Citrus Sinensis ID: 038837

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------
Protein Sequence
MAAAAHLTLLLVILFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHccHHHHHHHHHHcHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MAAAAHLTLLLVILFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRkvngksnyiEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRknnfdihnleskaldaeDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFsekhlpkltgmlvpylpgkgsILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Flexible Loop (DISEMBL)
MAAAAHLTLLLVILFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEesirkvngksnyIEERDKLVDDMTNKIHHLQSllskikddssRAEERLNALEEEIRLLWAASRKNNFDIHNLeskaldaedRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Low Complexity Region (SEG)
MAAAAHLTLLLVILFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSraeerlnaleeeirllWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Disordered region (IsUnstruct)
****AHLTLLLVILFWSFTLTSQ*******HLIAELQDAKLKIAGLETMLEESIRKV*****YI******V******IH**********************LEEEIRLLWAASRKNNFDIHNLE************VSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLS******
Disordered Region (DISOPRED)
***AAHLTLLLVIL***********************************************************************************************************************************************************************************HLPKLTGML*P*******I**SFMSQVQHQFKRFFLAFKK******************TAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Disordered Region (DISEMBL)
MAAAAHLTLLLVILFWSFTLT**********LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Disordered Region (DISPRO)
M***AHLTLLLVILFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAAAHLTLLLVILFWSFTLTSQNQQHSQQHLIAExxxxxxxxxxxxxxxxxxxxxVNGKSNYIEERDKLVDDMTNKIHHLQSLxxxxxxxxxxxxxxxxxxxxxIRLLWAASRKNNFDxxxxxxxxxxxxxxxxxxxxxxxxxxxxVTEQWIQxxxxxxxxxxxxxxxxxxxxxLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSSQFSKL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	287
297740426	247	unnamed protein product [Vitis vinifera]	0.857	0.995	0.638	3e-84
147778581	433	hypothetical protein VITISV_005069 [Viti	0.905	0.600	0.610	6e-83
358248291	274	uncharacterized protein LOC100795179 pre	0.881	0.923	0.492	2e-62
357446727	276	hypothetical protein MTR_2g014440 [Medic	0.850	0.884	0.510	2e-62
297851298	276	hypothetical protein ARALYDRAFT_473060 [	0.944	0.981	0.444	5e-58
449457763	291	PREDICTED: uncharacterized protein LOC10	0.909	0.896	0.475	1e-57
449484542	291	PREDICTED: uncharacterized protein LOC10	0.909	0.896	0.475	1e-57
79354936	277	uncharacterized protein [Arabidopsis tha	0.944	0.978	0.446	1e-57
44917437	277	At1g28410 [Arabidopsis thaliana] gi|4577	0.944	0.978	0.446	3e-57
255536731	529	conserved hypothetical protein [Ricinus	0.871	0.472	0.478	6e-57

>gi|297740426|emb|CBI30608.3| unnamed protein product [Vitis vinifera]

 Score =  317 bits (812), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 157/246 (63%), Positives = 194/246 (78%)

Query: 40  KLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERL 99
           KL+I  LET++EE ++  N K  Y+++R+KL+++ ++KIHHLQS+L  IK DSS A ERL
Sbjct: 2   KLRITQLETVMEEIVQNFNEKYLYLKQREKLIEEFSHKIHHLQSVLYSIKGDSSHANERL 61

Query: 100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLE 159
            ALEEE+RLLWAASRKNNFD+H LESKA DAEDRL  VS QVE+++++VTEQWIQIQ LE
Sbjct: 62  AALEEEVRLLWAASRKNNFDLHTLESKAQDAEDRLNVVSKQVEQLADVVTEQWIQIQQLE 121

Query: 160 QALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSILISFMSQ 219
           QAL MAELRA   +RQ+   RCTFLKF+ +    HL K+ GML PYL G+GS L S+ S+
Sbjct: 122 QALQMAELRALKAKRQVSMMRCTFLKFINNLFGNHLEKVFGMLDPYLFGRGSTLSSYKSR 181

Query: 220 VQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPILAAWVL 279
             HQ KR + A K +HHELQGFIKQEM K + TAALAN+ELVFFVASALITFPI+ AW+L
Sbjct: 182 FLHQLKRMWSAAKAYHHELQGFIKQEMEKYEFTAALANDELVFFVASALITFPIMGAWML 241

Query: 280 LSSQFS 285
           +SSQF 
Sbjct: 242 VSSQFC 247

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147778581|emb|CAN60307.1| hypothetical protein VITISV_005069 [Vitis vinifera]

 Score =  313 bits (802), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 160/262 (61%), Positives = 199/262 (75%), Gaps = 2/262 (0%)

Query: 19  TLTSQNQQHSQQHL--IAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTN 76
            L SQ+   +QQ +  I ELQ+ KL+I  LET++EE ++  N K  Y+++R+KL+++ ++
Sbjct: 27  PLNSQSPCGNQQGVNSICELQEMKLRITQLETVMEEIVQNFNEKYLYLKQREKLIEEFSH 86

Query: 77  KIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEE 136
           KIHHLQS+L  IK DSS A ERL ALEEE+RLLWAASRKNNFD+H LESKA DAEDRL  
Sbjct: 87  KIHHLQSVLYSIKGDSSHANERLAALEEEVRLLWAASRKNNFDLHTLESKAQDAEDRLNM 146

Query: 137 VSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLP 196
           VS QVE++++ VTEQWIQIQ LEQAL MAELRA   +RQ+   RCTFLKF+ +    HL 
Sbjct: 147 VSKQVEQLADXVTEQWIQIQQLEQALQMAELRALKAKRQVSMMRCTFLKFINNLFGNHLE 206

Query: 197 KLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALA 256
           K+ GML PYL G+GS L S+ S+  HQ KR + A K +HHELQGFIKQE  K + TAALA
Sbjct: 207 KVFGMLDPYLFGRGSTLSSYKSRFLHQLKRMWSAAKAYHHELQGFIKQEXEKYEFTAALA 266

Query: 257 NEELVFFVASALITFPILAAWV 278
           N+ELVFFVASALITFPI+ AW+
Sbjct: 267 NDELVFFVASALITFPIMGAWI 288

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248291|ref|NP_001239856.1| uncharacterized protein LOC100795179 precursor [Glycine max] gi|255644426|gb|ACU22718.1| unknown [Glycine max]

 Score =  245 bits (626), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 127/258 (49%), Positives = 180/258 (69%), Gaps = 5/258 (1%)

Query: 25  QQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSL 84
           Q     H  +++    LKIA LE++LEES  ++  +  ++EE ++ +++++ KIHHL S 
Sbjct: 22  QTQPNYHYASQISQINLKIAHLESVLEESNTRLKERDAHLEECERRMNELSEKIHHLHST 81

Query: 85  LSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKM 144
           LS +K DS  +E +  ALEEE++LLW   R+NNFD+H LESKA DAE++LEE++ +VEKM
Sbjct: 82  LSAMKADSLHSERQYTALEEEVQLLWHTLRRNNFDLHILESKAQDAEEKLEELTSRVEKM 141

Query: 145 SEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVP 204
            +IV EQWIQ+QHLEQALH+ ++R    QR     RCTF+KF+       L  L   L  
Sbjct: 142 GDIVNEQWIQVQHLEQALHITKMRTLKAQRLTSVTRCTFMKFINVL----LDDLRA-LHS 196

Query: 205 YLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFV 264
           Y+ G+ +I+ S +SQ   Q KR     KK+HH+LQGFIK  M +N+LTA++AN+ELVFF+
Sbjct: 197 YVFGERTIVSSLISQTLDQLKRCSSLTKKYHHQLQGFIKDLMERNELTASIANDELVFFL 256

Query: 265 ASALITFPILAAWVLLSS 282
           ASALITFP+++AW+LLSS
Sbjct: 257 ASALITFPLMSAWMLLSS 274

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357446727|ref|XP_003593639.1| hypothetical protein MTR_2g014440 [Medicago truncatula] gi|355482687|gb|AES63890.1| hypothetical protein MTR_2g014440 [Medicago truncatula]

 Score =  245 bits (625), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 127/249 (51%), Positives = 179/249 (71%), Gaps = 5/249 (2%)

Query: 34  AELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSS 93
           +++    LKIA LE++LE++ +K+  +  Y++E +  ++ +++KIHHL S LS IKDDS 
Sbjct: 33  SQINQINLKIAHLESVLEQTNKKLTERDLYLQEFENRINHISDKIHHLHSTLSSIKDDSL 92

Query: 94  RAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWI 153
            AE R+ AL+EE++LLW A RKNNFD+H L+SKA D E  LEEV+ +VEKMS IVTEQWI
Sbjct: 93  HAETRIKALDEEVQLLWDALRKNNFDLHILKSKAEDNEKSLEEVTSRVEKMSGIVTEQWI 152

Query: 154 QIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPYLPGKGSIL 213
           Q+QHLEQALH+A++RA   Q Q+   RCTFLKF+ +            +  ++ G+  I+
Sbjct: 153 QVQHLEQALHIAKMRALKAQWQVSLRRCTFLKFINNIYHD-----LRAVESFVFGERPIV 207

Query: 214 ISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVASALITFPI 273
            SF+S+    FKR     KK+HH+LQG +K  M +N+LTA+LAN+ELVFF+ SALITFP+
Sbjct: 208 GSFISKALDYFKRCCSMTKKYHHQLQGSVKDLMKRNELTASLANDELVFFLVSALITFPL 267

Query: 274 LAAWVLLSS 282
           ++AW+LLSS
Sbjct: 268 MSAWMLLSS 276

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297851298|ref|XP_002893530.1| hypothetical protein ARALYDRAFT_473060 [Arabidopsis lyrata subsp. lyrata] gi|297339372|gb|EFH69789.1| hypothetical protein ARALYDRAFT_473060 [Arabidopsis lyrata subsp. lyrata]

 Score =  230 bits (587), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 124/279 (44%), Positives = 185/279 (66%), Gaps = 8/279 (2%)

Query: 6   HLTLLLVILFWSFTLTSQNQQ-HSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYI 64
           HL  L  I+     L+S+ QQ  S Q+L+ +L  AKL+I  LE +LE +I+K++ K+ Y+
Sbjct: 4   HLAALFFIITPLCVLSSEVQQIGSNQNLVNDLDAAKLRIPQLEAVLEATIQKLDAKTLYL 63

Query: 65  EERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLE 124
           +ER+KL+    ++IH LQ+     K      ++R++ LEEE++LLWAA R  NF++H LE
Sbjct: 64  KEREKLIQVAESQIHDLQAASYIDKSGLPLVQKRISELEEEVKLLWAALRTTNFELHVLE 123

Query: 125 SKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFL 184
            KA +A+D+L+  +L+VE+M+E+VTEQWIQ+QHLEQ      +R  N +R    +RC F+
Sbjct: 124 DKAREAKDKLKAKALEVEQMTEVVTEQWIQVQHLEQ------MREFNNRRHHTPSRCPFV 177

Query: 185 KFVKDFSEKHLPKLTGMLVPYLPGKGSILI-SFMSQVQHQFKRFFLAFKKFHHELQGFIK 243
           K + D   KHLPK+      +  GK  + +  +++Q   Q K  + A  K+HH+LQGFI+
Sbjct: 178 KLMSDIQRKHLPKVDEAFDIHWKGKKVLSVQPYLTQALSQLKSLWAAITKYHHQLQGFIE 237

Query: 244 QEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSS 282
            EM + ++TAALAN E+VFF+ASALITFP+  AW+LLSS
Sbjct: 238 HEMERTEITAALANREVVFFMASALITFPVFGAWILLSS 276

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457763|ref|XP_004146617.1| PREDICTED: uncharacterized protein LOC101213056 [Cucumis sativus]

 Score =  229 bits (584), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 124/261 (47%), Positives = 176/261 (67%)

Query: 26  QHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLL 85
           Q     LI EL   KL+I+ LE++LEES + +  KSN ++ ++KL++D+++KI +L+S +
Sbjct: 31  QSGNDALIHELLGIKLRISHLESVLEESKQNLTEKSNELKAQEKLIEDVSHKIQYLESAI 90

Query: 86  SKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMS 145
           S +K   S  +ER+  LE+E+R LW A RKNNFDIH L++K  +AE++LEEV+ QVEK S
Sbjct: 91  SDMKRKISSDDERIAVLEDEVRRLWDAKRKNNFDIHLLKAKVQEAEEKLEEVTSQVEKKS 150

Query: 146 EIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPY 205
            I++EQWIQI+HLEQAL M++++A  V++Q    RCTF+K V       L K    L  +
Sbjct: 151 SIISEQWIQIRHLEQALEMSKIQALKVRQQFALTRCTFVKLVNTRFANQLQKAFQTLNHH 210

Query: 206 LPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVA 265
           +  K   L S ++   H F+R +   KK+HHELQ  IKQEM +N+  A LAN EL+FF+A
Sbjct: 211 VFSKVPTLSSRVTGAIHYFQRVYEEAKKYHHELQRLIKQEMERNEYAAHLANPELIFFLA 270

Query: 266 SALITFPILAAWVLLSSQFSK 286
           SAL  FPI  AW+ LSS FS+
Sbjct: 271 SALAIFPIFGAWMFLSSWFSR 291

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449484542|ref|XP_004156911.1| PREDICTED: uncharacterized protein LOC101232017 [Cucumis sativus]

 Score =  229 bits (583), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 124/261 (47%), Positives = 176/261 (67%)

Query: 26  QHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLL 85
           Q     LI EL   KL+I+ LE++LEES + +  KSN ++ ++KL++D+++KI +L+S +
Sbjct: 31  QSGNDALIHELLGIKLRISHLESVLEESKQNLTEKSNELKAQEKLIEDVSHKIQYLESAI 90

Query: 86  SKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMS 145
           S +K   S  +ER+  LE+E+R LW A RKNNFDIH L++K  +AE++LEEV+ QVEK S
Sbjct: 91  SDMKRKISSDDERIAVLEDEVRRLWDAKRKNNFDIHLLKAKVQEAEEKLEEVTSQVEKKS 150

Query: 146 EIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLTGMLVPY 205
            I++EQWIQI+HLEQAL M++++A  V++Q    RCTF+K V       L K    L  +
Sbjct: 151 SIISEQWIQIRHLEQALEMSKIQALKVRQQFALTRCTFVKLVNTRFANQLQKAFQTLNHH 210

Query: 206 LPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEELVFFVA 265
           +  K   L S ++   H F+R +   KK+HHELQ  IKQEM +N+  A LAN EL+FF+A
Sbjct: 211 VFSKVPTLSSRVTGAIHYFQRVYEEAKKYHHELQRLIKQEMERNEYAAHLANPELIFFLA 270

Query: 266 SALITFPILAAWVLLSSQFSK 286
           SAL  FPI  AW+ LSS FS+
Sbjct: 271 SALAIFPIFGAWMFLSSWFSR 291

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79354936|ref|NP_174163.2| uncharacterized protein [Arabidopsis thaliana] gi|332192853|gb|AEE30974.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  229 bits (583), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 125/280 (44%), Positives = 185/280 (66%), Gaps = 9/280 (3%)

Query: 6   HLTLLLVILFWSFTLTSQNQQH--SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNY 63
           HL  L  I+   F  +SQ QQ   S Q+LI +L  AKL+I+ LE +LE +I+K++GK+ Y
Sbjct: 4   HLAALFFIISPLFVFSSQVQQQIGSNQNLINDLDSAKLRISQLEAVLEATIQKLDGKTLY 63

Query: 64  IEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNL 123
           ++ER+KL+     +I  LQS     K      ++R++ LEEE++LLWAA R  NF++H L
Sbjct: 64  LKEREKLIQVAETQILDLQSASYIDKSGLPLVQKRISELEEEVKLLWAALRTTNFELHVL 123

Query: 124 ESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTF 183
           E KA +A+++L+  +L+VE+M+E+VTEQWIQ+QHLEQ      +R  N +R    +RC F
Sbjct: 124 EDKAREAKNKLKAKALEVEQMTEVVTEQWIQVQHLEQ------MREFNNRRHHTPSRCPF 177

Query: 184 LKFVKDFSEKHLPKLTGMLVPYLPGKGSILI-SFMSQVQHQFKRFFLAFKKFHHELQGFI 242
           +K + D   KHLPK+      +  GK  + +  ++++   Q K  + A  K+HH+LQGFI
Sbjct: 178 VKLMSDIQRKHLPKVDEAFDIHWKGKKVLSVQPYLTKALSQLKSLWAAVTKYHHQLQGFI 237

Query: 243 KQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSS 282
           + EM + ++TAALAN E+VFF+ASALITFP+  AW+LLSS
Sbjct: 238 EHEMERTEITAALANREVVFFMASALITFPVFGAWMLLSS 277

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|44917437|gb|AAS49043.1| At1g28410 [Arabidopsis thaliana] gi|45773882|gb|AAS76745.1| At1g28410 [Arabidopsis thaliana]

 Score =  228 bits (580), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 125/280 (44%), Positives = 184/280 (65%), Gaps = 9/280 (3%)

Query: 6   HLTLLLVILFWSFTLTSQNQQH--SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNY 63
           HL  L  I+   F  +SQ QQ   S Q+LI +L  AKL+I+ LE +LE +I+K++GK+ Y
Sbjct: 4   HLAALFFIISPLFVFSSQVQQQIGSNQNLINDLDSAKLRISQLEAVLEATIQKLDGKTLY 63

Query: 64  IEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNL 123
           ++ER+KL+     +I  LQS     K      ++R + LEEE++LLWAA R  NF++H L
Sbjct: 64  LKEREKLIQVAETQILDLQSASYIDKSGLPLVQKRTSELEEEVKLLWAALRTTNFELHVL 123

Query: 124 ESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTF 183
           E KA +A+++L+  +L+VE+M+E+VTEQWIQ+QHLEQ      +R  N +R    +RC F
Sbjct: 124 EDKAREAKNKLKAKALEVEQMTEVVTEQWIQVQHLEQ------MREFNNRRHHTPSRCPF 177

Query: 184 LKFVKDFSEKHLPKLTGMLVPYLPGKGSILI-SFMSQVQHQFKRFFLAFKKFHHELQGFI 242
           +K + D   KHLPK+      +  GK  + +  ++++   Q K  + A  K+HH+LQGFI
Sbjct: 178 VKLMSDIQRKHLPKVDEAFDIHWKGKKVLSVQPYLTKALSQLKSLWAAVTKYHHQLQGFI 237

Query: 243 KQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSS 282
           + EM + ++TAALAN E+VFF+ASALITFP+  AW+LLSS
Sbjct: 238 EHEMERTEITAALANREVVFFMASALITFPVFGAWMLLSS 277

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255536731|ref|XP_002509432.1| conserved hypothetical protein [Ricinus communis] gi|223549331|gb|EEF50819.1| conserved hypothetical protein [Ricinus communis]

 Score =  226 bits (577), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 121/253 (47%), Positives = 167/253 (66%), Gaps = 3/253 (1%)

Query: 20  LTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIH 79
           LTSQ+Q  +  HL+ +L +AKLK+A  E+ LEE ++K   K  Y+++++K + D    + 
Sbjct: 22  LTSQDQHSTNHHLLTQLHEAKLKVAQFESSLEEIVQKAEAKELYLKKQEKQIQDSEKTLS 81

Query: 80  HLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSL 139
            L   LS +K  S   +E+++ALEEE+R+LWA SRKNNFDIH L+SKA DAEDRL+ V  
Sbjct: 82  DLHFTLSNLKSGSLLTDEKVHALEEEVRVLWATSRKNNFDIHVLQSKAQDAEDRLQVVHS 141

Query: 140 QVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPKLT 199
           QVEKM++IV+EQWIQIQ  E AL + ++     QR++   RC+FLKF+ D S K+LP   
Sbjct: 142 QVEKMADIVSEQWIQIQQFEHALQLRQMTMLKAQRRVGPPRCSFLKFMNDLSSKYLP--- 198

Query: 200 GMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMVKNKLTAALANEE 259
             L P          S++ Q  +Q +RFF   K+ HHELQG I+QEM +++LTA LAN+E
Sbjct: 199 SSLRPLGLNSFGNWRSYIFQTLNQLRRFFSTMKESHHELQGLIRQEMERHELTARLANKE 258

Query: 260 LVFFVASALITFP 272
           LVFFV    I FP
Sbjct: 259 LVFFVKVKSIDFP 271

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	287
TAIR|locus:2032520	277	AT1G28410 "AT1G28410" [Arabido	0.944	0.978	0.421	1.5e-51
TAIR|locus:2128166	437	AT4G31340 "AT4G31340" [Arabido	0.578	0.379	0.248	5.9e-14
TAIR|locus:2061067	440	AT2G24420 [Arabidopsis thalian	0.337	0.220	0.247	2.6e-13

TAIR|locus:2032520 AT1G28410 "AT1G28410" [Arabidopsis thaliana (taxid:3702)]

 Score = 535 (193.4 bits), Expect = 1.5e-51, P = 1.5e-51
 Identities = 118/280 (42%), Positives = 172/280 (61%)

Query:     6 HLTLLLVILFWSFTLTSQNQQH--SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNY 63
             HL  L  I+   F  +SQ QQ   S Q+LI +L  AKL+I+ LE +LE +I+K++GK+ Y
Sbjct:     4 HLAALFFIISPLFVFSSQVQQQIGSNQNLINDLDSAKLRISQLEAVLEATIQKLDGKTLY 63

