body component Spc42p; InterP	87.65
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	87.54
PRK02119	73	hypothetical protein; Provisional	87.3
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	87.3
KOG0249	916	consensus LAR-interacting protein and related prot	87.22
COG4942	420	Membrane-bound metallopeptidase [Cell division and	87.2
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	86.86
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	86.8
PF04201	162	TPD52: Tumour protein D52 family; InterPro: IPR007	86.67
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	86.48
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	86.43
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	86.38
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	86.32
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	86.21
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	86.18
PF11068	131	YlqD: YlqD protein; InterPro: IPR021297 This bacte	86.05
KOG4398	359	consensus Predicted coiled-coil protein [General f	85.96
PF10779	71	XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemoly	85.94
PF02050	123	FliJ: Flagellar FliJ protein; InterPro: IPR012823	85.68
PRK04406	75	hypothetical protein; Provisional	85.63
PF05278	269	PEARLI-4: Arabidopsis phospholipase-like protein (	85.58
PRK12704	520	phosphodiesterase; Provisional	85.57
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	85.52
PF14817	632	HAUS5: HAUS augmin-like complex subunit 5	85.44
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	85.43
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	85.3
KOG2991	330	consensus Splicing regulator [RNA processing and m	85.27
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	85.16
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	85.03
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	84.99
PRK02793	72	phi X174 lysis protein; Provisional	84.99
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	84.84
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	84.76
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	84.59
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	84.47
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	84.41
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	84.39
PF11594	106	Med28: Mediator complex subunit 28; InterPro: IPR0	84.32
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	84.19
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	84.17
PF13863	126	DUF4200: Domain of unknown function (DUF4200)	84.15
COG2433	652	Uncharacterized conserved protein [Function unknow	84.14
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	84.05
KOG0962	1294	consensus DNA repair protein RAD50, ABC-type ATPas	83.99
KOG4673	961	consensus Transcription factor TMF, TATA element m	83.9
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	83.88
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	83.87
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	83.84
KOG0288	459	consensus WD40 repeat protein TipD [General functi	83.73
PF09787	511	Golgin_A5: Golgin subfamily A member 5; InterPro:	83.68
PF10158	131	LOH1CR12: Tumour suppressor protein; InterPro: IPR	83.66
KOG4687	389	consensus Uncharacterized coiled-coil protein [Fun	83.66
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	83.64
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	83.55
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	83.54
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	83.52
PRK10803	263	tol-pal system protein YbgF; Provisional	83.46
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	83.4
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	83.02
PF13747	89	DUF4164: Domain of unknown function (DUF4164)	82.99
PF12240	205	Angiomotin_C: Angiomotin C terminal; InterPro: IPR	82.64
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	82.64
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	82.56
PRK00846	77	hypothetical protein; Provisional	82.55
PF04100	383	Vps53_N: Vps53-like, N-terminal ; InterPro: IPR007	82.49
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	82.27
TIGR02559	158	HrpB7 type III secretion protein HrpB7. This famil	82.27
PRK04863	1486	mukB cell division protein MukB; Provisional	82.2
PF06818	202	Fez1: Fez1; InterPro: IPR009638 This family repres	82.08
PRK10361	475	DNA recombination protein RmuC; Provisional	82.01
KOG1899	861	consensus LAR transmembrane tyrosine phosphatase-i	81.61
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	81.51
PF09486	158	HrpB7: Bacterial type III secretion protein (HrpB7	81.5
TIGR03495	135	phage_LysB phage lysis regulatory protein, LysB fa	81.49
PRK01156	895	chromosome segregation protein; Provisional	81.4
KOG0971	1243	consensus Microtubule-associated protein dynactin	81.39
PF02994	370	Transposase_22: L1 transposable element; InterPro:	81.39
PRK00295	68	hypothetical protein; Provisional	81.3
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	81.19
PF06120	301	Phage_HK97_TLTM: Tail length tape measure protein;	81.13
PRK10803	263	tol-pal system protein YbgF; Provisional	81.09
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	81.08
COG1322	448	Predicted nuclease of restriction endonuclease-lik	81.05
PRK00106	535	hypothetical protein; Provisional	81.05
PRK01156	895	chromosome segregation protein; Provisional	81.0
PF14932	256	HAUS-augmin3: HAUS augmin-like complex subunit 3	80.96
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	80.85
KOG0996	1293	consensus Structural maintenance of chromosome pro	80.75
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	80.64
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	80.6
PRK04778	569	septation ring formation regulator EzrA; Provision	80.54
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	80.48
PF08647	96	BRE1: BRE1 E3 ubiquitin ligase; InterPro: IPR01395	80.4
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	80.3
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	80.29
KOG0971	1243	consensus Microtubule-associated protein dynactin	80.12
PF05278	269	PEARLI-4: Arabidopsis phospholipase-like protein (	80.09

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

Probab=96.82  E-value=0.037  Score=45.14  Aligned_cols=78  Identities=21%  Similarity=0.321  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           35 KITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        35 kIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      |+-.-++-.|+..+|..+..|-+...+|+..|..|+.|+..||..|- ++.....+......+......++-.|+|-|.
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            44455778899999999999999999999999999999999999996 3333333333333333333333334444443

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=96.64  E-value=0.039  Score=51.03  Aligned_cols=108  Identities=19%  Similarity=0.248  Sum_probs=51.3

Q ss_pred             CCCChHHHHhhCCCCchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHH--
Q 028818           11 TFDLPEEVLQVLPSDPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIE-------SIYSSLS--   81 (203)
Q Consensus        11 ~f~lp~eil~vLP~DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s-------~Le~~L~--   81 (203)
                      .|.+..-|+.+|       |-++-  ..+++..-...++.++..+++++.++...|.+++.+..       .++.++.  
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            566666666655       22222  22222222334444455555555444444444444433       3333333  


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 028818           82 -DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (203)
Q Consensus        82 -~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (203)
                       .++....++...+.++.+.|...++.+..++.+++.--+.++..+.
T Consensus        88 ~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~rlra~Y  134 (428)
T PRK11637         88 SRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAAQLDAAF  134 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             4444555555555555555555555555555555444444444333

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

Probab=96.61  E-value=0.04  Score=46.15  Aligned_cols=82  Identities=26%  Similarity=0.434  Sum_probs=28.3

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      ++.|+..+..++..|+.++.++...|.+|+..+..|+..+.   ..|+.....+..|..|..+|--+...+...+.+|+.
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   333344444444444444444444444444444444


Q ss_pred             HHHHH
Q 028818          118 FRKTL  122 (203)
Q Consensus       118 FKk~L  122 (203)
                      =-+.|
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.

>PRK10884 SH3 domain-containing protein; Provisional

Probab=96.61  E-value=0.028  Score=48.67  Aligned_cols=69  Identities=26%  Similarity=0.381  Sum_probs=42.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      -...|+-.||.|+..|+.+|++-+...   ..+...+    +.++..+.+...+|.+||+.|...+..+..++..|
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            455788899999999999998765432   2222222    23333555555556666666666666665555443

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=96.24  E-value=0.076  Score=53.10  Aligned_cols=83  Identities=29%  Similarity=0.415  Sum_probs=73.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      ++-.+|.+||.|+..|+..+.+..+.|..|+.++..+...+.      -.+.....++..|.++-..=...|.-|.|.++
T Consensus       426 ~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~e~~~~ve~L~~~l~  505 (652)
T COG2433         426 KLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLA  505 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888999999999999999999999999999999999988877      44556777889999999988999999999999


Q ss_pred             HHHHHHHHH
Q 028818          114 KLEVFRKTL  122 (203)
Q Consensus       114 KLE~FKk~L  122 (203)
                      +|+.+++-.
T Consensus       506 ~l~k~~~lE  514 (652)
T COG2433         506 ELRKMRKLE  514 (652)
T ss_pred             HHHHHHhhh
Confidence            999888843

>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=96.20  E-value=0.12  Score=49.48  Aligned_cols=68  Identities=22%  Similarity=0.298  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------------HHHHHHHHHHHHHHHHHHHHHH
Q 028818           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------------------------DKLGQAQADKERLSKENEALTN  103 (203)
Q Consensus        49 E~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-------------------------~rL~~a~ee~~kL~~E~~~La~  103 (203)
                      |.=++.||..+....++..+|+.+-..+|..|+                         -.-..+++|++.|.+|+++|+.
T Consensus       284 eelar~Lr~~I~~VarENs~LqrQKle~e~~l~a~qeakek~~KEAqareaklqaec~rQ~qlaLEEKaaLrkerd~L~k  363 (442)
T PF06637_consen  284 EELARSLRAGIERVARENSDLQRQKLEAEQGLQASQEAKEKAGKEAQAREAKLQAECARQTQLALEEKAALRKERDSLAK  363 (442)
T ss_pred             HHHHHHHhhhHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444566666666666666666666666665554                         1223467888999999999999


Q ss_pred             HHHHHhhhHHHHH
Q 028818          104 TVRKLQRDVSKLE  116 (203)
Q Consensus       104 TvKkL~rDvaKLE  116 (203)
                      .+-...|+++.|+
T Consensus       364 eLeekkreleql~  376 (442)
T PF06637_consen  364 ELEEKKRELEQLK  376 (442)
T ss_pred             HHHHHHHHHHHHH
Confidence            9988888887654

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

>PRK11637 AmiB activator; Provisional

Probab=96.19  E-value=0.12  Score=47.70  Aligned_cols=68  Identities=9%  Similarity=0.180  Sum_probs=27.4

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (203)
                      .+...++.++..|..++.+-...|.+++.++..++.++.    ...++..+++++.+.+...++++-|.+.+
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            333334444444444444333333333333333333333    44444444444444444444444443333

>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=96.15  E-value=0.086  Score=38.89  Aligned_cols=65  Identities=28%  Similarity=0.435  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 028818           54 ALRSQLAEKDSRIAELQSQIESIYS---SLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (203)
Q Consensus        54 ~LR~~LaEKd~~i~~Lq~r~s~Le~---~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (203)
                      .|-..|+|||..|+.|.+.-..|-.   .+..-++..+..+..+.++.+.|...+.++..++..|+.+
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            4667899999999999955554443   3334444444455555555555555555555555544443

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.

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

Probab=96.13  E-value=0.07  Score=44.70  Aligned_cols=72  Identities=18%  Similarity=0.344  Sum_probs=45.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhhHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTV-RKLQRDVSKL  115 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~Tv-KkL~rDvaKL  115 (203)
                      .+...+..|+.++..|...+.||...+..|++-+..|.-++.    .+.+...+|.+||+.|.... ++-+++..+|
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            344444455555555555666666666666666666665554    88999999999999998763 4444554443

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.

>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=95.92  E-value=0.55  Score=38.87  Aligned_cols=84  Identities=26%  Similarity=0.389  Sum_probs=64.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           40 AISTRVSDLESEHSALRSQLA-------EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La-------EKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      -+..||-+||+|+........       .+.+.|..|+.+++.+...+.    ....+...|.+||..|.....+.+..|
T Consensus        21 sle~~v~~LEreLe~~q~~~e~~~~daEn~k~eie~L~~el~~lt~el~----~L~~EL~~l~sEk~~L~k~lq~~q~kv   96 (140)
T PF10473_consen   21 SLEDHVESLERELEMSQENKECLILDAENSKAEIETLEEELEELTSELN----QLELELDTLRSEKENLDKELQKKQEKV   96 (140)
T ss_pred             hHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            577889999998776655433       344455666666666666555    888999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcc
Q 028818          113 SKLEVFRKTLVQSLK  127 (203)
Q Consensus       113 aKLE~FKk~LmqSLq  127 (203)
                      +-||.....+-.-|+
T Consensus        97 ~eLE~~~~~~~~~l~  111 (140)
T PF10473_consen   97 SELESLNSSLENLLQ  111 (140)
T ss_pred             HHHHHHhHHHHHHHH
Confidence            999988776655444

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

>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=95.85  E-value=0.21  Score=39.94  Aligned_cols=30  Identities=20%  Similarity=0.297  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +.+|+.+++++.+.+..++.+...++..+.
T Consensus        75 ~~rL~~~~~~~ere~~~~~~~~~~l~~~~~  104 (151)
T PF11559_consen   75 VERLKEQLEELERELASAEEKERQLQKQLK  104 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555555555555555555555555555

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=95.78  E-value=0.2  Score=45.94  Aligned_cols=88  Identities=17%  Similarity=0.233  Sum_probs=67.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-HHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRD-VSKL  115 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rD-vaKL  115 (203)
                      ....|+..|+.+...++....|....|.-|+.++..|..+|.   +.|..+.++....+...+.|...+.+.-.+ +..|
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            345667777778888888888888888888888888888877   666677777777777777777777666544 8889


Q ss_pred             HHHHHHHHhhcc
Q 028818          116 EVFRKTLVQSLK  127 (203)
Q Consensus       116 E~FKk~LmqSLq  127 (203)
                      +.||..+..-|.
T Consensus       193 ~~~~~~~~~~l~  204 (343)
T PRK09039        193 NRYRSEFFGRLR  204 (343)
T ss_pred             HHhHHHHHHHHH
Confidence            999999976664

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

Probab=95.28  E-value=0.37  Score=43.03  Aligned_cols=21  Identities=33%  Similarity=0.544  Sum_probs=10.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLA   60 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La   60 (203)
                      .|..-|+.+|.++..+|.++.
T Consensus        56 ~le~qv~~~e~ei~~~r~r~~   76 (239)
T COG1579          56 DLENQVSQLESEIQEIRERIK   76 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            444445555555555554443

>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=95.19  E-value=0.34  Score=38.76  Aligned_cols=68  Identities=22%  Similarity=0.404  Sum_probs=52.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      ..|+..+.+++..+..-...+..|+.+++.++.++.    .+..+...|.++...+..++|.+..++.||.+
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            345555666666666666777788888888888776    77788888888888999999999988888874

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.

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

Probab=95.07  E-value=0.81  Score=40.91  Aligned_cols=72  Identities=17%  Similarity=0.344  Sum_probs=49.1

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHH---------HHHHHHHHHHHHHHHHHHHhhhH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQA---------DKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~e---------e~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      +.++.+|..+++..+.+++..+.+|+.+++.++..++   .|+..+..         +...|..|.+.+......|+.++
T Consensus        33 l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~le~el  112 (239)
T COG1579          33 LKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDEL  112 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567788888888899999999999999998888888   44444332         23455555555555555555555


Q ss_pred             HHHH
Q 028818          113 SKLE  116 (203)
Q Consensus       113 aKLE  116 (203)
                      +.|.
T Consensus       113 ~~l~  116 (239)
T COG1579         113 AELM  116 (239)
T ss_pred             HHHH
Confidence            5443

>PHA02562 46 endonuclease subunit; Provisional

Probab=95.04  E-value=0.54  Score=43.91  Aligned_cols=97  Identities=11%  Similarity=0.245  Sum_probs=58.7

Q ss_pred             HhhCCCCchhhHHHHHHHHHH--------HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           19 LQVLPSDPFEQLDVARKITSI--------AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQAD   90 (203)
Q Consensus        19 l~vLP~DP~EQLdlarkIts~--------A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee   90 (203)
                      ...++..|.+--.+-.+|...        ..+.++..++.++..|+.++.+....+..++..+..++..+...+....++
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            344555555555555555433        456677778888888888888888888877777777766555444444444


Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           91 KERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        91 ~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      ..+|..+...|...+..|..++..|
T Consensus       222 ~~~l~~~~~~l~~~l~~l~~~i~~l  246 (562)
T PHA02562        222 YDELVEEAKTIKAEIEELTDELLNL  246 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555444444444444333

>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=95.04  E-value=0.81  Score=38.88  Aligned_cols=85  Identities=24%  Similarity=0.368  Sum_probs=42.9

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH----
Q 028818           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSK----  114 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK----  114 (203)
                      +..+..++..+..||..+.+....|.+.++++..+..++.   ..|....+...+..+....+.+.++...+.+.+    
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            4445555555556666666666666666666666666555   333322333333444444444444444444443    


Q ss_pred             HHHHHHHHHhhc
Q 028818          115 LEVFRKTLVQSL  126 (203)
Q Consensus       115 LE~FKk~LmqSL  126 (203)
                      +..=++.+++.|
T Consensus       142 l~~~r~~l~~~l  153 (302)
T PF10186_consen  142 LARRRRQLIQEL  153 (302)
T ss_pred             HHHHHHHHHHHH
Confidence            444555666644

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=94.90  E-value=1.6  Score=37.55  Aligned_cols=90  Identities=17%  Similarity=0.192  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           30 LDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        30 LdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      |+|..+-..+||......||+....|...|.+..+.|.++..+=-.-+.+...+|+...+.-..+...|-.+...+..|.
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            56778888899999999999999999999999999999997655555555557777777777777777777777777787


Q ss_pred             hhHHHHHHHH
Q 028818          110 RDVSKLEVFR  119 (203)
Q Consensus       110 rDvaKLE~FK  119 (203)
                      ++|..|+.=+
T Consensus       203 ~ei~~l~~~~  212 (221)
T PF05700_consen  203 QEIEQLKRKA  212 (221)
T ss_pred             HHHHHHHHHH
Confidence            7777665433

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

>PRK03918 chromosome segregation protein; Provisional

Probab=94.76  E-value=1.3  Score=43.77  Aligned_cols=93  Identities=25%  Similarity=0.297  Sum_probs=38.7

Q ss_pred             CCCCchhhHHHHHHHHHHHHHHhhhhhHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHH
Q 028818           22 LPSDPFEQLDVARKITSIAISTRVSDLESEH----------SALRSQLAEKDSRIAELQSQIESIYSSLS------DKLG   85 (203)
Q Consensus        22 LP~DP~EQLdlarkIts~A~atRVs~LE~E~----------~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~------~rL~   85 (203)
                      +..|-|+++.-..+-....+..++..|+..+          ..++.++.+....+..++.++..++..+.      ..|.
T Consensus       155 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~i~~~l~~l~~~~~~l~~ei~~l~~e~~~l~~~~~~~~~~l~~l~  234 (880)
T PRK03918        155 LGLDDYENAYKNLGEVIKEIKRRIERLEKFIKRTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELE  234 (880)
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444433333344445544444433          23333333444444444444444444443      1333


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSK  114 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (203)
                      ...++...|.++...|....+.+..++.+
T Consensus       235 ~~~~~~~~l~~~~~~l~~~~~~l~~~i~~  263 (880)
T PRK03918        235 ELKEEIEELEKELESLEGSKRKLEEKIRE  263 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444333333

>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=94.73  E-value=0.89  Score=42.19  Aligned_cols=87  Identities=31%  Similarity=0.449  Sum_probs=52.9

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHh
Q 028818           39 IAISTRVSDLESEHSALRSQLA-EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT--------VRKLQ  109 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~La-EKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~T--------vKkL~  109 (203)
                      |.+..|+.+|-.|-..|=.+|. |...++.-|+.++..|+....    .......+|.+|+-.|.+|        |.+|.
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 344455555555555554332    2233344677777777666        57899


Q ss_pred             hhHHHHHHHHHHHHhhcccc
Q 028818          110 RDVSKLEVFRKTLVQSLKDD  129 (203)
Q Consensus       110 rDvaKLE~FKk~LmqSLq~d  129 (203)
                      +.+++|++=||.|=..|..-
T Consensus       185 Kqm~~l~~eKr~Lq~~l~~~  204 (310)
T PF09755_consen  185 KQMDKLEAEKRRLQEKLEQP  204 (310)
T ss_pred             HHHHHHHHHHHHHHHHHccc
Confidence            99999999999988877643

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

Probab=94.54  E-value=1.4  Score=36.10  Aligned_cols=80  Identities=18%  Similarity=0.346  Sum_probs=42.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      ....+...|+.|+..+...+.+...++..+++....+...+.   .++....+...++.+|-..|.+-++.+.+.+..++
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            345555556666666666666655555555555544443333   55556666666666665555533333334444433


Q ss_pred             HHH
Q 028818          117 VFR  119 (203)
Q Consensus       117 ~FK  119 (203)
                      ...
T Consensus       165 ~~~  167 (191)
T PF04156_consen  165 SQL  167 (191)
T ss_pred             HHH
Confidence            333

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 [].

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

Probab=94.24  E-value=2.4  Score=39.36  Aligned_cols=96  Identities=22%  Similarity=0.303  Sum_probs=76.5

Q ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH-----------------H
Q 028818           30 LDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQ-----------------A   89 (203)
Q Consensus        30 LdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~-----------------e   89 (203)
                      |.-...-|..||..||...+.--..|-.++.+-...|++++.-+..|+.++.   +-|+.|.                 .
T Consensus       238 l~~Q~~~vn~al~~Ri~et~~ak~~Le~ql~~~~~ei~~~e~~i~~L~~ai~~k~~~lkvaqTRL~~R~~RP~vElcrD~  317 (384)
T PF03148_consen  238 LRAQADAVNAALRKRIHETQEAKNELEWQLKKTLQEIAEMEKNIEDLEKAIRDKEGPLKVAQTRLENRTQRPNVELCRDP  317 (384)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhHhcCCchHHHHhh
Confidence            3344455777999999998888888888888888899999999999998888   2233222                 2


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Q 028818           90 DKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS  125 (203)
Q Consensus        90 e~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS  125 (203)
                      -+..|..|-..|..++.+|+..+...+..-+.|...
T Consensus       318 ~q~~L~~Ev~~l~~~i~~L~~~L~~a~~~l~~L~~~  353 (384)
T PF03148_consen  318 PQYGLIEEVKELRESIEALQEKLDEAEASLQKLERT  353 (384)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            237899999999999999999999999888888763

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

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

Probab=94.21  E-value=1.2  Score=36.29  Aligned_cols=76  Identities=20%  Similarity=0.329  Sum_probs=49.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSR----------IAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVR  106 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~----------i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvK  106 (203)
                      ++-.|++.||.++..+..+|.+-...          ...|+.|+..||.+|-   .+|+.+.+........-+-+...|+
T Consensus        39 sL~~K~~~lE~eld~~~~~l~~~k~~lee~~~~~~~~E~l~rriq~LEeele~ae~~L~e~~ekl~e~d~~ae~~eRkv~  118 (143)
T PF12718_consen   39 SLQKKNQQLEEELDKLEEQLKEAKEKLEESEKRKSNAEQLNRRIQLLEEELEEAEKKLKETTEKLREADVKAEHFERKVK  118 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            67788888888888877776643332          2446677777777776   6666666666666666666666666


Q ss_pred             HHhhhHHHH
Q 028818          107 KLQRDVSKL  115 (203)
Q Consensus       107 kL~rDvaKL  115 (203)
                      .|......+
T Consensus       119 ~le~~~~~~  127 (143)
T PF12718_consen  119 ALEQERDQW  127 (143)
T ss_pred             HHHhhHHHH
Confidence            665554443

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 [].

>PRK02224 chromosome segregation protein; Provisional

Probab=94.20  E-value=1.7  Score=43.22  Aligned_cols=13  Identities=15%  Similarity=0.376  Sum_probs=5.1

Q ss_pred             CchhhHHHHHHHH
Q 028818           25 DPFEQLDVARKIT   37 (203)
Q Consensus        25 DP~EQLdlarkIt   37 (203)
                      +|-+-.++-.+|.
T Consensus       147 ~p~~R~~ii~~l~  159 (880)
T PRK02224        147 TPSDRQDMIDDLL  159 (880)
T ss_pred             CHHHHHHHHHHHh
Confidence            4433333333333

>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=94.16  E-value=1.9  Score=32.83  Aligned_cols=79  Identities=20%  Similarity=0.281  Sum_probs=56.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH-------HHHHH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV-------SKLEV  117 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv-------aKLE~  117 (203)
                      +-++|.+...++..+..|-..+..+++++..|+.+..    .+.++.-.+-+-+++|.+-+|+|+..+       ++|..
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            4578889999999999999999999999999999988    555555555555555555555555554       44555


Q ss_pred             HHHHHHhhcc
Q 028818          118 FRKTLVQSLK  127 (203)
Q Consensus       118 FKk~LmqSLq  127 (203)
                      .=+.+++.|.
T Consensus        81 ~E~~~~~~l~   90 (96)
T PF08647_consen   81 TEKEFVRKLK   90 (96)
T ss_pred             HHHHHHHHHH
Confidence            5555555543

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=93.94  E-value=1.5  Score=42.88  Aligned_cols=43  Identities=16%  Similarity=0.311  Sum_probs=33.5

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Q 028818           39 IAISTRVSDLESEHSALRSQLAE--KDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaE--Kd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .++..+...+|.|+..+..+|..  ....|..|++++..++..+.
T Consensus       394 ~~~~~~~~~~e~el~~l~~~l~~~~~~e~i~~l~e~l~~l~~~l~  438 (650)
T TIGR03185       394 SQLLKELRELEEELAEVDKKISTIPSEEQIAQLLEELGEAQNELF  438 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHH
Confidence            47778889999999999999974  34677777777777777665

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.

>PHA02562 46 endonuclease subunit; Provisional

Probab=93.83  E-value=0.93  Score=42.36  Aligned_cols=38  Identities=16%  Similarity=0.274  Sum_probs=16.8

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSS   79 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~   79 (203)
                      ..|+..++.++..+|..+.++-..+..|+.++..|+..
T Consensus       336 ~~~i~el~~~i~~~~~~i~~~~~~~~~l~~ei~~l~~~  373 (562)
T PHA02562        336 SKKLLELKNKISTNKQSLITLVDKAKKVKAAIEELQAE  373 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34444444444444444444444444444444444443

>KOG3990 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.70  E-value=0.31  Score=44.72  Aligned_cols=34  Identities=29%  Similarity=0.413  Sum_probs=31.1

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~   78 (203)
                      +..|+.||++|+..|.+||+.|-+-.++++.|-.
T Consensus       227 i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKa  260 (305)
T KOG3990|consen  227 IQKLKEEIARLKKLLHQKDQLILEKDKQISNLKA  260 (305)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCc
Confidence            4689999999999999999999999999998765

>PRK10884 SH3 domain-containing protein; Provisional

Probab=93.68  E-value=1.1  Score=38.82  Aligned_cols=66  Identities=14%  Similarity=0.237  Sum_probs=41.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      ++...+..|+.+...++++..   ...++|++++...+....    ...++|.+|.+|...+.+.+..|+..+
T Consensus        97 ~le~el~~l~~~l~~~~~~~~---~~~~~l~~~~~~~~~~~~----~L~~~n~~L~~~l~~~~~~~~~l~~~~  162 (206)
T PRK10884         97 DLENQVKTLTDKLNNIDNTWN---QRTAEMQQKVAQSDSVIN----GLKEENQKLKNQLIVAQKKVDAANLQL  162 (206)
T ss_pred             HHHHHHHHHHHHHHHHHhHHH---HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            677888888888888877654   555566666666555554    455555555555555555555554443

>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=93.59  E-value=0.92  Score=42.12  Aligned_cols=72  Identities=21%  Similarity=0.415  Sum_probs=58.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHH----------------HHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAE----------------KDSRI---AELQSQIESIYSSLSDKLGQAQADKERLSKENEA  100 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaE----------------Kd~~i---~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~  100 (203)
                      .+..|+..++.++.-||.+++.                |...|   +.+++++..|+..|+    ...++.+.|..|+|.
T Consensus        90 ~Lrqkl~E~qGD~KlLR~~la~~r~~~~~~~~~~~~~ere~lV~qLEk~~~q~~qLe~d~q----s~lDEkeEl~~ERD~  165 (319)
T PF09789_consen   90 ELRQKLNEAQGDIKLLREKLARQRVGDEGIGARHFPHEREDLVEQLEKLREQIEQLERDLQ----SLLDEKEELVTERDA  165 (319)
T ss_pred             HHHHHHHHHhchHHHHHHHHHhhhhhhccccccccchHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence            6777888888888888877653                44444   556678888888888    999999999999999


Q ss_pred             HHHHHHHHhhhHHHH
Q 028818          101 LTNTVRKLQRDVSKL  115 (203)
Q Consensus       101 La~TvKkL~rDvaKL  115 (203)
                      ...-+-+||.++..+
T Consensus       166 yk~K~~RLN~ELn~~  180 (319)
T PF09789_consen  166 YKCKAHRLNHELNYI  180 (319)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999988653

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

Probab=93.56  E-value=1.1  Score=43.55  Aligned_cols=71  Identities=18%  Similarity=0.236  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818           54 ALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus        54 ~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      +++.|+.--...-..+..++...|.+|+    ...+|+.+|.+|+-.+..|++.|.+++-.+|+.+=.+.+-+.+
T Consensus        31 ~~~aq~~~~~a~~~ai~a~~~~~E~~l~----~Lq~e~~~l~e~~v~~~a~~~~~t~~~~~~en~~~r~~~eir~  101 (459)
T KOG0288|consen   31 RLSAQLVILRAESRAIKAKLQEKELELN----RLQEENTQLNEERVREEATEKTLTVDVLIAENLRIRSLNEIRE  101 (459)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333444444444444444    4445566666666666677777777777777766655554443

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=93.49  E-value=1.4  Score=32.32  Aligned_cols=58  Identities=26%  Similarity=0.407  Sum_probs=37.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           47 DLESEHSALRSQLAEKDSRIAELQ---SQIESIYSSLS-DKLGQAQADKERLSKENEALTNTV  105 (203)
Q Consensus        47 ~LE~E~~~LR~~LaEKd~~i~~Lq---~r~s~Le~~L~-~rL~~a~ee~~kL~~E~~~La~Tv  105 (203)
                      +||+++..||..|.-=.+++...+   +.+.. |+.-. .+|..+-+++.+|..|+..|..-.
T Consensus         2 ~Lea~~~~Lr~rLd~~~rk~~~~~~~~k~L~~-ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el   63 (69)
T PF14197_consen    2 KLEAEIATLRNRLDSLTRKNSVHEIENKRLRR-ERDSAERQLGDAYEENNKLKEENEALRKEL   63 (69)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            588888888888854333333222   22222 32222 677788888888888888887663

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

Probab=93.38  E-value=1.7  Score=39.64  Aligned_cols=77  Identities=19%  Similarity=0.334  Sum_probs=44.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      ++...+..||.|...|.+.|.+=+..-.+|.+.+..++.+..          .......-+...+.+|+++|.+++.-..
T Consensus        47 ~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q~~~~~  126 (314)
T PF04111_consen   47 ELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQYEYAS  126 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666666666666555555555555555555544          1112222333455677777777777777


Q ss_pred             hhHHHHH
Q 028818          110 RDVSKLE  116 (203)
Q Consensus       110 rDvaKLE  116 (203)
                      .++.+|+
T Consensus       127 ~~L~~L~  133 (314)
T PF04111_consen  127 NQLDRLR  133 (314)
T ss_dssp             HHHHCHH
T ss_pred             HHHHHHH
Confidence            6666665

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.

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

Probab=93.29  E-value=1.8  Score=42.87  Aligned_cols=83  Identities=17%  Similarity=0.344  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHHHH------hhhhhHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHH---HHHHHHHHHHHHH
Q 028818           31 DVARKITSIAIST------RVSDLESEHSALRSQLAEKDSRI-------AELQSQIESIYSSLS---DKLGQAQADKERL   94 (203)
Q Consensus        31 dlarkIts~A~at------RVs~LE~E~~~LR~~LaEKd~~i-------~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL   94 (203)
                      .=||++..-+-+.      -+.+|+.|+..||.++.++....       .+...+++.+++++.   .|.+...++...|
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            3466776665443      36678888888888888874443       455667777887777   7888888888888


Q ss_pred             HHHHHHHHHHHHHHhhhHH
Q 028818           95 SKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        95 ~~E~~~La~TvKkL~rDva  113 (203)
                      .+|+..|-..+..+..++.
T Consensus       175 k~en~rl~~~l~~~r~~ld  193 (546)
T KOG0977|consen  175 KAENSRLREELARARKQLD  193 (546)
T ss_pred             HHHhhhhHHHHHHHHHHHH
Confidence            8888888877777665444

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=93.20  E-value=1.9  Score=43.18  Aligned_cols=18  Identities=22%  Similarity=0.390  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHHHHhhh
Q 028818           94 LSKENEALTNTVRKLQRD  111 (203)
Q Consensus        94 L~~E~~~La~TvKkL~rD  111 (203)
                      |.++.+.+...+..+...
T Consensus       901 l~~~~~~l~~~~~~~~~~  918 (1164)
T TIGR02169       901 LERKIEELEAQIEKKRKR  918 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            333333333333333333

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=93.06  E-value=2.1  Score=37.45  Aligned_cols=75  Identities=27%  Similarity=0.403  Sum_probs=55.8

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      -|--+||++..-+...+++-+.....|+.-+.-...+=+   ++-..+.++-..|..|+...-.++.+|+|.|.-|+.
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            455567777777766666666666666654443332222   788889999999999999999999999999998874

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

Probab=93.00  E-value=1.2  Score=44.98  Aligned_cols=39  Identities=33%  Similarity=0.486  Sum_probs=34.3

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           37 TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIES   75 (203)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~   75 (203)
                      ..-+...|...||.|+.+||..|..|++.+..|+..+..
T Consensus       539 ~~e~~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~  577 (697)
T PF09726_consen  539 CAESCRQRRRQLESELKKLRRELKQKEEQIRELESELQE  577 (697)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344688999999999999999999999999999887743

; GO: 0016021 integral to membrane

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

Probab=93.00  E-value=2  Score=37.09  Aligned_cols=53  Identities=25%  Similarity=0.366  Sum_probs=33.0

Q ss_pred             hHHHHHHHHHHH------HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           29 QLDVARKITSIA------ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        29 QLdlarkIts~A------~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ||.-|..+..-|      +..|+..+|.++.+.-.++..-...|.+|+.++..+...|.
T Consensus       100 ~l~ea~~~~ee~e~k~~E~~rkl~~~E~~Le~aEeR~e~~E~ki~eLE~el~~~~~~lk  158 (237)
T PF00261_consen  100 QLKEAKRRAEEAERKYEEVERKLKVLEQELERAEERAEAAESKIKELEEELKSVGNNLK  158 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHHHHH
Confidence            555565555543      45666666776666666666666666666666666655554

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 ....

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

Probab=92.88  E-value=3.3  Score=33.84  Aligned_cols=41  Identities=24%  Similarity=0.460  Sum_probs=17.6

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +..++..++++...++.....-.......++++..++..+.
T Consensus       100 l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~  140 (191)
T PF04156_consen  100 LQERIQELESELEKLKEDLQELRELLKSVEERLDSLDESIK  140 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444333344444444444444443

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 [].

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

Probab=92.81  E-value=5.6  Score=34.09  Aligned_cols=77  Identities=18%  Similarity=0.309  Sum_probs=52.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      .....|..+..|..+|+.-|..-...+.+|+.++...+..-.      .|+....++...|.-|...|...+.++.++-.
T Consensus        45 ~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y~kdK~~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~Erd  124 (201)
T PF13851_consen   45 RNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNYEKDKQSLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERD  124 (201)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455567777777777777777777777777777766665433      66777777777777777777777776666655


Q ss_pred             HHH
Q 028818          114 KLE  116 (203)
Q Consensus       114 KLE  116 (203)
                      -|.
T Consensus       125 eL~  127 (201)
T PF13851_consen  125 ELY  127 (201)
T ss_pred             HHH
Confidence            544

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

Probab=92.63  E-value=3.2  Score=37.92  Aligned_cols=84  Identities=27%  Similarity=0.410  Sum_probs=52.0

Q ss_pred             hHHHHHHHHHHHHHH-------hhh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           29 QLDVARKITSIAIST-------RVS---DLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKEN   98 (203)
Q Consensus        29 QLdlarkIts~A~at-------RVs---~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~   98 (203)
                      -++|.||=..||+..       ||-   .|-.....+|.+|.|-...-.+|.+++..++..+-    ..+++...|..||
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            357788888887642       221   33344556677777666667777777778887776    4455555555555


Q ss_pred             HHHHHHHHHHhhhHHHHH
Q 028818           99 EALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        99 ~~La~TvKkL~rDvaKLE  116 (203)
                      +.|..-.|+|-..|.+|+
T Consensus       180 s~LeE~~~~l~~ev~~L~  197 (290)
T COG4026         180 SRLEEMLKKLPGEVYDLK  197 (290)
T ss_pred             HHHHHHHHhchhHHHHHH
Confidence            555555555555555544

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=92.58  E-value=1.3  Score=37.98  Aligned_cols=61  Identities=30%  Similarity=0.431  Sum_probs=38.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVR  106 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-------~rL~~a~ee~~kL~~E~~~La~TvK  106 (203)
                      ..|..++..+..++.+++..|..|+.++.-....++       .|...+..++..|..|...|-+.++
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            566777788888888888888888888877777666       3334444444444444444444443

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=92.53  E-value=5.1  Score=32.89  Aligned_cols=46  Identities=15%  Similarity=0.335  Sum_probs=20.0

Q ss_pred             CchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           25 DPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIE   74 (203)
Q Consensus        25 DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s   74 (203)
                      --||||.    |-...|..++..=..|+.+||.....--+.+...++++.
T Consensus        42 iDFeqLk----ien~~l~~kIeERn~eL~~Lk~~~~~~v~~L~h~keKl~   87 (177)
T PF13870_consen   42 IDFEQLK----IENQQLNEKIEERNKELLKLKKKIGKTVQILTHVKEKLH   87 (177)
T ss_pred             HHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3466663    334444444444444444444444333333333333333

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

Probab=92.52  E-value=3.2  Score=37.52  Aligned_cols=28  Identities=18%  Similarity=0.414  Sum_probs=11.9

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 028818          100 ALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (203)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (203)
                      .|...+..++..+..++.-|..+...++
T Consensus       234 el~~el~~l~~~i~~~~~~k~~l~~eI~  261 (325)
T PF08317_consen  234 ELQEELEELEEKIEELEEQKQELLAEIA  261 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444444333

>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=92.45  E-value=2.5  Score=31.32  Aligned_cols=35  Identities=20%  Similarity=0.402  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           82 DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      ..+....++++.|....++|...|..|+..|.+|.
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            34448888888999999999999999999998874

>KOG2685 consensus Cystoskeletal protein Tektin [Cytoskeleton]

Probab=92.37  E-value=6.6  Score=38.02  Aligned_cols=97  Identities=25%  Similarity=0.335  Sum_probs=78.3

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHH------------
Q 028818           28 EQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-----DKLGQAQAD------------   90 (203)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-----~rL~~a~ee------------   90 (203)
                      .||..=.-.+..||..|+...+.=..+|.-+++.+.++|++.+..|..++.++.     -|+.+.+-+            
T Consensus       263 n~lr~Q~~~ve~af~~ri~etqdar~kL~~ql~k~leEi~~~e~~I~~le~airdK~~pLKVAqTRle~Rt~RPnvELCr  342 (421)
T KOG2685|consen  263 NDLRTQADAVELAFKKRIRETQDARNKLEWQLAKTLEEIADAENNIEALERAIRDKEGPLKVAQTRLENRTYRPNVELCR  342 (421)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccccHHHHHHHHHHcccCCchHHHH
Confidence            344444445667999999999999999999999999999999999999999998     344444433            


Q ss_pred             ---HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Q 028818           91 ---KERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ  124 (203)
Q Consensus        91 ---~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lmq  124 (203)
                         +-.|-.|--.|-.||..|...+++=|.=++.|..
T Consensus       343 D~AQ~~L~~EV~~l~~t~~~L~~kL~eA~~~l~~L~~  379 (421)
T KOG2685|consen  343 DQAQYRLVDEVHELDDTVAALKEKLDEAEDSLKLLVN  379 (421)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               3578888888889998888888887777777665

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

Probab=92.15  E-value=1.8  Score=38.49  Aligned_cols=84  Identities=23%  Similarity=0.328  Sum_probs=62.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------------------------------------
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS--------------------------------------------   81 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~--------------------------------------------   81 (203)
                      ..|+.++..+.+++.+-...|..|+.-+..++....                                            
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            468889999999999999999999999988885411                                            


Q ss_pred             ----HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH------HHHHHhhcccc
Q 028818           82 ----DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF------RKTLVQSLKDD  129 (203)
Q Consensus        82 ----~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F------Kk~LmqSLq~d  129 (203)
                          ..=-.-.++|..|.+|.+.+.+++.+|.++|++|++=      |=--|||.+..
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                0001224677888888888888888888888877652      34467888764

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

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=92.02  E-value=2.2  Score=38.93  Aligned_cols=90  Identities=21%  Similarity=0.291  Sum_probs=55.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH--------HHHHHHHHHHHH---------
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQA--------QADKERLSKENE---------   99 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a--------~ee~~kL~~E~~---------   99 (203)
                      .+.++...+|.+...|+....++.-.+..++.++..++..+.   .++...        ......|...-+         
T Consensus       258 ~l~~~l~~le~~l~~l~~~y~~~hP~v~~l~~~i~~l~~~l~~e~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l  337 (444)
T TIGR03017       258 NLKTDIARAESKLAELSQRLGPNHPQYKRAQAEINSLKSQLNAEIKKVTSSVGTNSRILKQREAELREALENQKAKVLEL  337 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467888888888888888888888888888888888888775   122111        111111211111         


Q ss_pred             -HHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 028818          100 -ALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (203)
Q Consensus       100 -~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (203)
                       ........|.||+.--+..=..|++.+++-
T Consensus       338 ~~~~~~~~~L~r~~~~~~~~y~~ll~r~~e~  368 (444)
T TIGR03017       338 NRQRDEMSVLQRDVENAQRAYDAAMQRYTQT  368 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             122345566667766666666777766554

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.

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=91.99  E-value=2.3  Score=47.55  Aligned_cols=90  Identities=23%  Similarity=0.341  Sum_probs=79.1

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-----------DKLGQAQADKERLSKENEALTNTVR  106 (203)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-----------~rL~~a~ee~~kL~~E~~~La~TvK  106 (203)
                      ..+++....+|+.|...||.++.|=...+.+|+.+++.+..+++           .++....+.+.+|++.-..+...+.
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            34899999999999999999999999999999999999888877           3456677778888888899999999


Q ss_pred             HHhhhHHHHHHHHHHHHhhcc
Q 028818          107 KLQRDVSKLEVFRKTLVQSLK  127 (203)
Q Consensus       107 kL~rDvaKLE~FKk~LmqSLq  127 (203)
                      -++.-.++||.-|..|+|-+.
T Consensus      1397 ~~~~~~~~Lek~k~~l~~el~ 1417 (1930)
T KOG0161|consen 1397 AANAKNASLEKAKNRLQQELE 1417 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHhHHH
Confidence            999999999999999988554

>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=91.96  E-value=4.1  Score=32.81  Aligned_cols=20  Identities=25%  Similarity=0.448  Sum_probs=9.8

Q ss_pred             HHHHhhhHHHHHHHHHHHHh
Q 028818          105 VRKLQRDVSKLEVFRKTLVQ  124 (203)
Q Consensus       105 vKkL~rDvaKLE~FKk~Lmq  124 (203)
                      |--|.-||.-|+.+=|..++
T Consensus        98 veEL~~Dv~DlK~myr~Qi~  117 (120)
T PF12325_consen   98 VEELRADVQDLKEMYREQID  117 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            34445555555554444443

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 [].

>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=91.91  E-value=4.8  Score=40.01  Aligned_cols=89  Identities=18%  Similarity=0.276  Sum_probs=42.8

Q ss_pred             HHHhhCCCCchhhHHHHHHH--------HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------
Q 028818           17 EVLQVLPSDPFEQLDVARKI--------TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------   81 (203)
Q Consensus        17 eil~vLP~DP~EQLdlarkI--------ts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-------   81 (203)
                      ++|-|.|..-+-|-.|-..-        ....+...+..|+.++.+|...|.........|+.+...+.....       
T Consensus       130 DmLvV~~ka~~lQ~qlE~~qkE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e~L~~~~kel~~~~e~l~~E~~  209 (546)
T PF07888_consen  130 DMLVVTTKAQLLQNQLEECQKEKEELLKENEQLEEEVEQLREEVERLEAELEQEEEEMEQLKQQQKELTESSEELKEERE  209 (546)
T ss_pred             ceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56777777545443333211        112445555555555666666665555555555554444443332       


Q ss_pred             ---HHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           82 ---DKLGQAQADKERLSKENEALTNTV  105 (203)
Q Consensus        82 ---~rL~~a~ee~~kL~~E~~~La~Tv  105 (203)
                         .++..+.+++.+|..+...|...+
T Consensus       210 ~L~~q~~e~~~ri~~LEedi~~l~qk~  236 (546)
T PF07888_consen  210 SLKEQLAEARQRIRELEEDIKTLTQKE  236 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               223334444444444444444444

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=91.77  E-value=3.5  Score=37.79  Aligned_cols=30  Identities=13%  Similarity=0.118  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ...+|.+|++=+..|...+.++..++.+++
T Consensus       206 L~~lk~~l~~~~~ei~~~~~~l~e~~~~l~  235 (312)
T smart00787      206 LDRAKEKLKKLLQEIMIKVKKLEELEEELQ  235 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444

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

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

Probab=91.73  E-value=8.5  Score=33.64  Aligned_cols=72  Identities=21%  Similarity=0.277  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 028818           51 EHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (203)
Q Consensus        51 E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (203)
                      |+..+|.++..-...+..|+.+...|+..+.       ..+.........|..|...|-..+....++...|-..|-.|
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            3444555555444444444444444444443       33333444555666666666666666666666666666544

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 ....

>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=91.71  E-value=1.1  Score=36.48  Aligned_cols=32  Identities=28%  Similarity=0.441  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (203)
Q Consensus        49 E~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L   80 (203)
                      ..++..|+.++.+-...+..|+..+..|...+
T Consensus        78 d~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~  109 (169)
T PF07106_consen   78 DAEIKELREELAELKKEVKSLEAELASLSSEP  109 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            33444444444444444444444444444333

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 [].

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

Probab=91.58  E-value=6.4  Score=39.38  Aligned_cols=76  Identities=22%  Similarity=0.333  Sum_probs=39.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------------DKLGQAQADKERLSKENEALTNTVRK  107 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~------------~rL~~a~ee~~kL~~E~~~La~TvKk  107 (203)
                      -|..|+..|-.++..|+.....=-++|.+|+..+..|..++.            ..-....++...|.+|+..|...+..
T Consensus        26 ~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eLk~q~~~~~~~~~pa~pse~E~~Lq~E~~~L~kElE~L~~qlqa  105 (617)
T PF15070_consen   26 QWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSELKNQMAEPPPPEPPAGPSEVEQQLQAEAEHLRKELESLEEQLQA  105 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666665555555555566655555555444            11112333445555565555555555


Q ss_pred             HhhhHHHH
Q 028818          108 LQRDVSKL  115 (203)
Q Consensus       108 L~rDvaKL  115 (203)
                      ..++...|
T Consensus       106 qv~~ne~L  113 (617)
T PF15070_consen  106 QVENNEQL  113 (617)
T ss_pred             HHHHHHHH
Confidence            44443333

>PRK02224 chromosome segregation protein; Provisional

Probab=91.57  E-value=4.6  Score=40.23  Aligned_cols=12  Identities=8%  Similarity=-0.006  Sum_probs=6.8

Q ss_pred             CchhhHHHHHHH
Q 028818           25 DPFEQLDVARKI   36 (203)
Q Consensus        25 DP~EQLdlarkI   36 (203)
                      +-||+++-..+=
T Consensus       162 ~~~e~~~~~~~~  173 (880)
T PRK02224        162 GKLEEYRERASD  173 (880)
T ss_pred             HHHHHHHHHHHH
Confidence            666666554433

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

Probab=91.53  E-value=2.4  Score=40.80  Aligned_cols=39  Identities=21%  Similarity=0.443  Sum_probs=20.9

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .|..+...|++.+...+.+....-..|++.+..++.++.
T Consensus        38 ~~l~q~q~ei~~~~~~i~~~~~~~~kL~~~lk~~e~~i~   76 (420)
T COG4942          38 KQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEIA   76 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455555566665555555555555555555544444443

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

Probab=91.49  E-value=1.2  Score=48.29  Aligned_cols=77  Identities=25%  Similarity=0.375  Sum_probs=50.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH----------HHH-------HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLA----------EKD-------SRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENE   99 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La----------EKd-------~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~   99 (203)
                      ||.+++..+|..+...|..|.          +-+       +.|.++.+++..+|..|.   .-+..+..+..-|++|.+
T Consensus      1198 ay~s~f~~me~kl~~ir~il~~~svs~~~i~~l~~~~~~lr~~l~~~~e~L~~~E~~Lsdi~~~~~~a~~~LesLq~~~~ 1277 (1758)
T KOG0994|consen 1198 AYASRFLDMEEKLEEIRAILSAPSVSAEDIAQLASATESLRRQLQALTEDLPQEEETLSDITNSLPLAGKDLESLQREFN 1277 (1758)
T ss_pred             hhHhHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhccchhhhhHHHHHHHHH
Confidence            889999999988888887772          112       222233333333333333   223344556678999999


Q ss_pred             HHHHHHHHHhhhHHHHH
Q 028818          100 ALTNTVRKLQRDVSKLE  116 (203)
Q Consensus       100 ~La~TvKkL~rDvaKLE  116 (203)
                      .|-+|+|.|...+.||+
T Consensus      1278 ~l~~~~keL~e~~~~ik 1294 (1758)
T KOG0994|consen 1278 GLLTTYKELREQLEKIK 1294 (1758)
T ss_pred             HHHHHHHHHHHHHHHhh
Confidence            99999999999888865

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

Probab=91.26  E-value=5.7  Score=34.07  Aligned_cols=99  Identities=24%  Similarity=0.324  Sum_probs=56.8

Q ss_pred             ChHHHHhhCCCCchhhHHHHHHHHHH---------HHHHhhhh----------hHHHHHHHHHHHHHH-------HHHHH
Q 028818           14 LPEEVLQVLPSDPFEQLDVARKITSI---------AISTRVSD----------LESEHSALRSQLAEK-------DSRIA   67 (203)
Q Consensus        14 lp~eil~vLP~DP~EQLdlarkIts~---------A~atRVs~----------LE~E~~~LR~~LaEK-------d~~i~   67 (203)
                      |-++|...==+||-..|+.=.+..+.         ++..|+.+          +-.+..++-.++.++       +.+|.
T Consensus        55 l~e~v~~l~idd~~~~f~~~~~tl~~LE~~GFnV~~l~~RL~kLL~lk~~~~~~~e~~k~le~~~~~~~~~~~~~e~~i~  134 (190)
T PF05266_consen   55 LAEKVKKLQIDDSRSSFESLMKTLSELEEHGFNVKFLRSRLNKLLSLKDDQEKLLEERKKLEKKIEEKEAELKELESEIK  134 (190)
T ss_pred             HHHHHHHcccCCcHHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence            44455555556666666655555443         44444443          344455666666655       77777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           68 ELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        68 ~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      +|+.++..|+.+.+    .....+..-.+|...|..-+.+++.++...|
T Consensus       135 ~Le~ki~el~~~~~----~~~~~ke~~~~ei~~lks~~~~l~~~~~~~e  179 (190)
T PF05266_consen  135 ELEMKILELQRQAA----KLKEKKEAKDKEISRLKSEAEALKEEIENAE  179 (190)
T ss_pred             HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777776654    2333333334666666666666666666554

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

Probab=91.16  E-value=0.4  Score=42.16  Aligned_cols=35  Identities=31%  Similarity=0.473  Sum_probs=32.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIE   74 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s   74 (203)
                      -|.+.+.++|.||..||+-|+-|++|..+|..|+-
T Consensus        48 elr~EL~kvEeEI~TLrqVLaAKerH~~ELKRKLG   82 (208)
T KOG4010|consen   48 ELRTELAKVEEEIVTLRQVLAAKERHAAELKRKLG   82 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            68889999999999999999999999999998863

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=91.15  E-value=2.4  Score=41.44  Aligned_cols=70  Identities=21%  Similarity=0.298  Sum_probs=37.4

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHhh
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLG----QAQADKERLSKENEALTNTVRKLQR  110 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~----~a~ee~~kL~~E~~~La~TvKkL~r  110 (203)
                      +..+|..++.++..|..+=..=..+...|++|-..++..++.++.    +..++..+|++|+..|...+-.|.+
T Consensus        64 lva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~  137 (472)
T TIGR03752        64 LVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQR  137 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455555555555444443344556777777777777773332    3344555555555555555555544

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.