Query:    64 IEERDKLVDDMTNKIHHLQSLLSKIKDDSSXXXXXXXXXXXXXXXXWAASRKNNFDIHNL 123
             ++ER+KL+     +I  LQS     K                    WAA R  NF++H L
Sbjct:    64 LKEREKLIQVAETQILDLQSASYIDKSGLPLVQKRISELEEEVKLLWAALRTTNFELHVL 123

Query:   124 ESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTF 183
             E KA +A+++L+  +L+VE+M+E+VTEQWIQ+QHLEQ      +R  N +R    +RC F
Sbjct:   124 EDKAREAKNKLKAKALEVEQMTEVVTEQWIQVQHLEQ------MREFNNRRHHTPSRCPF 177

Query:   184 LKFVKDFSEKHLPKLTGMLVPYLPGKGSILIS-FMSQVQHQFKRFFLAFKKFHHELQGFI 242
             +K + D   KHLPK+      +  GK  + +  ++++   Q K  + A  K+HH+LQGFI
Sbjct:   178 VKLMSDIQRKHLPKVDEAFDIHWKGKKVLSVQPYLTKALSQLKSLWAAVTKYHHQLQGFI 237

Query:   243 KQEMVKNKLTAALANEELVFFVASALITFPILAAWVLLSS 282
             + EM + ++TAALAN E+VFF+ASALITFP+  AW+LLSS
Sbjct:   238 EHEMERTEITAALANREVVFFMASALITFPVFGAWMLLSS 277

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2128166 AT4G31340 "AT4G31340" [Arabidopsis thaliana (taxid:3702)]

 Score = 126 (49.4 bits), Expect = 5.9e-14, Sum P(2) = 5.9e-14
 Identities = 45/181 (24%), Positives = 84/181 (46%)

Query:     1 MAAAAHLTLLLV-ILFWSFTLTSQNQQHSQQHLIAE------LQDAKLKIAGLETMLEES 53
             MAAA  + LLL+ +LF +      ++    +   ++      L     KI  LE+ ++E 
Sbjct:     1 MAAAKLVALLLLALLFTTSVFADADEPEVSEAAGSDGSSKIHLDQLNAKIRALESQIDEK 60

Query:    54 IRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSXXXXXXXXXXXXXXXXWAAS 113
              R+V GK   + E++KL+ +  +KI  LQ+ +S ++   S                    
Sbjct:    61 TREVQGKDEVVAEKEKLLKEREDKIASLQTEVSSLQKKGSSDSAKQLGKAQARADELEKQ 120

Query:   114 ---RKN-----NFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMA 165
                 KN     N +  + E++  +AE +L E++  ++K+ +   EQ  +I  LE+A+ +A
Sbjct:   121 VEVLKNFLEQKNKEKDSTEARTNEAEKKLRELNSSLDKLQKTNEEQKNKIGKLERAIKIA 180

Query:   166 E 166
             E
Sbjct:   181 E 181

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0006007 "glucose catabolic process" evidence=RCA

GO:0042732 "D-xylose metabolic process" evidence=RCA

TAIR|locus:2061067 AT2G24420 [Arabidopsis thaliana (taxid:3702)]

 Score = 125 (49.1 bits), Expect = 2.6e-13, Sum P(2) = 2.6e-13
 Identities = 24/97 (24%), Positives = 51/97 (52%)

Query:   188 KDFSEKHLPKLTGMLVPYLPGKGSILISFMSQVQHQFKRFFLAFKKFHHELQGFIKQEMV 247
             K FS+ ++ ++     P++    + +  + ++  H +K F  +   +HH+LQ  ++ ++ 
Sbjct:   318 KKFSKPYVDQVATATKPHVDKVRATMKPYTTKTVHYYKEFLESASTYHHQLQANVESKLK 377

Query:   248 KNKLTAALANEELVFFVASALITFPILAAWVLLSSQF 284
              ++L    A +E ++F ASAL+  PI   +  L S F
Sbjct:   378 SHELLEPFATKEFIWFAASALLALPIFIVYKFLCSLF 414

GO:0005576 "extracellular region" evidence=ISM

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

---

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: GSVIVG00003052001 SubName- Full=Chromosome chr10 scaffold_138, whole genome shotgun sequence; (236 aa) (Vitis vinifera)

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	287
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-06
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	2e-05
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	3e-05
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	3e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.003
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.003
COG1579	239	COG1579, COG1579, Zn-ribbon protein, possibly nucl	0.003

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

 Score = 47.4 bits (113), Expect = 5e-06
 Identities = 33/156 (21%), Positives = 78/156 (50%)

Query: 21  TSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHH 80
           +S  Q+   + L  EL + + ++  LE  L+    ++    + +EE  + ++++  ++  
Sbjct: 661 SSLAQKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEE 720

Query: 81  LQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQ 140
           L+  L+ ++++  + + RL  LEEE+  L     +    +  LE +    E+ L ++  +
Sbjct: 721 LKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEE 780

Query: 141 VEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQL 176
           +E++ E       +++ LE+ L  AE R   ++R+L
Sbjct: 781 IEELEEKRQALQEELEELEEELEEAERRLDALEREL 816

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 36/149 (24%), Positives = 68/149 (45%)

Query: 32  LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDD 91
           L  EL++ + ++   E  LEE   ++      +EE    V ++  +I  LQ  L  + ++
Sbjct: 237 LREELEELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANE 296

Query: 92  SSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQ 151
            SR E++   L E +  L     +    +  LESK  +  + L E+  ++E++ E +   
Sbjct: 297 ISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESL 356

Query: 152 WIQIQHLEQALHMAELRAANVQRQLMYAR 180
             +++ LE  L   E R   ++ QL   R
Sbjct: 357 EAELEELEAELEELESRLEELEEQLETLR 385

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

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

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 28/142 (19%), Positives = 72/142 (50%)

Query: 35  ELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSR 94
           +L++ + ++  L+  L     ++    + +EE ++ ++++  ++  LQ  L +++++   
Sbjct: 710 QLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELES 769

Query: 95  AEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQ 154
            EE L  L+EEI  L    +    ++  LE +  +AE RL+ +  ++E + +       +
Sbjct: 770 LEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQE 829

Query: 155 IQHLEQALHMAELRAANVQRQL 176
           I+ LE+ +   E +   ++ +L
Sbjct: 830 IEELEEEIEELEEKLDELEEEL 851

Length = 1163

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 34/146 (23%), Positives = 75/146 (51%)

Query: 31  HLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKD 90
            L  ++++ + KIA LE  L E  +++      +E+  K +++++ +I  L+  L++++ 
Sbjct: 681 ELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKDLARLEA 740

Query: 91  DSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTE 150
           +  + EER+  L +E+  L A   +    +   E +  +AE  +EE+  Q+E++ E +  
Sbjct: 741 EVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKA 800

Query: 151 QWIQIQHLEQALHMAELRAANVQRQL 176
               +  L   L +    AAN++ +L
Sbjct: 801 LREALDELRAELTLLNEEAANLRERL 826

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 36/170 (21%), Positives = 69/170 (40%), Gaps = 21/170 (12%)

Query: 18  FTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNK 77
                +  +     L  EL + + +I  LE  LEE+      +    E   ++ +     
Sbjct: 738 LEAEVEQLEERIAQLSKELTELEAEIEELEERLEEA------EEELAEAEAEIEE----- 786

Query: 78  IHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEV 137
              L++ + ++K++     E L+ L  E+ LL   +      + +LE +    E RLE++
Sbjct: 787 ---LEAQIEQLKEELKALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDL 843

Query: 138 SLQVEKMSEIVT-------EQWIQIQHLEQALHMAELRAANVQRQLMYAR 180
             Q+E++SE +        E    I+ LE  L       A+++  L   R
Sbjct: 844 EEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLR 893

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 41.6 bits (98), Expect = 4e-04
 Identities = 26/144 (18%), Positives = 67/144 (46%), Gaps = 2/144 (1%)

Query: 19  TLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKI 78
            L     + +  +   E  + + ++  LE  +  + R++      IEE  + ++ +  +I
Sbjct: 804 ALDELRAELTLLN--EEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEI 861

Query: 79  HHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVS 138
             L+ L+ +++ +         +LEE + LL +   + + ++  LESK  +    LEE+ 
Sbjct: 862 EELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELESKRSELRRELEELR 921

Query: 139 LQVEKMSEIVTEQWIQIQHLEQAL 162
            ++ ++   +    ++I +L++ L
Sbjct: 922 EKLAQLELRLEGLEVRIDNLQERL 945

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

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

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 34/147 (23%), Positives = 71/147 (48%), Gaps = 14/147 (9%)

Query: 30  QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIK 89
           + L  EL++ + +++ LE  LEE   ++      IEE    ++++  ++  LQ  L ++K
Sbjct: 235 KELRKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELK 294

Query: 90  DDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVT 149
           ++    E  ++ L E +                LE++  + E+RLEE+  ++E + E + 
Sbjct: 295 EEIEELEGEISLLRERLE--------------ELENELEELEERLEELKEKIEALKEELE 340

Query: 150 EQWIQIQHLEQALHMAELRAANVQRQL 176
           E+   ++ LEQ L   E     ++ +L
Sbjct: 341 ERETLLEELEQLLAELEEAKEELEEKL 367

Length = 1163

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

 Score = 40.4 bits (95), Expect = 0.001
 Identities = 30/172 (17%), Positives = 75/172 (43%), Gaps = 19/172 (11%)

Query: 24  NQQHSQQHLIAELQDAKLKIAGLETMLE--------ESIRKVNGKSNYIEE-------RD 68
           N +   + L A +++ +  +  LE  L           I ++  + + +EE       R 
Sbjct: 755 NVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEARL 814

Query: 69  KLVDDMTNKIHHLQSLLSK----IKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLE 124
           + ++   N++   +  L K    +++     +E++ ++E+EI  L     +   ++  LE
Sbjct: 815 REIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELE 874

Query: 125 SKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQL 176
           +   D E RL ++  + +++   + E   +I+ LE  +     R + ++ +L
Sbjct: 875 AALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKL 926

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

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

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 29/148 (19%), Positives = 72/148 (48%), Gaps = 7/148 (4%)

Query: 23  QNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQ 82
           ++ +  ++ L  E+++ + +I  LE  L+E   +       +EE +K ++++  ++  L+
Sbjct: 817 ESLEQRRERLEQEIEELEEEIEELEEKLDELEEE-------LEELEKELEELKEELEELE 869

Query: 83  SLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVE 142
           +   +++D+    EE    LEEE+R L +   +   +I  L  +  + E +LE + +++ 
Sbjct: 870 AEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEELEAKLERLEVELP 929

Query: 143 KMSEIVTEQWIQIQHLEQALHMAELRAA 170
           ++ E + E++      E    +  L   
Sbjct: 930 ELEEELEEEYEDTLETELEREIERLEEE 957

Length = 1163

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

 Score = 38.5 bits (90), Expect = 0.003
 Identities = 31/165 (18%), Positives = 76/165 (46%), Gaps = 11/165 (6%)

Query: 23  QNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNY-------IEERDKLVDDMT 75
           +  Q     L  E+++ + +I+ L   LEE   ++             IE   + +++  
Sbjct: 284 EELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEELEERE 343

Query: 76  NKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKAL----DAE 131
             +  L+ LL+++++     EE+L+AL EE+  L+ A R+   ++    ++      + +
Sbjct: 344 TLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEAELAEIRNELEELK 403

Query: 132 DRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQL 176
             +E +  ++E++SE + +   +++ LE  L   +     +  +L
Sbjct: 404 REIESLEERLERLSERLEDLKEELKELEAELEELQTELEELNEEL 448

Length = 1163

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

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 19/118 (16%), Positives = 51/118 (43%), Gaps = 1/118 (0%)

Query: 34  AELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMT-NKIHHLQSLLSKIKDDS 92
            +L   + ++  L   + E  +++      +EE +K + D+   +   ++  + +++ + 
Sbjct: 244 RQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGELEAEI 303

Query: 93  SRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTE 150
           +  E  +   E E+        K   +I  L ++  + E  +EE   + +K++E   E
Sbjct: 304 ASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAE 361

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

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

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 26/143 (18%), Positives = 60/143 (41%), Gaps = 9/143 (6%)

Query: 20  LTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIH 79
           L+   ++ S+        + KL    LE    E   ++        +  + +  +  +I 
Sbjct: 800 LSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEK--EIQELQEQRIDLKEQIKSIEKEIE 857

Query: 80  HLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSL 139
           +L     +++++    E  L  LE  +  L         +   LE++  + E ++EE+  
Sbjct: 858 NLNGKKEELEEELEELEAALRDLESRLGDLKK-------ERDELEAQLRELERKIEELEA 910

Query: 140 QVEKMSEIVTEQWIQIQHLEQAL 162
           Q+EK  + ++E   +++ LE+ L
Sbjct: 911 QIEKKRKRLSELKAKLEALEEEL 933

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

>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 33/168 (19%), Positives = 77/168 (45%), Gaps = 7/168 (4%)

Query: 24  NQQHSQQHLIAELQDAKLKIAGLETMLEESIRKV----NGKSNYIEERDKLVDDMTNKIH 79
           N        I +L   K ++      + ++++K        +  +E  +  ++D+ N++ 
Sbjct: 3   NNNLKSLLAIQKLDLEKDRLEPRIKEIRKALKKAKAELEALNKALEALEIELEDLENQVS 62

Query: 80  HLQSLLSKIKDDSSRAEERLNAL--EEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEV 137
            L+S + +I++   RAEE+L+A+  E E+R L    +     I++LE +  +  + +E++
Sbjct: 63  QLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKL 122

Query: 138 SLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLK 185
             ++E + E +      +   E  L   E+     + Q + ++   LK
Sbjct: 123 EKEIEDLKERLERLEKNLAEAEARLE-EEVAEIREEGQELSSKREELK 169

Length = 239

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	287
PRK09039	343	hypothetical protein; Validated	97.9
PRK11637	428	AmiB activator; Provisional	97.76
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	97.55
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	97.49
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	97.45
PRK11637	428	AmiB activator; Provisional	97.36
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	97.26
KOG0996	1293	consensus Structural maintenance of chromosome pro	97.2
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	97.14
PF00261	237	Tropomyosin: Tropomyosin; InterPro: IPR000533 Trop	96.97
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	96.94
PRK09039	343	hypothetical protein; Validated	96.92
PRK02224	880	chromosome segregation protein; Provisional	96.92
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	96.89
PRK02224	880	chromosome segregation protein; Provisional	96.83
PHA02562	562	46 endonuclease subunit; Provisional	96.58
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	96.47
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	96.43
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	96.42
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	96.38
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	96.35
COG4942	420	Membrane-bound metallopeptidase [Cell division and	96.31
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	96.22
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	96.11
PF04582	326	Reo_sigmaC: Reovirus sigma C capsid protein; Inter	96.11
PRK03918	880	chromosome segregation protein; Provisional	96.11
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	96.1
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	96.06
PRK03918	880	chromosome segregation protein; Provisional	96.03
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	95.99
PHA02562	562	46 endonuclease subunit; Provisional	95.98
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	95.95
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	95.87
PF15619	194	Lebercilin: Ciliary protein causing Leber congenit	95.78
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	95.63
PF06818	202	Fez1: Fez1; InterPro: IPR009638 This family repres	95.59
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	95.48
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	95.45
PRK04863	1486	mukB cell division protein MukB; Provisional	95.45
KOG0161	1930	consensus Myosin class II heavy chain [Cytoskeleto	95.42
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	95.38
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	95.35
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	95.28
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	95.27
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	95.24
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	95.11
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	95.02
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	94.99
PF10481	307	CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR0	94.85
PF10186	302	Atg14: UV radiation resistance protein and autopha	94.81
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	94.75
KOG0933	1174	consensus Structural maintenance of chromosome pro	94.74
PF05911	769	DUF869: Plant protein of unknown function (DUF869)	94.71
KOG4809	654	consensus Rab6 GTPase-interacting protein involved	94.64
COG2433	652	Uncharacterized conserved protein [Function unknow	94.36
PRK04778	569	septation ring formation regulator EzrA; Provision	94.32
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	94.32
KOG0996	1293	consensus Structural maintenance of chromosome pro	94.29
TIGR01843	423	type_I_hlyD type I secretion membrane fusion prote	94.23
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	94.19
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	94.18
PRK01156	895	chromosome segregation protein; Provisional	94.14
TIGR03185	650	DNA_S_dndD DNA sulfur modification protein DndD. T	94.08
PF14662	193	CCDC155: Coiled-coil region of CCDC155	93.93
PF11570	136	E2R135: Coiled-coil receptor-binding R-domain of c	93.65
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	93.55
PF06008	264	Laminin_I: Laminin Domain I; InterPro: IPR009254 L	93.55
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	93.42
PRK10929	1109	putative mechanosensitive channel protein; Provisi	93.37
PRK10884	206	SH3 domain-containing protein; Provisional	93.25
PF00038	312	Filament: Intermediate filament protein; InterPro:	93.15
PRK04778	569	septation ring formation regulator EzrA; Provision	93.02
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	93.0
PF05483	786	SCP-1: Synaptonemal complex protein 1 (SCP-1); Int	93.0
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	92.97
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	92.94
PF12761	195	End3: Actin cytoskeleton-regulatory complex protei	92.9
PF09730	717	BicD: Microtubule-associated protein Bicaudal-D; I	92.86
PRK12705	508	hypothetical protein; Provisional	92.77
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	92.77
KOG4674	1822	consensus Uncharacterized conserved coiled-coil pr	92.66
KOG0963	629	consensus Transcription factor/CCAAT displacement	92.61
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	92.59
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	92.56
PF09403	126	FadA: Adhesion protein FadA; InterPro: IPR018543 F	92.56
PRK04863	1486	mukB cell division protein MukB; Provisional	92.53
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	92.35
PF11802	268	CENP-K: Centromere-associated protein K; InterPro:	92.32
PF02994	370	Transposase_22: L1 transposable element; InterPro:	92.23
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	92.17
PF05335	188	DUF745: Protein of unknown function (DUF745); Inte	92.06
PF12128	1201	DUF3584: Protein of unknown function (DUF3584); In	92.06
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	91.96
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	91.88
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	91.66
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	91.66
KOG0933	1174	consensus Structural maintenance of chromosome pro	91.51
PF05278	269	PEARLI-4: Arabidopsis phospholipase-like protein (	91.46
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	91.32
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	91.31
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	91.28
KOG0243	1041	consensus Kinesin-like protein [Cytoskeleton]	91.26
PF04582	326	Reo_sigmaC: Reovirus sigma C capsid protein; Inter	91.25
COG5185	622	HEC1 Protein involved in chromosome segregation, i	91.24
TIGR02977	219	phageshock_pspA phage shock protein A. Members of	91.24
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	91.19
PF05010	207	TACC: Transforming acidic coiled-coil-containing p	91.14
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	91.11
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	91.1
KOG0976	1265	consensus Rho/Rac1-interacting serine/threonine ki	91.0
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	90.9
KOG0980	980	consensus Actin-binding protein SLA2/Huntingtin-in	90.75
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	90.58
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	90.55
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	90.54
TIGR03007	498	pepcterm_ChnLen polysaccharide chain length determ	90.46
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	90.25
PF12795	240	MscS_porin: Mechanosensitive ion channel porin dom	90.16
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	90.11
COG5185	622	HEC1 Protein involved in chromosome segregation, i	90.11
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	90.11
COG2433	652	Uncharacterized conserved protein [Function unknow	90.04
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	89.89
PRK11281	1113	hypothetical protein; Provisional	89.89
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	89.85
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	89.82
PF06160	560	EzrA: Septation ring formation regulator, EzrA ; I	89.76
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	89.61
KOG1003	205	consensus Actin filament-coating protein tropomyos	89.58
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	89.58
PRK00736	68	hypothetical protein; Provisional	89.54
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	89.5
PF06705	247	SF-assemblin: SF-assemblin/beta giardin	89.49
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	89.42
PF01920	106	Prefoldin_2: Prefoldin subunit; InterPro: IPR00277	89.39
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	89.36
PF08702	146	Fib_alpha: Fibrinogen alpha/beta chain family; Int	89.34
COG1842	225	PspA Phage shock protein A (IM30), suppresses sigm	89.14
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	89.11
PRK02119	73	hypothetical protein; Provisional	89.11
TIGR01000	457	bacteriocin_acc bacteriocin secretion accessory pr	89.02
PRK10698	222	phage shock protein PspA; Provisional	89.02
TIGR03017	444	EpsF chain length determinant protein EpsF. Sequen	88.98
PRK10884	206	SH3 domain-containing protein; Provisional	88.9
PRK00295	68	hypothetical protein; Provisional	88.85
PRK04406	75	hypothetical protein; Provisional	88.8
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	88.72
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	88.71
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	88.62
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	88.49
KOG1899	861	consensus LAR transmembrane tyrosine phosphatase-i	88.37
PRK00846	77	hypothetical protein; Provisional	88.27
PF02994	370	Transposase_22: L1 transposable element; InterPro:	88.08
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	88.07
TIGR02680	1353	conserved hypothetical protein TIGR02680. Members	87.93
KOG0994	1758	consensus Extracellular matrix glycoprotein Lamini	87.91
PRK04325	74	hypothetical protein; Provisional	87.89
TIGR01005	754	eps_transp_fam exopolysaccharide transport protein	87.7
PRK02793	72	phi X174 lysis protein; Provisional	87.69
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	87.64
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	87.62
PF10186	302	Atg14: UV radiation resistance protein and autopha	87.54
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	87.42
KOG0964	1200	consensus Structural maintenance of chromosome pro	87.35
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	87.29
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	87.22
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	87.16
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	87.1
KOG4673	961	consensus Transcription factor TMF, TATA element m	87.05
KOG3433	203	consensus Protein involved in meiotic recombinatio	87.02
PF13166	712	AAA_13: AAA domain	86.97
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	86.83
PF13166	712	AAA_13: AAA domain	86.43
TIGR02473	141	flagell_FliJ flagellar export protein FliJ. Member	86.41
KOG0243	1041	consensus Kinesin-like protein [Cytoskeleton]	86.18
PF06008	264	Laminin_I: Laminin Domain I; InterPro: IPR009254 L	86.16
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	86.08
PRK15422	79	septal ring assembly protein ZapB; Provisional	85.91
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	85.73
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	85.69
KOG0979	1072	consensus Structural maintenance of chromosome pro	85.49
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	85.46
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	85.28
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	85.24
PF05622	713	HOOK: HOOK protein; InterPro: IPR008636 This famil	85.17
KOG0963	629	consensus Transcription factor/CCAAT displacement	85.1
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	85.06
PF06818	202	Fez1: Fez1; InterPro: IPR009638 This family repres	85.01
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	84.78
PRK12704	520	phosphodiesterase; Provisional	84.65
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	84.55
COG3206	458	GumC Uncharacterized protein involved in exopolysa	84.54
PF05483	786	SCP-1: Synaptonemal complex protein 1 (SCP-1); Int	84.14
PF14992	280	TMCO5: TMCO5 family	83.94
PF01576	859	Myosin_tail_1: Myosin tail; InterPro: IPR002928 Mu	83.87
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	83.84
PF10481	307	CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR0	83.79
PF10205	102	KLRAQ: Predicted coiled-coil domain-containing pro	83.64
PF10212	518	TTKRSYEDQ: Predicted coiled-coil domain-containing	83.24
KOG0239	670	consensus Kinesin (KAR3 subfamily) [Cytoskeleton]	83.24
KOG0964	1200	consensus Structural maintenance of chromosome pro	83.12
PF04508	23	Pox_A_type_inc: Viral A-type inclusion protein rep	83.09
PRK11281	1113	hypothetical protein; Provisional	82.9
PRK00888	105	ftsB cell division protein FtsB; Reviewed	82.74
PF05557	722	MAD: Mitotic checkpoint protein; InterPro: IPR0086	82.7
PF05557	722	MAD: Mitotic checkpoint protein; InterPro: IPR0086	82.7
PF09787	511	Golgin_A5: Golgin subfamily A member 5; InterPro:	82.47
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	82.47
PF14073	178	Cep57_CLD: Centrosome localisation domain of Cep57	82.41
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	82.38
KOG4673	961	consensus Transcription factor TMF, TATA element m	82.29
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	82.25
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	81.94
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	81.67
PF13747	89	DUF4164: Domain of unknown function (DUF4164)	81.58
KOG0976	1265	consensus Rho/Rac1-interacting serine/threonine ki	81.35
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	81.18
COG4372	499	Uncharacterized protein conserved in bacteria with	81.17
PF15450	531	DUF4631: Domain of unknown function (DUF4631)	81.15
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	80.84
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	80.76
PF10168	717	Nup88: Nuclear pore component; InterPro: IPR019321	80.74
PF06160	560	EzrA: Septation ring formation regulator, EzrA ; I	80.67
PRK00106	535	hypothetical protein; Provisional	80.65
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	80.44
PF05739	63	SNARE: SNARE domain; InterPro: IPR000727 The proce	80.43
PRK10929	1109	putative mechanosensitive channel protein; Provisi	80.38
KOG1962	216	consensus B-cell receptor-associated protein and r	80.31
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	80.25
KOG0018	1141	consensus Structural maintenance of chromosome pro	80.09