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

Probab=91.15  E-value=7  Score=35.37  Aligned_cols=21  Identities=24%  Similarity=0.404  Sum_probs=10.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLA   60 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La   60 (203)
                      .+..|-..|+.|+..||+...
T Consensus       181 ~l~~~~~~L~~e~~~Lk~~~~  201 (325)
T PF08317_consen  181 KLRERKAELEEELENLKQLVE  201 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            344555555555555555444

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

Probab=91.09  E-value=7  Score=33.50  Aligned_cols=85  Identities=21%  Similarity=0.302  Sum_probs=58.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH--HHHHHH-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           40 AISTRVSDLESEHSALRSQLA--EKDSRI-AELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La--EKd~~i-~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      -+.--+..++.|+..||.+|.  +||... ..++.|+..++..|.   ---....+...+|..|++.|-.+....-.||.
T Consensus        59 ~L~epL~~a~~e~~eL~k~L~~y~kdK~~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~~~i~evq  138 (201)
T PF13851_consen   59 RLSEPLKKAEEEVEELRKQLKNYEKDKQSLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYRKFESAIQEVQ  138 (201)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344556778888888888887  555443 344555555555554   22236677888999999999988888888888


Q ss_pred             HHHHHHHHHHh
Q 028818          114 KLEVFRKTLVQ  124 (203)
Q Consensus       114 KLE~FKk~Lmq  124 (203)
                      .==.||-.|++
T Consensus       139 Qk~~~kn~lLE  149 (201)
T PF13851_consen  139 QKTGLKNLLLE  149 (201)
T ss_pred             HHHHHHHHHHH
Confidence            77777766654

>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]

Probab=91.02  E-value=10  Score=37.35  Aligned_cols=85  Identities=28%  Similarity=0.398  Sum_probs=56.6

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHH------------------------HHHHHHHHHHHHHHHHHHH-------HHHHH
Q 028818           37 TSIAISTRVSDLESEHSALRSQLAE------------------------KDSRIAELQSQIESIYSSL-------SDKLG   85 (203)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~LaE------------------------Kd~~i~~Lq~r~s~Le~~L-------~~rL~   85 (203)
                      ..|-+-.||.+||.|-+-|-.+|.+                        --.||.-|+..|..|-..|       +.++.
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            3456778999999999988887742                        1234455555555544444       45555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ  124 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lmq  124 (203)
                      +-.++.....+||..|   -+||.+.|.|=|++=|+|-.
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   47899999999999888865

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

Probab=90.95  E-value=3.6  Score=42.28  Aligned_cols=88  Identities=19%  Similarity=0.293  Sum_probs=56.3

Q ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH------------HHHH
Q 028818           35 KITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLS------------KENE   99 (203)
Q Consensus        35 kIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~------------~E~~   99 (203)
                      |++--|+++- -+-|+|+..|+++|..--..-..+++|++.||.+|.   -.|+.+++++.+.-            +.+.
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            5555666654 356888888888888888888888888888888888   66777777664332            2333


Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHH
Q 028818          100 ALTNTVRKLQRDVSKLEVFRKTLV  123 (203)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~Lm  123 (203)
                      .|...+-.+++.++++.+=-.+|-
T Consensus        89 ~le~~l~e~~~~l~~~~~e~~~l~  112 (769)
T PF05911_consen   89 ELEAKLAELSKRLAESAAENSALS  112 (769)
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHH
Confidence            444444445554444443333333

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=90.68  E-value=5.4  Score=33.90  Aligned_cols=30  Identities=23%  Similarity=0.436  Sum_probs=16.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           47 DLESEHSALRSQLAEKDSRIAELQSQIESI   76 (203)
Q Consensus        47 ~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~L   76 (203)
                      .++..+..|..++.+....|.+|++++..+
T Consensus        66 ~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~   95 (188)
T PF03962_consen   66 KRQNKLEKLQKEIEELEKKIEELEEKIEEA   95 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555555555544

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

>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=90.61  E-value=4.5  Score=35.76  Aligned_cols=41  Identities=12%  Similarity=0.115  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-cccccCC
Q 028818           92 ERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS-LKDDEDA  132 (203)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS-Lq~d~~~  132 (203)
                      .++..|++...+.+.++..++.+|+.+=-.+..+ |+-+.-.
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            3445667777777888888888888877777777 6665543

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.

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

Probab=90.61  E-value=1.6  Score=44.10  Aligned_cols=84  Identities=26%  Similarity=0.430  Sum_probs=53.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHhhhHHHHH
Q 028818           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYS---SLSDKLGQAQADKERLSKENEALTNT-------VRKLQRDVSKLE  116 (203)
Q Consensus        47 ~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~---~L~~rL~~a~ee~~kL~~E~~~La~T-------vKkL~rDvaKLE  116 (203)
                      +||+|+.+||..|.--...-.||+.+++.|+.   .+..=|.+..++++.|+.....|...       +..|.|.++-..
T Consensus       422 rLE~dvkkLraeLq~~Rq~E~ELRsqis~l~~~Er~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DKq~l~~LEkrL~eE~  501 (697)
T PF09726_consen  422 RLEADVKKLRAELQSSRQSEQELRSQISSLTNNERSLKSELSQLRQENEQLQNKLQNLVQARQQDKQSLQQLEKRLAEER  501 (697)
T ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            79999999999999999999999999776655   33355556666666666655555432       223333333333


Q ss_pred             HHHHHHHhhccccc
Q 028818          117 VFRKTLVQSLKDDE  130 (203)
Q Consensus       117 ~FKk~LmqSLq~d~  130 (203)
                      .-|..|=..|+++-
T Consensus       502 ~~R~~lEkQL~eEr  515 (697)
T PF09726_consen  502 RQRASLEKQLQEER  515 (697)
T ss_pred             HHHHHHHHHHHHHH
Confidence            34444444555543

; GO: 0016021 integral to membrane

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

Probab=90.59  E-value=8.4  Score=42.16  Aligned_cols=111  Identities=20%  Similarity=0.257  Sum_probs=74.0

Q ss_pred             ChHHHHh-hCCCCchhhHHHHHHHHHH---------------HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           14 LPEEVLQ-VLPSDPFEQLDVARKITSI---------------AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIY   77 (203)
Q Consensus        14 lp~eil~-vLP~DP~EQLdlarkIts~---------------A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le   77 (203)
                      +.++||. +||.+|.+=..|+-+|...               +=..|+..|++|+.+-|.....-.....+.++-+...+
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            4455554 7999999888888777654               33578999999999988887755555555555555555


Q ss_pred             HHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH----HHHHHHHh
Q 028818           78 SSLS----------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE----VFRKTLVQ  124 (203)
Q Consensus        78 ~~L~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE----~FKk~Lmq  124 (203)
                      .+..          .-+..+.+...|.++|-..-..++..-+..|++||    .+|...||
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          34455666667777777666666666666666554    45555554

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

Probab=90.57  E-value=6  Score=38.89  Aligned_cols=85  Identities=13%  Similarity=0.200  Sum_probs=50.0

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHHH
Q 028818           28 EQLDVARKITSIAISTRVSDLES-EHSALRSQLAEKDSRIAELQSQIESIYSSLS-----------------DKLGQAQA   89 (203)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~-E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-----------------~rL~~a~e   89 (203)
                      .||+--|+--.    .+++++|. ++..+|+.+.++-....+|+...+.++.+-+                 ..|....|
T Consensus       328 sqleSqr~y~e----~~~~e~~qsqlen~k~~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~E  403 (493)
T KOG0804|consen  328 SQLESQRKYYE----QIMSEYEQSQLENQKQYYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKEERE  403 (493)
T ss_pred             hhhhHHHHHHH----HHHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47777665443    77777776 7888887777666555554433333333222                 33334556


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           90 DKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        90 e~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      ++..|.+..+...+++|+++....+.-
T Consensus       404 ~n~~l~knq~vw~~kl~~~~e~~~~~~  430 (493)
T KOG0804|consen  404 ENKKLIKNQDVWRGKLKELEEREKEAL  430 (493)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence            666666666666667777666555443

>smart00787 Spc7 Spc7 kinetochore protein

Probab=90.52  E-value=6.7  Score=35.99  Aligned_cols=77  Identities=16%  Similarity=0.274  Sum_probs=34.2

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKD----SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd----~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      +..|...|+.|+..||+.-.|-+    .....+++++..+..++           ....++-..+..++..++-++....
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            34444445555555544444422    23444444444443333           3334444444444444444444444


Q ss_pred             HHHHHHHhhccc
Q 028818          117 VFRKTLVQSLKD  128 (203)
Q Consensus       117 ~FKk~LmqSLq~  128 (203)
                      .-|..+...+++
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.

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

Probab=90.51  E-value=2.5  Score=37.26  Aligned_cols=73  Identities=14%  Similarity=0.218  Sum_probs=55.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFR  119 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FK  119 (203)
                      +.+++...||++..+++++.+...+.|+-.+       .-.    ....++++.|.++.++|....+-|.-+|+|++-=+
T Consensus        78 ~~ks~~qeLe~~L~~~~qk~~tl~e~~en~K-------~~~----e~tEer~~el~kklnslkk~~e~lr~el~k~~e~d  146 (203)
T KOG3433|consen   78 DRKSVLQELESQLATGSQKKATLGESIENRK-------AGR----EETEERTDELTKKLNSLKKILESLRWELAKIQETD  146 (203)
T ss_pred             HHHHHHHHHHHHHHHhhhhHhHHHHHHHHHH-------hhh----hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            6788999999999999999888877665443       111    24556666999999999999999999999987544


Q ss_pred             HHHH
Q 028818          120 KTLV  123 (203)
Q Consensus       120 k~Lm  123 (203)
                      -++.
T Consensus       147 pqv~  150 (203)
T KOG3433|consen  147 PQVF  150 (203)
T ss_pred             HHHH
Confidence            4443

>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=90.44  E-value=1.6  Score=33.19  Aligned_cols=41  Identities=27%  Similarity=0.447  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028818           71 SQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRD  111 (203)
Q Consensus        71 ~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (203)
                      .++-.|+..|.   +|.....+++.||..||.-|..-|..|.+.
T Consensus        23 ~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~~   66 (80)
T PF10224_consen   23 QEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMSS   66 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34555666666   888899999999999999999999988654

The exact function is unknown.

>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=90.10  E-value=11  Score=32.05  Aligned_cols=82  Identities=24%  Similarity=0.321  Sum_probs=45.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      ....|+..|..++..+|..+.++.+.+.++++.+......+.   ...........++..+...+...+..+.+.+..-.
T Consensus        67 ~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~r  146 (302)
T PF10186_consen   67 ELRERLERLRERIERLRKRIEQKRERLEELRESLEQRRSRLSASQDLVESRQEQLEELQNELEERKQRLSQLQSQLARRR  146 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            556777788888888888888777777777666666555554   22222222233333333334444444444444443


Q ss_pred             HHHHH
Q 028818          117 VFRKT  121 (203)
Q Consensus       117 ~FKk~  121 (203)
                      ...-.
T Consensus       147 ~~l~~  151 (302)
T PF10186_consen  147 RQLIQ  151 (302)
T ss_pred             HHHHH
Confidence            33333

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

>PF14362 DUF4407: Domain of unknown function (DUF4407)

Probab=90.05  E-value=13  Score=32.81  Aligned_cols=83  Identities=14%  Similarity=0.257  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----H-----------HHHHHHHHHHHHHHHHHHHHHH----HHHH
Q 028818           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----D-----------KLGQAQADKERLSKENEALTNT----VRKL  108 (203)
Q Consensus        48 LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----~-----------rL~~a~ee~~kL~~E~~~La~T----vKkL  108 (203)
                      +..++..+...++..+..+..+++++..+...++    +           +-+.+.+.....+.+.+.+.++    +..|
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            4446666666666666666666666666666665    1           2344444444444444444444    4444


Q ss_pred             h----hhHHHHHHHHHHHHhhccccc
Q 028818          109 Q----RDVSKLEVFRKTLVQSLKDDE  130 (203)
Q Consensus       109 ~----rDvaKLE~FKk~LmqSLq~d~  130 (203)
                      +    ...+.|...+.......+.+.
T Consensus       213 ~~~~~~~~~~l~~~~~~~~a~~~~~~  238 (301)
T PF14362_consen  213 DAQIAARKARLDEARQAKVAEFQAII  238 (301)
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHhHhh
Confidence            4    555666666666666555544

>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=90.03  E-value=5.8  Score=40.23  Aligned_cols=64  Identities=19%  Similarity=0.268  Sum_probs=39.3

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVR  106 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvK  106 (203)
                      .++..||..|..+......+|.+-.+.+..|+++...|.    +|+..+.+.+++|.+.-+.+.+.+.
T Consensus       561 ~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  561 EEIQRRVKLLKQQKEQQLKELQELQEERKSLRESAEKLA----ERYEEAKDKQEKLMKRVDRVLQLLN  624 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            467777777777777666666666666666655554444    4555666666666665555554443

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 [].

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

Probab=89.99  E-value=13  Score=32.93  Aligned_cols=42  Identities=19%  Similarity=0.312  Sum_probs=23.1

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L   80 (203)
                      ..+..++..++.++..++.++..-.+.+..++.++..++..+
T Consensus       140 ~~~~~~~~~l~~~i~~~~~~i~~~~~~l~~~~~~l~~~~~~~  181 (423)
T TIGR01843       140 STLRAQLELILAQIKQLEAELAGLQAQLQALRQQLEVISEEL  181 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355566666666666666666555555555555544444433

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.

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=89.95  E-value=11  Score=36.99  Aligned_cols=68  Identities=22%  Similarity=0.259  Sum_probs=41.7

Q ss_pred             ChHHHHhhCCCCchhhHHHHHHH---------HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           14 LPEEVLQVLPSDPFEQLDVARKI---------TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        14 lp~eil~vLP~DP~EQLdlarkI---------ts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      |-+.+-.+|==+++++|.-=-.+         ....+..++..||.++..+..++.+....+..++.++..++..+.
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            44556666666677776421111         112555677777777777777777777667666666666666554

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.

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

Probab=89.89  E-value=4.1  Score=37.96  Aligned_cols=41  Identities=20%  Similarity=0.343  Sum_probs=27.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL   80 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L   80 (203)
                      .+..++..||.+...|+....++.-.+.+|++++..++..+
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            44566777777777777766666666666666666666654

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=89.64  E-value=6.8  Score=29.02  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKL  108 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL  108 (203)
                      ...++|.+|..|+......++.|
T Consensus        43 ~L~~en~~L~~e~~~~~~rl~~L   65 (72)
T PF06005_consen   43 ELKEENEQLKQERNAWQERLRSL   65 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445555555555555554444

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.

>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=89.62  E-value=2.6  Score=38.38  Aligned_cols=58  Identities=28%  Similarity=0.433  Sum_probs=44.2

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~  103 (203)
                      ..++..++.+....+.+|.++...+.++++++..|+.++.    .+..++.+|..+......
T Consensus       220 ~~~l~~a~~~l~~~~~~L~~~~~~l~~l~~~l~~l~~~~~----~~~~e~~~l~~~~~~~~~  277 (344)
T PF12777_consen  220 RQKLEEAEAELEEAEEQLAEKQAELAELEEKLAALQKEYE----EAQKEKQELEEEIEETER  277 (344)
T ss_dssp             HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHh
Confidence            4677788888888899999999999999988888888887    566666666665544443

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.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=89.57  E-value=3.3  Score=30.36  Aligned_cols=55  Identities=24%  Similarity=0.415  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH----HHHHHH
Q 028818           63 DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL----EVFRKT  121 (203)
Q Consensus        63 d~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL----E~FKk~  121 (203)
                      +..|..|+.++..+++.+.    ....++..|..||+..+..+-....+..+|    |++|+.
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            4678889999998888776    778889999999999888887777766654    455554

>TIGR00606 rad50 rad50

Probab=89.57  E-value=4.6  Score=42.87  Aligned_cols=75  Identities=4%  Similarity=0.214  Sum_probs=37.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           40 AISTRVSDLESEHSALRSQLAEK--DSRIAELQSQIESIYSSLS--------DKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEK--d~~i~~Lq~r~s~Le~~L~--------~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      ++...+..++.+-+.++..|.-+  ...+.+++.++..|+.++.        .-+....++...|..++..|..++++|.
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            44444445555555555555544  5555666666666665554        2233344444445444444444555544


Q ss_pred             hhHHH
Q 028818          110 RDVSK  114 (203)
Q Consensus       110 rDvaK  114 (203)
                      .+|+.
T Consensus      1082 ~qi~~ 1086 (1311)
T TIGR00606      1082 KEIKH 1086 (1311)
T ss_pred             HHHHH
Confidence            44444

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

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

Probab=89.54  E-value=5.9  Score=39.63  Aligned_cols=86  Identities=26%  Similarity=0.423  Sum_probs=53.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKD----------------SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd----------------~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~  103 (203)
                      ....||..||..+..|+.++++..                +.+..|++++..|+..|+    .-..++..|..-+.....
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            567899999999999999887332                234556666666666555    444455566555555555


Q ss_pred             HHHHHhhhHHHHHHHH---HHHHhhcccc
Q 028818          104 TVRKLQRDVSKLEVFR---KTLVQSLKDD  129 (203)
Q Consensus       104 TvKkL~rDvaKLE~FK---k~LmqSLq~d  129 (203)
                      .+..|.+.|..++...   ..|+..++.|
T Consensus       123 rL~ELE~~le~~~e~~~D~~kLLe~lqsd  151 (617)
T PF15070_consen  123 RLAELEEELERLQEQQEDRQKLLEQLQSD  151 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence            5666666665555542   3344444443

>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=89.52  E-value=7.4  Score=38.75  Aligned_cols=81  Identities=19%  Similarity=0.328  Sum_probs=41.0

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      .++...+.|-..|......=......|++++..|+.+|.          .+..........|.+|++.|.....++...+
T Consensus       143 ~qlE~~qkE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e~L~~~~kel~~~~e~l~~E~~~L~~q~~e~~~ri  222 (546)
T PF07888_consen  143 NQLEECQKEKEELLKENEQLEEEVEQLREEVERLEAELEQEEEEMEQLKQQQKELTESSEELKEERESLKEQLAEARQRI  222 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444333444555666666665554          1222333444556666666666666665555


Q ss_pred             HHHHHHHHHHH
Q 028818          113 SKLEVFRKTLV  123 (203)
Q Consensus       113 aKLE~FKk~Lm  123 (203)
                      ..||.=.++|-
T Consensus       223 ~~LEedi~~l~  233 (546)
T PF07888_consen  223 RELEEDIKTLT  233 (546)
T ss_pred             HHHHHHHHHHH
Confidence            55554444443

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 [].

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

Probab=89.37  E-value=7.2  Score=34.37  Aligned_cols=78  Identities=22%  Similarity=0.400  Sum_probs=47.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKER-------LSKENEALTNTVRKLQ  109 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~k-------L~~E~~~La~TvKkL~  109 (203)
                      -|--|+..+|.+..+.+..|.+....+..|.++...++.+-.   .+-..+.+++..       ..+|+..|+.-+..+.
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            466788889999999999998888888888777766555433   333334444433       3456666666776666


Q ss_pred             hhHHHHHH
Q 028818          110 RDVSKLEV  117 (203)
Q Consensus       110 rDvaKLE~  117 (203)
                      ..+++|+.
T Consensus        89 ~~i~~l~e   96 (246)
T PF00769_consen   89 AEIARLEE   96 (246)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66666554

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.

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=89.31  E-value=11  Score=30.96  Aligned_cols=79  Identities=22%  Similarity=0.355  Sum_probs=62.6

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (203)
                      -+|.-|...|..++.||...+..|+.++..-=..|.   .+|.....++..+..+-......+.++..++.+++.=+..+
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            356677889999999999999999988876666666   88888888888888888888888888888887776655544


Q ss_pred             Hh
Q 028818          123 VQ  124 (203)
Q Consensus       123 mq  124 (203)
                      -.
T Consensus       125 ~~  126 (177)
T PF13870_consen  125 RK  126 (177)
T ss_pred             HH
Confidence            44

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=89.23  E-value=3.7  Score=40.52  Aligned_cols=28  Identities=14%  Similarity=0.258  Sum_probs=18.7

Q ss_pred             HHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 028818          102 TNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (203)
Q Consensus       102 a~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (203)
                      ......|.|++.-.+..=..|++.+++-
T Consensus       375 ~~e~~~L~Re~~~~~~~Y~~ll~r~~e~  402 (754)
T TIGR01005       375 QVDLDALQRDAAAKRQLYESYLTNYRQA  402 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555677777777776666777766554

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.

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=89.19  E-value=5.7  Score=44.66  Aligned_cols=89  Identities=20%  Similarity=0.363  Sum_probs=71.6

Q ss_pred             hhHHHHHHHHH-----HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 028818           28 EQLDVARKITS-----IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENE   99 (203)
Q Consensus        28 EQLdlarkIts-----~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~   99 (203)
                      |.++++-.|..     .+..+.=.+||.+|..|...|+|......-..+|+..+.....   .-|..-.+.+.+|...|.
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            33444444443     3666777889999999999999999999999999998888777   788888899999999999


Q ss_pred             HHHHHHHHHhhhHHHHH
Q 028818          100 ALTNTVRKLQRDVSKLE  116 (203)
Q Consensus       100 ~La~TvKkL~rDvaKLE  116 (203)
                      +|..+||.|.-.+..+|
T Consensus      1776 ~LE~~~kdLq~rL~e~E 1792 (1930)
T KOG0161|consen 1776 SLERQVKDLQLRLDEAE 1792 (1930)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999998876555544

>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=89.18  E-value=6.3  Score=40.34  Aligned_cols=89  Identities=19%  Similarity=0.286  Sum_probs=58.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHH----------HHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIE-------SIYSSLS----------DKLGQAQADKERLSKENEALT  102 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s-------~Le~~L~----------~rL~~a~ee~~kL~~E~~~La  102 (203)
                      .|..|+..||.|+..+|..+......+..|.....       .+|.+..          -|=...++|...|.+||=+|.
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            57889999999999999998866555544443333       3333322          222344567788888888888


Q ss_pred             HHHHHHhhhHHHHHHHHHHHHhhcccc
Q 028818          103 NTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (203)
Q Consensus       103 ~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (203)
                      .+|-.|...=--+|.||--+ ..|.+|
T Consensus       111 Kqvs~Lk~sQvefE~~Khei-~rl~Ee  136 (717)
T PF09730_consen  111 KQVSVLKQSQVEFEGLKHEI-KRLEEE  136 (717)
T ss_pred             HHHHHHHHhHHHHHHHHHHH-HHHHHH
Confidence            88888777666677776443 334443

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

>TIGR02231 conserved hypothetical protein

Probab=89.02  E-value=5.2  Score=38.07  Aligned_cols=78  Identities=18%  Similarity=0.276  Sum_probs=49.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSL---------------------SDKLGQAQADKERLSKEN   98 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L---------------------~~rL~~a~ee~~kL~~E~   98 (203)
                      +...++..|+.++..|+.++++-...+..++.++.-|+.--                     .+-+....++..+|..+.
T Consensus        68 ~~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (525)
T TIGR02231        68 PDPERLAELRKQIRELEAELRDLEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTED  147 (525)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34557777777777777777777777766666665554432                     022223334556666777


Q ss_pred             HHHHHHHHHHhhhHHHHHH
Q 028818           99 EALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        99 ~~La~TvKkL~rDvaKLE~  117 (203)
                      ..|...+++|.+.+++|+.
T Consensus       148 ~~~~~~~~~~~~~l~~l~~  166 (525)
T TIGR02231       148 REAERRIRELEKQLSELQN  166 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            7777777777777777644

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.