>PRK09039 hypothetical protein; Validated

Probab=97.90  E-value=0.0065  Score=58.87  Aligned_cols=198  Identities=13%  Similarity=0.120  Sum_probs=127.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhc-------cchhHHHHHHH
Q 038837           29 QQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKD-------DSSRAEERLNA  101 (287)
Q Consensus        29 ~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk-------~s~~aee~i~e  101 (287)
                      ++-|..++...+.++..|+++|.+.+.-|.--......++..+.+...++..++..-+-|..       ....++.++..
T Consensus        41 q~fLs~~i~~~~~eL~~L~~qIa~L~e~L~le~~~~~~l~~~l~~l~~~l~~a~~~r~~Le~~~~~~~~~~~~~~~~~~~  120 (343)
T PRK09039         41 QFFLSREISGKDSALDRLNSQIAELADLLSLERQGNQDLQDSVANLRASLSAAEAERSRLQALLAELAGAGAAAEGRAGE  120 (343)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcchHHHHHHH
Confidence            56777788888888888888888877666666666666676676666666666655554422       12244566777


Q ss_pred             HHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhchhh
Q 038837          102 LEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARC  181 (287)
Q Consensus       102 LEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~p~~~  181 (287)
                      |+.+...++......+.+...|.......++.+..|...|+-.+.-..++..+|..+++.|..|-.+  |++.=.. -+.
T Consensus       121 l~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~--~~~~l~~-~~~  197 (343)
T PRK09039        121 LAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQ--RVQELNR-YRS  197 (343)
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHH-hHH
Confidence            7788877777777777777777777777777888888888888888889999999998888876544  2221111 123


Q ss_pred             HHHHHHHHhhc-ccccchh-c----ccCCcccCCcccccchHHHHHHHHHHHHH
Q 038837          182 TFLKFVKDFSE-KHLPKLT-G----MLVPYLPGKGSILISFMSQVQHQFKRFFL  229 (287)
Q Consensus       182 ~f~k~~~~~~~-ph~~kv~-~----~~~py~~~~~~~skpyi~~~~~~~k~~l~  229 (287)
                      .|..=++++.. +--.++. .    ..+++|..++.-..|.-.......-..+.
T Consensus       198 ~~~~~l~~~~~~~~~iri~g~~~~~~~~vlF~~gsa~L~~~~~~~L~~ia~~l~  251 (343)
T PRK09039        198 EFFGRLREILGDREGIRIVGDRFVFQSEVLFPTGSAELNPEGQAEIAKLAAALI  251 (343)
T ss_pred             HHHHHHHHHhCCCCCcEEECCEEEecCCceeCCCCcccCHHHHHHHHHHHHHHH
Confidence            34333343332 1111111 1    33577777777777876555444443333

>PRK11637 AmiB activator; Provisional

Probab=97.76  E-value=0.0042  Score=61.08  Aligned_cols=7  Identities=0%  Similarity=0.273  Sum_probs=2.5

Q ss_pred             HHHHHHH
Q 038837           32 LIAELQD   38 (287)
Q Consensus        32 l~~eL~q   38 (287)
                      ++.++.+
T Consensus        52 l~~qi~~   58 (428)
T PRK11637         52 IQQDIAA   58 (428)
T ss_pred             HHHHHHH
Confidence            3333333

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

Probab=97.55  E-value=0.0052  Score=52.84  Aligned_cols=122  Identities=22%  Similarity=0.243  Sum_probs=75.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      .+|+.|-+.+..++..+|..+....++...++..|..+.       +++..|+++++.+...-..+..++.+-++.    
T Consensus         3 ~~lk~E~d~a~~r~e~~e~~~K~le~~~~~~E~EI~sL~-------~K~~~lE~eld~~~~~l~~~k~~lee~~~~----   71 (143)
T PF12718_consen    3 QALKLEADNAQDRAEELEAKVKQLEQENEQKEQEITSLQ-------KKNQQLEEELDKLEEQLKEAKEKLEESEKR----   71 (143)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHhHHHH----
Confidence            468889999999999999998887766555555555554       666666666665533333333333333222    


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQAL  162 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Al  162 (287)
                      ....+..+..+..||..+..+++++.+.+.+|.....-.++=-++++.+|+-.
T Consensus        72 ~~~~E~l~rriq~LEeele~ae~~L~e~~ekl~e~d~~ae~~eRkv~~le~~~  124 (143)
T PF12718_consen   72 KSNAEQLNRRIQLLEEELEEAEKKLKETTEKLREADVKAEHFERKVKALEQER  124 (143)
T ss_pred             HHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhH
Confidence            22333566666677777777777777777777776666666555666555533

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 [].

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

Probab=97.49  E-value=0.0091  Score=52.15  Aligned_cols=98  Identities=24%  Similarity=0.388  Sum_probs=62.2

Q ss_pred             HHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837           65 EERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus        65 ~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      .++++.+.+.+..+..+++++..++.+.....+.....++.++.++........+...+.....+.+..++++...++.+
T Consensus        91 ~~l~~el~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~  170 (191)
T PF04156_consen   91 QQLQEELDQLQERIQELESELEKLKEDLQELRELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERL  170 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444455666666666666655544555556666666666666666666666666666777778888888888877


Q ss_pred             hhhhHHHHHHHHHHHHHH
Q 038837          145 SEIVTEQWIQIQHLEQAL  162 (287)
Q Consensus       145 ~ki~~EQ~~qIqk~E~Al  162 (287)
                      +.....+..++++.+.-+
T Consensus       171 ~~~~~~l~~~~~~~~~l~  188 (191)
T PF04156_consen  171 QENLQQLEEKIQELQELL  188 (191)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            666666666666555433

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 [].

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=97.45  E-value=0.0078  Score=64.25  Aligned_cols=14  Identities=0%  Similarity=-0.090  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHH
Q 038837          222 HQFKRFFLAFKKFH  235 (287)
Q Consensus       222 ~~~k~~l~sA~~yH  235 (287)
                      ..|...++.|---|
T Consensus       535 ~~y~~Aie~~lg~~  548 (1164)
T TIGR02169       535 ERYATAIEVAAGNR  548 (1164)
T ss_pred             HHHHHHHHHHhhhh
Confidence            45666666655433

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.

>PRK11637 AmiB activator; Provisional

Probab=97.36  E-value=0.029  Score=55.29  Aligned_cols=6  Identities=17%  Similarity=0.169  Sum_probs=2.2

Q ss_pred             HHHHHH
Q 038837          134 LEEVSL  139 (287)
Q Consensus       134 v~eL~s  139 (287)
                      +..|..
T Consensus       221 l~~L~~  226 (428)
T PRK11637        221 LTGLES  226 (428)
T ss_pred             HHHHHH
Confidence            333333

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=97.26  E-value=0.018  Score=61.19  Aligned_cols=56  Identities=18%  Similarity=0.275  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHh
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLS   86 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~   86 (287)
                      .+..+++.++..+..++..+.+...++......+.++...+++....+..++..+.
T Consensus       674 ~l~~e~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~  729 (1179)
T TIGR02168       674 ERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQIS  729 (1179)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44556666666666666666666655555555555555544444444444443333

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.

>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=97.20  E-value=0.013  Score=64.52  Aligned_cols=146  Identities=19%  Similarity=0.298  Sum_probs=93.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH---hhhhcCchhhHHHHhHHhHHH-----h-hhHHHHHHHHhhhhccchh-HHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEES---IRKVNGKSNYIEERDKLVDDM-----T-NKIHHLQSLLSKIKDDSSR-AEERLNA  101 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~---~qel~~Kd~~l~e~Ek~i~ek-----s-~kI~sLqsEi~sLkk~s~~-aee~i~e  101 (287)
                      +..++..|+..|+++|....-.   .+.++.+...|+++++.+.+.     . ..|..||+.|+.+-.-..- -..++..
T Consensus       832 ~~~~~~~l~~~i~~~E~~~~k~~~d~~~l~~~~~~ie~l~kE~e~~qe~~~Kk~~i~~lq~~i~~i~~e~~q~qk~kv~~  911 (1293)
T KOG0996|consen  832 LAELIEYLESQIAELEAAVLKKVVDKKRLKELEEQIEELKKEVEELQEKAAKKARIKELQNKIDEIGGEKVQAQKDKVEK  911 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhhchhhHHhHHHHHH
Confidence            3345566666666666663222   233455566788888877776     3 7789999999988333222 2233555


Q ss_pred             HHHHHHHHHHHHhhhhhh--------------hhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 038837          102 LEEEIRLLWAASRKNNFD--------------IHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAEL  167 (287)
Q Consensus       102 LEkQVe~L~~elekqn~~--------------~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~  167 (287)
                      +-+|++.|.+++++++..              ...+|..-.+++++++.|+.++..+..-..|+...+.+++.+++-+..
T Consensus       912 ~~~~~~~l~~~i~k~~~~i~~s~~~i~k~q~~l~~le~~~~~~e~e~~~L~e~~~~~~~k~~E~~~~~~e~~~~~~E~k~  991 (1293)
T KOG0996|consen  912 INEQLDKLEADIAKLTVAIKTSDRNIAKAQKKLSELEREIEDTEKELDDLTEELKGLEEKAAELEKEYKEAEESLKEIKK  991 (1293)
T ss_pred             HHHHHHHHHHHHHHhHHHHhcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555666665555554433              344555666666777777777777777778888888888888888777


Q ss_pred             HHHHHHhhhh
Q 038837          168 RAANVQRQLM  177 (287)
Q Consensus       168 ~~~k~q~ea~  177 (287)
                      .+..+..+-.
T Consensus       992 ~~~~~k~~~e 1001 (1293)
T KOG0996|consen  992 ELRDLKSELE 1001 (1293)
T ss_pred             HHHHHHHHHH
Confidence            7666654433

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

Probab=97.14  E-value=0.01  Score=54.40  Aligned_cols=123  Identities=22%  Similarity=0.279  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWA  111 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~  111 (287)
                      ++.+++.+..++..++..+.+       ......+.|..+..+..+|..|+.+++..-..-..+..++.++++..+.-. 
T Consensus         6 l~~eld~~~~~~~~~~~~l~~-------~~~~~~~aE~e~~~l~rri~~lE~~le~~eerL~~~~~kL~~~e~~~de~e-   77 (237)
T PF00261_consen    6 LKDELDEAEERLEEAEEKLKE-------AEKRAEKAEAEVASLQRRIQLLEEELERAEERLEEATEKLEEAEKRADESE-   77 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH-
Confidence            444555555555555444444       557777788888888888888887776553333344444444444433332 


Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELR  168 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~  168 (287)
                            .....||.|....+.|+..|-.+|..+..+..+=..+....++-|.+.+..
T Consensus        78 ------r~~k~lE~r~~~~eeri~~lE~~l~ea~~~~ee~e~k~~E~~rkl~~~E~~  128 (237)
T PF00261_consen   78 ------RARKVLENREQSDEERIEELEQQLKEAKRRAEEAERKYEEVERKLKVLEQE  128 (237)
T ss_dssp             ------HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             ------HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                  222344444444444444444444444444443333333333333333333

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 ....

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

Probab=96.97  E-value=0.037  Score=50.68  Aligned_cols=128  Identities=20%  Similarity=0.263  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLW  110 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~  110 (287)
                      ....++..|+.+|..||..++.....|..-...|.+.++...+.......|++.       ....++++..||.++....
T Consensus        33 ~aE~e~~~l~rri~~lE~~le~~eerL~~~~~kL~~~e~~~de~er~~k~lE~r-------~~~~eeri~~lE~~l~ea~  105 (237)
T PF00261_consen   33 KAEAEVASLQRRIQLLEEELERAEERLEEATEKLEEAEKRADESERARKVLENR-------EQSDEERIEELEQQLKEAK  105 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHHHHCHHHHHHHHH-------HHHHHHHHHHCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHHHHHHHHH
Confidence            345677788888888888888888778877888888887777777777777776       4456778888888887776


Q ss_pred             HHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 038837          111 AASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANV  172 (287)
Q Consensus       111 ~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~  172 (287)
                      ...+...       .+..++..|+..+...|+.++.-.+.--.+|..+|.-|+.+...+-..
T Consensus       106 ~~~ee~e-------~k~~E~~rkl~~~E~~Le~aEeR~e~~E~ki~eLE~el~~~~~~lk~l  160 (237)
T PF00261_consen  106 RRAEEAE-------RKYEEVERKLKVLEQELERAEERAEAAESKIKELEEELKSVGNNLKSL  160 (237)
T ss_dssp             HHHHHHH-------HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHhhhchhHHHHHHHHHHHHHHHHHh
Confidence            5554433       344466666666666666666666666677777777777666655443

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 ....

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

Probab=96.94  E-value=0.18  Score=55.50  Aligned_cols=211  Identities=17%  Similarity=0.211  Sum_probs=112.5

Q ss_pred             HHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHH-------HHHHHHHHHHHHHHH
Q 038837           41 LKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEER-------LNALEEEIRLLWAAS  113 (287)
Q Consensus        41 ~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~-------i~eLEkQVe~L~~el  113 (287)
                      .+|......+++-.+.++++...+.++--.+..+...|..+...+..+++--.+.+++       +.++.+.|+.|.+.+
T Consensus       302 ~ki~~~~~k~~~~r~k~teiea~i~~~~~e~~~~d~Ei~~~r~~~~~~~re~~~~~~~~~~~~n~i~~~k~~~d~l~k~I  381 (1074)
T KOG0250|consen  302 EKIEEKQGKIEEARQKLTEIEAKIGELKDEVDAQDEEIEEARKDLDDLRREVNDLKEEIREIENSIRKLKKEVDRLEKQI  381 (1074)
T ss_pred             HHHHHHHHHHHHHhhhhhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333344444444444443334444444444444444444434444444       444455555555555


Q ss_pred             hhhhhhh-hhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhchh--hHHHHHH---
Q 038837          114 RKNNFDI-HNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYAR--CTFLKFV---  187 (287)
Q Consensus       114 ekqn~~~-~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~p~~--~~f~k~~---  187 (287)
                      .+-+.+. ..+.+.-.+.|+|++.|..+||+++..+..-....+++=++...-++++...+.+-.-.+  -.+.+|.   
T Consensus       382 ~~~~~~~~~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~~~~l~~  461 (1074)
T KOG0250|consen  382 ADLEKQTNNELGSELEERENKLEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENISEELKD  461 (1074)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555554 566777788999999999999999999888888888888877777777655544422111  1122211   


Q ss_pred             --------HHhhcccccchhcccCCcccC-----CcccccchHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHH
Q 038837          188 --------KDFSEKHLPKLTGMLVPYLPG-----KGSILISFMSQVQH--------QFKRFFLAFKKFHHELQGFIKQEM  246 (287)
Q Consensus       188 --------~~~~~ph~~kv~~~~~py~~~-----~~~~skpyi~~~~~--------~~k~~l~sA~~yH~qvQ~~I~~~L  246 (287)
                              -...+||++.+....+-....     .|+ ...||+-.-+        +++.++.+-----|.=+..+++.|
T Consensus       462 lk~~k~dkvs~FG~~m~~lL~~I~r~~~~f~~~P~GP-lG~~Vtl~~~KWa~aIE~~L~n~lnaFiv~sh~D~~~Lr~i~  540 (1074)
T KOG0250|consen  462 LKKTKTDKVSAFGPNMPQLLRAIERRKRRFQTPPKGP-LGKYVTLKEPKWALAIERCLGNLLNAFIVTSHKDARILRAIM  540 (1074)
T ss_pred             HHhcccchhhhcchhhHHHHHHHHHHHhcCCCCCCCC-ccceeEecCcHHHHHHHHHHHHhhhhheeCCHhhHHHHHHHH
Confidence                    112357776665443332211     112 3556644333        444444433222334455678888


Q ss_pred             Hhccch
Q 038837          247 VKNKLT  252 (287)
Q Consensus       247 ~~hElt  252 (287)
                      .++-+-
T Consensus       541 ~~~~~~  546 (1074)
T KOG0250|consen  541 RRLKIP  546 (1074)
T ss_pred             HHcCCC
Confidence            877654

>PRK09039 hypothetical protein; Validated

Probab=96.92  E-value=0.027  Score=54.60  Aligned_cols=69  Identities=14%  Similarity=0.200  Sum_probs=33.1

Q ss_pred             hhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH
Q 038837           75 TNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus        75 s~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      ......|..++...+.-+..+.-+|.-|..||+.|++.+......+...|.+-.++..++++|..+|+.
T Consensus       115 ~~~~~~l~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~  183 (343)
T PRK09039        115 EGRAGELAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNV  183 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444555554444444444444555555555555554444444444444444444444444444443

>PRK02224 chromosome segregation protein; Provisional

Probab=96.92  E-value=0.04  Score=58.35  Aligned_cols=59  Identities=14%  Similarity=0.235  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      ..+..++++++..+..|+..++...+++...+....+++....+...++..|+..++.+
T Consensus       275 ~~l~~~i~~~~~~~~~le~e~~~l~~~l~~~~~~~~~l~~~~~~l~~k~~el~~~l~~~  333 (880)
T PRK02224        275 EELAEEVRDLRERLEELEEERDDLLAEAGLDDADAEAVEARREELEDRDEELRDRLEEC  333 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56778888999999999988888888888777777777777777777777777776544

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

Probab=96.89  E-value=0.06  Score=57.04  Aligned_cols=121  Identities=17%  Similarity=0.253  Sum_probs=96.1

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHH-----------
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAE-----------   96 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~ae-----------   96 (287)
                      .+..++.+|+++|.+.-.|++.+.+.++....=...+..+|+.+.|--..=+.++..+..-++..-.+|           
T Consensus       454 ~Er~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DKq~l~~LEkrL~eE~~~R~~lEkQL~eErk~r~~ee~~aar~~~~~~  533 (697)
T PF09726_consen  454 NERSLKSELSQLRQENEQLQNKLQNLVQARQQDKQSLQQLEKRLAEERRQRASLEKQLQEERKARKEEEEKAARALAQAQ  533 (697)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhccccch
Confidence            446788899999999999999999988887777788999999999998999999999988744422111           


Q ss_pred             -----------HHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhH-------hHHHHHHHHHHHHHHHhhhh
Q 038837           97 -----------ERLNALEEEIRLLWAASRKNNFDIHNLESKAL-------DAEDRLEEVSLQVEKMSEIV  148 (287)
Q Consensus        97 -----------e~i~eLEkQVe~L~~elekqn~~~~~LEsrA~-------dAEkkv~eL~sklek~~ki~  148 (287)
                                 .+..+||.|+.+|..|+..-...+..+|..+.       +.++..+.|-+-|.-|++-|
T Consensus       534 ~~r~e~~e~~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr~~~~e~~~~~e~L~~aL~amqdk~  603 (697)
T PF09726_consen  534 ATRQECAESCRQRRRQLESELKKLRRELKQKEEQIRELESELQELRKYEKESEKDTEVLMSALSAMQDKN  603 (697)
T ss_pred             hccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH
Confidence                       23789999999999999999888888888773       33456777777777776654

; GO: 0016021 integral to membrane

>PRK02224 chromosome segregation protein; Provisional

Probab=96.83  E-value=0.063  Score=56.87  Aligned_cols=42  Identities=10%  Similarity=0.183  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHH
Q 038837           44 AGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLL   85 (287)
Q Consensus        44 a~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi   85 (287)
                      ..++..|.+....+......+.+.+..+.+....+..|..++
T Consensus       261 ~~l~~~i~~~e~~~~~l~~~i~~~~~~~~~le~e~~~l~~~l  302 (880)
T PRK02224        261 EDLRETIAETEREREELAEEVRDLRERLEELEEERDDLLAEA  302 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            333333333333333333444444444444444444444444

>PHA02562 46 endonuclease subunit; Provisional

Probab=96.58  E-value=0.16  Score=50.72  Aligned_cols=49  Identities=16%  Similarity=0.255  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           40 KLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        40 k~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      ..++..|+..|.+...++..-++.|.+++..+.....++..++.++..+
T Consensus       233 ~~~l~~l~~~i~~l~~~i~~~~~~L~~l~~~~~~~~~~l~~~~~~~~~~  281 (562)
T PHA02562        233 KAEIEELTDELLNLVMDIEDPSAALNKLNTAAAKIKSKIEQFQKVIKMY  281 (562)
T ss_pred             HHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3333333444444433344444555556666666666666666665555

>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=96.47  E-value=0.26  Score=51.07  Aligned_cols=87  Identities=17%  Similarity=0.296  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      ..|......|+..+..|++.++....+|........+++...+++...-..|..|.+.|+........+|.+||..+..|
T Consensus       153 eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e~L~~~~kel~~~~e~l~~E~~~L~~q~~e~~~ri~~LEedi~~l  232 (546)
T PF07888_consen  153 EELLKENEQLEEEVEQLREEVERLEAELEQEEEEMEQLKQQQKELTESSEELKEERESLKEQLAEARQRIRELEEDIKTL  232 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555557777778888888888888888888888888888888888899999999999777777888889999888888


Q ss_pred             HHHHhhh
Q 038837          110 WAASRKN  116 (287)
Q Consensus       110 ~~elekq  116 (287)
                      ......+
T Consensus       233 ~qk~~E~  239 (546)
T PF07888_consen  233 TQKEKEQ  239 (546)
T ss_pred             HHHHHHH
Confidence            7666433

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 [].

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

Probab=96.43  E-value=0.17  Score=56.02  Aligned_cols=66  Identities=21%  Similarity=0.271  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      +.+++.+++.++..++..+.+...+++.....+.+..++...+..+..-..+...++++++..+..
T Consensus       851 ~~~~~~~~~~~~~~l~~~~~~~~~l~~~l~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~  916 (1163)
T COG1196         851 LEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLRERLEE  916 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444555555555555555555555555555555555555555555555555555555554443

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

Probab=96.42  E-value=0.21  Score=43.00  Aligned_cols=114  Identities=14%  Similarity=0.220  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hcc--chhHHHHHHHHHHHHHHH
Q 038837           33 IAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDD--SSRAEERLNALEEEIRLL  109 (287)
Q Consensus        33 ~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~--s~~aee~i~eLEkQVe~L  109 (287)
                      ....+++..++..||.....+.+++.+=.-.+..+|..+.....++.....-++.- +.+  .-....+|.-||++++..
T Consensus        13 ~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~lee~~~~~~~~E~l~rriq~LEeele~a   92 (143)
T PF12718_consen   13 QDRAEELEAKVKQLEQENEQKEQEITSLQKKNQQLEEELDKLEEQLKEAKEKLEESEKRKSNAEQLNRRIQLLEEELEEA   92 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHhhHHHHHHHHHHH
Confidence            34556666677777766666666666666777777766666666666665555544 211  112334466666666666


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      .+.+..-+.+..-..-+|...|++|..|...-+..++
T Consensus        93 e~~L~e~~ekl~e~d~~ae~~eRkv~~le~~~~~~E~  129 (143)
T PF12718_consen   93 EKKLKETTEKLREADVKAEHFERKVKALEQERDQWEE  129 (143)
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhHHHHHH
Confidence            6666666666666666666666666666655555443

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 [].

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

Probab=96.38  E-value=0.22  Score=46.67  Aligned_cols=47  Identities=19%  Similarity=0.252  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH
Q 038837           97 ERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus        97 e~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      .....|+.+++.++..+.+.+.+...+..+-..-++.+..+..++.+
T Consensus        89 ~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~  135 (239)
T COG1579          89 RELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLER  135 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444433333333333333333333333

>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=96.35  E-value=0.28  Score=50.86  Aligned_cols=94  Identities=19%  Similarity=0.212  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHH---------------------HHHHHhhh
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHH---------------------LQSLLSKI   88 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~s---------------------LqsEi~sL   88 (287)
                      ..|..+..+++.+|..||..|...++.....+..+.++..+..+++.....                     ++.+.+.|
T Consensus       209 ~~L~~q~~e~~~ri~~LEedi~~l~qk~~E~e~~~~~lk~~~~elEq~~~eLk~rLk~~~~~~~~~~~~~~~~~~e~e~L  288 (546)
T PF07888_consen  209 ESLKEQLAEARQRIRELEEDIKTLTQKEKEQEKELDKLKELKAELEQLEAELKQRLKETVVQLKQEETQAQQLQQENEAL  288 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHH
Confidence            566677788889999999999888888766655555554444444433322                     22233333


Q ss_pred             hccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhH
Q 038837           89 KDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNL  123 (287)
Q Consensus        89 kk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~L  123 (287)
                      +..--.+++++.+-+.++..|.++++....-.+..
T Consensus       289 keqLr~~qe~lqaSqq~~~~L~~EL~~~~~~RDrt  323 (546)
T PF07888_consen  289 KEQLRSAQEQLQASQQEAELLRKELSDAVNVRDRT  323 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334455667777888888888887776654333

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 [].

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

Probab=96.31  E-value=0.59  Score=47.07  Aligned_cols=61  Identities=18%  Similarity=0.173  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQ  160 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~  160 (287)
                      .++-++++.|.+++.........+++.=.+-+.-+-+...+..++...-.|+++-.++++.
T Consensus       157 ~~~~~~i~~l~~~~~~l~~~~~~iaaeq~~l~~~~~eq~~q~~kl~~~~~E~kk~~~~l~~  217 (420)
T COG4942         157 PARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNS  217 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5666667777766666666666665555555555555555555555555555555554433

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=96.22  E-value=0.24  Score=44.85  Aligned_cols=96  Identities=14%  Similarity=0.236  Sum_probs=49.7

Q ss_pred             hHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhH--hHHHHHHHHHHHHHHHh
Q 038837           68 DKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKAL--DAEDRLEEVSLQVEKMS  145 (287)
Q Consensus        68 Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~--dAEkkv~eL~sklek~~  145 (287)
                      |.-=.+++.-|+.-.+|+-+|+..--.+.++..+++..+.....++.+.+.....|+..+.  .... -++|+.+|+.++
T Consensus        53 e~~e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r~~~~klk~~~~el~k~~~~l~~L~~L~~dknL~e-ReeL~~kL~~~~  131 (194)
T PF15619_consen   53 EDTEAELPQLLQRHNEEVRVLRERLRKSQEQERELERKLKDKDEELLKTKDELKHLKKLSEDKNLAE-REELQRKLSQLE  131 (194)
T ss_pred             HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchh-HHHHHHHHHHHH
Confidence            3333666666777777777665544444444444444444444444444444443333222  1111 256666666666


Q ss_pred             hhhHHHHHHHHHHHHHHHH
Q 038837          146 EIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       146 ki~~EQ~~qIqk~E~Alk~  164 (287)
                      ....+.-.+|+.+|+-+..
T Consensus       132 ~~l~~~~~ki~~Lek~leL  150 (194)
T PF15619_consen  132 QKLQEKEKKIQELEKQLEL  150 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            6666666666666664443

>TIGR00606 rad50 rad50

Probab=96.11  E-value=1.1  Score=50.44  Aligned_cols=23  Identities=9%  Similarity=0.209  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 038837          221 QHQFKRFFLAFKKFHHELQGFIK  243 (287)
Q Consensus       221 ~~~~k~~l~sA~~yH~qvQ~~I~  243 (287)
                      +..|+.-+..-...+.+++.++.
T Consensus       943 ~~~~~~~~~~~~~~~~~i~~y~~  965 (1311)
T TIGR00606       943 VNDIKEKVKNIHGYMKDIENKIQ  965 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555443

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

>PF04582 Reo_sigmaC: Reovirus sigma C capsid protein; InterPro: IPR007662 Protein sigmaC in its native state was shown to be a homotrimer

Probab=96.11  E-value=0.01  Score=57.72  Aligned_cols=140  Identities=16%  Similarity=0.230  Sum_probs=30.6

Q ss_pred             HHHHhhccccCcccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccch
Q 038837           14 LFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSS   93 (287)
Q Consensus        14 ~~~~~~~~s~~~~~~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~   93 (287)
                      +.+++++||---..+     .+|.+++.++.+||+.++..+.-+.+=...+..++-.++++...|+.++++|.+|     
T Consensus        13 V~LILslTss~s~s~-----GDLs~I~eRLsaLEssv~sL~~SVs~lss~iSdLss~L~~l~~sl~~~~s~L~sL-----   82 (326)
T PF04582_consen   13 VGLILSLTSSISTSP-----GDLSPIRERLSALESSVASLSDSVSSLSSTISDLSSDLQDLASSLADMTSELNSL-----   82 (326)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHhhhcccCCCCCCc-----ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----
Confidence            456777776422222     5788999999999999999886666666666666666666666666666666555     


Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Q 038837           94 RAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMA  165 (287)
Q Consensus        94 ~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~a  165 (287)
                        ...|..|+..|..|..++-.........++-..+.-..|..+...+-+|..-+.-|--.|-.+|+.++--
T Consensus        83 --sstV~~lq~Sl~~lsssVs~lS~~ls~h~ssIS~Lqs~v~~lsTdvsNLksdVSt~aL~ItdLe~RV~~L  152 (326)
T PF04582_consen   83 --SSTVTSLQSSLSSLSSSVSSLSSTLSDHSSSISDLQSSVSALSTDVSNLKSDVSTQALNITDLESRVKAL  152 (326)
T ss_dssp             -------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHHHhhhHHhhhhhhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhcchHhhHHHHHHHH
Confidence              2345566666666666666666777777777778888889999999999999999999999999988743

It was demonstrated that the sigmaC subunits are not covalently bound via disulphide linkages and the formation of an intrachain disulphide bond between the two cysteine residues of the sigmaC polypeptide may have a negative effect on oligomer stability. The susceptibility of the trimer to pH, temperature, ionic strength, chemical denaturants and detergents indicates that hydrophobic interactions contribute much more to oligomer stability than do ionic interactions and hydrogen bonding [].; PDB: 2VRS_C 2JJL_A 2BSF_A 2BT7_A 2BT8_A.

>PRK03918 chromosome segregation protein; Provisional

Probab=96.11  E-value=0.43  Score=50.44  Aligned_cols=28  Identities=14%  Similarity=0.262  Sum_probs=11.2

Q ss_pred             hHHhhhHhHHHHHHHHHHHHHHHhhhhH
Q 038837          122 NLESKALDAEDRLEEVSLQVEKMSEIVT  149 (287)
Q Consensus       122 ~LEsrA~dAEkkv~eL~sklek~~ki~~  149 (287)
                      .++.+...++.++.++..+++.+++...
T Consensus       663 ~l~~~~~~l~~~l~~l~~~~~~l~~~i~  690 (880)
T PRK03918        663 ELREEYLELSRELAGLRAELEELEKRRE  690 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444444444444444333333

>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=96.10  E-value=0.021  Score=44.12  Aligned_cols=65  Identities=18%  Similarity=0.254  Sum_probs=42.3

Q ss_pred             HhHHhHHHhhhHHHHHHHHhhhhccchhHH-------HHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHH
Q 038837           67 RDKLVDDMTNKIHHLQSLLSKIKDDSSRAE-------ERLNALEEEIRLLWAASRKNNFDIHNLESKALDAE  131 (287)
Q Consensus        67 ~Ek~i~eks~kI~sLqsEi~sLkk~s~~ae-------e~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAE  131 (287)
                      +++.+.||...|+.|+.|-+.|-+.-..-.       .++.++|+++..|++.+++...+...|+.++..+|
T Consensus         3 l~~~l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~l~~~E   74 (74)
T PF12329_consen    3 LEKKLAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEERLKRAE   74 (74)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence            456677777777777777777722222211       33677777777777777777777777777766543

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.

>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=96.06  E-value=0.35  Score=51.99  Aligned_cols=62  Identities=18%  Similarity=0.375  Sum_probs=47.6

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHhhhh------------cCchh-hHHHHhHHhHHHhhhHHHH-------HHHHh
Q 038837           27 HSQQHLIAELQDAKLKIAGLETMLEESIRKV------------NGKSN-YIEERDKLVDDMTNKIHHL-------QSLLS   86 (287)
Q Consensus        27 ~~~~~l~~eL~qLk~kIa~LES~i~e~~qel------------~~Kd~-~l~e~Ek~i~eks~kI~sL-------qsEi~   86 (287)
                      .++... ..+..+...+.+|++.++.+.++.            -.+|. ..+-..++|.+|..+|.+|       ++||.
T Consensus       177 ~~~~~~-~~~~~~e~~~~~le~lle~~e~~~~~~r~~l~~~~~~~~~~a~t~alq~~ie~Kd~ki~~lEr~l~~le~Ei~  255 (775)
T PF10174_consen  177 EDNEAL-RRIREAEARIMRLESLLERKEKEHMEAREQLHRRLQMERDDAETEALQTVIEEKDTKIASLERMLRDLEDEIY  255 (775)
T ss_pred             hhhHHH-HHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444 478999999999999999998888            13333 4445688889999998886       99999


Q ss_pred             hhh
Q 038837           87 KIK   89 (287)
Q Consensus        87 sLk   89 (287)
                      .|+
T Consensus       256 ~L~  258 (775)
T PF10174_consen  256 RLR  258 (775)
T ss_pred             HHH
Confidence            993

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 [].

>PRK03918 chromosome segregation protein; Provisional

Probab=96.03  E-value=0.28  Score=51.88  Aligned_cols=35  Identities=14%  Similarity=0.150  Sum_probs=14.2

Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      +.+..+.+...++.+..+.+.++..+..+++.+.+
T Consensus       660 ~~~~l~~~~~~l~~~l~~l~~~~~~l~~~i~~l~~  694 (880)
T PRK03918        660 EYEELREEYLELSRELAGLRAELEELEKRREEIKK  694 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333344444444444444444444444443333

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

Probab=95.99  E-value=0.043  Score=48.83  Aligned_cols=96  Identities=19%  Similarity=0.248  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLW  110 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~  110 (287)
                      .++.||.++...-..+..++...+.+       +.+++..+.+....|..|+.++..|...-.+-++.+.++++-++.|+
T Consensus        78 ~l~~ELael~r~~~el~~~L~~~~~~-------l~~l~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~  150 (194)
T PF08614_consen   78 KLQEELAELYRSKGELAQQLVELNDE-------LQELEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQ  150 (194)
T ss_dssp             -------------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccc-------cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555555555544       44444555555555555666655553333444566666666666666


Q ss_pred             HHHhhhhhhhhhHHhhhHhHHHH
Q 038837          111 AASRKNNFDIHNLESKALDAEDR  133 (287)
Q Consensus       111 ~elekqn~~~~~LEsrA~dAEkk  133 (287)
                      +|+-..|-....+|.+....++-
T Consensus       151 DE~~~L~l~~~~~e~k~~~l~~E  173 (194)
T PF08614_consen  151 DELQALQLQLNMLEEKLRKLEEE  173 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666665555444444443333

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.

>PHA02562 46 endonuclease subunit; Provisional

Probab=95.98  E-value=0.68  Score=46.38  Aligned_cols=43  Identities=12%  Similarity=0.152  Sum_probs=19.0

Q ss_pred             HHHhhhHHHHHHHHhhhhccchh-------HHHHHHHHHHHHHHHHHHHh
Q 038837           72 DDMTNKIHHLQSLLSKIKDDSSR-------AEERLNALEEEIRLLWAASR  114 (287)
Q Consensus        72 ~eks~kI~sLqsEi~sLkk~s~~-------aee~i~eLEkQVe~L~~ele  114 (287)
                      .....+|..|++++.++..+-.+       .+..+..++.++..+++++.
T Consensus       230 ~~l~~~l~~l~~~i~~l~~~i~~~~~~L~~l~~~~~~~~~~l~~~~~~~~  279 (562)
T PHA02562        230 KTIKAEIEELTDELLNLVMDIEDPSAALNKLNTAAAKIKSKIEQFQKVIK  279 (562)
T ss_pred             HHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444555555555333333       22334444444444444443

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

Probab=95.95  E-value=0.24  Score=54.56  Aligned_cols=97  Identities=19%  Similarity=0.177  Sum_probs=66.9

Q ss_pred             HHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHH--HhhhhccchhHHHH-HHHHHHHHHHHHHHHhhhhhhhhhH
Q 038837           47 ETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSL--LSKIKDDSSRAEER-LNALEEEIRLLWAASRKNNFDIHNL  123 (287)
Q Consensus        47 ES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsE--i~sLkk~s~~aee~-i~eLEkQVe~L~~elekqn~~~~~L  123 (287)
                      |..|++....++..+..+.+.++.++.+...|++|.|.  ....+-+..+...+ |...+++|+...+.+++...+.+.+
T Consensus       688 e~~l~e~~~~~~~l~~~~~q~~~~~~~~~~em~el~n~~e~~~~~~~~~~~l~~ei~~~~~eIe~~~~~~e~l~~e~e~~  767 (1074)
T KOG0250|consen  688 EKNLEELEKKLRELSEHIEQIKRRIRKKRAEMTELKNTAEEKQVDISKLEDLAREIKKKEKEIEEKEAPLEKLKEELEHI  767 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566666666667777778888888888888888883  44444445554443 6777777777777777777777777


Q ss_pred             HhhhHhHHHHHHHHHHHHHH
Q 038837          124 ESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus       124 EsrA~dAEkkv~eL~sklek  143 (287)
                      +.+++..+........++..
T Consensus       768 ~~e~~e~~~~~~~~~~~l~~  787 (1074)
T KOG0250|consen  768 ELEAQELEEYYAAGREKLQG  787 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            77777777766655555543

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

Probab=95.87  E-value=0.56  Score=44.70  Aligned_cols=27  Identities=11%  Similarity=0.135  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKV   57 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel   57 (287)
                      .+..++.+++.++.+|+..+......+
T Consensus        78 ~~~~~l~~l~~~~~~l~a~~~~l~~~~  104 (423)
T TIGR01843        78 DVEADAAELESQVLRLEAEVARLRAEA  104 (423)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344566666666666655554433333

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.