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

Probab=89.00  E-value=7.6  Score=40.81  Aligned_cols=24  Identities=29%  Similarity=0.509  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           92 ERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      ..|.++-+.+...+..+...+.++
T Consensus       887 ~~l~~~l~~~~~~~~~~~~~~~~~  910 (1163)
T COG1196         887 EELEEELRELESELAELKEEIEKL  910 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333

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

Probab=88.84  E-value=5.4  Score=42.50  Aligned_cols=34  Identities=29%  Similarity=0.392  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Q 028818           92 ERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQS  125 (203)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqS  125 (203)
                      ..+..++...++-.+-|.+.|.+||..-..|-..
T Consensus       390 ~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e  423 (1074)
T KOG0250|consen  390 NELGSELEERENKLEQLKKEVEKLEEQINSLREE  423 (1074)
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455666666677777777777777744444433

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

Probab=88.79  E-value=11  Score=37.80  Aligned_cols=73  Identities=22%  Similarity=0.409  Sum_probs=51.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      |++++..+-=.-+.+|.....+|+.+|..|+++...|-.++.      .-...-.++.++|.+|-+-.--..-+|.+.|
T Consensus       320 ~mk~K~~~~~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         320 AMKQKSQEWPGKLEKLKSEIELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLTKSV  398 (622)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHH
Confidence            333333333344778888889999999999999999998887      5556666777777777666655555555554

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

Probab=88.59  E-value=2.3  Score=42.93  Aligned_cols=56  Identities=29%  Similarity=0.477  Sum_probs=42.7

Q ss_pred             HHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 028818           55 LRSQLA----EKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQR  110 (203)
Q Consensus        55 LR~~La----EKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~r  110 (203)
                      ||+||.    +|++++..+..++..+.......|.....+.++|+.||.-|.+-+|.+..
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    78888888888888888777766667777778888888888887777653

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

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

Probab=88.55  E-value=12  Score=39.40  Aligned_cols=40  Identities=20%  Similarity=0.368  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Q 028818           85 GQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQ  124 (203)
Q Consensus        85 ~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~Lmq  124 (203)
                      .....+...|......+.+.++.+.+++.++..-...+.+
T Consensus       442 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  481 (1163)
T COG1196         442 EELNEELEELEEQLEELRDRLKELERELAELQEELQRLEK  481 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555555666666666666666665554444433

>TIGR00606 rad50 rad50

Probab=88.41  E-value=11  Score=40.20  Aligned_cols=52  Identities=12%  Similarity=0.227  Sum_probs=33.1

Q ss_pred             HHHHHHHHH-HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           30 LDVARKITS-IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        30 LdlarkIts-~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +.++.++.. ..|..++..|..++..++..+.+.+..|..|+.++..+...+.
T Consensus       874 lkl~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  926 (1311)
T TIGR00606       874 LQIGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQEKE  926 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            334443433 2566666667777777777777777777777777776666664

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

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

Probab=88.39  E-value=8.1  Score=38.78  Aligned_cols=42  Identities=19%  Similarity=0.415  Sum_probs=26.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ++.+|...++..+..|...+.+|..+|..|+.....|-..+-
T Consensus       284 ~~~~k~~~~~~~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~Ie  325 (581)
T KOG0995|consen  284 QMKSKKQHMEKKLEMLKSEIEEKEEEIEKLQKENDELKKQIE  325 (581)
T ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555666666666666666666666666666666666655543

>PRK09039 hypothetical protein; Validated

Probab=88.07  E-value=6.1  Score=36.39  Aligned_cols=9  Identities=11%  Similarity=0.191  Sum_probs=3.2

Q ss_pred             HHHHHHHHH
Q 028818           72 QIESIYSSL   80 (203)
Q Consensus        72 r~s~Le~~L   80 (203)
                      ++..++.+|
T Consensus       117 ~~~~l~~~L  125 (343)
T PRK09039        117 RAGELAQEL  125 (343)
T ss_pred             HHHHHHHHH
Confidence            333333333

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=87.96  E-value=8.3  Score=33.83  Aligned_cols=64  Identities=17%  Similarity=0.248  Sum_probs=39.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      ..|+.|++.||.-+..=.+....|..+...+|.+-+   +++....++|.+|..|.+-|....+-|+
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            345666666666666666666666666666666655   5555566666666666665555555543

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

Probab=87.91  E-value=2.9  Score=32.45  Aligned_cols=22  Identities=14%  Similarity=0.234  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhH
Q 028818           91 KERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        91 ~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      ..++..+-+.|..+++-++|.+
T Consensus        74 l~el~G~~~~l~~~l~~v~~~~   95 (106)
T PF10805_consen   74 LAELRGELKELSARLQGVSHQL   95 (106)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHH
Confidence            3334444444444444444433

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

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

Probab=87.90  E-value=13  Score=32.40  Aligned_cols=20  Identities=30%  Similarity=0.368  Sum_probs=11.9

Q ss_pred             HHHhhhhhHHHHHHHHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLA   60 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~La   60 (203)
                      |-.||..||.+-..|..++.
T Consensus        16 YIekVr~LE~~N~~Le~~i~   35 (312)
T PF00038_consen   16 YIEKVRFLEQENKRLESEIE   35 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhHHHHH
Confidence            55666666666555555554

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 ....

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

Probab=87.87  E-value=6.6  Score=39.73  Aligned_cols=73  Identities=23%  Similarity=0.277  Sum_probs=42.6

Q ss_pred             HhhhhhHHHHHHHHHHHHHH------H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 028818           43 TRVSDLESEHSALRSQLAEK------D--SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEK------d--~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (203)
                      +|+-.||.|++.||.+++.-      +  ..|..+...+...|...+--.........-|++|+....++|.+|.+.+..
T Consensus       249 ~ri~~lE~e~e~L~~ql~~~N~~~~~~~~~~i~~~~~~L~~kd~~i~~L~~di~~~~~S~~~e~e~~~~qI~~le~~l~~  328 (629)
T KOG0963|consen  249 QRIVFLEREVEQLREQLAKANSSKKLAKIDDIDALGSVLNQKDSEIAQLSNDIERLEASLVEEREKHKAQISALEKELKA  328 (629)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhhccCCchHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67888899999998887621      1  223444444444444443222333344455666777777777777766654


Q ss_pred             H
Q 028818          115 L  115 (203)
Q Consensus       115 L  115 (203)
                      .
T Consensus       329 ~  329 (629)
T KOG0963|consen  329 K  329 (629)
T ss_pred             H
Confidence            3

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

Probab=87.85  E-value=3.2  Score=36.83  Aligned_cols=71  Identities=24%  Similarity=0.392  Sum_probs=38.4

Q ss_pred             HHHhhhhhHH------HHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028818           41 ISTRVSDLES------EHSALRSQLAE---KDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (203)
Q Consensus        41 ~atRVs~LE~------E~~~LR~~LaE---Kd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (203)
                      +-.+.-.+++      +...+|.++.-   ..+.+..+.+....|+.+++    ....+-+++++.+++|..++..++++
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            3444444454      55555555542   23334444444445554444    45555566666666666666666666


Q ss_pred             HHHH
Q 028818          112 VSKL  115 (203)
Q Consensus       112 vaKL  115 (203)
                      -++|
T Consensus       195 ydrL  198 (216)
T KOG1962|consen  195 YDRL  198 (216)
T ss_pred             HHHH
Confidence            6655

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

Probab=87.83  E-value=9.1  Score=35.65  Aligned_cols=100  Identities=26%  Similarity=0.401  Sum_probs=55.6

Q ss_pred             chhhHHHHHHHHHHHHHH---hhhhhHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----
Q 028818           26 PFEQLDVARKITSIAIST---RVSDLESEHSALRSQLAE-KDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKE----   97 (203)
Q Consensus        26 P~EQLdlarkIts~A~at---RVs~LE~E~~~LR~~LaE-Kd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E----   97 (203)
                      |..|=+|++|=..-=++-   |+..=|.||..||.||+- ++.-|++=   --..|++|.  |++|+.|+.+|..-    
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            567888988665544433   223334556666666552 22222221   222344443  78999999888764    


Q ss_pred             HHHHHHHHH-------HHhhhHHHHHHHHHH--HH--hhccccc
Q 028818           98 NEALTNTVR-------KLQRDVSKLEVFRKT--LV--QSLKDDE  130 (203)
Q Consensus        98 ~~~La~TvK-------kL~rDvaKLE~FKk~--Lm--qSLq~d~  130 (203)
                      |++|+..=|       ..|-+--|||+|=+.  |-  .+++|+.
T Consensus       137 rssL~ekDkGiQKYFvDINiQN~KLEsLLqsMElAq~g~~rde~  180 (305)
T PF15290_consen  137 RSSLAEKDKGIQKYFVDINIQNKKLESLLQSMELAQSGSLRDEG  180 (305)
T ss_pred             HhhhchhhhhHHHHHhhhhhhHhHHHHHHHHHHHHHhccccccC
Confidence            455555433       344566789998663  22  2566653

>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=87.77  E-value=9.7  Score=30.35  Aligned_cols=65  Identities=29%  Similarity=0.358  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           48 LESEHSALRSQLA-EKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        48 LE~E~~~LR~~La-EKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      |=.|-..||.+.. =|...| +=|.+...|...|.   ..|+...+|+.-|.=-|+.|...|-.|+-++.
T Consensus         3 la~eYsKLraQ~~vLKKaVi-eEQ~k~~~L~e~Lk~ke~~LRk~eqE~dSL~FrN~QL~kRV~~LQ~El~   71 (102)
T PF10205_consen    3 LAQEYSKLRAQNQVLKKAVI-EEQAKNAELKEQLKEKEQALRKLEQENDSLTFRNQQLTKRVEVLQEELE   71 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456666777666 344444 33456666666555   23335555555555555555555544444444

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.

>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=87.72  E-value=10  Score=39.07  Aligned_cols=72  Identities=32%  Similarity=0.391  Sum_probs=44.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      |.-.+-..|-+++.+||..|.+|...+...+..+..++.+..          +.+.....+...|++..++|..+++.=.
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            455556667777777777777777777666666666665544          4445555555666666666666665433


Q ss_pred             hh
Q 028818          110 RD  111 (203)
Q Consensus       110 rD  111 (203)
                      +.
T Consensus       413 ~q  414 (775)
T PF10174_consen  413 RQ  414 (775)
T ss_pred             HH
Confidence            33

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 [].

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

Probab=87.70  E-value=19  Score=36.22  Aligned_cols=88  Identities=18%  Similarity=0.334  Sum_probs=54.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------
Q 028818           40 AISTRVSDLESEHSALRSQL-------AEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVR------  106 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~L-------aEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvK------  106 (203)
                      +..+|...|+-..++|+..+       ..-..+...+...++.+-.++    ....+++.+|+++++.|-+.|.      
T Consensus       256 k~~~~~eslre~~~~L~~D~nK~~~y~~~~~~k~~~~~~~l~~l~~Ei----e~kEeE~e~lq~~~d~Lk~~Ie~Q~iS~  331 (581)
T KOG0995|consen  256 KDPGKEESLREKKARLQDDVNKFQAYVSQMKSKKQHMEKKLEMLKSEI----EEKEEEIEKLQKENDELKKQIELQGISG  331 (581)
T ss_pred             cCcchHHHHHHHHHHHHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHhcCCCH
Confidence            34445555555555444444       444444444444444444444    4888999999999999988875      


Q ss_pred             -----------HHhhhHHHHHHHHHHHHhhcccccC
Q 028818          107 -----------KLQRDVSKLEVFRKTLVQSLKDDED  131 (203)
Q Consensus       107 -----------kL~rDvaKLE~FKk~LmqSLq~d~~  131 (203)
                                 +|.|+|.++..=+-.|++.+-+-+.
T Consensus       332 ~dve~mn~Er~~l~r~l~~i~~~~d~l~k~vw~~~l  367 (581)
T KOG0995|consen  332 EDVERMNLERNKLKRELNKIQSELDRLSKEVWELKL  367 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence                       4666777766666666666655543

>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=87.70  E-value=12  Score=29.86  Aligned_cols=23  Identities=30%  Similarity=0.527  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 028818           55 LRSQLAEKDSRIAELQSQIESIY   77 (203)
Q Consensus        55 LR~~LaEKd~~i~~Lq~r~s~Le   77 (203)
                      |+.+|.+|+..|..++..+.+|.
T Consensus        31 L~e~Lk~ke~~LRk~eqE~dSL~   53 (102)
T PF10205_consen   31 LKEQLKEKEQALRKLEQENDSLT   53 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333

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.

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

Probab=87.69  E-value=5.1  Score=36.61  Aligned_cols=76  Identities=18%  Similarity=0.222  Sum_probs=54.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFR  119 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FK  119 (203)
                      -++.+...+-.|-..|+..+.+++....++|+|+..|+.+.+    ...++-.+|-.|-..|......|.-.|.-+|.|.
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            566777888888888899999999888888888888888776    5555555555566666655555655555555554

>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=87.67  E-value=13  Score=29.92  Aligned_cols=72  Identities=25%  Similarity=0.403  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818           53 SALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEAL---TNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus        53 ~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~L---a~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      .+|-..+.-++-.+..|+.++..|+.+=.    .+.++..+|.++++.+   ...+..|.+++..|+.==.++++=|++
T Consensus        19 e~L~s~lr~~E~E~~~l~~el~~l~~~r~----~l~~Eiv~l~~~~e~~~~~~~~~~~L~~el~~l~~ry~t~LellGE   93 (120)
T PF12325_consen   19 ERLQSQLRRLEGELASLQEELARLEAERD----ELREEIVKLMEENEELRALKKEVEELEQELEELQQRYQTLLELLGE   93 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            34444444555556666666666665554    5666666666666444   445556666666666544455554443

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 [].

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

Probab=87.65  E-value=8.8  Score=29.24  Aligned_cols=52  Identities=19%  Similarity=0.271  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTN  103 (203)
Q Consensus        48 LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~  103 (203)
                      |=.+-..|+.+|.+|+++|..|..-+.+|...|+    .-.+-+.+|+.+...+..
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            3456788999999999999988877777776666    667777777777766654

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.

>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=87.54  E-value=2.8  Score=30.06  Aligned_cols=38  Identities=26%  Similarity=0.474  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           66 IAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRK  107 (203)
Q Consensus        66 i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKk  107 (203)
                      |.+|+.++..++..+.    ....++.+|.++...+..+||+
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            3455555555555443    3333444444444444444433

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) [].

>PRK02119 hypothetical protein; Provisional

Probab=87.30  E-value=4.5  Score=29.84  Aligned_cols=29  Identities=24%  Similarity=0.320  Sum_probs=14.6

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818          100 ALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      .|..+|.+.++++++|+.-=+.|.+.|.+
T Consensus        27 ~LN~~v~~Qq~~id~L~~ql~~L~~rl~~   55 (73)
T PRK02119         27 ELNQALIEQQFVIDKMQVQLRYMANKLKD   55 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444555555555555554555555544

>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=87.30  E-value=19  Score=31.23  Aligned_cols=40  Identities=15%  Similarity=0.292  Sum_probs=19.2

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      -.|+.++..|...|.+.+..-.+.+..|+.....++..+.
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            3445555555555555444444444444444444444443

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.

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

Probab=87.22  E-value=11  Score=39.34  Aligned_cols=73  Identities=22%  Similarity=0.292  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIE-----------SIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s-----------~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      +.+|+.++.++...++.+..|..           +.+.-|+   ...-+++|+++.|..|-+++.+++-.++++=.||-+
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            55566666666666655554432           1222233   456688999999999999999999999999998888


Q ss_pred             HHHHHHh
Q 028818          118 FRKTLVQ  124 (203)
Q Consensus       118 FKk~Lmq  124 (203)
                      |+-.|-+
T Consensus       245 d~E~Lr~  251 (916)
T KOG0249|consen  245 DIEDLRG  251 (916)
T ss_pred             hHHHHHH
Confidence            8876655

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

Probab=87.20  E-value=11  Score=36.37  Aligned_cols=68  Identities=15%  Similarity=0.264  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 028818           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKT  121 (203)
Q Consensus        50 ~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~  121 (203)
                      .+....+..++++...|.+-+++...|+.+|.    ....++..+..+....++++++++++++-++.-+..
T Consensus        38 ~~l~q~q~ei~~~~~~i~~~~~~~~kL~~~lk----~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~l~~  105 (420)
T COG4942          38 KQLKQIQKEIAALEKKIREQQDQRAKLEKQLK----SLETEIASLEAQLIETADDLKKLRKQIADLNARLNA  105 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHH
Confidence            44566666666666667666666666666665    555666666666666666666666666555544333

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=86.86  E-value=12  Score=32.26  Aligned_cols=43  Identities=16%  Similarity=0.230  Sum_probs=35.0

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ..+..-+.+...|++.||.+|-.....+.+++.++-..+.++.
T Consensus        57 ~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r~~~~klk~~~~el~   99 (194)
T PF15619_consen   57 AELPQLLQRHNEEVRVLRERLRKSQEQERELERKLKDKDEELL   99 (194)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566677888889999999988888888888888888887776

>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=86.80  E-value=9  Score=31.73  Aligned_cols=32  Identities=31%  Similarity=0.533  Sum_probs=29.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQS   71 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~   71 (203)
                      +...++..++.|...|+.+|.+.+..|.+|+.
T Consensus        17 ~~K~~~~~~~~e~~~~k~ql~~~d~~i~~Lk~   48 (155)
T PF06810_consen   17 APKAKVDKVKEERDNLKTQLKEADKQIKDLKK   48 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            57899999999999999999999999999987

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

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

Probab=86.67  E-value=13  Score=31.90  Aligned_cols=35  Identities=29%  Similarity=0.454  Sum_probs=30.9

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQI   73 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~   73 (203)
                      ..|..-+.++|.||..||+-|+-|.++.++|++|+
T Consensus        32 eeLr~EL~KvEeEI~TLrqvL~aKer~~~eLKrkL   66 (162)
T PF04201_consen   32 EELRSELAKVEEEIQTLRQVLAAKERHCAELKRKL   66 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            34566688899999999999999999999999885

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 [].

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

Probab=86.48  E-value=5.9  Score=44.34  Aligned_cols=54  Identities=33%  Similarity=0.514  Sum_probs=41.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENE   99 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~   99 (203)
                      .+|.++|++|...|.+|+++|++|..+...+...++.++.....++..|.++-.
T Consensus      1310 ~kL~~ei~~Lk~el~~ke~~~~el~~~~~~~q~~~k~qld~l~~e~~~lt~~~~ 1363 (1822)
T KOG4674|consen 1310 EKLKSEISRLKEELEEKENLIAELKKELNRLQEKIKKQLDELNNEKANLTKELE 1363 (1822)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456778999999999999999999999998886666555555555555544433

>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=86.43  E-value=18  Score=30.33  Aligned_cols=80  Identities=16%  Similarity=0.221  Sum_probs=50.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFR  119 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FK  119 (203)
                      +....+-.|..+...|..+...+...-...+.++..+|..+...-+........|+.++..|...++.+.-.+++|+.=.
T Consensus        47 ~~~~e~~~L~~d~e~L~~q~~~ek~~r~~~e~~l~~~Ed~~~~e~k~L~~~v~~Le~e~r~L~~~~~~~~~q~~rlee~e  126 (158)
T PF09744_consen   47 EHEVELELLREDNEQLETQYEREKELRKQAEEELLELEDQWRQERKDLQSQVEQLEEENRQLELKLKNLSDQSSRLEERE  126 (158)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccchhH
Confidence            33334445555555555555544444455556666667666655566677777888888888877777777777776433

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

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

Probab=86.38  E-value=5.1  Score=28.92  Aligned_cols=31  Identities=26%  Similarity=0.398  Sum_probs=13.8

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhhccccc
Q 028818          100 ALTNTVRKLQRDVSKLEVFRKTLVQSLKDDE  130 (203)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~LmqSLq~d~  130 (203)
                      .|..+|...++++.+|+.-=+.|...|.+-.
T Consensus        22 ~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen   22 ELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3444555555555555555555555555433

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.

>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=86.32  E-value=8.7  Score=39.58  Aligned_cols=65  Identities=26%  Similarity=0.383  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHH
Q 028818           33 ARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALT  102 (203)
Q Consensus        33 arkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----------~rL~~a~ee~~kL~~E~~~La  102 (203)
                      +.+..+.+.++|+       .+++.+|..|+..|..++.++..++.+..          .-|..+.++...|+.+++.|-
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            3455666666663       45555555555555555555555544443          122344455555555555544


Q ss_pred             HH
Q 028818          103 NT  104 (203)
Q Consensus       103 ~T  104 (203)
                      .-
T Consensus       350 ~r  351 (775)
T PF10174_consen  350 FR  351 (775)
T ss_pred             HH
Confidence            33

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 [].

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=86.21  E-value=16  Score=33.40  Aligned_cols=16  Identities=31%  Similarity=0.397  Sum_probs=9.3

Q ss_pred             hhhhHHHHHHHHHHHH
Q 028818           45 VSDLESEHSALRSQLA   60 (203)
Q Consensus        45 Vs~LE~E~~~LR~~La   60 (203)
                      |-.|.+++..||.++.
T Consensus       284 v~~l~~~i~~l~~~l~  299 (444)
T TIGR03017       284 YKRAQAEINSLKSQLN  299 (444)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4555666666666654

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.

>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=86.18  E-value=15  Score=30.39  Aligned_cols=70  Identities=23%  Similarity=0.346  Sum_probs=37.0

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      +.+....|+.|...||..-.+=+......+.||+.|+....   ..|....++..++.+   .+...|-.|..++.
T Consensus        64 lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~~E~ek~q~~e---~~~~~ve~L~~ql~  136 (140)
T PF10473_consen   64 LTSELNQLELELDTLRSEKENLDKELQKKQEKVSELESLNSSLENLLQEKEQEKVQLKE---ESKSAVEMLQKQLK  136 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHh
Confidence            44455556666666664333333344455555777776665   444566666444433   34445555554443

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

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

Probab=86.05  E-value=9.7  Score=31.13  Aligned_cols=62  Identities=23%  Similarity=0.340  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 028818           62 KDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENE-----ALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (203)
Q Consensus        62 Kd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~-----~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (203)
                      |+....+|++++..+|.+|+    +..-+..++..|..     .+.+--...+...++++..|+.|.+-++
T Consensus        18 K~~l~~~l~~~i~~~d~el~----QLefq~kr~~~e~~~~~~~~~~~i~~q~~~e~~~r~e~k~~l~~ql~   84 (131)
T PF11068_consen   18 KEELLQELQEQIQQLDQELQ----QLEFQGKRMIKEIKKQNAQQIQSIQQQFEQEKQERLEQKNQLLQQLE   84 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67778888888888888887    55666666666654     4444446667777777777777766544

; PDB: 4DCI_C.

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

Probab=85.96  E-value=5.6  Score=37.32  Aligned_cols=82  Identities=21%  Similarity=0.261  Sum_probs=60.3

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH----HHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV----SKLE  116 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv----aKLE  116 (203)
                      .+.|..+||.-|..=   -.|...-+..+.+..+.++. |.+|+..-.++..+++.-|.-|-+-|+++.-||    .||+
T Consensus         3 ~k~~~~~~~~~i~k~---nee~~~~~~~~~k~~e~~qk-l~sr~~~~~ekke~i~r~n~k~~d~v~~~~~~~~~~~erl~   78 (359)
T KOG4398|consen    3 CKMRIEQLKQTICKG---NEEMEKNSEGLLKTKEKNQK-LYSRAQRHQEKKEKIQRHNRKLGDLVEKKTIDLRSHYERLA   78 (359)
T ss_pred             hhHHHHHHHHHHhcC---cHHHHHhHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhhhhcchHHHHHHHHHHHHHHHHH
Confidence            456666666555433   23555556666665555444 336888999999999999999999999988764    7999


Q ss_pred             HHHHHHHhhc
Q 028818          117 VFRKTLVQSL  126 (203)
Q Consensus       117 ~FKk~LmqSL  126 (203)
                      +++++-++-|
T Consensus        79 ~lr~shi~el   88 (359)
T KOG4398|consen   79 NLRRSHILEL   88 (359)
T ss_pred             HHHHHHHHHH
Confidence            9999987755

>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=85.94  E-value=4.8  Score=29.02  Aligned_cols=46  Identities=15%  Similarity=0.417  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           68 ELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        68 ~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      ++++|+..+|..+-    ...++..+|..-...+...++.++.++.+++.
T Consensus         3 ~i~e~l~~ie~~l~----~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~   48 (71)
T PF10779_consen    3 DIKEKLNRIETKLD----NHEERIDKLEKRDAANEKDIKNLNKQLEKIKS   48 (71)
T ss_pred             HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555554332    44455555555555666667777777777765

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

Probab=85.68  E-value=11  Score=27.07  Aligned_cols=81  Identities=22%  Similarity=0.375  Sum_probs=54.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKD-----SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd-----~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (203)
                      .+..++..|+.+...+...+....     ..+...+.-+..|+..+.    ........+..+-..+-..+....+++.+
T Consensus        16 ~~~~~l~~L~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~l~~~i~----~~~~~~~~~~~~~~~~r~~l~~a~~~~k~   91 (123)
T PF02050_consen   16 EAEEQLEQLQQERQEYQEQLSESQQGVSVAQLRNYQRYISALEQAIQ----QQQQELERLEQEVEQAREELQEARRERKK   91 (123)
T ss_dssp             HHHHHHHHHHHHHHHHHHT-----SGGGHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566677777777777777776666     555555555555555544    77777888888888888888888899988


Q ss_pred             HHHHHHHHHh
Q 028818          115 LEVFRKTLVQ  124 (203)
Q Consensus       115 LE~FKk~Lmq  124 (203)
                      +|.++-.-..
T Consensus        92 ~e~L~e~~~~  101 (123)
T PF02050_consen   92 LEKLKERRRE  101 (123)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            8888765443

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.

>PRK04406 hypothetical protein; Provisional

Probab=85.63  E-value=6.9  Score=29.07  Aligned_cols=16  Identities=25%  Similarity=0.501  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q 028818           66 IAELQSQIESIYSSLS   81 (203)
Q Consensus        66 i~~Lq~r~s~Le~~L~   81 (203)
                      |..|++|+..||..+.
T Consensus         6 ~~~le~Ri~~LE~~lA   21 (75)
T PRK04406          6 IEQLEERINDLECQLA   21 (75)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3456666666666554

>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=85.58  E-value=12  Score=34.24  Aligned_cols=64  Identities=17%  Similarity=0.337  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 028818           51 EHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (203)
Q Consensus        51 E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (203)
                      |....+.++..+..++..+++.+...|..+.   .|+....++..+|..|...|..+|..+.--|.|
T Consensus       194 eke~~~r~l~~~~~ELe~~~EeL~~~Eke~~e~~~~i~e~~~rl~~l~~~~~~l~k~~~~~~sKV~k  260 (269)
T PF05278_consen  194 EKEEKDRKLELKKEELEELEEELKQKEKEVKEIKERITEMKGRLGELEMESTRLSKTIKSIKSKVEK  260 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444444   455555555666666666666666666544444

>PRK12704 phosphodiesterase; Provisional

Probab=85.57  E-value=30  Score=33.80  Aligned_cols=12  Identities=8%  Similarity=0.473  Sum_probs=6.1

Q ss_pred             HHHHHHhhcccc
Q 028818          118 FRKTLVQSLKDD  129 (203)
Q Consensus       118 FKk~LmqSLq~d  129 (203)
                      .|+.||..+.++
T Consensus       155 a~~~l~~~~~~~  166 (520)
T PRK12704        155 AKEILLEKVEEE  166 (520)
T ss_pred             HHHHHHHHHHHH
Confidence            455555555444

>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=85.52  E-value=3.7  Score=34.04  Aligned_cols=68  Identities=21%  Similarity=0.312  Sum_probs=32.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAE-LQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~-Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (203)
                      .+..++..+|.+...++.+.......... ..+....++.++.    ...++..+...|.+.|..+++.|+++
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            45555555566555555554433222221 1122222233332    44444445566666666666666653

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

>PF14817 HAUS5: HAUS augmin-like complex subunit 5

Probab=85.44  E-value=17  Score=36.73  Aligned_cols=78  Identities=22%  Similarity=0.360  Sum_probs=60.0

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH-------HHHHHHHHHHHHHHHHhhhHH
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKE-------RLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~-------kL~~E~~~La~TvKkL~rDva  113 (203)
                      |=..|+.||++||..+.+-+..|..++..++.-|.++.   ++++....+..       +-..+...|..-.++|+..|.
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   55555555443       344566677777777777777


Q ss_pred             HHHHHHHH
Q 028818          114 KLEVFRKT  121 (203)
Q Consensus       114 KLE~FKk~  121 (203)
                      .|+...|.
T Consensus       160 ~~q~~~R~  167 (632)
T PF14817_consen  160 QLQDIQRK  167 (632)
T ss_pred             HHHHHHhh
Confidence            77766554

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

Probab=85.43  E-value=9.3  Score=29.65  Aligned_cols=31  Identities=16%  Similarity=0.200  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 028818           88 QADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (203)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (203)
                      .++..+|.-+-..+...++.++..+.-++..
T Consensus        64 ~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~   94 (106)
T PF10805_consen   64 RDDVHDLQLELAELRGELKELSARLQGVSHQ   94 (106)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            4555566666666666666666555554433

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

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=85.30  E-value=32  Score=33.61  Aligned_cols=12  Identities=8%  Similarity=0.476  Sum_probs=6.2

Q ss_pred             HHHHHHhhcccc
Q 028818          118 FRKTLVQSLKDD  129 (203)
Q Consensus       118 FKk~LmqSLq~d  129 (203)
                      .|..||..+.++
T Consensus       149 ak~~l~~~~~~~  160 (514)
T TIGR03319       149 AKEILLEEVEEE  160 (514)
T ss_pred             HHHHHHHHHHHH
Confidence            455555555444

>KOG2991 consensus Splicing regulator [RNA processing and modification]

Probab=85.27  E-value=5.7  Score=36.95  Aligned_cols=71  Identities=27%  Similarity=0.367  Sum_probs=54.8

Q ss_pred             HHHHHHHHhhhhhHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           36 ITSIAISTRVSDLESEH-------SALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTV  105 (203)
Q Consensus        36 Its~A~atRVs~LE~E~-------~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~Tv  105 (203)
                      |.-+|--+|+.+||.|.       ..||.+-.|=+.+|.+|-+-|......+.   .+|+..+.++..|.+++..+...|
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            34467778999999885       46777777888888888888877777655   888888888888888887776665


Q ss_pred             H
Q 028818          106 R  106 (203)
Q Consensus       106 K  106 (203)
                      +
T Consensus       309 ~  309 (330)
T KOG2991|consen  309 G  309 (330)
T ss_pred             c
Confidence            4

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=85.16  E-value=11  Score=37.31  Aligned_cols=17  Identities=29%  Similarity=0.350  Sum_probs=9.5

Q ss_pred             hhhhhHHHHHHHHHHHH
Q 028818           44 RVSDLESEHSALRSQLA   60 (203)
Q Consensus        44 RVs~LE~E~~~LR~~La   60 (203)
                      +|..+++++..|++++.
T Consensus       317 ~v~~l~~qi~~l~~~i~  333 (754)
T TIGR01005       317 RVVAAKSSLADLDAQIR  333 (754)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            35555556666665554

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.

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=85.03  E-value=8.3  Score=32.89  Aligned_cols=21  Identities=43%  Similarity=0.615  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHhhhHHHH
Q 028818           95 SKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        95 ~~E~~~La~TvKkL~rDvaKL  115 (203)
                      ...|+.|.+-+.||..|+.+|
T Consensus        94 ~~~N~~L~~dl~klt~~~~~l  114 (182)
T PF15035_consen   94 RKANEALQEDLQKLTQDWERL  114 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            456666666666666666653

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

Probab=84.99  E-value=7.9  Score=39.86  Aligned_cols=61  Identities=28%  Similarity=0.396  Sum_probs=45.4

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEAL  101 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~L  101 (203)
                      +..|+..+-+|...|...|.+|+..|.+|.+.-+..|..+.   .||....-+|.-|.=|-..|
T Consensus        97 ~~~~l~~~~~e~~~l~~~l~~~~~~i~~l~~~~~~~e~~~~~l~~~l~~~eken~~Lkye~~~~  160 (769)
T PF05911_consen   97 LSKRLAESAAENSALSKALQEKEKLIAELSEEKSQAEAEIEDLMARLESTEKENSSLKYELHVL  160 (769)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456666777788888889999999999999999998876   66666666665555544444

The function of this family is unknown.

>PRK02793 phi X174 lysis protein; Provisional

Probab=84.99  E-value=6.9  Score=28.74  Aligned_cols=26  Identities=27%  Similarity=0.298  Sum_probs=10.8

Q ss_pred             HHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818          103 NTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus       103 ~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      ..|-..+++++.|+.-=+.|.+.|.+
T Consensus        29 ~~v~~Qq~~I~~L~~~l~~L~~rl~~   54 (72)
T PRK02793         29 VTVTAHEMEMAKLRDHLRLLTEKLKA   54 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33444444444444444444444433

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=84.84  E-value=11  Score=40.68  Aligned_cols=42  Identities=21%  Similarity=0.354  Sum_probs=38.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +=..|+..|+.++..|+.++++.++.+..|+.++..|..++.
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            445689999999999999999999999999999999999877

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.

>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=84.76  E-value=25  Score=30.41  Aligned_cols=53  Identities=13%  Similarity=0.126  Sum_probs=26.6

Q ss_pred             hhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           28 EQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        28 EQLdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .+++-+..........+. ....++..+-++-.+-.+.|..|++++..|+....
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            345555555555444442 23334555555555555555555555555555443

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.

>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=84.59  E-value=13  Score=26.94  Aligned_cols=56  Identities=30%  Similarity=0.395  Sum_probs=36.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      +.||+||+.       |...-.+|. ++-.-...+..||..+...|..|..|.+.|...+..+.
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 34444444448888999888888888777777666553

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

>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=84.47  E-value=7.8  Score=28.53  Aligned_cols=35  Identities=34%  Similarity=0.505  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 028818           84 LGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (203)
Q Consensus        84 L~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (203)
                      +.+..++..+|.+-.-.+.++||||...+..+|.-
T Consensus        14 Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~   48 (74)
T PF12329_consen   14 IAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQ   48 (74)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            34778888888888888888888888888777643

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.

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=84.41  E-value=4.7  Score=39.49  Aligned_cols=48  Identities=31%  Similarity=0.412  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           58 QLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTV  105 (203)
Q Consensus        58 ~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~Tv  105 (203)
                      +|++-.....+|++++..|..+++   .++....++.++|..|+..|..++
T Consensus        70 ALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql  120 (475)
T PRK13729         70 ATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV  120 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            344444455555555555544443   222233333334444444444443

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.39  E-value=9.9  Score=34.68  Aligned_cols=28  Identities=29%  Similarity=0.526  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           88 QADKERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      ......+.+|++.+-.-+|+|+.+++.|
T Consensus        65 ~~k~~~~~~~i~~~~~eik~l~~eI~~~   92 (265)
T COG3883          65 QSKIDELQKEIDQSKAEIKKLQKEIAEL   92 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333334444444444444444444333

>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=84.32  E-value=8.8  Score=30.82  Aligned_cols=52  Identities=27%  Similarity=0.379  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHHHhh--------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           30 LDVARKITSIAISTRV--------SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        30 LdlarkIts~A~atRV--------s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ||+||+.-+.-+-.|.        ..|+-|+..||..|+-|++.+..+.+++...+.-|.
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            8999988887666664        368899999999999999999999999988887665

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 [].

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

Probab=84.19  E-value=9.9  Score=30.03  Aligned_cols=26  Identities=27%  Similarity=0.426  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 028818           85 GQAQADKERLSKENEALTNTVRKLQR  110 (203)
Q Consensus        85 ~~a~ee~~kL~~E~~~La~TvKkL~r  110 (203)
                      ....++|+.|.-||..|-..+.++..
T Consensus        32 ~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen   32 QELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            37888999999999888877777665

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=84.17  E-value=11  Score=32.09  Aligned_cols=24  Identities=13%  Similarity=0.235  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           94 LSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        94 L~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      ++.++....+.|..|.+.-..|+.
T Consensus       161 ~~~~~k~~~~ei~~lk~~~~ql~~  184 (189)
T PF10211_consen  161 RQEEEKKHQEEIDFLKKQNQQLKA  184 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444445555555555554443

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 [].

>PF13863 DUF4200: Domain of unknown function (DUF4200)

Probab=84.15  E-value=17  Score=27.83  Aligned_cols=55  Identities=22%  Similarity=0.270  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 028818           68 ELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (203)
Q Consensus        68 ~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (203)
                      .|++.+...+.-|.   .+...|.....+=.+.+.....-+++|..+++.|...+..+
T Consensus        43 ~l~~~~~~f~~flken~~k~~rA~k~a~~e~k~~~~k~~ei~~l~~~l~~l~~~~~k~  100 (126)
T PF13863_consen   43 ELEEDVIKFDKFLKENEAKRERAEKRAEEEKKKKEEKEAEIKKLKAELEELKSEISKL  100 (126)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444   44444444444444444444444444444444444443333

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=84.14  E-value=19  Score=36.62  Aligned_cols=83  Identities=23%  Similarity=0.405  Sum_probs=47.1

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH----HHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS----KLE  116 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva----KLE  116 (203)
                      +-.++..+|.-+.+|+....+=.+.+.+|++.+..|+..|. +++.-.......-+|-..+...+.+|++.+.    +.|
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 4444444444445555555555555555543    345


Q ss_pred             HHHHHHHh
Q 028818          117 VFRKTLVQ  124 (203)
Q Consensus       117 ~FKk~Lmq  124 (203)
                      -+|+.|-+
T Consensus       499 ~L~~~l~~  506 (652)
T COG2433         499 ELERKLAE  506 (652)
T ss_pred             HHHHHHHH
Confidence            55555544

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

Probab=84.05  E-value=30  Score=31.58  Aligned_cols=71  Identities=20%  Similarity=0.297  Sum_probs=37.6

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRD  111 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (203)
                      ...-+..++.|+..|...-.+..+++.+|++....++.++.   ..+....++..+.-++.+.+....-.+..+
T Consensus        41 ~~~~~~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e  114 (314)
T PF04111_consen   41 SEEDIEELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEE  114 (314)
T ss_dssp             -HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445666777777777777777777777777777776665   333333333334444444444333333333

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.

>KOG0962 consensus DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair]

Probab=83.99  E-value=13  Score=40.57  Aligned_cols=80  Identities=21%  Similarity=0.363  Sum_probs=55.8

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH-----
Q 028818           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS-----  113 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva-----  113 (203)
                      +.+..++..++.|+..|+-|+.+-+  ++..++++..|+....    ...-+.+.+..+...+.+.++++.+++.     
T Consensus      1011 ~~l~~q~~e~~re~~~ld~Qi~~~~--~~~~~ee~~~L~~~~~----~l~se~~~~lg~~ke~e~~i~~~k~eL~~~~~k 1084 (1294)
T KOG0962|consen 1011 RNLERKLKELERELSELDKQILEAD--IKSVKEERVKLEEERE----KLSSEKNLLLGEMKQYESQIKKLKQELREKDFK 1084 (1294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhH--HHHHHHHHHHHHHHHH----HhhhHhhHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence            3666777777777777777777655  6666666666666665    5555667777777788888888888887     


Q ss_pred             -HHHHHHHHHHh
Q 028818          114 -KLEVFRKTLVQ  124 (203)
Q Consensus       114 -KLE~FKk~Lmq  124 (203)
                       ..++|++.++.
T Consensus      1085 d~~~nyr~~~ie 1096 (1294)
T KOG0962|consen 1085 DAEKNYRKALIE 1096 (1294)
T ss_pred             cHHHHHHHHHHH
Confidence             46666666654

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

Probab=83.90  E-value=11  Score=39.17  Aligned_cols=38  Identities=32%  Similarity=0.404  Sum_probs=28.5

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .|+.|++|..+|++.|+.|.+.-..+++-|..+.+++-
T Consensus       496 ~i~~L~sE~~~lk~il~~Kee~Ek~~~E~I~k~~ae~~  533 (961)
T KOG4673|consen  496 LITKLQSEENKLKSILRDKEETEKLLQETIEKHQAELT  533 (961)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence            68889999999999999888776666665555555543

>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=83.88  E-value=30  Score=30.62  Aligned_cols=52  Identities=17%  Similarity=0.401  Sum_probs=31.1

Q ss_pred             HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           60 AEKDSRIAEL---QSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        60 aEKd~~i~~L---q~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      .||.+|..+|   ..-++.||..+.    .+..+..+..+.-..|-.-+..|-..|.++
T Consensus        46 ~Er~~h~eeLrqI~~DIn~lE~iIk----qa~~er~~~~~~i~r~~eey~~Lk~~in~~  100 (230)
T PF10146_consen   46 QERMAHVEELRQINQDINTLENIIK----QAESERNKRQEKIQRLYEEYKPLKDEINEL  100 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3888888777   667777887776    555555555554444444444444444443

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.

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

Probab=83.87  E-value=15  Score=36.68  Aligned_cols=41  Identities=22%  Similarity=0.420  Sum_probs=19.1

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +..++..++.++..|+..+..-..++.+.+.....++.++.
T Consensus       340 l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~  380 (594)
T PF05667_consen  340 LESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELK  380 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444444444444444444444444444

>TIGR00634 recN DNA repair protein RecN

Probab=83.84  E-value=8.9  Score=37.04  Aligned_cols=46  Identities=26%  Similarity=0.328  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH-----HHHHHHHHhhccc
Q 028818           83 KLGQAQADKERLSKENEALTNTVRKLQRDVSKL-----EVFRKTLVQSLKD  128 (203)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL-----E~FKk~LmqSLq~  128 (203)
                      .+....++..+|.++.+.+...+.++...+++.     +.|.+.+..-|++
T Consensus       340 ~l~~~~~~le~L~~el~~l~~~l~~~a~~Ls~~R~~~a~~l~~~v~~~l~~  390 (563)
T TIGR00634       340 QLDDSDESLEALEEEVDKLEEELDKAAVALSLIRRKAAERLAKRVEQELKA  390 (563)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            334444566777778888888888888887777     6777777776654

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

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

Probab=83.73  E-value=22  Score=34.76  Aligned_cols=36  Identities=22%  Similarity=0.311  Sum_probs=23.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      -.|++|.+.++.++.+|+.++.+||+....+-.++.
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            346666667777777777777777666665554443

>PF09787 Golgin_A5: Golgin subfamily A member 5; InterPro: IPR019177 This entry represents a family of proteins involved in maintaining Golgi structure

Probab=83.68  E-value=4.6  Score=38.84  Aligned_cols=72  Identities=29%  Similarity=0.406  Sum_probs=59.2

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           37 TSIAISTRVSDLESEHSALRSQLAEKD--SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~LaEKd--~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      ....+..|+..-|.|+..||.+|..|.  ..-.+|+.|+..|...|+    +.....+.|..||.+|.-+..++.+.+
T Consensus       356 ~~s~~~~k~~~ke~E~q~lr~~l~~~~~~s~~~elE~rl~~lt~~Li----~KQ~~lE~l~~ek~al~lqlErl~~~l  429 (511)
T PF09787_consen  356 QKSPLQLKLKEKESEIQKLRNQLSARASSSSWNELESRLTQLTESLI----QKQTQLESLGSEKNALRLQLERLETQL  429 (511)
T ss_pred             hcChHHHHHHHHHHHHHHHHHHHHHHhccCCcHhHHHHHhhccHHHH----HHHHHHHHHHhhhhhccccHHHHHHHH
Confidence            455788889999999999999999887  334689999999988887    777788899999999988777766543

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 [].

>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=83.66  E-value=17  Score=29.64  Aligned_cols=56  Identities=30%  Similarity=0.509  Sum_probs=38.7

Q ss_pred             HHHhhCCCCchhhHHHHHHH-------------HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           17 EVLQVLPSDPFEQLDVARKI-------------TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIE   74 (203)
Q Consensus        17 eil~vLP~DP~EQLdlarkI-------------ts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s   74 (203)
                      +++.-|-+.|+-.|  +.|+             .++++..|+...|.++.++-.++.|+...+...-+.++
T Consensus        19 ~~leklds~~~l~L--c~R~Q~HL~~cA~~Va~~Q~~L~~riKevd~~~~~l~~~~~erqk~~~k~ae~L~   87 (131)
T PF10158_consen   19 EVLEKLDSRPVLRL--CSRYQEHLNQCAEAVAFDQNALAKRIKEVDQEIAKLLQQMVERQKRFAKFAEQLE   87 (131)
T ss_pred             HHHHccChHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47777777776654  3332             34588888888899998888888887766655544443

The exact function of these proteins is not known.

>KOG4687 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=83.66  E-value=5.5  Score=37.45  Aligned_cols=87  Identities=16%  Similarity=0.218  Sum_probs=40.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHhhh
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQ--------ADKERLSKENEALTNTVRKLQRD  111 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~--------ee~~kL~~E~~~La~TvKkL~rD  111 (203)
                      |+-.+...-=.-++.|++.|..=..+-..|..++.+|+..|. +|..-.        +...+---|+..|+.-+-+-.++
T Consensus        20 AlhqK~~aKtdairiL~QdLEkfe~Ekd~~a~~aETLeln~e-alere~eLlaa~gc~a~~e~gterqdLaa~i~etkee   98 (389)
T KOG4687|consen   20 ALHQKCGAKTDAIRILGQDLEKFENEKDGLAARAETLELNLE-ALERELELLAACGCDAKIEFGTERQDLAADIEETKEE   98 (389)
T ss_pred             HHHHHhcccHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH-HHHhhhHHHHhcCCCchhhccchhhHHHHHHHHHHHH
Confidence            333333333333455555555444444445555555555553 111100        01122223556666666666666


Q ss_pred             HHHHHHHHHHHHhhcc
Q 028818          112 VSKLEVFRKTLVQSLK  127 (203)
Q Consensus       112 vaKLE~FKk~LmqSLq  127 (203)
                      --||-+=+..|.+.+.
T Consensus        99 NlkLrTd~eaL~dq~a  114 (389)
T KOG4687|consen   99 NLKLRTDREALLDQKA  114 (389)
T ss_pred             hHhhhHHHHHHHHHHH
Confidence            6666666666655443

>KOG4643 consensus Uncharacterized coiled-coil protein [Function unknown]

Probab=83.64  E-value=9.3  Score=40.96  Aligned_cols=67  Identities=19%  Similarity=0.353  Sum_probs=52.4

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKL  108 (203)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL  108 (203)
                      +.+++.-..-||.-|+.||++|.||.....+|+.-+..++.++.    ..++++..+..|..+...-.++|
T Consensus       172 ~~hL~velAdle~kir~LrqElEEK~enll~lr~eLddleae~~----klrqe~~e~l~ea~ra~~yrdel  238 (1195)
T KOG4643|consen  172 NLHLEVELADLEKKIRTLRQELEEKFENLLRLRNELDDLEAEIS----KLRQEIEEFLDEAHRADRYRDEL  238 (1195)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhhhhhhhHH
Confidence            45888888999999999999999999999999999999888886    55666666666555544444333

>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=83.55  E-value=12  Score=38.02  Aligned_cols=51  Identities=20%  Similarity=0.347  Sum_probs=27.8

Q ss_pred             HHHHHHH-HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Q 028818           53 SALRSQL-AEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTN  103 (203)
Q Consensus        53 ~~LR~~L-aEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~  103 (203)
                      ..||.+- ..-+..-.++++|+..|..+..   .+|..+.++..+|...-..|+.
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 3334446778888877777766   3444444444444443333433

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 [].

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=83.54  E-value=14  Score=34.64  Aligned_cols=66  Identities=15%  Similarity=0.299  Sum_probs=32.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAEL------------QSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~L------------q~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (203)
                      .++.++.++..|+.++++....+.++            +.|+..+...   .+..+.++..++..+.+.+...+.+....
T Consensus       237 ~~~~~~~~i~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~l~~~~~~l~~~~~~l~~a~~~  313 (457)
T TIGR01000       237 ILATIQQQIDQLQKSIASYQVQKAGLTKSTASNYASSQNSKLAQLKEQ---QLAKVKQEITDLNQKLLELESKIKSLKED  313 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhccCCccchhhhhhHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566666666666666665555554            3333333322   22344444455555555555555444443


Q ss_pred             H
Q 028818          112 V  112 (203)
Q Consensus       112 v  112 (203)
                      +
T Consensus       314 l  314 (457)
T TIGR01000       314 S  314 (457)
T ss_pred             H
Confidence            3

This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.

>TIGR00634 recN DNA repair protein RecN

Probab=83.52  E-value=4.5  Score=39.03  Aligned_cols=57  Identities=18%  Similarity=0.214  Sum_probs=42.8

Q ss_pred             CchhhHHHHHHHHHH-HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           25 DPFEQLDVARKITSI-AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        25 DP~EQLdlarkIts~-A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +|.+|+++--.+... .+..++..+..+...++.+|.+......++++++..++.++.
T Consensus       142 ~~~~~~~lLD~~~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~~~~~~~eld~L~~ql~  199 (563)
T TIGR00634       142 RPDEQRQLLDTFAGANEKVKAYRELYQAWLKARQQLKDRQQKEQELAQRLDFLQFQLE  199 (563)
T ss_pred             CHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence            888998887776653 577777778888888888887777777777777777766665

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

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=83.46  E-value=11  Score=33.41  Aligned_cols=63  Identities=11%  Similarity=0.169  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        49 E~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      |..+.+|-+.+.-....+.+|+.|+..|+.++.    ..+-.++.++-+.+.+...-|.|..|+..+
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            333333334444444555666666666666665    445555566666666666677777777764

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

Probab=83.40  E-value=34  Score=36.39  Aligned_cols=41  Identities=29%  Similarity=0.488  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH-----------HHHHHHHHHh
Q 028818           84 LGQAQADKERLSKENEALTNTVRKLQRDVSK-----------LEVFRKTLVQ  124 (203)
Q Consensus        84 L~~a~ee~~kL~~E~~~La~TvKkL~rDvaK-----------LE~FKk~Lmq  124 (203)
                      +..+.+.+.+..++|.+|..+|.++.|....           ||.||+.|..
T Consensus       454 le~~~~s~~~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~~le~l~~El~~  505 (980)
T KOG0980|consen  454 LESAEQSIDDVEEENTNLNDQLEELQRAAGRAETKTESQAKALESLRQELAL  505 (980)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            4445556667777778888877777765544           5666665543

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.02  E-value=16  Score=33.37  Aligned_cols=23  Identities=26%  Similarity=0.378  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKL  108 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL  108 (203)
                      ...++..+|.++.+.|.++++..
T Consensus        77 ~~~~eik~l~~eI~~~~~~I~~r   99 (265)
T COG3883          77 QSKAEIKKLQKEIAELKENIVER   99 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444455555555555444443

>PF13747 DUF4164: Domain of unknown function (DUF4164)

Probab=82.99  E-value=17  Score=27.66  Aligned_cols=25  Identities=28%  Similarity=0.454  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           83 KLGQAQADKERLSKENEALTNTVRK  107 (203)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKk  107 (203)
                      +|-.+..+.++|..-+..++..++.
T Consensus        54 eLD~~~ar~~~Le~~~~Evs~rL~~   78 (89)
T PF13747_consen   54 ELDQAEARANRLEEANREVSRRLDS   78 (89)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            3335555555555555555444443

>PF12240 Angiomotin_C: Angiomotin C terminal; InterPro: IPR024646 This domain represents the C-terminal region of angiomotin

Probab=82.64  E-value=34  Score=30.34  Aligned_cols=80  Identities=19%  Similarity=0.319  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH-------------------------------HHHHHHHHHHHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS--DKLGQ-------------------------------AQADKERLSKEN   98 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~--~rL~~-------------------------------a~ee~~kL~~E~   98 (203)
                      +..|+.+|.||++.|-.|+.-+...|..+-  ..+++                               ..++...-....
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            455788899999999999988888876654  11111                               012222223334


Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhhcccccC
Q 028818           99 EALTNTVRKLQRDVSKLEVFRKTLVQSLKDDED  131 (203)
Q Consensus        99 ~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d~~  131 (203)
                      -.+.+.||.|+..+..=++.=|.|=|..+.+..
T Consensus       139 qemE~RIK~LhaqI~EKDAmIkVLQqrs~~~~~  171 (205)
T PF12240_consen  139 QEMENRIKALHAQIAEKDAMIKVLQQRSRKDPG  171 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCC
Confidence            567888999999999988888888887776664

Angiomotin regulates the action of angiogenesis-inhibitor angiostatin []. The C-terminal region of angiomotin appears to be involved in directing the protein chemotactically [].