>PF15619 Lebercilin: Ciliary protein causing Leber congenital amaurosis disease

Probab=95.78  E-value=1.4  Score=39.86  Aligned_cols=118  Identities=14%  Similarity=0.175  Sum_probs=78.2

Q ss_pred             hhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHH---------------HHhhhhh
Q 038837           54 IRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWA---------------ASRKNNF  118 (287)
Q Consensus        54 ~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~---------------elekqn~  118 (287)
                      .+.|..-++.=.++-.+|.-....|..|...+-..+....+.+.++.+.+.++.++.+               +-++...
T Consensus        46 ~kAL~k~e~~e~~Lpqll~~h~eEvr~Lr~~LR~~q~~~r~~~~klk~~~~el~k~~~~l~~L~~L~~dknL~eReeL~~  125 (194)
T PF15619_consen   46 EKALQKYEDTEAELPQLLQRHNEEVRVLRERLRKSQEQERELERKLKDKDEELLKTKDELKHLKKLSEDKNLAEREELQR  125 (194)
T ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchhHHHHHH
Confidence            3345445555567788888889999999888877766666666665555544444442               3445566


Q ss_pred             hhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHH----HHHHHHHHHHHHHHHHHHHHH
Q 038837          119 DIHNLESKALDAEDRLEEVSLQVEKMSEIVTE----QWIQIQHLEQALHMAELRAAN  171 (287)
Q Consensus       119 ~~~~LEsrA~dAEkkv~eL~sklek~~ki~~E----Q~~qIqk~E~Alk~ae~~~~k  171 (287)
                      +.+.++.++.++++++.+|.-+++-..+.-.-    ...++..+...++.+.++.-.
T Consensus       126 kL~~~~~~l~~~~~ki~~Lek~leL~~k~~~rql~~e~kK~~~~~~~~~~l~~ei~~  182 (194)
T PF15619_consen  126 KLSQLEQKLQEKEKKIQELEKQLELENKSFRRQLASEKKKHKEAQEEVKSLQEEIQR  182 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77778888888888888888888776665332    245666666666666665443

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=95.63  E-value=0.56  Score=54.82  Aligned_cols=140  Identities=23%  Similarity=0.229  Sum_probs=72.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      ..++.+..++-..+..+++++++..+.........++.+..+++....|..++..+..+.......+.++..|++++..+
T Consensus       897 ~~~~~~k~~le~~l~~~~~~~e~~ee~~~~le~~~~~~~~e~~~l~~~~~~~E~~~~k~~~Ek~~~e~~~~~l~~e~~~~  976 (1930)
T KOG0161|consen  897 ERLRAEKQELEKELKELKERLEEEEEKNAELERKKRKLEQEVQELKEQLEELELTLQKLELEKNAAENKLKNLEEEINSL  976 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444445555555555555555544444444444444555555666666555555555444555556666666666655


Q ss_pred             HHHHhhhhhhhhhHH--------------hhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 038837          110 WAASRKNNFDIHNLE--------------SKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRA  169 (287)
Q Consensus       110 ~~elekqn~~~~~LE--------------srA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~  169 (287)
                      ...+.+.++++-.+|              .+++.+.|...-|.+.++.+++....++....++|.+.+-.+.++
T Consensus       977 ~e~~~kL~kekk~lEe~~~~l~~~l~~~eek~~~l~k~~~kle~~l~~le~~le~e~~~r~e~Ek~~rkle~el 1050 (1930)
T KOG0161|consen  977 DENISKLSKEKKELEERIRELQDDLQAEEEKAKSLNKAKAKLEQQLDDLEVTLEREKRIRMELEKAKRKLEGEL 1050 (1930)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555554444444444              444444444444445555555555555555555554444333333

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

Probab=95.59  E-value=0.44  Score=43.69  Aligned_cols=91  Identities=20%  Similarity=0.294  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhh-------hHHHHHHHHhhhhccchhH-------
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTN-------KIHHLQSLLSKIKDDSSRA-------   95 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~-------kI~sLqsEi~sLkk~s~~a-------   95 (287)
                      ..||.+|.+++.+....++.+.+....+.+|...++.+++.++.+.+       ++..|..|+..|+.....+       
T Consensus        34 v~Lr~ql~e~~~~l~~~~~~~~~l~~~~~~K~~ELE~ce~ELqr~~~Ea~lLrekl~~le~El~~Lr~~l~~~~~~~~~~  113 (202)
T PF06818_consen   34 VSLRAQLRELRAELRNKESQIQELQDSLRTKQLELEVCENELQRKKNEAELLREKLGQLEAELAELREELACAGRLKRQC  113 (202)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhHhHHHhHHHHHHHhCHHHHhhhhhhhhHHHHHHHHHHHHhhccchhhh
Confidence            56788888888888888888888888888888888888777666554       4444455555442221111       


Q ss_pred             ----------------HHHHHHHHHHHHHHHHHHhhhhhhh
Q 038837           96 ----------------EERLNALEEEIRLLWAASRKNNFDI  120 (287)
Q Consensus        96 ----------------ee~i~eLEkQVe~L~~elekqn~~~  120 (287)
                                      ..-+..|..+|+.|+.+|..-+...
T Consensus       114 ~~l~~~deak~~~~~~~~~~~~l~~e~erL~aeL~~er~~~  154 (202)
T PF06818_consen  114 QLLSESDEAKAQRQAGEDELGSLRREVERLRAELQRERQRR  154 (202)
T ss_pred             ccccccchhHHhhccccccchhHHHHHHHHHHHHHHHHHhH
Confidence                            1115667778888887777655443

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

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

Probab=95.48  E-value=1  Score=47.13  Aligned_cols=83  Identities=16%  Similarity=0.171  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhcc---chhHHHHHHHHHHHHHHH
Q 038837           33 IAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDD---SSRAEERLNALEEEIRLL  109 (287)
Q Consensus        33 ~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~---s~~aee~i~eLEkQVe~L  109 (287)
                      ..++++|+.+|..|++.|++...+++.-...+.+.+..+.++......++.++...++-   -.++++++..|+..|+.-
T Consensus       327 ~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l~~k~~~lL~d~e~ni~kL~~~v~~s  406 (594)
T PF05667_consen  327 EQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKLKKKTVELLPDAEENIAKLQALVEAS  406 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            46778888888888888888888888888888999999999999999999988755433   556777776666666554


Q ss_pred             HHHHhh
Q 038837          110 WAASRK  115 (287)
Q Consensus       110 ~~elek  115 (287)
                      ..-+..
T Consensus       407 ~~rl~~  412 (594)
T PF05667_consen  407 EQRLVE  412 (594)
T ss_pred             HHHHHH
Confidence            443333

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

Probab=95.45  E-value=0.085  Score=46.93  Aligned_cols=108  Identities=15%  Similarity=0.238  Sum_probs=45.6

Q ss_pred             HhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhH
Q 038837           70 LVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVT  149 (287)
Q Consensus        70 ~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~  149 (287)
                      .+.+.+.++..|+.|+..+.+..+....++..+..+++.|...+......+..++......+.++..|...++...+.+.
T Consensus        68 ~~~~le~~~~~l~~ELael~r~~~el~~~L~~~~~~l~~l~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e  147 (194)
T PF08614_consen   68 QISSLEQKLAKLQEELAELYRSKGELAQQLVELNDELQELEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANE  147 (194)
T ss_dssp             ----------------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555677777888888887777777788888888888888888888888888888888888888888888877777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 038837          150 EQWIQIQHLEQALHMAELRAANVQRQLM  177 (287)
Q Consensus       150 EQ~~qIqk~E~Alk~ae~~~~k~q~ea~  177 (287)
                      ....-+.-+-=.+-++|+.+.+.+.|-.
T Consensus       148 ~l~DE~~~L~l~~~~~e~k~~~l~~En~  175 (194)
T PF08614_consen  148 ILQDELQALQLQLNMLEEKLRKLEEENR  175 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7666666666666667777666666643

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.

>PRK04863 mukB cell division protein MukB; Provisional

Probab=95.45  E-value=0.81  Score=52.49  Aligned_cols=135  Identities=19%  Similarity=0.168  Sum_probs=76.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      ...|.=+++.    +.......+..++|..++..+.+.+.++.+...++..|+.+.+...+.....++ +..+..++..+
T Consensus       279 eERR~liEEA----ag~r~rk~eA~kkLe~tE~nL~rI~diL~ELe~rL~kLEkQaEkA~kyleL~ee-~lr~q~ei~~l  353 (1486)
T PRK04863        279 NERRVHLEEA----LELRRELYTSRRQLAAEQYRLVEMARELAELNEAESDLEQDYQAASDHLNLVQT-ALRQQEKIERY  353 (1486)
T ss_pred             HHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence            3444444444    556688888888899999999999999999999999999998877443222221 22223334444


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRA  169 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~  169 (287)
                      ..+++..+......+.....++..+.++..+++.++.-..+...++.++++++..++.+.
T Consensus       354 ~~~LeELee~Lee~eeeLeeleeeleeleeEleelEeeLeeLqeqLaelqqel~elQ~el  413 (1486)
T PRK04863        354 QADLEELEERLEEQNEVVEEADEQQEENEARAEAAEEEVDELKSQLADYQQALDVQQTRA  413 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444444444444444444444444444444444444444444433

>KOG0161 consensus Myosin class II heavy chain [Cytoskeleton]

Probab=95.42  E-value=0.63  Score=54.47  Aligned_cols=44  Identities=16%  Similarity=0.209  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038837          132 DRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQ  175 (287)
Q Consensus       132 kkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~e  175 (287)
                      +....|-..+..++....+-+.++.++++-++..+.++...+.+
T Consensus      1041 k~~rkle~el~~~~e~~~~~~~~~~el~~~l~kke~El~~l~~k 1084 (1930)
T KOG0161|consen 1041 KAKRKLEGELKDLQESIEELKKQKEELDNQLKKKESELSQLQSK 1084 (1930)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333334443344444444444444444444444444444333

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

Probab=95.38  E-value=0.75  Score=40.13  Aligned_cols=23  Identities=17%  Similarity=0.273  Sum_probs=8.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhc
Q 038837           36 LQDAKLKIAGLETMLEESIRKVN   58 (287)
Q Consensus        36 L~qLk~kIa~LES~i~e~~qel~   58 (287)
                      +.++..++.+++..+.+...++.
T Consensus        90 l~~l~~el~~l~~~~~~~~~~l~  112 (191)
T PF04156_consen   90 LQQLQEELDQLQERIQELESELE  112 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333334444444333333333

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 [].

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

Probab=95.35  E-value=0.91  Score=47.74  Aligned_cols=116  Identities=21%  Similarity=0.241  Sum_probs=72.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhh-------hhcCchhhHHHHhHHhHHHhhhHHHHHH---HHhhhhccchhHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIR-------KVNGKSNYIEERDKLVDDMTNKIHHLQS---LLSKIKDDSSRAEERL   99 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~q-------el~~Kd~~l~e~Ek~i~eks~kI~sLqs---Ei~sLkk~s~~aee~i   99 (287)
                      ..|..++..|+-.+..|+..+....+       -...+++-|.++|..+++.........+   .+.|-|.+-+.|-.+.
T Consensus        83 ~~Lq~E~~~L~kElE~L~~qlqaqv~~ne~Ls~L~~EqEerL~ELE~~le~~~e~~~D~~kLLe~lqsdk~t~SRAlsQN  162 (617)
T PF15070_consen   83 QQLQAEAEHLRKELESLEEQLQAQVENNEQLSRLNQEQEERLAELEEELERLQEQQEDRQKLLEQLQSDKATASRALSQN  162 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHhH
Confidence            46667777777777777666554432       2345666667766666655555433333   3334466677788888


Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHH-HHHHHHHHHHhh
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRL-EEVSLQVEKMSE  146 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv-~eL~sklek~~k  146 (287)
                      .+|.+|+..|+...-+.+.++-.|.+... +|..| .+|..++..++.
T Consensus       163 ~eLK~QL~Elq~~Fv~ltne~~elt~~lq-~Eq~~~keL~~kl~~l~~  209 (617)
T PF15070_consen  163 RELKEQLAELQDAFVKLTNENMELTSALQ-SEQHVKKELQKKLGELQE  209 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHhhHHHH-HHHHHHHHHHHHHHHHHH
Confidence            99999999999888888777655544433 33333 355555555543

>TIGR00606 rad50 rad50

Probab=95.28  E-value=0.84  Score=51.33  Aligned_cols=23  Identities=26%  Similarity=0.293  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Q 038837           32 LIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      +..+++.++.++..++..++...
T Consensus       756 le~~l~~~~~~le~~~~~l~~~~  778 (1311)
T TIGR00606       756 VNRDIQRLKNDIEEQETLLGTIM  778 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444333

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

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.27  E-value=1.8  Score=41.34  Aligned_cols=57  Identities=11%  Similarity=0.074  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQ  156 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIq  156 (287)
                      .-.+++=..|..--.+.+.+..+|++...+.|..+..|+++.....+....-+....
T Consensus       151 e~qk~dk~~Le~kq~~l~~~~e~l~al~~e~e~~~~~L~~qk~e~~~l~~~~aa~~a  207 (265)
T COG3883         151 EQQKEDKKSLEEKQAALEDKLETLVALQNELETQLNSLNSQKAEKNALIAALAAKEA  207 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444554455566667777777888888888888887776666554444433

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

Probab=95.24  E-value=0.7  Score=43.35  Aligned_cols=47  Identities=23%  Similarity=0.332  Sum_probs=19.9

Q ss_pred             HhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Q 038837          113 SRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLE  159 (287)
Q Consensus       113 lekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E  159 (287)
                      .++.+.+.++++.+...+++.+.+|.-+++++++--++-..++..+|
T Consensus        91 ~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~~e  137 (239)
T COG1579          91 LRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLE  137 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444444444443344444333

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=95.11  E-value=1.6  Score=48.83  Aligned_cols=58  Identities=12%  Similarity=0.157  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHH-hHHhHHHhhhHHHHHHHHhh
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEER-DKLVDDMTNKIHHLQSLLSK   87 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~-Ek~i~eks~kI~sLqsEi~s   87 (287)
                      ..++.+++.++..+..|.+...+...+.+.--..|+.. ......+..++..++.+...
T Consensus       355 ~~~~~~~~~l~~~~~~Lt~~~~di~~ky~~~~~~l~~~~~~~~~~~~~~~~~~~e~~~~  413 (1201)
T PF12128_consen  355 PEWRNELENLQEQLDLLTSKHQDIESKYNKLKQKLEEAFNRQQERLQAQQDEIREEKAE  413 (1201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666777777777777776666666555544444332 44455555555555555443

>PF05701 WEMBL: Weak chloroplast movement under blue light; InterPro: IPR008545 This family consists of several plant proteins of unknown function

Probab=95.02  E-value=0.86  Score=46.63  Aligned_cols=72  Identities=13%  Similarity=0.280  Sum_probs=32.4

Q ss_pred             hHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHH
Q 038837           71 VDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVE  142 (287)
Q Consensus        71 i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skle  142 (287)
                      .......+.+...|++..+..--.+.+-+..|..-|+.|+.++++.+.++..+..+...+...|..|+.++.
T Consensus       276 ~~~~~~~l~s~~~ELe~ak~~L~~~k~E~~~L~~~vesL~~ELe~~K~el~~lke~e~~a~~~v~~L~~eL~  347 (522)
T PF05701_consen  276 SSELQSSLASAKKELEEAKKELEKAKEEASSLRASVESLRSELEKEKEELERLKEREKEASSEVSSLEAELN  347 (522)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhHHHHHH
Confidence            333334444444444444333333333344444444444444444444444444444444444444444443

Several sequences in this family are described as being myosin heavy chain-like.

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

Probab=94.99  E-value=0.42  Score=50.83  Aligned_cols=105  Identities=21%  Similarity=0.179  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHH-------HhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           37 QDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDD-------MTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        37 ~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~e-------ks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      +.+|.+...||+.+.....||+.|++.+..+|..+++       ...++..|.+.+              ..|++.-..|
T Consensus       541 e~~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr~~~~e~~~~~e~L~~aL--------------~amqdk~~~L  606 (697)
T PF09726_consen  541 ESCRQRRRQLESELKKLRRELKQKEEQIRELESELQELRKYEKESEKDTEVLMSAL--------------SAMQDKNQHL  606 (697)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHH--------------HHHHHHHHHH
Confidence            4589999999999999999999999999998876632       223444455544              3344444444


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHH
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQI  155 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qI  155 (287)
                      .+-|-.-+.=+-.|=+-.+||.+.++.+...+-+=++-..|-|.+|
T Consensus       607 E~sLsaEtriKldLfsaLg~akrq~ei~~~~~~~~d~ei~~lk~ki  652 (697)
T PF09726_consen  607 ENSLSAETRIKLDLFSALGDAKRQLEIAQGQLRKKDKEIEELKAKI  652 (697)
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445444444444555556666666666555555444444444333

; GO: 0016021 integral to membrane

>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []

Probab=94.85  E-value=0.58  Score=44.97  Aligned_cols=117  Identities=19%  Similarity=0.199  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 038837           41 LKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDI  120 (287)
Q Consensus        41 ~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~  120 (287)
                      -||..||++++...+|=.-|---|+-+|--.+---.+...=.++++.||+..-..-+....||+..++|.+|+---....
T Consensus        18 qKIqelE~QldkLkKE~qQrQfQleSlEAaLqKQKqK~e~ek~e~s~LkREnq~l~e~c~~lek~rqKlshdlq~Ke~qv   97 (307)
T PF10481_consen   18 QKIQELEQQLDKLKKERQQRQFQLESLEAALQKQKQKVEEEKNEYSALKRENQSLMESCENLEKTRQKLSHDLQVKESQV   97 (307)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHhhHHHhhhHHHH
Confidence            48999999999988877777777777776665555555555666666666666666667778888888888776666666


Q ss_pred             hhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 038837          121 HNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMY  178 (287)
Q Consensus       121 ~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~p  178 (287)
                      .-||...+-+.+                     +|..+|+-++.-+.+|-|.|..+.+
T Consensus        98 ~~lEgQl~s~Kk---------------------qie~Leqelkr~KsELErsQ~~~~~  134 (307)
T PF10481_consen   98 NFLEGQLNSCKK---------------------QIEKLEQELKRCKSELERSQQAASS  134 (307)
T ss_pred             HHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            666655555544                     6666666666666777777766653

Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].

>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=94.81  E-value=2.7  Score=38.32  Aligned_cols=25  Identities=32%  Similarity=0.308  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      ..++.+|.+++.....|...|++.-
T Consensus        23 ~~~~~~l~~~~~~~~~l~~~i~~~l   47 (302)
T PF10186_consen   23 LELRSELQQLKEENEELRRRIEEIL   47 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566777777777777777777644

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

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=94.75  E-value=0.65  Score=48.36  Aligned_cols=84  Identities=13%  Similarity=0.205  Sum_probs=56.8

Q ss_pred             HHhHHHhhhHHHHHHHHhhh--hccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837           69 KLVDDMTNKIHHLQSLLSKI--KDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus        69 k~i~eks~kI~sLqsEi~sL--kk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      +.+.+...+|..++.+++.+  +-...++++.+..+++..+.+.+++.+.+.++..++.+....++.++.+..+++++.+
T Consensus       391 ~~~~~~~~~~~~~e~el~~l~~~l~~~~~~e~i~~l~e~l~~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~  470 (650)
T TIGR03185       391 DAKSQLLKELRELEEELAEVDKKISTIPSEEQIAQLLEELGEAQNELFRSEAEIEELLRQLETLKEAIEALRKTLDEKTK  470 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444445566666666666  2234445567777777777777777777777777777777777777777777777666


Q ss_pred             hhHHHH
Q 038837          147 IVTEQW  152 (287)
Q Consensus       147 i~~EQ~  152 (287)
                      ...+..
T Consensus       471 ~~~~~~  476 (650)
T TIGR03185       471 QKINAF  476 (650)
T ss_pred             HHHhhh
Confidence            655433

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.

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=94.74  E-value=0.84  Score=50.41  Aligned_cols=127  Identities=20%  Similarity=0.275  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHH----HhhhHHHHHHHHhhhhcc----chhHHHH-----
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDD----MTNKIHHLQSLLSKIKDD----SSRAEER-----   98 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~e----ks~kI~sLqsEi~sLkk~----s~~aee~-----   98 (287)
                      +-.++.+++..|-.+|++|.+...-++..++.++.+|+-+.+    ++.....|+.+|.-.+..    +..-++.     
T Consensus       739 ~~~~~~~~~e~v~e~~~~Ike~~~~~k~~~~~i~~lE~~~~d~~~~re~rlkdl~keik~~k~~~e~~~~~~ek~~~e~e  818 (1174)
T KOG0933|consen  739 LLDDLKELLEEVEESEQQIKEKERALKKCEDKISTLEKKMKDAKANRERRLKDLEKEIKTAKQRAEESSKELEKRENEYE  818 (1174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346788888999999999999888888888888888776654    556677777777766322    2222221     


Q ss_pred             -----HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 038837           99 -----LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHL  158 (287)
Q Consensus        99 -----i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~  158 (287)
                           ..+|+++++.++..++..+.....|++...+.+-+|...-..+++.+.-..+|+.+.+..
T Consensus       819 ~l~lE~e~l~~e~~~~k~~l~~~~~~~~~l~~e~~~l~~kv~~~~~~~~~~~~el~~~k~k~~~~  883 (1174)
T KOG0933|consen  819 RLQLEHEELEKEISSLKQQLEQLEKQISSLKSELGNLEAKVDKVEKDVKKAQAELKDQKAKQRDI  883 (1174)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHHHhh
Confidence                 467777777777777777777777777777777777777777777777666777665543

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

Probab=94.71  E-value=0.87  Score=49.07  Aligned_cols=131  Identities=21%  Similarity=0.250  Sum_probs=86.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLW  110 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~  110 (287)
                      +-......+..++-.+++.-++..-.|.+=.+.++.....++|.+.+|..|++++.+.++..+.++.++..+        
T Consensus       586 a~~~~~~el~eelE~le~eK~~Le~~L~~~~d~lE~~~~qL~E~E~~L~eLq~eL~~~keS~s~~E~ql~~~--------  657 (769)
T PF05911_consen  586 ADTSEKKELEEELEKLESEKEELEMELASCQDQLESLKNQLKESEQKLEELQSELESAKESNSLAETQLKAM--------  657 (769)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------
Confidence            333444455555555555555555555556677888888888888999999999988777777666665443        


Q ss_pred             HHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038837          111 AASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQ  175 (287)
Q Consensus       111 ~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~e  175 (287)
                            ......++.++.++|..++++..|+..++.-..+-+.--..++.--+-.++++.+...+
T Consensus       658 ------~e~~e~le~~~~~~e~E~~~l~~Ki~~Le~Ele~er~~~~e~~~kc~~Le~el~r~~~~  716 (769)
T PF05911_consen  658 ------KESYESLETRLKDLEAEAEELQSKISSLEEELEKERALSEELEAKCRELEEELERMKKE  716 (769)
T ss_pred             ------HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhHHHHHHHHHHhhhcc
Confidence                  33445777888888888888888888887776665555555555444444555554443

The function of this family is unknown.