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

Probab=82.64  E-value=11  Score=32.08  Aligned_cols=30  Identities=20%  Similarity=0.366  Sum_probs=16.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAEL   69 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~L   69 (203)
                      +...++.+|..++..++.++.+-...|..+
T Consensus        66 ~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~   95 (188)
T PF03962_consen   66 KRQNKLEKLQKEIEELEKKIEELEEKIEEA   95 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555566666666666666555555444

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

>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=82.56  E-value=22  Score=28.14  Aligned_cols=30  Identities=33%  Similarity=0.431  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +..||.++.+-...|.+|+..+..+...|.
T Consensus        61 L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~   90 (132)
T PF07926_consen   61 LQQLREELQELQQEINELKAEAESAKAELE   90 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555554444444

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

>PRK00846 hypothetical protein; Provisional

Probab=82.55  E-value=9.7  Score=28.80  Aligned_cols=26  Identities=8%  Similarity=0.134  Sum_probs=11.0

Q ss_pred             HHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818          103 NTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus       103 ~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      .+|.+.++.+++|..--+.|...|.+
T Consensus        34 ~~v~~qq~~I~~L~~ql~~L~~rL~~   59 (77)
T PRK00846         34 EALADARLTGARNAELIRHLLEDLGK   59 (77)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444443444444444

>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=82.49  E-value=17  Score=33.99  Aligned_cols=25  Identities=28%  Similarity=0.571  Sum_probs=15.3

Q ss_pred             HHHHHHHhhhHHHHHHHHHHHHhhc
Q 028818          102 TNTVRKLQRDVSKLEVFRKTLVQSL  126 (203)
Q Consensus       102 a~TvKkL~rDvaKLE~FKk~LmqSL  126 (203)
                      ..+|+.+.+|+.+|..=||+|.+|+
T Consensus        84 E~~V~~it~dIk~LD~AKrNLT~SI  108 (383)
T PF04100_consen   84 EQMVQEITRDIKQLDNAKRNLTQSI  108 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666666665543

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

Probab=82.27  E-value=29  Score=29.16  Aligned_cols=99  Identities=19%  Similarity=0.235  Sum_probs=49.0

Q ss_pred             CCchhhHHHHHHHHHHHH---HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Q 028818           24 SDPFEQLDVARKITSIAI---STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----DKLGQAQADKERLSK   96 (203)
Q Consensus        24 ~DP~EQLdlarkIts~A~---atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----~rL~~a~ee~~kL~~   96 (203)
                      .||..-|+.+++=...+|   ..-|...-+....|..++.+-...+..+++++   +.+|.    +.-+.+..+...+..
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 EDPEKMLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQA---ELALAAGREDLAREALQRKADLEE   98 (221)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHcCCHHHHHHHHHHHHHHHH
Confidence            367766666653222221   22233333333444444444444444444443   33333    444566666666666


Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHhh
Q 028818           97 ENEALTNTVRKLQRDVSKLEVFRKTLVQS  125 (203)
Q Consensus        97 E~~~La~TvKkL~rDvaKLE~FKk~LmqS  125 (203)
                      +...|..++..+...+.+|+..-+.|-..
T Consensus        99 ~~~~l~~~~~~~~~~~~~l~~~l~~l~~k  127 (221)
T PF04012_consen   99 QAERLEQQLDQAEAQVEKLKEQLEELEAK  127 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666666666666666665544444433

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 [].

>TIGR02559 HrpB7 type III secretion protein HrpB7

Probab=82.27  E-value=26  Score=29.92  Aligned_cols=64  Identities=17%  Similarity=0.240  Sum_probs=52.9

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHH
Q 028818           37 TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS------DKLGQAQADKERLSKENEA  100 (203)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~------~rL~~a~ee~~kL~~E~~~  100 (203)
                      -.-.+.-++..+|.+...+++-|..|...|+..+..+..++..+.      ++|..+.|.......+-+.
T Consensus        80 yr~vl~~~~~~aE~~~aaa~~al~~~~~~laa~~r~iaRn~a~id~c~eR~~~l~ra~ea~~edA~dEEa  149 (158)
T TIGR02559        80 YRDVLEAHLGAAEQAEAAARAALQALAAALAAKKREIARLDAQIDVCRERAERLRRAGEAAREEALEEEA  149 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHH
Confidence            334567889999999999999999999999999999999999998      7777777776666555443

This family of genes is found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia.

>PRK04863 mukB cell division protein MukB; Provisional

Probab=82.20  E-value=22  Score=39.14  Aligned_cols=21  Identities=29%  Similarity=0.365  Sum_probs=10.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLA   60 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La   60 (203)
                      .+..|+..|+.++...+..+.
T Consensus       318 ELe~rL~kLEkQaEkA~kyle  338 (1486)
T PRK04863        318 ELNEAESDLEQDYQAASDHLN  338 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            455555555555555544444

>PF06818 Fez1: Fez1; InterPro: IPR009638 This family represents the eukaryotic Fez1 protein

Probab=82.08  E-value=14  Score=32.51  Aligned_cols=68  Identities=28%  Similarity=0.380  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        50 ~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      +||-.||.+|.+-...+...+.++..|..++.   .-|.....+......|...|-..+-+|..+++.|..
T Consensus        31 ~Eiv~Lr~ql~e~~~~l~~~~~~~~~l~~~~~~K~~ELE~ce~ELqr~~~Ea~lLrekl~~le~El~~Lr~  101 (202)
T PF06818_consen   31 SEIVSLRAQLRELRAELRNKESQIQELQDSLRTKQLELEVCENELQRKKNEAELLREKLGQLEAELAELRE  101 (202)
T ss_pred             hHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhHhHHHhHHHHHHHhCHHHHhhhhhhhhHHHHHHHHH
Confidence            45555555555555555555555555555554   333456666666666777777777777777766543

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

>PRK10361 DNA recombination protein RmuC; Provisional

Probab=82.01  E-value=30  Score=33.96  Aligned_cols=76  Identities=25%  Similarity=0.391  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHhhh---------HH
Q 028818           51 EHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTV--------RKLQRD---------VS  113 (203)
Q Consensus        51 E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~Tv--------KkL~rD---------va  113 (203)
                      ++..++..+.+-.....+|+.++.........++....+-..+|..+-.+|++.+        ...|+.         =.
T Consensus        68 ~l~~~~~~~~~~~~~~~~l~~~le~~~~~~~ek~~~l~~~~~~L~~~F~~LA~~ile~k~~~f~~~~~~~l~~ll~Pl~e  147 (475)
T PRK10361         68 EVRSLQSINTSLEADLREVTTRMEAAQQHADDKIRQMINSEQRLSEQFENLANRIFEHSNRRVDEQNRQSLNSLLSPLRE  147 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence            3333333333333333333333333333333556666666667777777777643        112221         13


Q ss_pred             HHHHHHHHHHhhc
Q 028818          114 KLEVFRKTLVQSL  126 (203)
Q Consensus       114 KLE~FKk~LmqSL  126 (203)
                      +|+.|++.+-.+-
T Consensus       148 ~l~~f~~~v~~~~  160 (475)
T PRK10361        148 QLDGFRRQVQDSF  160 (475)
T ss_pred             HHHHHHHHHHHHH
Confidence            5778888776543

>KOG1899 consensus LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only]

Probab=81.61  E-value=21  Score=36.94  Aligned_cols=85  Identities=18%  Similarity=0.225  Sum_probs=61.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHH---HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI---YSS---LS-DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~L---e~~---L~-~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      +|-++...=-.|++.||.+++||+..+..|++++..-   +..   ++ .+|+.+.+....-.++++..+.-.+.+....
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            5555555555679999999999999999988776532   222   22 6888888888888888888887777776666


Q ss_pred             HHHHHHHHHHHh
Q 028818          113 SKLEVFRKTLVQ  124 (203)
Q Consensus       113 aKLE~FKk~Lmq  124 (203)
                      .|.....+-+|.
T Consensus       308 ~k~~~iv~i~qg  319 (861)
T KOG1899|consen  308 DKNAQIVRILQG  319 (861)
T ss_pred             hhhhhhhhhhcC
Confidence            666555555544

>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=81.51  E-value=11  Score=30.69  Aligned_cols=42  Identities=31%  Similarity=0.441  Sum_probs=25.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLA--EKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La--EKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .+...++.|++|...|+..+.  |-...|.+|+..+..++..|.
T Consensus        90 ~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~  133 (169)
T PF07106_consen   90 ELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLE  133 (169)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566666666666666666663  555556666666665555554

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 [].

>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=81.50  E-value=14  Score=31.16  Aligned_cols=43  Identities=26%  Similarity=0.307  Sum_probs=39.6

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      --+.-|+..+|.+...|++.|..|...|...+..|..++..+.
T Consensus        82 ~~l~~~~~~~e~~~a~l~~~l~~~~~~ia~~~raIarn~a~id  124 (158)
T PF09486_consen   82 DVLEERVRAAEAELAALRQALRAAEDEIAATRRAIARNDARID  124 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Confidence            3466799999999999999999999999999999999999887

>TIGR03495 phage_LysB phage lysis regulatory protein, LysB family

Probab=81.49  E-value=15  Score=30.29  Aligned_cols=29  Identities=17%  Similarity=0.223  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSL   80 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L   80 (203)
                      ...||..+......+...+..+..+..+|
T Consensus        21 ~~~l~~~~~~a~~~~~~~~~~l~~~~~qL   49 (135)
T TIGR03495        21 LRNARADLERANRVLKAQQAELASKANQL   49 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence            34444444444444444444444444444

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.

>PRK01156 chromosome segregation protein; Provisional

Probab=81.40  E-value=26  Score=35.36  Aligned_cols=13  Identities=31%  Similarity=0.335  Sum_probs=4.9

Q ss_pred             HHHHHHHHHHHHH
Q 028818           92 ERLSKENEALTNT  104 (203)
Q Consensus        92 ~kL~~E~~~La~T  104 (203)
                      ..|..+...|..+
T Consensus       698 ~~l~~~i~~l~~~  710 (895)
T PRK01156        698 ARLESTIEILRTR  710 (895)
T ss_pred             HHHHHHHHHHHhh
Confidence            3333333333333

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=81.39  E-value=7.7  Score=41.35  Aligned_cols=31  Identities=26%  Similarity=0.533  Sum_probs=17.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIE   74 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s   74 (203)
                      -++.|++-..+|..++.+-+..|.+|+++|.
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            3445555555566666666666666666553

>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition

Probab=81.39  E-value=3.8  Score=38.07  Aligned_cols=33  Identities=18%  Similarity=0.423  Sum_probs=0.8

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQI   73 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~   73 (203)
                      +..++..|..|+..++....+.-..|..+..+.
T Consensus       103 l~~~~~elkkEie~IKk~q~e~~~~i~~~~~~~  135 (370)
T PF02994_consen  103 LKKRIKELKKEIENIKKNQSEMKLEIENLKKKL  135 (370)
T ss_dssp             ---------------H-----------------
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhHH
Confidence            456667777888888866655544444444333

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.

>PRK00295 hypothetical protein; Provisional

Probab=81.30  E-value=15  Score=26.68  Aligned_cols=15  Identities=20%  Similarity=0.271  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHH
Q 028818           66 IAELQSQIESIYSSL   80 (203)
Q Consensus        66 i~~Lq~r~s~Le~~L   80 (203)
                      |.+|+.|++-.|..+
T Consensus         7 i~~LE~kla~qE~ti   21 (68)
T PRK00295          7 VTELESRQAFQDDTI   21 (68)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            445554444444333

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=81.19  E-value=46  Score=31.16  Aligned_cols=39  Identities=18%  Similarity=0.287  Sum_probs=26.3

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~   78 (203)
                      .+.+|...+++++..+.+++...+..+..++.....++.
T Consensus       162 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  200 (457)
T TIGR01000       162 KSQTQNEAAEKTKAQLDQQISKTDQKLQDYQALKNAISN  200 (457)
T ss_pred             hhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            455666777777777777777777777776666654444

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=81.13  E-value=45  Score=30.90  Aligned_cols=74  Identities=18%  Similarity=0.255  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHH----HHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLS--------------DKLG----QAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        48 LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~--------------~rL~----~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      |-+.+++++..|.+-.+.|.+|++++..|..++.              ..+.    ...+-..+|.+=.+.|+..-.+|+
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            3445666666666666666666666666665552              1111    111223333333344555556666


Q ss_pred             hhHHHHHHHHHH
Q 028818          110 RDVSKLEVFRKT  121 (203)
Q Consensus       110 rDvaKLE~FKk~  121 (203)
                      +-++|+...-++
T Consensus       152 q~~~k~~~~q~~  163 (301)
T PF06120_consen  152 QMQSKASETQAT  163 (301)
T ss_pred             HHHHHHHHHHHH
Confidence            666665554443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=81.09  E-value=8.8  Score=33.97  Aligned_cols=61  Identities=20%  Similarity=0.322  Sum_probs=25.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEA  100 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~  100 (203)
                      +...||..||..+..-.+.+.|-...|.+||..|..|-..+.   -.|.+..+++..|-.+-|.
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            344566666655544333333444444444444433333333   2222444444444444433

>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=81.08  E-value=20  Score=26.54  Aligned_cols=13  Identities=38%  Similarity=0.534  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHHH
Q 028818           96 KENEALTNTVRKL  108 (203)
Q Consensus        96 ~E~~~La~TvKkL  108 (203)
                      .+|..|..-..+|
T Consensus        39 ~e~~~L~~en~~L   51 (72)
T PF06005_consen   39 EENEELKEENEQL   51 (72)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3333333333333

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.

>COG1322 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]

Probab=81.05  E-value=50  Score=32.11  Aligned_cols=15  Identities=40%  Similarity=0.667  Sum_probs=9.6

Q ss_pred             HHHHHHHHHhhcccc
Q 028818          115 LEVFRKTLVQSLKDD  129 (203)
Q Consensus       115 LE~FKk~LmqSLq~d  129 (203)
                      ++.|+++|-+++...
T Consensus       141 ~e~f~e~l~~~~~~s  155 (448)
T COG1322         141 LEKFREQLEQRIHES  155 (448)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            677777776655443

>PRK00106 hypothetical protein; Provisional

Probab=81.05  E-value=58  Score=32.36  Aligned_cols=12  Identities=8%  Similarity=0.285  Sum_probs=6.8

Q ss_pred             HHHHHHhhcccc
Q 028818          118 FRKTLVQSLKDD  129 (203)
Q Consensus       118 FKk~LmqSLq~d  129 (203)
                      .|..||..+.++
T Consensus       170 ak~~l~~~~~~~  181 (535)
T PRK00106        170 AREIILAETENK  181 (535)
T ss_pred             HHHHHHHHHHHH
Confidence            455666655554

>PRK01156 chromosome segregation protein; Provisional

Probab=81.00  E-value=34  Score=34.53  Aligned_cols=18  Identities=17%  Similarity=0.508  Sum_probs=7.6

Q ss_pred             HHHhhhHHHHHHHHHHHH
Q 028818          106 RKLQRDVSKLEVFRKTLV  123 (203)
Q Consensus       106 KkL~rDvaKLE~FKk~Lm  123 (203)
                      +++..-+..|+.|++.|.
T Consensus       729 ~~~~~~~~~l~~~r~~l~  746 (895)
T PRK01156        729 KKIKKAIGDLKRLREAFD  746 (895)
T ss_pred             HHHHHHHHHHHHHHHHhh
Confidence            333334444444444433

>PF14932 HAUS-augmin3: HAUS augmin-like complex subunit 3

Probab=80.96  E-value=35  Score=30.04  Aligned_cols=39  Identities=26%  Similarity=0.181  Sum_probs=26.4

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ..|..||.|+..|+.....+...+..|+...+.+...+.
T Consensus        68 ~~le~Le~el~~l~~~~~~~~~~~~~lq~~~~~~~~~~~  106 (256)
T PF14932_consen   68 EDLEALEEELEALQEYKELYEQLRNKLQQLDSSLSQELS  106 (256)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456678888888877777777777777755555544443

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=80.85  E-value=25  Score=32.45  Aligned_cols=81  Identities=21%  Similarity=0.297  Sum_probs=51.8

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----hhhHHH
Q 028818           42 STRVSDLESEHSALRSQLAEKDSRI---AELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKL----QRDVSK  114 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEKd~~i---~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL----~rDvaK  114 (203)
                      ..|+.-|--|-.-+|.+|-.+-+.-   .--..|.+.+|.++.    ...+++.+|+.||+.|-..-+.|    +.-+..
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            4555666556666666664321110   112345566666554    88889999999999998776665    445677


Q ss_pred             HHHHHHHHHhhc
Q 028818          115 LEVFRKTLVQSL  126 (203)
Q Consensus       115 LE~FKk~LmqSL  126 (203)
                      ||-++..||.+=
T Consensus       134 le~~~~~l~~~~  145 (292)
T KOG4005|consen  134 LELLRQELAELK  145 (292)
T ss_pred             HHHHHHHHHhhH
Confidence            888888888753

>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=80.75  E-value=19  Score=39.25  Aligned_cols=81  Identities=22%  Similarity=0.259  Sum_probs=46.3

Q ss_pred             hCCCCchhhHHHHHHHHH-----HHHHHhhhhhHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHH
Q 028818           21 VLPSDPFEQLDVARKITS-----IAISTRVSDLESEHSALRSQ--------------LAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        21 vLP~DP~EQLdlarkIts-----~A~atRVs~LE~E~~~LR~~--------------LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      |.+-+|.+==.+.+..--     +++..++..+|..++.||..              +..=...|+.|+.++..+|.++.
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            556666554344333322     24444444444444444443              33334466777777778887765


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHH
Q 028818           82 ------DKLGQAQADKERLSKENEAL  101 (203)
Q Consensus        82 ------~rL~~a~ee~~kL~~E~~~L  101 (203)
                            .+|+...+....|.+|.+.|
T Consensus       852 k~~~d~~~l~~~~~~ie~l~kE~e~~  877 (1293)
T KOG0996|consen  852 KKVVDKKRLKELEEQIEELKKEVEEL  877 (1293)
T ss_pred             hccCcHHHHHHHHHHHHHHHHHHHHH
Confidence                  66676666677777777777

>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=80.64  E-value=15  Score=29.66  Aligned_cols=44  Identities=14%  Similarity=0.234  Sum_probs=24.1

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .+.+..|+..|+.++...+-.-.+=...-.+|+..+.+|..+--
T Consensus        11 ~~el~n~La~Le~slE~~K~S~~eL~kqkd~L~~~l~~L~~q~~   54 (107)
T PF09304_consen   11 QNELQNRLASLERSLEDEKTSQGELAKQKDQLRNALQSLQAQNA   54 (107)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHHHHH
Confidence            45677788888888877765544333333335555555554443

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.

>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=80.60  E-value=11  Score=26.18  Aligned_cols=35  Identities=31%  Similarity=0.485  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRK  120 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk  120 (203)
                      ....++++|.+|++.|...++.|..|-+.+|.+=|
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            44455566677777777777777667777776655

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

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=80.54  E-value=31  Score=33.62  Aligned_cols=49  Identities=22%  Similarity=0.424  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH----------HHHHhhhHHHHHHHHHHHHhhccccc
Q 028818           82 DKLGQAQADKERLSKENEALTNT----------VRKLQRDVSKLEVFRKTLVQSLKDDE  130 (203)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~T----------vKkL~rDvaKLE~FKk~LmqSLq~d~  130 (203)
                      ..|.++.+.+..|..|-+.|...          ++.+..++..|+.=-+.+...+....
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            56678888889999999999888          88999888888877776666655443

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

Probab=80.48  E-value=41  Score=29.84  Aligned_cols=42  Identities=21%  Similarity=0.380  Sum_probs=23.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .+..+...+.+++..++.++..-...+..++.++..++.++.
T Consensus       134 ~~~~~~~~~~~~~~~l~~~i~~~~~~i~~~~~~l~~~~~~l~  175 (423)
T TIGR01843       134 LFESRKSTLRAQLELILAQIKQLEAELAGLQAQLQALRQQLE  175 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555555555555554

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.

>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=80.40  E-value=23  Score=26.92  Aligned_cols=35  Identities=14%  Similarity=0.188  Sum_probs=19.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        47 ~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .||..+.+|-...+.-|+.+.++.+....++.++.
T Consensus        28 ~lE~k~~rl~~Ek~kadqkyfa~mr~~d~l~~e~k   62 (96)
T PF08647_consen   28 ILEQKKLRLEAEKAKADQKYFAAMRSKDALDNEMK   62 (96)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            34555555555555555555555555555555554

>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=80.30  E-value=27  Score=31.85  Aligned_cols=66  Identities=15%  Similarity=0.307  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 028818           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSK  114 (203)
Q Consensus        49 E~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (203)
                      |-+.+..|.+..-+.-.+.++++.+...-.+++..+....+....|..+..+|...++|-..++.+
T Consensus       143 E~~lr~~R~~a~~r~~e~~~iE~~l~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER  208 (267)
T PF10234_consen  143 EVELREERQRALARPLELNEIEKALKEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELER  208 (267)
T ss_pred             hHhHHHHHHHHHcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555666677766677777777776666666666777788888999999999999988887776654

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 [].

>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=80.29  E-value=44  Score=31.16  Aligned_cols=85  Identities=18%  Similarity=0.322  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHH---HHHHHHHHHHHHHHH
Q 028818           31 DVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESI-----------YSSLS---DKLGQAQADKERLSK   96 (203)
Q Consensus        31 dlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~L-----------e~~L~---~rL~~a~ee~~kL~~   96 (203)
                      .+-..|...++..|+..||.|-..||.....=......++++-..|           -..+.   .=|....+++...++
T Consensus       155 ~~~~~~~le~Lq~Klk~LEeEN~~LR~Ea~~L~~et~~~EekEqqLv~dcv~QL~~An~qia~LseELa~k~Ee~~rQQE  234 (306)
T PF04849_consen  155 SSQKCIQLEALQEKLKSLEEENEQLRSEASQLKTETDTYEEKEQQLVLDCVKQLSEANQQIASLSEELARKTEENRRQQE  234 (306)
T ss_pred             ccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHH
Confidence            3344566678999999999999999987664332222333222211           11111   223355566666666


Q ss_pred             HHHHHHHHHHHHhhhHHHH
Q 028818           97 ENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        97 E~~~La~TvKkL~rDvaKL  115 (203)
                      |..+|..+|-.|++.+..+
T Consensus       235 EIt~LlsqivdlQ~r~k~~  253 (306)
T PF04849_consen  235 EITSLLSQIVDLQQRCKQL  253 (306)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            6666666666666555544

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 [].