>KOG4809 consensus Rab6 GTPase-interacting protein involved in endosome-to-TGN transport [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.64  E-value=1.6  Score=45.53  Aligned_cols=148  Identities=16%  Similarity=0.141  Sum_probs=90.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhH-------------------------------------
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVD-------------------------------------   72 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~-------------------------------------   72 (287)
                      ....-++-.|++.+..+|-.|+-..|.|+.||+.|.++....+                                     
T Consensus       239 ~~~~~e~~llr~t~~~~e~riEtqkqtl~ardesIkkLlEmLq~kgmg~~~~~~df~~~~~~a~~~~h~r~~~er~IerL  318 (654)
T KOG4809|consen  239 LTTKEEQFLLRSTDPSGEQRIETQKQTLDARDESIKKLLEMLQRKGMGRSNQPRDFTKANLSAHEMAHMRMKVERIIERL  318 (654)
T ss_pred             hhHHHHHHHHHhcCchHHHHHHHHHhhhhhHHHHHHHHHHHHHHhhcccccchhhHHHHHHhHHHHHhhhchHHHHHHHh
Confidence            3445677888999999999999999999999999998843322                                     


Q ss_pred             ---------HHhhhHHHHHHHHhhh-------hccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHH
Q 038837           73 ---------DMTNKIHHLQSLLSKI-------KDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEE  136 (287)
Q Consensus        73 ---------eks~kI~sLqsEi~sL-------kk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~e  136 (287)
                               ||..+|.+..-|.--|       .....+.+++...|.+..-.|.....+-.++.-++|--.+--..+.-.
T Consensus       319 keqr~rderE~~EeIe~~~ke~kdLkEkv~~lq~~l~eke~sl~dlkehassLas~glk~ds~Lk~leIalEqkkEec~k  398 (654)
T KOG4809|consen  319 KEQRERDERERLEEIESFRKENKDLKEKVNALQAELTEKESSLIDLKEHASSLASAGLKRDSKLKSLEIALEQKKEECSK  398 (654)
T ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHH
Confidence                     2222233222222222       111222333344555555555555555556655555555555555566


Q ss_pred             HHHHHHHHhhh------hHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 038837          137 VSLQVEKMSEI------VTEQWIQIQHLEQALHMAELRAANVQRQLM  177 (287)
Q Consensus       137 L~sklek~~ki------~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~  177 (287)
                      ++++|.+..++      +.|=-.+|+++|.+.-.-+.+..+||.+..
T Consensus       399 me~qLkkAh~~~ddar~~pe~~d~i~~le~e~~~y~de~~kaqaevd  445 (654)
T KOG4809|consen  399 MEAQLKKAHNIEDDARMNPEFADQIKQLEKEASYYRDECGKAQAEVD  445 (654)
T ss_pred             HHHHHHHHHHhhHhhhcChhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666666555      334446777777777777777777777654

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=94.36  E-value=0.69  Score=48.60  Aligned_cols=157  Identities=18%  Similarity=0.166  Sum_probs=96.3

Q ss_pred             ccCcccchHHHHHHH---HHHHHHHHHHHHHHHHH---hhhhcCchhhHHH-----H-hHHh-----HHHhhhHHHHHHH
Q 038837           22 SQNQQHSQQHLIAEL---QDAKLKIAGLETMLEES---IRKVNGKSNYIEE-----R-DKLV-----DDMTNKIHHLQSL   84 (287)
Q Consensus        22 s~~~~~~~~~l~~eL---~qLk~kIa~LES~i~e~---~qel~~Kd~~l~e-----~-Ek~i-----~eks~kI~sLqsE   84 (287)
                      |-+-.+++++|.+-+   +..+.|+.+.|..+.+.   .+...-|+..|..     . ++.+     +|+.-+++..--+
T Consensus       337 ~~~ddH~RDALAAA~kAY~~yk~kl~~vEr~~~~~g~~~d~~rika~VIrG~~l~eal~~~~e~~~p~e~~~~~~~e~~e  416 (652)
T COG2433         337 SVSDDHERDALAAAYKAYLAYKPKLEKVERKLPELGIWKDVERIKALVIRGYPLAEALSKVKEEERPREKEGTEEEERRE  416 (652)
T ss_pred             CCCCchHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHeecCCcHHHHHHHHHhhhccccccccccccccc
Confidence            446668899998887   67888999999988887   5555555554432     2 1111     1111222222222


Q ss_pred             HhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHH----------HHHHHHHHHHHhhhhHHHHHH
Q 038837           85 LSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDR----------LEEVSLQVEKMSEIVTEQWIQ  154 (287)
Q Consensus        85 i~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkk----------v~eL~sklek~~ki~~EQ~~q  154 (287)
                      +.+..+.-..-++++..|+.++..|+.+++.+..+++.|+++...+.++          ++.+-.+++.+++--.|++..
T Consensus       417 i~~~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~e~~~~  496 (652)
T COG2433         417 ITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKR  496 (652)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            2222222333455677777777777777777777777777777666544          445666677778888888888


Q ss_pred             HHHHHHHHHHHH-HHHHHHHhhhhc
Q 038837          155 IQHLEQALHMAE-LRAANVQRQLMY  178 (287)
Q Consensus       155 Iqk~E~Alk~ae-~~~~k~q~ea~p  178 (287)
                      +..||+-|-..+ |.+|.-.-+.+|
T Consensus       497 ve~L~~~l~~l~k~~~lE~sG~g~p  521 (652)
T COG2433         497 VEELERKLAELRKMRKLELSGKGTP  521 (652)
T ss_pred             HHHHHHHHHHHHHHHhhhhcCCCcc
Confidence            888887665544 333333344444

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=94.32  E-value=3.7  Score=42.31  Aligned_cols=100  Identities=16%  Similarity=0.170  Sum_probs=40.2

Q ss_pred             hHHhHHHhhhHHHHHHHHhhhhcc---chhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837           68 DKLVDDMTNKIHHLQSLLSKIKDD---SSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus        68 Ek~i~eks~kI~sLqsEi~sLkk~---s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      ...+.........|..|++.++..   +-+.-+.+..+++|+..|.+...........-..--.+.+++++++..+++.+
T Consensus       316 ~~~l~~~~e~~~~l~~Ei~~l~~sY~l~~~e~~~~~~lekeL~~Le~~~~~~~~~i~~~~~~ysel~e~leel~e~leei  395 (569)
T PRK04778        316 PDFLEHAKEQNKELKEEIDRVKQSYTLNESELESVRQLEKQLESLEKQYDEITERIAEQEIAYSELQEELEEILKQLEEI  395 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            334444444555555666655333   01111223333333333333333222222222222334444444555555444


Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHH
Q 038837          145 SEIVTEQWIQIQHLEQALHMAEL  167 (287)
Q Consensus       145 ~ki~~EQ~~qIqk~E~Alk~ae~  167 (287)
                      ++--.+-+..|+.++..-.-|+.
T Consensus       396 e~eq~ei~e~l~~Lrk~E~eAr~  418 (569)
T PRK04778        396 EKEQEKLSEMLQGLRKDELEARE  418 (569)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444444444333333

>PF05701 WEMBL: Weak chloroplast movement under blue light; InterPro: IPR008545 This family consists of several plant proteins of unknown function

Probab=94.32  E-value=3.2  Score=42.55  Aligned_cols=80  Identities=19%  Similarity=0.285  Sum_probs=35.5

Q ss_pred             HHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH
Q 038837           64 IEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus        64 l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      |......+......+.+|.+|++..|..-....++..+-...|..|..++.+.+.+...+.+.-.++.....++...|++
T Consensus       297 L~~~k~E~~~L~~~vesL~~ELe~~K~el~~lke~e~~a~~~v~~L~~eL~~~r~eLea~~~~e~~~k~~~~~l~~~Lqq  376 (522)
T PF05701_consen  297 LEKAKEEASSLRASVESLRSELEKEKEELERLKEREKEASSEVSSLEAELNKTRSELEAAKAEEEKAKEAMSELPKALQQ  376 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhHHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHH
Confidence            33333333333344444444444333333333344455555555555555555555555444444444333444444333

Several sequences in this family are described as being myosin heavy chain-like.

>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=94.29  E-value=2.3  Score=47.77  Aligned_cols=124  Identities=19%  Similarity=0.189  Sum_probs=74.4

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhcc----------------
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDD----------------   91 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~----------------   91 (287)
                      ..-..+..|.-+..+|.-||..|++...+       +.++++....-+..|+-+++|++.|..-                
T Consensus       399 ~~vk~~E~lK~~~~k~kKleke~ek~~~~-------~~e~e~~pe~~~~~i~~~~~ei~~L~~~~~~~~~~l~e~~~~l~  471 (1293)
T KOG0996|consen  399 EDVKREEKLKRLTSKIKKLEKEIEKARRK-------KSELEKAPEKARIEIQKCQTEIEQLEELLEKEERELDEILDSLK  471 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhh-------HHHHHhCchhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34445566666777777777777765533       3444444455555555566665544211                


Q ss_pred             ---chhHHHH------HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 038837           92 ---SSRAEER------LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHL  158 (287)
Q Consensus        92 ---s~~aee~------i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~  158 (287)
                         ....++.      ..-+.+++.....+++--.++..-|..+.+.+-++|++|..+|..+.....|-+.-+..+
T Consensus       472 ~~t~~~~~e~~~~ekel~~~~~~~n~~~~e~~vaesel~~L~~~~~~~~~~~e~lk~~L~~~~~~~~e~~~~l~~~  547 (1293)
T KOG0996|consen  472 QETEGIREEIEKLEKELMPLLKQVNEARSELDVAESELDILLSRHETGLKKVEELKGKLLASSESLKEKKTELDDL  547 (1293)
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               1111111      122334555556666777777778888888888999999999988776666555444433

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

Probab=94.23  E-value=3.4  Score=39.35  Aligned_cols=32  Identities=13%  Similarity=0.025  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHH
Q 038837          101 ALEEEIRLLWAASRKNNFDIHNLESKALDAED  132 (287)
Q Consensus       101 eLEkQVe~L~~elekqn~~~~~LEsrA~dAEk  132 (287)
                      ..+.++..++.++.....+...+++....++.
T Consensus       200 ~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~  231 (423)
T TIGR01843       200 ELERERAEAQGELGRLEAELEVLKRQIDELQL  231 (423)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444433333333333

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.

>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=94.19  E-value=1.7  Score=36.66  Aligned_cols=100  Identities=18%  Similarity=0.193  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHH
Q 038837           34 AELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAAS  113 (287)
Q Consensus        34 ~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~el  113 (287)
                      .-++.|.+.|.++|+.+....       +.++.++..=.+....|..|..+.+.           +.+..+++..|.+++
T Consensus        16 ~~ve~L~s~lr~~E~E~~~l~-------~el~~l~~~r~~l~~Eiv~l~~~~e~-----------~~~~~~~~~~L~~el   77 (120)
T PF12325_consen   16 QLVERLQSQLRRLEGELASLQ-------EELARLEAERDELREEIVKLMEENEE-----------LRALKKEVEELEQEL   77 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHH
Confidence            445666677777766666644       33444444444445555555555433           345555666677777


Q ss_pred             hhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHH
Q 038837          114 RKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQ  151 (287)
Q Consensus       114 ekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ  151 (287)
                      ...+.+-.++=-..++-...|+||-.+|.+|..+-..|
T Consensus        78 ~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~myr~Q  115 (120)
T PF12325_consen   78 EELQQRYQTLLELLGEKSEEVEELRADVQDLKEMYREQ  115 (120)
T ss_pred             HHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHH
Confidence            66666666665667777888999999988887776554

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 [].

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=94.18  E-value=2.3  Score=37.08  Aligned_cols=22  Identities=32%  Similarity=0.481  Sum_probs=16.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHH
Q 038837          148 VTEQWIQIQHLEQALHMAELRA  169 (287)
Q Consensus       148 ~~EQ~~qIqk~E~Alk~ae~~~  169 (287)
                      ..+-+..|..+++-..++++..
T Consensus       154 ~~~l~~~i~~l~rk~~~l~~~i  175 (177)
T PF13870_consen  154 VEELRKEIKELERKVEILEMRI  175 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Confidence            4456677888888888887764

>PRK01156 chromosome segregation protein; Provisional

Probab=94.14  E-value=1.6  Score=46.70  Aligned_cols=13  Identities=23%  Similarity=0.102  Sum_probs=5.5

Q ss_pred             cchhhhhhhhHHH
Q 038837          250 KLTAALANEELVF  262 (287)
Q Consensus       250 Elt~~lAtkeLvW  262 (287)
                      |-|.+|-.....+
T Consensus       833 Ept~~lD~~~~~~  845 (895)
T PRK01156        833 EPTAFLDEDRRTN  845 (895)
T ss_pred             CCCCcCCHHHHHH
Confidence            3344444444444

>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD

Probab=94.08  E-value=0.71  Score=48.05  Aligned_cols=54  Identities=13%  Similarity=0.141  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhcCc--hhhHHHHhHHhHHHhhhHHHHHHHHhh
Q 038837           34 AELQDAKLKIAGLETMLEESIRKVNGK--SNYIEERDKLVDDMTNKIHHLQSLLSK   87 (287)
Q Consensus        34 ~eL~qLk~kIa~LES~i~e~~qel~~K--d~~l~e~Ek~i~eks~kI~sLqsEi~s   87 (287)
                      .++.++..++..+|..|++..+.|..-  ++.++++++.+.+.+.+|..++.++..
T Consensus       391 ~~~~~~~~~~~~~e~el~~l~~~l~~~~~~e~i~~l~e~l~~l~~~l~~~~~~~~~  446 (650)
T TIGR03185       391 DAKSQLLKELRELEEELAEVDKKISTIPSEEQIAQLLEELGEAQNELFRSEAEIEE  446 (650)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345556666666666666666666543  234444454444444444444444433

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.

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=93.93  E-value=5  Score=36.73  Aligned_cols=38  Identities=21%  Similarity=0.337  Sum_probs=23.8

Q ss_pred             hhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 038837          125 SKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQAL  162 (287)
Q Consensus       125 srA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Al  162 (287)
                      +-+++-..++++|..-|+-.-.++.|-+-.|.++|+-+
T Consensus       151 a~l~e~t~~i~eL~~~ieEy~~~teeLR~e~s~LEeql  188 (193)
T PF14662_consen  151 AILSERTQQIEELKKTIEEYRSITEELRLEKSRLEEQL  188 (193)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33555555566666666666666666677777777654

>PF11570 E2R135: Coiled-coil receptor-binding R-domain of colicin E2; InterPro: IPR024566 Bacteriocins are protein antibiotics that kill bacteria closely related to the producing species

Probab=93.65  E-value=0.67  Score=40.00  Aligned_cols=101  Identities=15%  Similarity=0.197  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWA  111 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~  111 (287)
                      -++||++.+..|++|.+.+....+.+.+|-..+.+.++-+.|  .+|--+.---..+ -.+...-.+     .+|+.+++
T Consensus        13 a~aeL~~a~~~I~~~q~r~a~a~~~~~~r~seldqA~~~~~e--ae~k~~~~~a~~P-~~~~~~~wq-----lkvr~a~~   84 (136)
T PF11570_consen   13 ARAELDQADEDIATLQERQASAEQALNGRRSELDQANKKVKE--AEIKQDEFFANNP-PHEYGRGWQ-----LKVRRAQK   84 (136)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHCCCCTT-T-TSSCHHHHH-----HHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH--HHhcccccccCCC-ccccccHHH-----HHHHHHHH
Confidence            478999999999999999999999999999999999988888  2222111110111 112222222     56677777


Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhh
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEI  147 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki  147 (287)
                      ++.-.+.+..       -|++++.++++.|-..+.+
T Consensus        85 dv~nkq~~l~-------AA~~~l~~~~~el~~~~~a  113 (136)
T PF11570_consen   85 DVQNKQNKLK-------AAQKELNAADEELNRIQAA  113 (136)
T ss_dssp             HHHHHHHHHH-------HHHHHHHHHH-------HH
T ss_pred             HHHHHHHHHH-------HHHHHHHHhhhhhHHHHHH
Confidence            6655544433       4555555555555444333

Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism. Most colicins are able to translocate the outer membrane by a two-receptor system, where one receptor is used for the initial binding and the second for translocation. The initial binding is to cell surface receptors such as the porins OmpF, FepA, BtuB, Cir and FhuA. The presence of specific periplasmic proteins, such as TolA, TolB, TolC, or TonB, are required for translocation across the membrane []. Colicins are composed of domains with distinct functional roles. In general they contain a central R (receptor) domain that mediates receptor binding, an N-terminal T (translocation) domain that mediates translocation of the protein from the outer membrane receptor to the colicin's target within the cell, and a C-terminal C (catalytic) domain that performs the catalytic cleavage []. This entry represents the central R domain found in colicin-E2 and other colicins.; PDB: 2YSU_B 1UJW_B 2B5U_C 1JCH_A.

>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=93.55  E-value=4.6  Score=35.08  Aligned_cols=106  Identities=20%  Similarity=0.187  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWA  111 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~  111 (287)
                      +..+|...+++-+.|+..|.....+|..-..+.......-.-...-|.+|+.+++.+...-.+.+..+..+-++-+.|-+
T Consensus         8 v~~kLK~~~~e~dsle~~v~~LEreLe~~q~~~e~~~~daEn~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k   87 (140)
T PF10473_consen    8 VEEKLKESESEKDSLEDHVESLERELEMSQENKECLILDAENSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDK   87 (140)
T ss_pred             HHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555555555444433344444443333444445555555555533333344444444455555555


Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHH
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEV  137 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL  137 (287)
                      .+.+.+.+...||++-.+.+.-++++
T Consensus        88 ~lq~~q~kv~eLE~~~~~~~~~l~~~  113 (140)
T PF10473_consen   88 ELQKKQEKVSELESLNSSLENLLQEK  113 (140)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            55555555555555555544444433

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

>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells

Probab=93.55  E-value=4.4  Score=37.51  Aligned_cols=44  Identities=9%  Similarity=0.256  Sum_probs=24.0

Q ss_pred             HHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           45 GLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        45 ~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      .|++.++..+.+|++....+..-...+......+.+|..+++.|
T Consensus        21 ~l~~~~e~~~~~L~~~~~~~~~~~~~~~~~e~~l~~L~~d~~~L   64 (264)
T PF06008_consen   21 KLLSSIEDLTNQLRSYRSKLNPQKQQLDPLEKELESLEQDVENL   64 (264)
T ss_pred             HHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555555555555555555555555555555

Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex

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

Probab=93.42  E-value=2.9  Score=48.89  Aligned_cols=87  Identities=18%  Similarity=0.154  Sum_probs=56.5

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHH--------H
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEER--------L   99 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~--------i   99 (287)
                      +|..||.++...-.||..|.+.|+-...++--=+..+.++.-.++++...+..|+.+.+--|....+..++        +
T Consensus      1230 sN~~LRee~~~~~~k~qEl~~~i~kl~~el~plq~~l~el~~e~~~~~ael~~l~~e~~~wK~R~q~L~~k~k~~d~~~~ 1309 (1822)
T KOG4674|consen 1230 SNKVLREENEANLEKIQELRDKIEKLNFELAPLQNELKELKAELQEKVAELKKLEEENDRWKQRNQDLLEKYKDSDKNDY 1309 (1822)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHH
Confidence            34667777777777777777777777777666667777777777777777777777766555554443333        3


Q ss_pred             HHHHHHHHHHHHHHh
Q 038837          100 NALEEEIRLLWAASR  114 (287)
Q Consensus       100 ~eLEkQVe~L~~ele  114 (287)
                      ..|.++|..|++++.
T Consensus      1310 ~kL~~ei~~Lk~el~ 1324 (1822)
T KOG4674|consen 1310 EKLKSEISRLKEELE 1324 (1822)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            455555555555554

>PRK10929 putative mechanosensitive channel protein; Provisional

Probab=93.37  E-value=5.1  Score=45.00  Aligned_cols=155  Identities=16%  Similarity=0.241  Sum_probs=84.0

Q ss_pred             ccchHHHHHHHHHHHHH--------HHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHH
Q 038837           26 QHSQQHLIAELQDAKLK--------IAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEE   97 (287)
Q Consensus        26 ~~~~~~l~~eL~qLk~k--------Ia~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee   97 (287)
                      -++...++++|++++..        +..||.-++-. ++.+.=....++..+.+..-.+.+..++.+++++++.....-+
T Consensus        22 ~p~~~~iq~~l~~~~~~~~~~~k~~~~~l~~tl~~l-~~~~~~~~~~~~~~~~i~~ap~~~~~~~~~l~~~~~~~~~~~~  100 (1109)
T PRK10929         22 APDEKQITQELEQAKAAKTPAQAEIVEALQSALNWL-EERKGSLERAKQYQQVIDNFPKLSAELRQQLNNERDEPRSVPP  100 (1109)
T ss_pred             CCCHHHHHHHHHHhhcCCChhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhcccccccc
Confidence            36666788888877542        22333322221 1222223455666777888888888888888877433211111


Q ss_pred             H--HHHHHHHHHHHHHHHhhhhhhhhhHHhhh--------------HhHHHHHHHHHHHHHHH----hhhhHHHHHHHHH
Q 038837           98 R--LNALEEEIRLLWAASRKNNFDIHNLESKA--------------LDAEDRLEEVSLQVEKM----SEIVTEQWIQIQH  157 (287)
Q Consensus        98 ~--i~eLEkQVe~L~~elekqn~~~~~LEsrA--------------~dAEkkv~eL~sklek~----~ki~~EQ~~qIqk  157 (287)
                      +  ..+||.+.-.-..++-..+.+.....++.              .++-.++++.+..+...    ....+.| ...-+
T Consensus       101 ~~s~~~Leq~l~~~~~~L~~~q~~l~~~~~~~~~~~~~l~~~pq~~~~~~~~l~~i~~~L~~~~~~~~~l~~a~-~~~lq  179 (1109)
T PRK10929        101 NMSTDALEQEILQVSSQLLEKSRQAQQEQDRAREISDSLSQLPQQQTEARRQLNEIERRLQTLGTPNTPLAQAQ-LTALQ  179 (1109)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhchhhHHHHHHHHHHHHHHHhCCCCCCCcccHHH-HHHHH
Confidence            1  35555555544444444444444444444              55666666666655431    1122222 23346


Q ss_pred             HHHHHHHHHHHHHHHHhhhhchhhH
Q 038837          158 LEQALHMAELRAANVQRQLMYARCT  182 (287)
Q Consensus       158 ~E~Alk~ae~~~~k~q~ea~p~~~~  182 (287)
                      +|+++-.++..+.+....+.+.+..
T Consensus       180 ae~~~l~~~~~~l~~~l~s~~~~~~  204 (1109)
T PRK10929        180 AESAALKALVDELELAQLSANNRQE  204 (1109)
T ss_pred             HHHHHHHHHHHHHHHHHhccHHHHH
Confidence            7777777777777776666665543

>PRK10884 SH3 domain-containing protein; Provisional

Probab=93.25  E-value=0.83  Score=41.76  Aligned_cols=24  Identities=17%  Similarity=0.162  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q 038837           31 HLIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      .++..+.+|..+++.|+..+++..
T Consensus        90 ~~~~rlp~le~el~~l~~~l~~~~  113 (206)
T PRK10884         90 SLRTRVPDLENQVKTLTDKLNNID  113 (206)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555544433

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

Probab=93.15  E-value=7.4  Score=36.30  Aligned_cols=48  Identities=15%  Similarity=0.236  Sum_probs=22.5

Q ss_pred             hhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 038837          115 KNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQAL  162 (287)
Q Consensus       115 kqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Al  162 (287)
                      ..+.....+..........++.|..+++.+...+..--.+|..+|+-+
T Consensus       206 ~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~  253 (312)
T PF00038_consen  206 KSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELEQRL  253 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHHHH
Confidence            333333334444444445555555555555555554444444444433

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 ....