>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]

Probab=80.12  E-value=51  Score=35.58  Aligned_cols=85  Identities=24%  Similarity=0.335  Sum_probs=52.8

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HH---HHHHHH-HHHHHHHHHHHHHHHHHHHhhhH
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DK---LGQAQA-DKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-------~r---L~~a~e-e~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      .|..=|.||..||..+-=|.+...+++=|..-+|..|.       .+   +.+..+ -...|.+--..+..|+..|++|+
T Consensus       956 tle~re~eikeLkk~aKmkqeelSe~qvRldmaEkkLss~~k~~~h~v~~~~ek~ee~~a~lr~Ke~efeetmdaLq~di 1035 (1243)
T KOG0971|consen  956 TLEDRETEIKELKKSAKMKQEELSEAQVRLDLAEKKLSSAAKDADHRVEKVQEKLEETQALLRKKEKEFEETMDALQADI 1035 (1243)
T ss_pred             hHHhhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhhhhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444455555555555555555555555555555554       22   222222 23445555567889999999999


Q ss_pred             HHHHHHHHHHHhhccc
Q 028818          113 SKLEVFRKTLVQSLKD  128 (203)
Q Consensus       113 aKLE~FKk~LmqSLq~  128 (203)
                      ..||.=|-.|=+.|+.
T Consensus      1036 ~~lEsek~elKqrl~~ 1051 (1243)
T KOG0971|consen 1036 DQLESEKAELKQRLNS 1051 (1243)
T ss_pred             HHHHhhHHHHHHHhhh
Confidence            9999999999888865

>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=80.09  E-value=34  Score=31.43  Aligned_cols=64  Identities=22%  Similarity=0.442  Sum_probs=44.9

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      ..++...+.|...+...|.++...+.++++|+.    +..+||..+..+-.+|.+.-..+...|++..
T Consensus       199 ~r~l~~~~~ELe~~~EeL~~~Eke~~e~~~~i~----e~~~rl~~l~~~~~~l~k~~~~~~sKV~kf~  262 (269)
T PF05278_consen  199 DRKLELKKEELEELEEELKQKEKEVKEIKERIT----EMKGRLGELEMESTRLSKTIKSIKSKVEKFH  262 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344555566667777777777777777777774    3346677888888888887777777777764

---

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	203
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05

>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 = 48.7 bits (115), Expect = 4e-07
 Identities = 31/207 (14%), Positives = 61/207 (29%), Gaps = 57/207 (27%)

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 -GNSSFAEEREPECRSKSSSFFLNSNI 192
            G +  A +    C S      ++  I
Sbjct: 161 SGKTWVALD---VCLSYKVQCKMDFKI 184

>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 = 48.7 bits (115), Expect = 4e-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 = 7e-05
 Identities = 42/227 (18%), Positives = 68/227 (29%), Gaps = 70/227 (30%)

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 KLEVFRKTLVQSLKDDEDASTGATRIAKPTPNEDDAAVAPTGTSSVHSQISEGGN----- 168
              +  K L    +D               P E      P   S +   I +G       
Sbjct: 304 -KSLLLKYLDCRPQDL--------------PRE-VLTTNPRRLSIIAESIRDGLATWDNW 347

Query: 169 ------------SSFAEEREP-ECRSKSSSFFL---NSNIKL-VLCL 198
                        S     EP E R       +   +++I   +L L
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	203
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	96.99
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	96.97
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.63
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	96.62
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	96.39
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	95.94
3bas_A	89	Myosin heavy chain, striated muscle/general contro	95.5
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	95.14
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	95.11
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	94.74
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	94.4
3a7o_A	75	Autophagy protein 16; coiled-coil, coiled coil, cy	94.33
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	94.29
2b9c_A	147	Striated-muscle alpha tropomyosin; alpha-helix, co	94.28
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	94.19
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	94.16
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	93.58
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	93.38
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	93.33
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	93.21
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	93.01
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	93.0
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	92.84
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	92.83
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	92.62
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	92.47
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	92.41
2q6q_A	74	Spindle POLE BODY component SPC42; SPC42P, budding	92.27
4emc_A	190	Monopolin complex subunit CSM1; RWD domain, kineto	92.17
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	92.11
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	92.01
3jsv_C	94	NF-kappa-B essential modulator; ubiquitin, coiled-	91.98
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	91.97
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	91.95
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	91.81
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	91.64
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	91.36
4fm3_A	98	Uncharacterized hypothetical protein; PF14346 fami	91.15
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	91.11
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	89.97
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	89.79
2akf_A	32	Coronin-1A; coiled coil, protein binding; 1.20A {S	89.69
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	89.46
1x79_B	112	RAB GTPase binding effector protein 1; rabaptin5,	89.45
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	89.21
2e7s_A	135	RAB guanine nucleotide exchange factor SEC2; coile	88.45
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	88.31
1cii_A	602	Colicin IA; bacteriocin, ION channel formation, tr	88.08
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	87.91
2xnx_M	146	M protein, M1-BC1; cell adhesion, virulence factor	87.89
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	87.69
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	87.44
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	86.79
1x4t_A	92	Hypothetical protein LOC57905; structural genomics	86.52
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	86.42
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	86.41
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	86.34
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	86.26
1gk4_A	84	Vimentin; intermediate filament, dimer, parallel c	85.86
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	85.83
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	85.52
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	85.32
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	85.06
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	84.49
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	84.46
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	84.17
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	83.37
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	83.26
3mov_A	95	Lamin-B1; LMNB1, B-type lamins, intermediate filam	83.03
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	82.8
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	82.71
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	82.37
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	82.31
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	82.27
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	82.17
1x8y_A	86	Lamin A/C; structural protein, intermediate filame	81.93
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	81.92
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	81.81
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	81.71
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	81.14
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	80.4

>3u1c_A Tropomyosin alpha-1 chain; anti-parallel coiled coil, contractIle protein; 1.80A {Gallus gallus} PDB: 3u1a_A

Probab=96.99  E-value=0.035  Score=41.79  Aligned_cols=77  Identities=16%  Similarity=0.212  Sum_probs=63.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      .+.-|+..+|.++..+.+....++..|..|+.|+..++..|-   .+|..+.+....-.+-...-...|..|||-+.-||
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            567788899999999999999999999999999999999987   66776666655555555666678999999887776

>1c1g_A Tropomyosin; contractIle protein; 7.00A {Sus scrofa} SCOP: h.1.5.1 PDB: 2tma_A 2w49_A 2w4u_A

Probab=96.97  E-value=0.026  Score=43.73  Aligned_cols=42  Identities=12%  Similarity=0.173  Sum_probs=21.9

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      +|..+|..|+.++..+...+.+-...+..++.++..++..+.
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            455555555555555555555555555555555444444443

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=96.63  E-value=0.032  Score=44.38  Aligned_cols=71  Identities=14%  Similarity=0.212  Sum_probs=58.9

Q ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028818           37 TSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRD  111 (203)
Q Consensus        37 ts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rD  111 (203)
                      ++.=++.-.-++..+...|++++.+++..|++|...+.++...+-    .+.+++.+|.++++.|...+++|...
T Consensus        62 aALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e----~~~~e~~~l~~~~~~l~~~~~~le~~  132 (138)
T 3hnw_A           62 MYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAE----SSAKEIKELKSEINKYQKNIVKLETE  132 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555677777888899999999999999999999988887776654    88888888888888888888888643

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=96.62  E-value=0.085  Score=39.37  Aligned_cols=77  Identities=16%  Similarity=0.238  Sum_probs=63.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      .+.-|+..+|.++..+......++..|..|+.|+..++..+-   .+|..+.+....-.+....-...|..|||-+.-||
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            567788889999999999999999999999999999999987   67776666665555566666778999999887664

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

Probab=96.39  E-value=0.038  Score=55.90  Aligned_cols=80  Identities=18%  Similarity=0.318  Sum_probs=38.1

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRK  120 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk  120 (203)
                      ...+|..||.|+..|+.++.+-..+..+|++++..+...|+.++....+++.+|..+.+.|...+.+.+.+.+  |.+|.
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            3345555555555555555555555555555555555544444444444444444444444433333333222  23555


Q ss_pred             HH
Q 028818          121 TL  122 (203)
Q Consensus       121 ~L  122 (203)
                      .+
T Consensus      1060 ~~ 1061 (1080)
T 2dfs_A         1060 KL 1061 (1080)
T ss_dssp             HH
T ss_pred             HH
Confidence            55

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=95.94  E-value=0.095  Score=43.00  Aligned_cols=71  Identities=18%  Similarity=0.216  Sum_probs=52.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhhHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT-VRKLQRDVSK  114 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~T-vKkL~rDvaK  114 (203)
                      .+.+-...|+.++..|...+.+|...+..|++-+.+|..++.    .+.+...+|++||+.|... +++-+++-.+
T Consensus        72 ~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n----~lE~kl~kLq~EN~~LV~RWM~rk~qEAe~  143 (152)
T 3a7p_A           72 ILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENN----VLQQKLSDLKKEHSQLVARWLKKTEKETEA  143 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566667777777777777888888888888888777776    8889999999999988764 4455555444

>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=95.50  E-value=0.23  Score=36.52  Aligned_cols=70  Identities=20%  Similarity=0.269  Sum_probs=60.3

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      -+..++.++..|+..+..-.....+|+.+...|..+..   ..+..+.+.+.+|.+.+..|...++.|+..|.
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            45678999999999999888889999999888887766   44889999999999999999999999987653

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=95.14  E-value=0.14  Score=40.04  Aligned_cols=64  Identities=19%  Similarity=0.345  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           49 ESEHSALRSQLAEKDS---RIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        49 E~E~~~LR~~LaEKd~---~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      ..++..|++.++.++.   .|.-|+.++.-....+.    .=+.+-++++.|+..|...+..|+|++.+|+
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            3566667776666665   45555555555544444    5556678999999999999999999998873

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

Probab=95.11  E-value=0.024  Score=57.38  Aligned_cols=71  Identities=23%  Similarity=0.299  Sum_probs=21.2

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      ..+||.++..|..+|.++.+...+|++++..++..+.   ..|+...++..++.+|+..+.+.|+.|..++++|
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            4677888888888887777777777666655555444   4444444444455555555555555444444443

>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=94.74  E-value=0.94  Score=34.95  Aligned_cols=32  Identities=22%  Similarity=0.410  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           82 DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        82 ~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      +.+..+.+...+|...+..|...++-|+.++.
T Consensus        62 ~~l~e~EE~~~~L~~~k~eLe~~l~el~~rle   93 (129)
T 2fxo_A           62 DNLADAEERCDQLIKNKIQLEAKVKEMNKRLE   93 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444443

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=94.40  E-value=0.8  Score=38.48  Aligned_cols=41  Identities=27%  Similarity=0.368  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      ..+...|..++..|...++.|...-.-||+=.|...-||.|
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            44445555555566666666666666666666666666554

>3a7o_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.50A {Saccharomyces cerevisiae}

Probab=94.33  E-value=0.31  Score=35.81  Aligned_cols=61  Identities=18%  Similarity=0.192  Sum_probs=42.5

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      -+.|+.-+..||..|.+|+.+|..|++.+.---..    .....++..-|.=||+-|...+.+|.
T Consensus        13 ~~~~~~~l~~Lr~eL~~Ke~eI~~L~e~i~lk~kd----~ErLNDEiislNIENNlL~~rl~~l~   73 (75)
T 3a7o_A           13 DDALLNTLAILQKELKSKEQEIRRLKEVIALKNKN----TERLNDELISGTIENNVLQQKLSDLK   73 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc----HHHhhHHHHHhHHHHHHHHHHHHHHh
Confidence            34456678999999999999999999776522222    23556777788888888877665554

>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=94.29  E-value=0.28  Score=44.26  Aligned_cols=41  Identities=15%  Similarity=0.101  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccc
Q 028818           89 ADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDD  129 (203)
Q Consensus        89 ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d  129 (203)
                      ++..+|.+.-+.-..++..|.++++++..=.|+|++-+++.
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            33334444444444466677777777766666666666543

>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=94.28  E-value=0.73  Score=36.91  Aligned_cols=75  Identities=16%  Similarity=0.225  Sum_probs=68.5

Q ss_pred             HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           38 SIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        38 s~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      +++.--|+..||.++...+....+.++...+...|+.-++..|.   .|+..+...+..|..|...+.+++|.|...-
T Consensus        47 ~~~deEr~~~lE~qLkeak~~aeeadrKyeE~~RKl~~~E~dLeraeeRae~aE~k~~eLEeeL~~~~~nlKsLE~~e  124 (147)
T 2b9c_A           47 AQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEDKV  124 (147)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             hcccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhH
Confidence            34777899999999999999999999999999999999999999   9999999999999999999999999987544

>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=94.19  E-value=1.4  Score=35.86  Aligned_cols=77  Identities=22%  Similarity=0.286  Sum_probs=57.4

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      -+..|...+|.+|..|..+|.+-+.....-+..|..|+..+-   ++|.........+..+-+..-+.+..+.-++-.|+
T Consensus        67 kasqrEd~yEeqIk~L~~kLKEAE~RAE~AERsv~kLEk~id~lEd~L~~~Kek~~~i~~eLd~tl~el~~~~~~~~~~~  146 (155)
T 2efr_A           67 KYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEEMKQLEDKVEELLSKNYHLE  146 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHH
Confidence            677899999999999999999988888888888888888777   66777777777777777765555544444444443

>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=94.16  E-value=1.2  Score=34.41  Aligned_cols=76  Identities=18%  Similarity=0.353  Sum_probs=47.2

Q ss_pred             HHHhhhhhHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 028818           41 ISTRVSDLESEHSALRSQLA-------EKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQR  110 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~La-------EKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~r  110 (203)
                      +-.+..+|+.|...|..+|.       +++.....|..+-..|+..|.   .||..-.+.+..|..++..|...+..|..
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            34455566666666655554       444444445555555555555   66667777777777777777777777777


Q ss_pred             hHHHHH
Q 028818          111 DVSKLE  116 (203)
Q Consensus       111 DvaKLE  116 (203)
                      ++.-+|
T Consensus       119 ~led~e  124 (129)
T 2fxo_A          119 DIDDLE  124 (129)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776665

>3cvf_A Homer-3, homer protein homolog 3; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, phosphoprotein, polymorphism; 2.90A {Homo sapiens}

Probab=93.58  E-value=0.44  Score=35.14  Aligned_cols=70  Identities=24%  Similarity=0.377  Sum_probs=45.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 028818           46 SDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (203)
Q Consensus        46 s~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (203)
                      +.||++...+-++|.+-.....+|++||..|+..|.    .+..+...+..|-..|..+.   ---+..|--|+..|
T Consensus         2 ~~l~~e~e~~~~klq~~E~rN~~Le~~v~~le~~Le----~s~~~q~~~~~Elk~l~e~L---d~KI~eL~elRqgL   71 (79)
T 3cvf_A            2 SHMAAEREETQQKVQDLETRNAELEHQLRAMERSLE----EARAERERARAEVGRAAQLL---DVSLFELSELREGL   71 (79)
T ss_dssp             --------CTTHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH---hhHHHHHHHHHHHH
Confidence            358888888999999999999999999999999887    77777777777766665543   23333444444443

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=93.38  E-value=0.06  Score=47.19  Aligned_cols=69  Identities=17%  Similarity=0.303  Sum_probs=22.6

Q ss_pred             HHhhhhhHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           42 STRVSDLESEHSALRSQLAEK---DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEK---d~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      +..|..|+.|+..||.++.+-   .+.... ++|+..|+.++.    .....|.+|..+...+...+.+|..+|.+|
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            556667888888888888644   333333 444554444443    444455555555555555555555555554

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=93.33  E-value=1.9  Score=33.47  Aligned_cols=60  Identities=12%  Similarity=0.230  Sum_probs=37.8

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKD----SRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENE   99 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd----~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~   99 (203)
                      .+..++..|+.|+..+|.++..-.    ..|..||+.+..|-..-.   .+++...+.|..|.....
T Consensus         7 dL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R   73 (111)
T 2v66_B            7 DLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKR   73 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHH
Confidence            577888999999999998887433    345556666555544433   455555555555554443

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=93.21  E-value=0.67  Score=36.25  Aligned_cols=53  Identities=26%  Similarity=0.293  Sum_probs=34.2

Q ss_pred             hHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH
Q 028818           48 LESEHSALRSQ----LAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEA  100 (203)
Q Consensus        48 LE~E~~~LR~~----LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~  100 (203)
                      |-.|+.+||..    ..|-.+.|.+|+.||+.|+.+|.   .-...|..++..|..|...
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    35889999999999999999998   2223344455555544443

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=93.01  E-value=1.8  Score=35.93  Aligned_cols=66  Identities=18%  Similarity=0.353  Sum_probs=38.3

Q ss_pred             hhHHHHHHHHHHHH-HH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           47 DLESEHSALRSQLA-EK------DSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        47 ~LE~E~~~LR~~La-EK------d~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      .||.|+..|..+|. ||      ...|.+|+.|+..|+.++.    ...+.-.++..||..|..-|-.|.+.-+-+|
T Consensus        66 ~Leke~~~LQa~L~qEr~~r~q~se~~~elq~ri~~L~~El~----~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~~e  138 (168)
T 3o0z_A           66 QTDKDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQEEVK----HLKHNLEKVEGERKEAQDMLNHSEKEKNNLE  138 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            45556666666665 55      3456788888888888886    3333334444444444444444444444444

>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=93.00  E-value=0.74  Score=46.48  Aligned_cols=75  Identities=11%  Similarity=0.235  Sum_probs=44.4

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----------DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      ++..|+.++..++.++..-...+.+++.++..|+.++.          ..+..+.++..+|..++..|...++.|..++.
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            34456666667776666666666666666665555444          33444555566666666666666666666655


Q ss_pred             HHHHH
Q 028818          114 KLEVF  118 (203)
Q Consensus       114 KLE~F  118 (203)
                      .++.-
T Consensus       938 e~ee~  942 (1184)
T 1i84_S          938 EEEER  942 (1184)
T ss_dssp             HHHHC
T ss_pred             HHHHH
Confidence            54443

>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=92.84  E-value=1  Score=40.58  Aligned_cols=22  Identities=27%  Similarity=0.335  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHH
Q 028818           92 ERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        92 ~kL~~E~~~La~TvKkL~rDva  113 (203)
                      .+|.+|+..|...++.-.+.+.
T Consensus       540 ~~~~~~~~~le~~~~~~~~~~~  561 (597)
T 3oja_B          540 EDLEQENIALEKQLDNKRAKQA  561 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhhHHHHHHHhhhhhHHH
Confidence            3333455555544444444433

>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=92.83  E-value=0.44  Score=34.76  Aligned_cols=45  Identities=20%  Similarity=0.188  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEA  100 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~  100 (203)
                      +..|+..|.+|++.|...++++..||..|+    +..+++.+|+.|-+.
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~----ekd~eI~~LqseLDK   65 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELD----QKDELIQMLQNELDK   65 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Confidence            455666666666666666666665555554    444444455554443

>3hnw_A Uncharacterized protein; coiled-coil, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.20A {Eubacterium eligens}

Probab=92.62  E-value=1.4  Score=34.91  Aligned_cols=53  Identities=28%  Similarity=0.317  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           65 RIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        65 ~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      .+..|+.++..++.++.   ..|..+..+...+.+|+..|...+..|.+.+.+||+
T Consensus        76 ~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~  131 (138)
T 3hnw_A           76 MADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLET  131 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444   455588888999999999999999999999999985

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=92.47  E-value=2.5  Score=31.36  Aligned_cols=71  Identities=13%  Similarity=0.241  Sum_probs=46.2

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLE  116 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE  116 (203)
                      .|--||-.||.+-..|..++..-..      ...+.+...+..-+.........+..||..|...+..|..++..|+
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            5778999999998888766543211      1223333333344556667777777788888777777777766543

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=92.41  E-value=3.1  Score=34.88  Aligned_cols=76  Identities=8%  Similarity=0.118  Sum_probs=46.1

Q ss_pred             CchhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           25 DPFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALT  102 (203)
Q Consensus        25 DP~EQLdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La  102 (203)
                      ++-|-=+|-+.|.  .+..|.+.||.++..+-.++.++...+.+++.++..++..|...-....+....+.++...|.
T Consensus        88 ~~kE~~aL~kEie--~~~~~i~~lE~eile~~e~ie~~~~~l~~~~~~l~~~~~~l~~~~~~~~~~~~e~~~e~~~l~  163 (256)
T 3na7_A           88 SERELRSLNIEED--IAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLALELESLVENEVKNIKETQQIIF  163 (256)
T ss_dssp             SSSHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555555  445788888888888888888887778777777777777776322333333333333333333

>2q6q_A Spindle POLE BODY component SPC42; SPC42P, budding yeast, cell cycle; 1.97A {Saccharomyces cerevisiae}

Probab=92.27  E-value=1.1  Score=32.80  Aligned_cols=58  Identities=28%  Similarity=0.364  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      -..|-.+|.+|+++|..|..=+.+    |.+||-.-.+-+.||+.+...+..-+..|++|++
T Consensus         5 NKeL~~kl~~Kq~EI~rLnvlvgs----lR~KLiKYtelnKKLe~~~~~~q~s~~~l~k~~~   62 (74)
T 2q6q_A            5 NKELNFKLREKQNEIFELKKIAET----LRSKLEKYVDITKKLEDQNLNLQIKISDLEKKLS   62 (74)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHhhhhhHHHHhhcc
Confidence            456888999999999887655554    4456668889999999999999999988888764

>4emc_A Monopolin complex subunit CSM1; RWD domain, kinetochore-binding, kinetoch replication-replication complex; 3.05A {Saccharomyces cerevisiae} PDB: 3n7n_A 3n4x_A

Probab=92.17  E-value=0.5  Score=39.98  Aligned_cols=37  Identities=32%  Similarity=0.487  Sum_probs=34.0

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      |++|-+|...|+++|..|+.+|..|++++.+++....
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            6789999999999999999999999999999888774

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=92.11  E-value=3.2  Score=31.80  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=11.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLA   60 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La   60 (203)
                      -+...|+.|+.|+..|+.+-+
T Consensus        40 elrr~iq~L~~el~~l~~~~~   60 (129)
T 3tnu_B           40 EMNRMIQRLRAEIDNVKKQCA   60 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhHHH
Confidence            344556666666666655443

>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=92.01  E-value=2.4  Score=30.29  Aligned_cols=40  Identities=15%  Similarity=0.270  Sum_probs=18.4

Q ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           42 STRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        42 atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ..|+..+|.++.............|..|+.|+..+|..|-
T Consensus        19 ~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld   58 (81)
T 1ic2_A           19 LDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELD   58 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444444444444444443

>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=91.98  E-value=0.84  Score=34.81  Aligned_cols=66  Identities=20%  Similarity=0.351  Sum_probs=48.7

Q ss_pred             hHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           48 LESEHSALRSQLAEKD---SRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        48 LE~E~~~LR~~LaEKd---~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      ...+|..|++.++.+.   ..|.-|+.++.-....+.    .=+.+-+++..|+..|...+..|.+++.+|..
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            4566777887777666   566777777776666665    55667789999999999999999999998864

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=91.97  E-value=1  Score=50.68  Aligned_cols=84  Identities=19%  Similarity=0.294  Sum_probs=58.7

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-----------------DKLGQAQADKERLSKENEALTNTV  105 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-----------------~rL~~a~ee~~kL~~E~~~La~Tv  105 (203)
                      .++..+|.+....+++|.++.+.+.++++++..|+.++.                 .||..|..=...|..|+..=..++
T Consensus      2014 ~~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~~~~~ek~~L~~e~~~~~~kl~rA~~Li~gL~~Ek~RW~~~~ 2093 (3245)
T 3vkg_A         2014 EEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYATLIRETEQIKTESSKVKNKVDRSIALLDNLNSERGRWEQQS 2093 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccHHHHH
Confidence            466677777777777777777777777777777666654                 455556666677888888888888


Q ss_pred             HHHhhhHHHH------------------HHHHHHHHhhc
Q 028818          106 RKLQRDVSKL------------------EVFRKTLVQSL  126 (203)
Q Consensus       106 KkL~rDvaKL------------------E~FKk~LmqSL  126 (203)
                      +.|..+...|                  +.||+.|++..
T Consensus      2094 ~~l~~~~~~L~GD~LLaaafisY~G~f~~~~R~~l~~~W 2132 (3245)
T 3vkg_A         2094 ENFNTQMSTVVGDVVLASAFLAYIGFFDQNFRTDLMRKW 2132 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTGGGSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            8777766664                  45777777643

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=91.95  E-value=3.2  Score=34.79  Aligned_cols=28  Identities=14%  Similarity=0.220  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 028818           99 EALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (203)
Q Consensus        99 ~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (203)
                      ..+...+..+..+++.|..=+..|...|
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            3334444444445555554444555444

>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=91.81  E-value=2.6  Score=30.11  Aligned_cols=42  Identities=10%  Similarity=0.158  Sum_probs=31.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ||..|+..|+.|......++.+-...+.+.+.+...++..+.
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            678888888888888777777777777777777766666665

>3mq9_A Bone marrow stromal antigen 2 fused to maltose-BI periplasmic protein; HIV, antiviral protein; 2.80A {Escherichia coli}

Probab=91.64  E-value=5.9  Score=34.94  Aligned_cols=63  Identities=16%  Similarity=0.282  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           55 LRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        55 LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      |+++|.|=..-..+++.+.++....+-........+..+-++....|.+.|++||..+..+++
T Consensus       402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  464 (471)
T 3mq9_A          402 LQQELTEAQKGFQDVEAQAATANHTVMALMASLDAEKAQGQKKVEELEGEITTLNHKLQDASA  464 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444444333222111111122233334556677778888877665554

>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=91.36  E-value=3.2  Score=30.33  Aligned_cols=32  Identities=13%  Similarity=0.289  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      ....+...|..+...|...+..|.+.+..|+.
T Consensus        68 ~~~~~l~~l~~~i~~l~~~i~~l~~~~~~l~~   99 (112)
T 1l8d_A           68 KYHLDLNNSKNTLAKLIDRKSELERELRRIDM   99 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444433

>4fm3_A Uncharacterized hypothetical protein; PF14346 family protein, DUF4398, structural genomics, joint for structural genomics, JCSG; HET: PG4; 2.47A {Pseudomonas aeruginosa}