>PRK04778 septation ring formation regulator EzrA; Provisional

Probab=93.02  E-value=3.9  Score=42.18  Aligned_cols=105  Identities=19%  Similarity=0.232  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHH-------HHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAE-------ERLNALEE  104 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~ae-------e~i~eLEk  104 (287)
                      +..++++++.+|......|.+         ..+...+..+.+....|.+|-.-++.=....-.++       +.+..+++
T Consensus       254 i~~~i~~l~~~i~~~~~~l~~---------l~l~~~~~~~~~i~~~Id~Lyd~lekE~~A~~~vek~~~~l~~~l~~~~e  324 (569)
T PRK04778        254 IEKEIQDLKEQIDENLALLEE---------LDLDEAEEKNEEIQERIDQLYDILEREVKARKYVEKNSDTLPDFLEHAKE  324 (569)
T ss_pred             hHHHHHHHHHHHHHHHHHHHh---------cChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            445666666666665555555         55666666677777777777666664433322333       33566666


Q ss_pred             HHHHHHHHHhhhhhh---hhhHHhhhHhHHHHHHHHHHHHHHHh
Q 038837          105 EIRLLWAASRKNNFD---IHNLESKALDAEDRLEEVSLQVEKMS  145 (287)
Q Consensus       105 QVe~L~~elekqn~~---~~~LEsrA~dAEkkv~eL~sklek~~  145 (287)
                      +.+.|..+++..+..   .+.--.+....++.++++...++.+.
T Consensus       325 ~~~~l~~Ei~~l~~sY~l~~~e~~~~~~lekeL~~Le~~~~~~~  368 (569)
T PRK04778        325 QNKELKEEIDRVKQSYTLNESELESVRQLEKQLESLEKQYDEIT  368 (569)
T ss_pred             HHHHHHHHHHHHHHccccCchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666555   01112224444455555555544433

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

Probab=93.00  E-value=7.4  Score=40.90  Aligned_cols=118  Identities=15%  Similarity=0.203  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcC-------------------------------chhhHHHHhHHhHHHhhhH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNG-------------------------------KSNYIEERDKLVDDMTNKI   78 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~-------------------------------Kd~~l~e~Ek~i~eks~kI   78 (287)
                      .+|..+|++++..|..++..++....+++.                               .+.+|++++.+++..+.++
T Consensus       331 ~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l~~k~~~lL~d~e~ni~kL~~~v~~s~~rl  410 (594)
T PF05667_consen  331 EELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKLKKKTVELLPDAEENIAKLQALVEASEQRL  410 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHH
Confidence            677777777777777766555544433333                               3445555555555555555


Q ss_pred             HHHHHHHhhhhccchh----HHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhh
Q 038837           79 HHLQSLLSKIKDDSSR----AEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEI  147 (287)
Q Consensus        79 ~sLqsEi~sLkk~s~~----aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki  147 (287)
                      ..|+++-+.-...-.+    ..+....-+.+-.....+++..+.+...++..+..=|.....|..+++++.+-
T Consensus       411 ~~L~~qWe~~R~pL~~e~r~lk~~~~~~~~e~~~~~~~ik~~r~~~k~~~~e~~~Kee~~~qL~~e~e~~~k~  483 (594)
T PF05667_consen  411 VELAQQWEKHRAPLIEEYRRLKEKASNRESESKQKLQEIKELREEIKEIEEEIRQKEELYKQLVKELEKLPKD  483 (594)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence            5555544432111111    00111222233334445555666666666666666666666666666665443

>PF05483 SCP-1: Synaptonemal complex protein 1 (SCP-1); InterPro: IPR008827 Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex

Probab=93.00  E-value=7.3  Score=41.80  Aligned_cols=143  Identities=22%  Similarity=0.338  Sum_probs=104.8

Q ss_pred             hHHHHHHHHHHHHHHHH-------HHHHHHHH----hhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHH
Q 038837           29 QQHLIAELQDAKLKIAG-------LETMLEES----IRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEE   97 (287)
Q Consensus        29 ~~~l~~eL~qLk~kIa~-------LES~i~e~----~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee   97 (287)
                      +++|-++|...+.-...       ||..+.-.    .+-...|+..++++.+.-...+..++.|+..+.+|+....--..
T Consensus       291 qe~L~~eL~~~K~slq~~~~tq~~le~~lq~~~k~~~qlt~eKe~~~Ee~nk~k~~~s~~v~e~qtti~~L~~lL~~Eqq  370 (786)
T PF05483_consen  291 QEHLLQELEDIKQSLQESESTQKALEEDLQQATKTLIQLTEEKEAQMEELNKAKAQHSFVVTELQTTICNLKELLTTEQQ  370 (786)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46667777655544333       33333322    23335678888888888888899999999999999665555556


Q ss_pred             HHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 038837           98 RLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANV  172 (287)
Q Consensus        98 ~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~  172 (287)
                      ++..+|+|...|-.++.+-+.+.+..=---++-|-.+++|.-.|+.-++.-++ +.++.++...|+.++.++...
T Consensus       371 r~~~~ed~lk~l~~eLqkks~eleEmtk~k~~ke~eleeL~~~L~e~qkll~e-kk~~eki~E~lq~~eqel~~l  444 (786)
T PF05483_consen  371 RLKKNEDQLKILTMELQKKSSELEEMTKQKNNKEVELEELKKILAEKQKLLDE-KKQFEKIAEELQGTEQELTGL  444 (786)
T ss_pred             HHHHhHHHHHHHHHHHHHhhHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999988887755444455666688888888888886666 566888888899888887665

Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase [].; GO: 0007130 synaptonemal complex assembly, 0000795 synaptonemal complex

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

Probab=92.97  E-value=6.9  Score=35.44  Aligned_cols=144  Identities=16%  Similarity=0.160  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      ..|+.++.++|.+..+.+..+.+..++-+.=.+.|+..+..+.+...++...+..-.+|    ..+..++..+++++..|
T Consensus        30 ksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y~kdK~~L----~~~k~rl~~~ek~l~~L  105 (201)
T PF13851_consen   30 KSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNYEKDKQSL----QNLKARLKELEKELKDL  105 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Confidence            45788999999999999999999999999889999999988888877766655554333    23444556666666666


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH-HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK-MSEIVTEQWIQIQHLEQALHMAELRAANVQRQLM  177 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek-~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~  177 (287)
                      +-+-+-.......++..-.+...+.+..-..|.+ .+--|-=--++++.+..++...+..+..+-..+.
T Consensus       106 k~e~evL~qr~~kle~ErdeL~~kf~~~i~evqQk~~~kn~lLEkKl~~l~~~lE~keaqL~evl~~~n  174 (201)
T PF13851_consen  106 KWEHEVLEQRFEKLEQERDELYRKFESAIQEVQQKTGLKNLLLEKKLQALSEQLEKKEAQLNEVLAAAN  174 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            5554444444444443333333333322222211 0001111224566666666666666665555544

>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=92.94  E-value=3.2  Score=44.91  Aligned_cols=99  Identities=15%  Similarity=0.259  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      ..|+.+|.....+-..|-+.++....+|..|...+.++...+.........+.+||+-++..---.+.+|.-|.+.++.|
T Consensus       325 ~~lkesl~~ke~~~~~Lqsdve~Lr~rle~k~~~l~kk~~~~~~~qeE~~~~~~Ei~~l~d~~d~~e~ki~~Lq~kie~L  404 (775)
T PF10174_consen  325 EVLKESLRAKEQEAEMLQSDVEALRFRLEEKNSQLEKKQAQIEKLQEEKSRLQGEIEDLRDMLDKKERKINVLQKKIENL  404 (775)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55666677777777788888888888888888888888888888888888888888776444333445566666666666


Q ss_pred             HHHHhhhhhhhhhHHhhhH
Q 038837          110 WAASRKNNFDIHNLESKAL  128 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~  128 (287)
                      ...++.-......+..|..
T Consensus       405 ee~l~ekd~ql~~~k~Rl~  423 (775)
T PF10174_consen  405 EEQLREKDRQLDEEKERLS  423 (775)
T ss_pred             HHHHHHHHHHHHHHHHHHh
Confidence            6666555554444444444

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 [].

>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3

Probab=92.90  E-value=0.73  Score=42.11  Aligned_cols=92  Identities=20%  Similarity=0.281  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhh-HHHHhHHhHHHhhhHHHHHHHHhhhhcc--chhHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNY-IEERDKLVDDMTNKIHHLQSLLSKIKDD--SSRAEERLNALEEEI  106 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~-l~e~Ek~i~eks~kI~sLqsEi~sLkk~--s~~aee~i~eLEkQV  106 (287)
                      ..|+.||.+|..++...|...+.+...-+++-.. =.|+|.+..=|..+...+.+  ..-+.|  .....+-|..+|.||
T Consensus        99 vrLkrELa~Le~~l~~~~~~~~~~~~~~~~~~~lvk~e~EqLL~YK~~ql~~~~~--~~~~~~~~l~~v~~Dl~~ie~QV  176 (195)
T PF12761_consen   99 VRLKRELAELEEKLSKVEQAAESRRSDTDSKPALVKREFEQLLDYKERQLRELEE--GRSKSGKNLKSVREDLDTIEEQV  176 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccCCcchHHHHHHHHHHHHHHHHHHHHhhhc--cCCCCCCCHHHHHHHHHHHHHHH
Confidence            3366666666666666666666542222222233 34669999989999888876  222222  344566799999999


Q ss_pred             HHHHHHHhhhhhhhhhH
Q 038837          107 RLLWAASRKNNFDIHNL  123 (287)
Q Consensus       107 e~L~~elekqn~~~~~L  123 (287)
                      +.|..-|..-+.+.+.|
T Consensus       177 ~~Le~~L~~k~~eL~~L  193 (195)
T PF12761_consen  177 DGLESHLSSKKQELQQL  193 (195)
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            99999997766665554

>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=92.86  E-value=7.3  Score=41.93  Aligned_cols=76  Identities=17%  Similarity=0.175  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhH----HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038837           98 RLNALEEEIRLLWAASRKNNFDIHNLESKALDA----EDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQ  173 (287)
Q Consensus        98 ~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dA----Ekkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q  173 (287)
                      +......||..|+.++...+.+...++.+..+.    +..++.|..++...++...+...+|..+|.=|+.+-...-..+
T Consensus       360 Ky~vav~Ev~~Lk~ELk~Lk~k~~~~~~~~~~ek~~~~~e~q~L~ekl~~lek~~re~qeri~~LE~ELr~l~~~A~E~q  439 (717)
T PF09730_consen  360 KYKVAVSEVIQLKAELKALKSKYNELEERYKQEKDRLESEVQNLKEKLMSLEKSSREDQERISELEKELRALSKLAGESQ  439 (717)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhHH
Confidence            356667889999999999999999999999888    5667999999999999888888888888887776655544443

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

>PRK12705 hypothetical protein; Provisional

Probab=92.77  E-value=2.5  Score=43.65  Aligned_cols=17  Identities=18%  Similarity=0.301  Sum_probs=8.4

Q ss_pred             hhhHHHHHHHHHHHhhc
Q 038837            4 AAHLTLLLVILFWSFTL   20 (287)
Q Consensus         4 ~~~~~~~~~~~~~~~~~   20 (287)
                      ++-+.||+++++++|-.
T Consensus         4 ~~~~~~~~~~~~~~~~~   20 (508)
T PRK12705          4 SILLVILLLLIGLLLGV   20 (508)
T ss_pred             hHHHHHHHHHHHHHHHH
Confidence            33445555555555443

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

Probab=92.77  E-value=15  Score=38.70  Aligned_cols=122  Identities=20%  Similarity=0.306  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh--------------hccchhHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI--------------KDDSSRAEE   97 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL--------------kk~s~~aee   97 (287)
                      +..+++.|+.+-..|+-+|.++ .+..+|.+.+++   ....+..++.-+++=++.+              +..--..|+
T Consensus       233 i~~~ie~l~~~n~~l~e~i~e~-ek~~~~~eslre---~~~~L~~D~nK~~~y~~~~~~k~~~~~~~l~~l~~Eie~kEe  308 (581)
T KOG0995|consen  233 IANEIEDLKKTNRELEEMINER-EKDPGKEESLRE---KKARLQDDVNKFQAYVSQMKSKKQHMEKKLEMLKSEIEEKEE  308 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-hcCcchHHHHHH---HHHHHHhHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence            3345555666666666666643 233444444333   3333333333344333333              222223445


Q ss_pred             HHHHHHHHHHHHHHHHhhhhhhhhhHHhh---hHhHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 038837           98 RLNALEEEIRLLWAASRKNNFDIHNLESK---ALDAEDRLEEVSLQVEKMSEIVTEQWIQIQH  157 (287)
Q Consensus        98 ~i~eLEkQVe~L~~elekqn~~~~~LEsr---A~dAEkkv~eL~sklek~~ki~~EQ~~qIqk  157 (287)
                      .+..|.++++.|++-++.|+....-+|-.   -+..++-|+..+++++.+.+-+-+++.+|+.
T Consensus       309 E~e~lq~~~d~Lk~~Ie~Q~iS~~dve~mn~Er~~l~r~l~~i~~~~d~l~k~vw~~~l~~~~  371 (581)
T KOG0995|consen  309 EIEKLQKENDELKKQIELQGISGEDVERMNLERNKLKRELNKIQSELDRLSKEVWELKLEIED  371 (581)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            56777777777776666665544433322   2233444555556666655555555555543

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

Probab=92.66  E-value=4.7  Score=47.26  Aligned_cols=135  Identities=21%  Similarity=0.236  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHHhhhhcCchhhHHHH----hHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhh
Q 038837           41 LKIAGLETMLEESIRKVNGKSNYIEER----DKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKN  116 (287)
Q Consensus        41 ~kIa~LES~i~e~~qel~~Kd~~l~e~----Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekq  116 (287)
                      ++|-.|+-.|....+++..+.+.+.++    +.-+.+-...|..+++++.++...-.-+.+.+..|+-++..|.+.|+..
T Consensus       805 ~~i~eL~~el~~lk~klq~~~~~~r~l~~~~~~~l~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~le~k~~eL~k~l~~~  884 (1822)
T KOG4674|consen  805 SRIKELERELQKLKKKLQEKSSDLRELTNSLEKQLENAQNLVDELESELKSLLTSLDSVSTNIAKLEIKLSELEKRLKSA  884 (1822)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344444444444444444444444332    3344444455555555555554444445555666666666666666655


Q ss_pred             hhhhhhHHhh--hHhHHHHHHHHHHHHHHH----------hhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038837          117 NFDIHNLESK--ALDAEDRLEEVSLQVEKM----------SEIVTEQWIQIQHLEQALHMAELRAANVQRQ  175 (287)
Q Consensus       117 n~~~~~LEsr--A~dAEkkv~eL~sklek~----------~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~e  175 (287)
                      -.....+.+.  -.|+-.++..|...++++          ..-..+-...+...|++|...+.++-..+..
T Consensus       885 ~~~~~~l~~~~~~~d~~~~~~~Lr~~~eq~~~l~~~L~~a~s~i~~yqe~~~s~eqsl~~~ks~lde~~~~  955 (1822)
T KOG4674|consen  885 KTQLLNLDSKSSNEDATILEDTLRKELEEITDLKEELTDALSQIREYQEEYSSLEQSLESVKSELDETRLE  955 (1822)
T ss_pred             HHHHhhccccchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5555555433  333333333333333333          2222233334445566666555554444433

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

Probab=92.61  E-value=8.5  Score=40.72  Aligned_cols=76  Identities=24%  Similarity=0.264  Sum_probs=54.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhhhh--------hhHHhhhHhHHHHHHHHHHHHHHHhhhhHH----HHHHHHHHHHH
Q 038837           94 RAEERLNALEEEIRLLWAASRKNNFDI--------HNLESKALDAEDRLEEVSLQVEKMSEIVTE----QWIQIQHLEQA  161 (287)
Q Consensus        94 ~aee~i~eLEkQVe~L~~elekqn~~~--------~~LEsrA~dAEkkv~eL~sklek~~ki~~E----Q~~qIqk~E~A  161 (287)
                      ++...|..||.+|+.|...+.+.|...        +.+.....--|+-+..|+..+++++....+    -+.+|.++|+=
T Consensus       246 ~aq~ri~~lE~e~e~L~~ql~~~N~~~~~~~~~~i~~~~~~L~~kd~~i~~L~~di~~~~~S~~~e~e~~~~qI~~le~~  325 (629)
T KOG0963|consen  246 DAQQRIVFLEREVEQLREQLAKANSSKKLAKIDDIDALGSVLNQKDSEIAQLSNDIERLEASLVEEREKHKAQISALEKE  325 (629)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCchHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455668999999999999999888654        344444555667777888888887776543    34788888887


Q ss_pred             HHHHHHHH
Q 038837          162 LHMAELRA  169 (287)
Q Consensus       162 lk~ae~~~  169 (287)
                      ++-.-..+
T Consensus       326 l~~~~~~l  333 (629)
T KOG0963|consen  326 LKAKISEL  333 (629)
T ss_pred             HHHHHHHH
Confidence            76554443

>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=92.59  E-value=1.3  Score=38.30  Aligned_cols=41  Identities=24%  Similarity=0.318  Sum_probs=18.1

Q ss_pred             HHHHHHHHhhhhcc--chhHHHHHHHHHHHHHHHHHHHhhhhh
Q 038837           78 IHHLQSLLSKIKDD--SSRAEERLNALEEEIRLLWAASRKNNF  118 (287)
Q Consensus        78 I~sLqsEi~sLkk~--s~~aee~i~eLEkQVe~L~~elekqn~  118 (287)
                      +.+|.+|+.+|...  ..+...+|.+|++++..|...++....
T Consensus        95 ~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~  137 (169)
T PF07106_consen   95 VKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS  137 (169)
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33444444444221  223334455555555555554444443

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 [].

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=92.56  E-value=3.1  Score=40.59  Aligned_cols=135  Identities=13%  Similarity=0.181  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhcC--chhhHHH--HhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           34 AELQDAKLKIAGLETMLEESIRKVNG--KSNYIEE--RDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        34 ~eL~qLk~kIa~LES~i~e~~qel~~--Kd~~l~e--~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      .+|.+|+.++...+....+....+.+  ....+..  ....|.....++..++.++..+...-.+.--.+..+..|++.|
T Consensus       215 ~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~l~~le~~l~~l~~~y~~~hP~v~~l~~~i~~l  294 (444)
T TIGR03017       215 ARLNELSAQLVAAQAQVMDASSKEGGSSGKDALPEVIANPIIQNLKTDIARAESKLAELSQRLGPNHPQYKRAQAEINSL  294 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccCCcccchhhhcChHHHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHH
Confidence            45555555555555444433322221  1111111  2345566667777777777766322222222234444444444


Q ss_pred             HHHHhhhhhh-hhhHHhhhHhHHHHHHHHHHHHHHHhhh---hHHHHHHHHHHHHHHHHHHHH
Q 038837          110 WAASRKNNFD-IHNLESKALDAEDRLEEVSLQVEKMSEI---VTEQWIQIQHLEQALHMAELR  168 (287)
Q Consensus       110 ~~elekqn~~-~~~LEsrA~dAEkkv~eL~sklek~~ki---~~EQ~~qIqk~E~Alk~ae~~  168 (287)
                      ++.+.+.-.+ ...+++....+..++.+|...++...+-   ...+-.+...++|-+..++.-
T Consensus       295 ~~~l~~e~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~L~r~~~~~~~~  357 (444)
T TIGR03017       295 KSQLNAEIKKVTSSVGTNSRILKQREAELREALENQKAKVLELNRQRDEMSVLQRDVENAQRA  357 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4433322111 1112222233444444444444432221   222234455666666655544

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.