Probab=91.15  E-value=2.8  Score=31.99  Aligned_cols=87  Identities=13%  Similarity=0.246  Sum_probs=63.0

Q ss_pred             chhhHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           26 PFEQLDVARKITSIAISTRVSDLESEHSALRSQLAEKDSRIAEL---QSQIESIYSSLSDKLGQAQADKERLSKENEALT  102 (203)
Q Consensus        26 P~EQLdlarkIts~A~atRVs~LE~E~~~LR~~LaEKd~~i~~L---q~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La  102 (203)
                      |.|||.++..-+..|.+..++....|...-|.+|..-..-+.+=   +.|.-.=+.++-+||..+.-...|=++..+.|.
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            79999999999999999999999888888888887655544321   111111122333777788888888888888888


Q ss_pred             HHHHHHhhhH
Q 028818          103 NTVRKLQRDV  112 (203)
Q Consensus       103 ~TvKkL~rDv  112 (203)
                      ..|..|..++
T Consensus        85 ~~I~~LrqEl   94 (98)
T 4fm3_A           85 KSLKRLRKQL   94 (98)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            7777776654

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=91.11  E-value=3  Score=32.05  Aligned_cols=21  Identities=24%  Similarity=0.203  Sum_probs=12.7

Q ss_pred             HHHHhhhhhHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLA   60 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~La   60 (203)
                      -+...|+.|+.|+..|+.+-+
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            345566677777766665443

>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=89.97  E-value=0.7  Score=33.13  Aligned_cols=45  Identities=24%  Similarity=0.412  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 028818           60 AEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKL  115 (203)
Q Consensus        60 aEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKL  115 (203)
                      .-|+.+|.+|+.++..|+....           .|..||..|-..|..|...+..|
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            3588999999999887776554           46677777777777776665443

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus}

Probab=89.79  E-value=5.7  Score=33.27  Aligned_cols=67  Identities=12%  Similarity=0.221  Sum_probs=44.1

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSR----IAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVR  106 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~----i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvK  106 (203)
                      .+.+++..|..|+..+|.++..=...    |..|++.++.|.....   .+++...+.|..|.........++.
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            56677777777777777777643333    6677777766666555   6666777777777666666655554

>2akf_A Coronin-1A; coiled coil, protein binding; 1.20A {Synthetic}

Probab=89.69  E-value=0.43  Score=29.87  Aligned_cols=30  Identities=23%  Similarity=0.422  Sum_probs=21.9

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ||+||.|++.|.       ..+.+||+|+..||..+|
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       456678888888877765

>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=89.46  E-value=1.3  Score=32.30  Aligned_cols=37  Identities=19%  Similarity=0.287  Sum_probs=29.4

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      |-.|+..+..-..+|..||..|.+|+.++...|..++
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            6777777777777888888888888888888887776

>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=89.45  E-value=1.2  Score=34.83  Aligned_cols=15  Identities=20%  Similarity=0.140  Sum_probs=6.7

Q ss_pred             hhhHHHHHHHHHHHH
Q 028818           46 SDLESEHSALRSQLA   60 (203)
Q Consensus        46 s~LE~E~~~LR~~La   60 (203)
                      .+|..+.+.|+.+|.
T Consensus         9 ~~lq~~~~ql~~qL~   23 (112)
T 1x79_B            9 KKLQLMLRQANDQLE   23 (112)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            344444444444443

>2v66_B Nuclear distribution protein NUDE-like 1; structural protein, developmental protein, structural protei phosphorylation, transport, microtubule; 2.10A {Homo sapiens}

Probab=89.21  E-value=6.5  Score=30.49  Aligned_cols=77  Identities=19%  Similarity=0.296  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818           52 HSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus        52 ~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      .+.|+.+..-=...+.+++.|+.....+..........+..+|..+++.|..-++.|...-.-||.=.|...-||.|
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R~t~~SLeD   81 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSLED   81 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHhhHHH
Confidence            44455555544455555666655555444344455667777788888888888888888888888888888877765

>2e7s_A RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 3.00A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=88.45  E-value=2.5  Score=33.93  Aligned_cols=46  Identities=17%  Similarity=0.329  Sum_probs=29.4

Q ss_pred             CchhhHHHHHHHHHHHHHHhhhhhHH---HHHHHHHHHHHHHHHHHHHHH
Q 028818           25 DPFEQLDVARKITSIAISTRVSDLES---EHSALRSQLAEKDSRIAELQS   71 (203)
Q Consensus        25 DP~EQLdlarkIts~A~atRVs~LE~---E~~~LR~~LaEKd~~i~~Lq~   71 (203)
                      |=.++|-++|++.+. ...|+++||.   +...|...+..++..+..|+.
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            445788888875544 4677777776   455555556566666666655

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=88.31  E-value=7.2  Score=29.91  Aligned_cols=74  Identities=20%  Similarity=0.183  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 028818           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKT  121 (203)
Q Consensus        49 E~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~  121 (203)
                      ..|+..||..+..-...|..++.+-..||.++.       ..+..+......|..+...+-..+-...++-..|=+.|-.
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            345555555555555555555555555555554       2333444444445555555555555555555555555544


Q ss_pred             H
Q 028818          122 L  122 (203)
Q Consensus       122 L  122 (203)
                      |
T Consensus       117 L  117 (131)
T 3tnu_A          117 L  117 (131)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1cii_A Colicin IA; bacteriocin, ION channel formation, transmembrane protein; 3.00A {Escherichia coli} SCOP: f.1.1.1 h.4.3.1

Probab=88.08  E-value=3.5  Score=39.66  Aligned_cols=64  Identities=23%  Similarity=0.385  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        50 ~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      +|-.+||+.+.++...|..++.-++++...+.   .....+.+..+.+.+|+..+.+.+-.++..++
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            56788999999999999999999999988888   67788899999999999999888877776654

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=87.91  E-value=8.2  Score=31.55  Aligned_cols=29  Identities=21%  Similarity=0.243  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSK  114 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaK  114 (203)
                      ...++..-|+=+.+.+...+++|..+-.+
T Consensus       100 ~l~DEl~aLqlq~n~lE~kl~kLq~EN~~  128 (152)
T 3a7p_A          100 RLNAALISGTIENNVLQQKLSDLKKEHSQ  128 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555566666666666554433

>2xnx_M M protein, M1-BC1; cell adhesion, virulence factor, streptococcal toxic shock S; 3.30A {Streptococcus pyogenes}

Probab=87.89  E-value=0.51  Score=38.54  Aligned_cols=37  Identities=22%  Similarity=0.337  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (203)
                      ....+..||..++..+...-+.|.||+.-...-||+|
T Consensus        98 ~LeAE~aKLeEekQIseASRqgLrRDLeASReAKKql  134 (146)
T 2xnx_M           98 QLTIEKAKLEEEKQISDASRQSLRRDLDASREAKKQV  134 (146)
T ss_dssp             HHHHHHHHHGGGTTTC---------------------
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555555555555555543

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=87.69  E-value=7.8  Score=29.59  Aligned_cols=74  Identities=15%  Similarity=0.217  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 028818           49 ESEHSALRSQLAEKDSRIAELQSQIESIYSSLS-------DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKT  121 (203)
Q Consensus        49 E~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~-------~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~  121 (203)
                      ..|+..||..+..-...|..|+.+...||.++.       ..+..+......|..+...+-..+-...++-..|=+.|-.
T Consensus        35 k~Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EYq~LlnvKl~  114 (129)
T 3tnu_B           35 KHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQELMNTKLA  114 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666665       2334444444455555555555555555555555555544


Q ss_pred             H
Q 028818          122 L  122 (203)
Q Consensus       122 L  122 (203)
                      |
T Consensus       115 L  115 (129)
T 3tnu_B          115 L  115 (129)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=87.44  E-value=7.1  Score=28.87  Aligned_cols=46  Identities=13%  Similarity=0.272  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           64 SRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        64 ~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      ..|.+|+++-..|..+.+   +.-....++|.+|..|..+-...+..|-
T Consensus        27 mEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~LL   75 (81)
T 2jee_A           27 MEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQALL   75 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444443   1112355566777777777666666654

>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=86.79  E-value=4.9  Score=27.52  Aligned_cols=33  Identities=30%  Similarity=0.491  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (203)
                      ...++...|..+|..|...|..|...+..|..+
T Consensus        27 ~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~~   59 (63)
T 2wt7_A           27 TLQAETDQLEDEKSALQTEIANLLKEKEKLEFI   59 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555667777778888888888887777654

>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=86.52  E-value=0.93  Score=34.46  Aligned_cols=48  Identities=13%  Similarity=0.227  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           62 KDSRIAELQSQIESIYSSLS--DKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        62 Kd~~i~~Lq~r~s~Le~~L~--~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      +...|.|+-++++.++..--  -+++...++++||.+|+..-...++.|.
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            34556777777776654433  7888999999999999999999998875

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=86.42  E-value=1.1  Score=40.67  Aligned_cols=37  Identities=14%  Similarity=0.346  Sum_probs=20.5

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSS   79 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~   79 (203)
                      +++..|+.|+..|+++..+.++.|++++.++..++..
T Consensus         3 ~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~   39 (403)
T 4etp_A            3 SKIAALKEKIAALKEKIAALKEKIKDTELGMKELNEI   39 (403)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555666666666666666666666665554444433

>1wt6_A Myotonin-protein kinase; coiled-coil, kinase activation, DMPK, molecular replacement, transferase; 1.60A {Homo sapiens}

Probab=86.34  E-value=6.3  Score=29.31  Aligned_cols=56  Identities=21%  Similarity=0.260  Sum_probs=35.2

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           45 VSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKL  108 (203)
Q Consensus        45 Vs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL  108 (203)
                      -|.||+||..       |+..-.+| .++...-..++.+|+.+...|..|..|...|...++-|
T Consensus        16 QSALeaEIqA-------KQ~i~EEL-s~vr~~ni~~eskL~eae~rn~eL~~e~~~l~~~~eel   71 (81)
T 1wt6_A           16 QEALEEEVLT-------RQSLSREM-EAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELL   71 (81)
T ss_dssp             HHHHHHHHHH-------HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-------HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556666543       44444455 45554444555888899999998888866666555554

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=86.26  E-value=1.5  Score=32.71  Aligned_cols=34  Identities=38%  Similarity=0.569  Sum_probs=22.3

Q ss_pred             HHHHhhhhhHHH--------------HHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESE--------------HSALRSQLAEKDSRIAELQSQI   73 (203)
Q Consensus        40 A~atRVs~LE~E--------------~~~LR~~LaEKd~~i~~Lq~r~   73 (203)
                      -+.-||+.||+|              +..|+++|..|+..|.-|+.++
T Consensus        30 ~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l   77 (81)
T 3qh9_A           30 HLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQL   77 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            456677777754              6666777777777666666554

>1gk4_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, stutter; 2.3A {Homo sapiens} SCOP: h.1.20.1

Probab=85.86  E-value=7.9  Score=27.81  Aligned_cols=67  Identities=18%  Similarity=0.267  Sum_probs=46.6

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS  113 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva  113 (203)
                      ++.+....||..+..+.....   ..+.+++.++..+|.+|+    .+..+......|-..|-+.=-+|--+++
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   346788888999999888    6777777777777777776556655543

>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=85.83  E-value=4.1  Score=31.53  Aligned_cols=49  Identities=29%  Similarity=0.474  Sum_probs=32.0

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENE   99 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~   99 (203)
                      -+-.|++.||.|..+||..-.+=...|.+|+..+.           ....+|..|..||.
T Consensus        41 ~LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~eve-----------rL~~ENq~L~~e~~   89 (104)
T 3s9g_A           41 ELEKSLSRMEDENNRLRLESKRLDARVRELELELD-----------RLRAENLQLLTENE   89 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHH-----------HHHHHHHHHHHHHH
Confidence            56778999999999999885555555555554433           44445555555554

>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=85.52  E-value=4.6  Score=30.88  Aligned_cols=24  Identities=25%  Similarity=0.430  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           86 QAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      .+.++..+|+.|...|-..|++|.
T Consensus        72 ~~~~~~e~Lq~E~erLr~~v~~lE   95 (100)
T 1go4_E           72 RLREDHSQLQAECERLRGLLRAME   95 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            455667777777776666665543

>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=85.32  E-value=4.9  Score=31.87  Aligned_cols=34  Identities=15%  Similarity=0.296  Sum_probs=15.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           48 LESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        48 LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ||.+...-.+-|.+++.....-..-|..|-..|-
T Consensus        30 Lq~qLTqAQe~l~~~eaQAaTCNqTV~tL~~SL~   63 (121)
T 3mq7_A           30 LQQELTEAQKGFQDVEAQAATANHTVMALMASLD   63 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444444443

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=85.06  E-value=11  Score=28.73  Aligned_cols=70  Identities=16%  Similarity=0.244  Sum_probs=43.2

Q ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           43 TRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS----DKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        43 tRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~----~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      .+++..+.|+.+|+..|.+-...-...+.....++.+|-    +-..+|..+...-..++..+...+.+|...+
T Consensus        19 ~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTasLFeEAN~MVa~ar~e~~~~e~kn~~L~~qL   92 (97)
T 2eqb_B           19 RELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQL   92 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566667788888888888666666666666666666665    3344555555555555555555555555444

>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=84.49  E-value=9.7  Score=27.68  Aligned_cols=38  Identities=21%  Similarity=0.123  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 028818           90 DKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (203)
Q Consensus        90 e~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (203)
                      ...+...+...|...+..|...+..|+.-.+.|-+.+.
T Consensus        65 ~i~~~~~~l~~l~~~i~~l~~~i~~l~~~~~~l~~~~~  102 (112)
T 1l8d_A           65 LLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIK  102 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455566666666666666666666665555544443

>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=84.46  E-value=18  Score=33.88  Aligned_cols=73  Identities=10%  Similarity=0.166  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 028818           55 LRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQAD-KERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (203)
Q Consensus        55 LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee-~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (203)
                      |+..+.+++..+.++...+......|........+. +.+....-..|...+..|...|.+||..-.+++....
T Consensus       126 Iq~slk~~Q~Qi~en~n~~~~~~~~~e~~~~~i~~~~~~~~~~~i~~L~~~~~~l~~ki~~l~~~~~~~~~~~~  199 (464)
T 1m1j_B          126 IDNKLVKTQKQRKDNDIILSEYNTEMELHYNYIKDNLDNNIPSSLRVLRAVIDSLHKKIQKLENAIATQTDYCR  199 (464)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhhcccccccchhhHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            455556666666666655555555554111111111 1123344556677788888888888888887776554

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=84.17  E-value=2.8  Score=28.90  Aligned_cols=36  Identities=22%  Similarity=0.346  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 028818           83 KLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (203)
Q Consensus        83 rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (203)
                      +.....++...|..+|+.|...|..|.+++.-|..+
T Consensus        24 ~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~l   59 (63)
T 1ci6_A           24 EQEALTGECKELEKKNEALKERADSLAKEIQYLKDL   59 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555667788888888888898888888887543

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=83.37  E-value=18  Score=29.89  Aligned_cols=79  Identities=19%  Similarity=0.215  Sum_probs=37.9

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 028818           44 RVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS---DKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRK  120 (203)
Q Consensus        44 RVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~---~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk  120 (203)
                      -++.+|.-++.|+.++.-=...-..|++.+..|..+|.   .-..+..+.+..|+....+|..-++.+.--.+|++.=+|
T Consensus        42 ~~~~~E~~~rELq~~~~~L~~~k~~Leke~~~LQa~L~qEr~~r~q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r  121 (168)
T 3o0z_A           42 SISQLESLNRELQERNRILENSKSQTDKDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERK  121 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555444444555555555555555   112233333344444444444444444444444444444


Q ss_pred             HH
Q 028818          121 TL  122 (203)
Q Consensus       121 ~L  122 (203)
                      +|
T Consensus       122 ~L  123 (168)
T 3o0z_A          122 EA  123 (168)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=83.26  E-value=1.6  Score=35.42  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=25.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           47 DLESEHSALRSQLAEKDSRIAELQSQIESIYS   78 (203)
Q Consensus        47 ~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~   78 (203)
                      .||..++.|...|..|+..|.+|++|+..+|.
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   35 (198)
T 4ghu_A            4 LLESQLSRHDQMLSVHDIRLADMDLRFQVLET   35 (198)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            67888888888888888888888877776664

>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=82.80  E-value=11  Score=27.18  Aligned_cols=65  Identities=11%  Similarity=0.156  Sum_probs=37.9

Q ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 028818           41 ISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDV  112 (203)
Q Consensus        41 ~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDv  112 (203)
                      +.+..+.||.-+..+....   ...+..++..+..+|.+|+    .+..+......|-..|-+.=-+|--++
T Consensus         8 L~~q~~~Le~~l~e~E~~~---~~~l~~~q~~i~~lE~el~----~~r~e~~~ql~EYq~LlnvK~~Le~EI   72 (86)
T 1x8y_A            8 LQCQLAAKEAKLRDLEDSL---ARERDTSRRLLAEKEREMA----EMRARMQQQLDEYQELLDIKLALDMEI   72 (86)
T ss_dssp             ----CTTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence            3444455665555555543   3356667777777777776    666666666667666666555555544

>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=82.71  E-value=4.7  Score=27.40  Aligned_cols=34  Identities=21%  Similarity=0.374  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           84 LGQAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        84 L~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      +....++...|..+|+.|...|..|...++.|..
T Consensus        24 ~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk~   57 (62)
T 1jnm_A           24 IARLEEKVKTLKAQNSELASTANMLREQVAQLKQ   57 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455566777888888888888888777643

>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=82.37  E-value=4  Score=36.50  Aligned_cols=42  Identities=17%  Similarity=0.103  Sum_probs=30.5

Q ss_pred             HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           40 AISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        40 A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      ++..++++|..|+.+|...+...+..|..|+.++..++..++
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            355678888888888888888888888888877776655443

>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=82.31  E-value=9.2  Score=25.77  Aligned_cols=32  Identities=28%  Similarity=0.357  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEV  117 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~  117 (203)
                      ...++...|..+|..|...|..|..++..|..
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            33444556667777777777777777776654

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=82.27  E-value=12  Score=27.28  Aligned_cols=9  Identities=44%  Similarity=0.671  Sum_probs=4.5

Q ss_pred             HHhhhhhHH
Q 028818           42 STRVSDLES   50 (203)
Q Consensus        42 atRVs~LE~   50 (203)
                      ..||..||.
T Consensus         5 e~rv~~LEr   13 (83)
T 2xdj_A            5 EDRVTQLER   13 (83)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            345555554

>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=82.17  E-value=13  Score=35.92  Aligned_cols=59  Identities=24%  Similarity=0.291  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH---------------------HHHHHHHHHHhhc
Q 028818           68 ELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVS---------------------KLEVFRKTLVQSL  126 (203)
Q Consensus        68 ~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDva---------------------KLE~FKk~LmqSL  126 (203)
                      +|++++..|+..++    .-...+..|+.-.+.+...++||.-||+                     --|+.-|+|-|-.
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            45555555554444    1123334444444444444555554443                     2567889998855


Q ss_pred             cccc
Q 028818          127 KDDE  130 (203)
Q Consensus       127 q~d~  130 (203)
                      --|-
T Consensus       190 a~dL  193 (562)
T 3ghg_A          190 AKDL  193 (562)
T ss_dssp             TTCC
T ss_pred             hccc
Confidence            4443

>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=81.93  E-value=8  Score=28.01  Aligned_cols=66  Identities=15%  Similarity=0.246  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 028818           50 SEHSALRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNTVRKLQRDVSKLEVFRKTL  122 (203)
Q Consensus        50 ~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~L  122 (203)
                      .|+..||.+.+.....+.+++.++.       ..+.........|..|...+-..+....++-..|=+.|-.|
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            4666677766665555556555443       22234444455555555555555556666666665555443

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=81.92  E-value=5.4  Score=28.80  Aligned_cols=32  Identities=9%  Similarity=0.146  Sum_probs=16.9

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhhcccccC
Q 028818          100 ALTNTVRKLQRDVSKLEVFRKTLVQSLKDDED  131 (203)
Q Consensus       100 ~La~TvKkL~rDvaKLE~FKk~LmqSLq~d~~  131 (203)
                      .|..+|-+.++++++|..-=+.|.+.|++-.+
T Consensus        32 eLn~~v~~Qq~~Id~L~~ql~~L~~rl~~~~~   63 (78)
T 3efg_A           32 ELSEALADARLTGARNAELIRHLLEDLGKVRS   63 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTC-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            45556666666666666666666666655443

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=81.81  E-value=7.8  Score=28.39  Aligned_cols=43  Identities=19%  Similarity=0.356  Sum_probs=29.1

Q ss_pred             HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           39 IAISTRVSDLESEHSALRSQLAEKDSRIAELQSQIESIYSSLS   81 (203)
Q Consensus        39 ~A~atRVs~LE~E~~~LR~~LaEKd~~i~~Lq~r~s~Le~~L~   81 (203)
                      .-+..++..|..|+..||-++.+-...|..|++|-..+-..|-
T Consensus        23 ~~Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~rQrd~Y~dLD   65 (83)
T 2xdj_A           23 TQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQID   65 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566677777777777777777777777777766555544443

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=81.71  E-value=7.6  Score=28.77  Aligned_cols=33  Identities=33%  Similarity=0.468  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 028818           86 QAQADKERLSKENEALTNTVRKLQRDVSKLEVF  118 (203)
Q Consensus        86 ~a~ee~~kL~~E~~~La~TvKkL~rDvaKLE~F  118 (203)
                      ...++...|.+||..|-..|..|..+|..|..+
T Consensus        40 e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~Lr~l   72 (87)
T 1hjb_A           40 ETQHKVLELTAENERLQKKVEQLSRELSTLRNL   72 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455667889999999999999999998877543

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=81.14  E-value=4.5  Score=36.57  Aligned_cols=42  Identities=19%  Similarity=0.203  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcccccC
Q 028818           90 DKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKDDED  131 (203)
Q Consensus        90 e~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~d~~  131 (203)
                      +..+|.++...+...++.|+..+.+-|..+|.|-..+++-..
T Consensus        18 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~elkg   59 (403)
T 4etp_A           18 KIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQELRG   59 (403)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            333444444444444445555555666666666666665443

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=80.40  E-value=14  Score=26.67  Aligned_cols=46  Identities=17%  Similarity=0.311  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028818           55 LRSQLAEKDSRIAELQSQIESIYSSLSDKLGQAQADKERLSKENEALTNT  104 (203)
Q Consensus        55 LR~~LaEKd~~i~~Lq~r~s~Le~~L~~rL~~a~ee~~kL~~E~~~La~T  104 (203)
                      +-++|.+-.....+|++||..|+..|.    .+..+...+..|-..|..+
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            345566666667778888888887776    6666666666665555443

---

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	203
d1yf2a2	205	Bipartite methylase S protein MJ0130 {Methanocaldo	91.6
d1ydxa2	181	Bipartite methylase S protein MG438 {Mycoplasma ge	88.29
d1ydxa1	193	Bipartite methylase S protein MG438 {Mycoplasma ge	84.58
d1x4ta1	80	Pre-mRNA-splicing factor ISY1 homolog {Mouse (Mus	80.82

>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=91.60  E-value=0.17  Score=35.87  Aligned_cols=39  Identities=13%  Similarity=0.308  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhc
Q 028818           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSL  126 (203)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSL  126 (203)
                      .+++.+..+.-+.+-..+.++.+.+.+|+.+|+.|||.|
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            456666677777777888899999999999999999986

>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=88.29  E-value=0.46  Score=33.83  Aligned_cols=40  Identities=23%  Similarity=0.277  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcc
Q 028818           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLK  127 (203)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq  127 (203)
                      .+++.+..+--+.+-..+..+.+.+.+|+.+|+.|||.|=
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            4666777777778888999999999999999999999763

>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=84.58  E-value=0.95  Score=32.22  Aligned_cols=41  Identities=7%  Similarity=0.156  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhccc
Q 028818           88 QADKERLSKENEALTNTVRKLQRDVSKLEVFRKTLVQSLKD  128 (203)
Q Consensus        88 ~ee~~kL~~E~~~La~TvKkL~rDvaKLE~FKk~LmqSLq~  128 (203)
                      .+++.+..+--+.|-..+.++.+.+.+|+.+|+.|||.|=.
T Consensus       143 ~~eQ~~I~~~l~~ld~~i~~~~~~i~~l~~~~~~ll~~lft  183 (193)
T d1ydxa1         143 KNEQHAIANTLSVFDERLENLASLIEINRKLRDEYAHKLFS  183 (193)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            45555666666677778888889999999999999997643

>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=80.82  E-value=1.1  Score=31.52  Aligned_cols=49  Identities=12%  Similarity=0.194  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028818           61 EKDSRIAELQSQIESIYSSLS--DKLGQAQADKERLSKENEALTNTVRKLQ  109 (203)
Q Consensus        61 EKd~~i~~Lq~r~s~Le~~L~--~rL~~a~ee~~kL~~E~~~La~TvKkL~  109 (203)
                      =+...|.|+-.+++.+...--  .+++...++.+||.+|+..-...++.|.
T Consensus        23 wR~~iikEI~~kvs~Iqn~~L~e~~IRdLNDeINkL~reK~~WE~rI~eLG   73 (80)
T d1x4ta1          23 WRRQIIGEISKKVAQIQNAGLGEFRIRDLNDEINKLLREKGHWEVRIKELG   73 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            344566777777776654332  7888999999999999999999998875