>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices

Probab=92.56  E-value=2.9  Score=35.71  Aligned_cols=73  Identities=18%  Similarity=0.160  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHhhccccCcccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHH
Q 038837            7 LTLLLVILFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLL   85 (287)
Q Consensus         7 ~~~~~~~~~~~~~~~s~~~~~~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi   85 (287)
                      |+.|+++.|.+|..|.      ...+.+++++|......|+..=+.+-.+.+...+..+..=....++-..|......+
T Consensus         6 l~~~lllss~sfaA~~------~~~v~~~l~~LEae~q~L~~kE~~r~~~~k~~ae~a~~~L~~~~~~~~~i~e~~~kl   78 (126)
T PF09403_consen    6 LLGMLLLSSISFAATA------TASVESELNQLEAEYQQLEQKEEARYNEEKQEAEAAEAELAELKELYAEIEEKIEKL   78 (126)
T ss_dssp             -----------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccc------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            4456677777777665      345567888888888888776666655555544444333323333333333333333

; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.

>PRK04863 mukB cell division protein MukB; Provisional

Probab=92.53  E-value=3.3  Score=47.77  Aligned_cols=142  Identities=19%  Similarity=0.227  Sum_probs=106.7

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hccchhHHHHHHHHHHHH
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDDSSRAEERLNALEEEI  106 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~s~~aee~i~eLEkQV  106 (287)
                      -+..|+.+|.+++..-..+...+.+..++++.....+.....-++++......++.++..| -..-..+|+++..-.   
T Consensus       986 ~~~~Le~~Le~iE~~~~~areql~qaq~q~~q~~q~l~slksslq~~~e~L~E~eqe~~~~g~~~~~~~~~~~~~~~--- 1062 (1486)
T PRK04863        986 LNEKLRQRLEQAEQERTRAREQLRQAQAQLAQYNQVLASLKSSYDAKRQMLQELKQELQDLGVPADSGAEERARARR--- 1062 (1486)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccHHHHHHHhH---
Confidence            3467888888888888888888888888888888888888888889999999999999999 555666777765543   


Q ss_pred             HHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHH----------HHHHHHH------HHHHHHHHHHHHH
Q 038837          107 RLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTE----------QWIQIQH------LEQALHMAELRAA  170 (287)
Q Consensus       107 e~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~E----------Q~~qIqk------~E~Alk~ae~~~~  170 (287)
                      +.|...|+..+.....||-.-.-.+..++.|+.++++.++--.+          +|--+.+      .|+.|...+..-+
T Consensus      1063 ~~l~~~l~~~~~~~~~~~~~~~~re~EIe~L~kkL~~~~~e~~~~re~I~~aK~~W~~v~~~~~~~~~~~~l~~~~~~~~ 1142 (1486)
T PRK04863       1063 DELHARLSANRSRRNQLEKQLTFCEAEMDNLTKKLRKLERDYHEMREQVVNAKAGWCAVLRLVKDNGVERRLHRRELAYL 1142 (1486)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChhhhhhHhhhhcc
Confidence            67788888888888888888777888888887777776665443          3433332      3666665555544


Q ss_pred             HH
Q 038837          171 NV  172 (287)
Q Consensus       171 k~  172 (287)
                      ++
T Consensus      1143 ~~ 1144 (1486)
T PRK04863       1143 SA 1144 (1486)
T ss_pred             Cc
Confidence            44

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.35  E-value=11  Score=36.13  Aligned_cols=55  Identities=18%  Similarity=0.306  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLL   85 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi   85 (287)
                      ++..+...+-.+|.+|-.+|++...+.++.+..+.+.+..|.....+|..+.+-|
T Consensus        42 ~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I   96 (265)
T COG3883          42 ELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENI   96 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444445555555555555555555555444444444444444444444

>PF11802 CENP-K: Centromere-associated protein K; InterPro: IPR020993 Cenp-K is one of seven new Cenp-A-nucleosome distal (CAD) centromere components (the others being Cenp-L, Cenp-O, Cenp-P, Cenp-Q, Cenp-R and Cenp-S) that are identified as assembling on the Cenp-A nucleosome associated complex, NAC []

Probab=92.32  E-value=8.1  Score=37.03  Aligned_cols=50  Identities=28%  Similarity=0.370  Sum_probs=28.8

Q ss_pred             cCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hccchhHHHHHHHHHHHHHHHHH
Q 038837           58 NGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDDSSRAEERLNALEEEIRLLWA  111 (287)
Q Consensus        58 ~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~s~~aee~i~eLEkQVe~L~~  111 (287)
                      +.|++.|.+||..-++|.    -.||++... .....+++.++.-|--++..|.+
T Consensus        16 ~~~~~l~~eCEe~wk~me----~~q~kL~l~~~e~l~~s~~ql~ll~~~~k~L~a   66 (268)
T PF11802_consen   16 DAKEELIKECEELWKDME----ECQNKLSLIGTETLTDSDAQLSLLMMRVKCLTA   66 (268)
T ss_pred             hHHHHHHHHHHHHHHHHH----HHHHHHhhcCCCCCCCcchhHHHHHHHHHHHHH
Confidence            346677888887776665    378888555 44455555553333333333333

The Cenp-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. Cenp-K is centromere-associated through its interaction with one or more components of the Cenp-A NAC.; GO: 0005634 nucleus

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

Probab=92.23  E-value=0.31  Score=47.88  Aligned_cols=42  Identities=26%  Similarity=0.406  Sum_probs=20.5

Q ss_pred             HHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 038837          123 LESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       123 LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      |.+|..++|.++.++...++.+.....+...+|..+++-+.-
T Consensus       142 l~~Ri~e~Eeris~lEd~~~~i~~~~~~~~k~i~~l~~kl~D  183 (370)
T PF02994_consen  142 LNSRIDELEERISELEDRIEEIEQAIKELEKRIKKLEDKLDD  183 (370)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555544445555555554443

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.

>smart00787 Spc7 Spc7 kinetochore protein

Probab=92.17  E-value=4.3  Score=39.31  Aligned_cols=81  Identities=17%  Similarity=0.272  Sum_probs=45.7

Q ss_pred             hHHhHHHhhhHHHHHHHHhhhhccchhH-----------HHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHH
Q 038837           68 DKLVDDMTNKIHHLQSLLSKIKDDSSRA-----------EERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEE  136 (287)
Q Consensus        68 Ek~i~eks~kI~sLqsEi~sLkk~s~~a-----------ee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~e  136 (287)
                      ..++.+...+-+.|+.|+..|+......           .+++.++..++....++++..+.+...++++.++...+..+
T Consensus       171 ~~~~~~l~~~~~~L~~e~~~L~~~~~e~~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e  250 (312)
T smart00787      171 NSIKPKLRDRKDALEEELRQLKQLEDELEDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSE  250 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555666667777777775443331           13355555555555555555555555555555555555555


Q ss_pred             HHHHHHHHhhhh
Q 038837          137 VSLQVEKMSEIV  148 (287)
Q Consensus       137 L~sklek~~ki~  148 (287)
                      +...+..++++.
T Consensus       251 ~~~~I~~ae~~~  262 (312)
T smart00787      251 LNTEIAEAEKKL  262 (312)
T ss_pred             HHHHHHHHHHHH
Confidence            555555555543

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

>PF05335 DUF745: Protein of unknown function (DUF745); InterPro: IPR007999 This family consists of several uncharacterised Drosophila melanogaster proteins of unknown function

Probab=92.06  E-value=7.2  Score=35.34  Aligned_cols=100  Identities=19%  Similarity=0.242  Sum_probs=73.8

Q ss_pred             hhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHH
Q 038837           56 KVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLE  135 (287)
Q Consensus        56 el~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~  135 (287)
                      -|.||.-.++++|..++|-..-+..-.+.+.+-....-.+..-...-+.++..|+.-+..-..+..+.+..+..+-..+.
T Consensus        61 aL~GKq~iveqLe~ev~EAe~vV~ee~~sL~~aq~na~aA~~aa~~A~~q~~~L~~~l~~a~~nl~~a~~~a~~AQ~el~  140 (188)
T PF05335_consen   61 ALAGKQQIVEQLEQEVREAEAVVQEEKASLQQAQANAQAAQRAAQQAQQQLETLKAALKAAQANLANAEQVAEGAQQELA  140 (188)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35678899999999999988885555444443333334455557888999999999999999999999999999888888


Q ss_pred             HHHHHHHHHhhhhHHHHHHH
Q 038837          136 EVSLQVEKMSEIVTEQWIQI  155 (287)
Q Consensus       136 eL~sklek~~ki~~EQ~~qI  155 (287)
                      +-+.=|+...+-+++-.+++
T Consensus       141 eK~qLLeaAk~Rve~L~~QL  160 (188)
T PF05335_consen  141 EKTQLLEAAKRRVEELQRQL  160 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            87777777654444443333

>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins

Probab=92.06  E-value=9.6  Score=42.86  Aligned_cols=62  Identities=18%  Similarity=0.254  Sum_probs=34.5

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHH-------HhhhHHHHHHHHhhh
Q 038837           27 HSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDD-------MTNKIHHLQSLLSKI   88 (287)
Q Consensus        27 ~~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~e-------ks~kI~sLqsEi~sL   88 (287)
                      ....+|+.+++++...|..++...++..+.|+.....+.+....+..       ...++..|.++..++
T Consensus       600 ~~ee~L~~~l~~~~~~l~~~~~~~~~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  668 (1201)
T PF12128_consen  600 ASEEELRERLEQAEDQLQSAEERQEELEKQLKQINKKIEELKREITQAEQELKQAEQDLQRLKNEREQL  668 (1201)
T ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            44567888887777777766655555555554444444444443333       344444455554444

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

Probab=91.96  E-value=5  Score=39.95  Aligned_cols=78  Identities=14%  Similarity=0.235  Sum_probs=41.3

Q ss_pred             HHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhh--------------hhhHHhhhHhHHHHHHHHH
Q 038837           73 DMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFD--------------IHNLESKALDAEDRLEEVS  138 (287)
Q Consensus        73 eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~--------------~~~LEsrA~dAEkkv~eL~  138 (287)
                      ....+|..++.++..+...-.+.--++..+..|++.|++.+.+.-..              ...|.....+++..+..+.
T Consensus       251 ~l~~~l~~l~~~l~~l~~~y~~~hP~v~~l~~qi~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~  330 (498)
T TIGR03007       251 ELDGRIEALEKQLDALRLRYTDKHPDVIATKREIAQLEEQKEEEGSAKNGGPERGEIANPVYQQLQIELAEAEAEIASLE  330 (498)
T ss_pred             chHHHHHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHHhhccccccCcccccccChHHHHHHHHHHHHHHHHHHHH
Confidence            44556777777776663332333344677777777777666543211              2234444555555555555


Q ss_pred             HHHHHHhhhhHH
Q 038837          139 LQVEKMSEIVTE  150 (287)
Q Consensus       139 sklek~~ki~~E  150 (287)
                      .+++.+.+...+
T Consensus       331 ~~~~~l~~~~~~  342 (498)
T TIGR03007       331 ARVAELTARIER  342 (498)
T ss_pred             HHHHHHHHHHHH
Confidence            555554444333

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.

>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=91.88  E-value=5.3  Score=33.41  Aligned_cols=42  Identities=19%  Similarity=0.192  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQ  140 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sk  140 (287)
                      +.+|+.+|.-+-+.++...--+.-|++|...+++.-..+-.+
T Consensus        60 ~~eLqaki~ea~~~le~eK~ak~~l~~r~~k~~~dka~lel~  101 (107)
T PF09304_consen   60 IAELQAKIDEARRNLEDEKQAKLELESRLLKAQKDKAILELK  101 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            444444444444444442222223444444444444433333

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.

>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=91.66  E-value=7.2  Score=32.72  Aligned_cols=112  Identities=18%  Similarity=0.251  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHH-hHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEER-DKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~-Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      .|..++..++..+...++.+.....+++.-.....+. +++-+|+-.- +....++..++........++..|..+++..
T Consensus         7 ~l~~e~~~~~~~~~~~~~~~~~~~~dl~~q~~~a~~Aq~~YE~El~~H-a~~~~~L~~lr~e~~~~~~~~~~l~~~~~~a   85 (132)
T PF07926_consen    7 SLQSELQRLKEQEEDAEEQLQSLREDLESQAKIAQEAQQKYERELVKH-AEDIKELQQLREELQELQQEINELKAEAESA   85 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555555555555555444444444 3333333322 1123333333444444445555555555555


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      +..+....   .+|+.+-...++.+.++..+++.+..
T Consensus        86 ~~~l~~~e---~sw~~qk~~le~e~~~~~~r~~dL~~  119 (132)
T PF07926_consen   86 KAELEESE---ASWEEQKEQLEKELSELEQRIEDLNE  119 (132)
T ss_pred             HHHHHHHH---HhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55554322   13333344444444444444444433

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

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

Probab=91.66  E-value=6.1  Score=37.93  Aligned_cols=23  Identities=17%  Similarity=0.372  Sum_probs=12.2

Q ss_pred             HHhHHhHHHhhhHHHHHHHHhhh
Q 038837           66 ERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        66 e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      ....+..+....-+.|+.++.+|
T Consensus       174 ~l~~~~~~l~~~~~~L~~e~~~L  196 (325)
T PF08317_consen  174 QLDELLPKLRERKAELEEELENL  196 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444445555566666666

>KOG0933 consensus Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=91.51  E-value=5.8  Score=44.17  Aligned_cols=84  Identities=19%  Similarity=0.244  Sum_probs=49.9

Q ss_pred             HHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhh
Q 038837           47 ETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESK  126 (287)
Q Consensus        47 ES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsr  126 (287)
                      |+.+.+.+++++.....+++-.+....+...-..|+-|.+-+.+.-...+.+...++++++.|..++..+.-+....|.-
T Consensus       786 e~rlkdl~keik~~k~~~e~~~~~~ek~~~e~e~l~lE~e~l~~e~~~~k~~l~~~~~~~~~l~~e~~~l~~kv~~~~~~  865 (1174)
T KOG0933|consen  786 ERRLKDLEKEIKTAKQRAEESSKELEKRENEYERLQLEHEELEKEISSLKQQLEQLEKQISSLKSELGNLEAKVDKVEKD  865 (1174)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhH
Confidence            34445555555555555555555555555566667777777755555566667777777777777766666655555433


Q ss_pred             hHhH
Q 038837          127 ALDA  130 (287)
Q Consensus       127 A~dA  130 (287)
                      ...+
T Consensus       866 ~~~~  869 (1174)
T KOG0933|consen  866 VKKA  869 (1174)
T ss_pred             HHHH
Confidence            3333

>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=91.46  E-value=4.8  Score=38.50  Aligned_cols=131  Identities=20%  Similarity=0.217  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHhhccccC-cccch------HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHH
Q 038837            8 TLLLVILFWSFTLTSQN-QQHSQ------QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHH   80 (287)
Q Consensus         8 ~~~~~~~~~~~~~~s~~-~~~~~------~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~s   80 (287)
                      .++=+||+.+-+|-+.+ ..-+.      .+...+|.-.+.++.=|.+.+++.....+-. +.-+..+...+.+..+|..
T Consensus       126 ~yLe~Lc~IIqeLq~t~~~~LS~~dl~e~~~~l~DLesa~vkV~WLR~~L~Ei~Ea~e~~-~~~~~~e~eke~~~r~l~~  204 (269)
T PF05278_consen  126 YYLECLCDIIQELQSTPLKELSESDLKEMIATLKDLESAKVKVDWLRSKLEEILEAKEIY-DQHETREEEKEEKDRKLEL  204 (269)
T ss_pred             HHHHHHHHHHHHHhcCcHhhhhHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence            34557888888884332 22222      3444566667778888888888865432222 2223334444555566666


Q ss_pred             HHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837           81 LQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus        81 LqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      ...|++.+       .+...+.|++|..++.-+.....+...||.+-....+.+..+.+||++..+
T Consensus       205 ~~~ELe~~-------~EeL~~~Eke~~e~~~~i~e~~~rl~~l~~~~~~l~k~~~~~~sKV~kf~~  263 (269)
T PF05278_consen  205 KKEELEEL-------EEELKQKEKEVKEIKERITEMKGRLGELEMESTRLSKTIKSIKSKVEKFHG  263 (269)
T ss_pred             HHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            66666544       455677777777777777777777888888888888888888888887654

>smart00787 Spc7 Spc7 kinetochore protein

Probab=91.32  E-value=3.4  Score=39.95  Aligned_cols=56  Identities=20%  Similarity=0.172  Sum_probs=29.5

Q ss_pred             HHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 038837          105 EIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQ  160 (287)
Q Consensus       105 QVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~  160 (287)
                      +...++.++.++..+....-....+.+..+++++.+++....--.+...+|+++|+
T Consensus       205 eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~ae~  260 (312)
T smart00787      205 ELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAEK  260 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455555555555555444445555555555555555554444444555555554

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

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]

Probab=91.31  E-value=13  Score=39.89  Aligned_cols=79  Identities=24%  Similarity=0.239  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHH-------HHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH-------HHHHH
Q 038837           99 LNALEEEIRLLW-------AASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLE-------QALHM  164 (287)
Q Consensus        99 i~eLEkQVe~L~-------~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E-------~Alk~  164 (287)
                      |+.||+|...|.       +++..-...++..-..+.++.++++.|-.++++.++.-++=..++++++       .-++-
T Consensus       526 i~~leeq~~~lt~~~~~l~~el~~~~~~le~~kk~~~e~~~~~~~Lq~~~ek~~~~le~i~~~~~e~~~ele~~~~k~~r  605 (698)
T KOG0978|consen  526 IGKLEEQERGLTSNESKLIKELTTLTQSLEMLKKKAQEAKQSLEDLQIELEKSEAKLEQIQEQYAELELELEIEKFKRKR  605 (698)
T ss_pred             HHHHHHHHHHhhHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566666666555       5555555555555667778888888888777777766665555555444       44456


Q ss_pred             HHHHHHHHHhhhh
Q 038837          165 AELRAANVQRQLM  177 (287)
Q Consensus       165 ae~~~~k~q~ea~  177 (287)
                      +++++.+.++...
T Consensus       606 leEE~e~L~~kle  618 (698)
T KOG0978|consen  606 LEEELERLKRKLE  618 (698)
T ss_pred             HHHHHHHHHHHHH
Confidence            6777777766655

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

Probab=91.28  E-value=8.7  Score=34.35  Aligned_cols=24  Identities=13%  Similarity=0.394  Sum_probs=12.0

Q ss_pred             HHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           65 EERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        65 ~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      .-++..|+++...|..+...+...
T Consensus        26 ~~l~q~ird~e~~l~~a~~~~a~~   49 (221)
T PF04012_consen   26 KMLEQAIRDMEEQLRKARQALARV   49 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555555555555555444433

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 [].

>KOG0243 consensus Kinesin-like protein [Cytoskeleton]

Probab=91.26  E-value=8.5  Score=42.94  Aligned_cols=136  Identities=16%  Similarity=0.193  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHH-------HHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEER-------LNAL  102 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~-------i~eL  102 (287)
                      ..+-.||+.||..+.+-..    ++=-.-+++.|. +.|....++..+|..|..+++++.+.-.+..++       -..|
T Consensus       407 Kd~~~EIerLK~dl~AaRe----KnGvyisee~y~-~~e~e~~~~~~~ieele~el~~~~~~l~~~~e~~~~~~~~~~~l  481 (1041)
T KOG0243|consen  407 KDLYEEIERLKRDLAAARE----KNGVYISEERYT-QEEKEKKEMAEQIEELEEELENLEKQLKDLTELYMNQLEIKELL  481 (1041)
T ss_pred             HHHHHHHHHHHHHHHHhHh----hCceEechHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            4455677777777766521    111111222222 334444555555555555555553333333333       3578


Q ss_pred             HHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 038837          103 EEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAA  170 (287)
Q Consensus       103 EkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~  170 (287)
                      -++.++|+..++..+.+..+++..-.++...+.+-.--+.++.+.-..--.+--++-+.+..+.+.+.
T Consensus       482 ~~~~~~~k~~L~~~~~el~~~~ee~~~~~~~l~~~e~ii~~~~~se~~l~~~a~~l~~~~~~s~~d~s  549 (1041)
T KOG0243|consen  482 KEEKEKLKSKLQNKNKELESLKEELQQAKATLKEEEEIISQQEKSEEKLVDRATKLRRSLEESQDDLS  549 (1041)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888888888887776666666554333332322222222111223344455555555544

>PF04582 Reo_sigmaC: Reovirus sigma C capsid protein; InterPro: IPR007662 Protein sigmaC in its native state was shown to be a homotrimer

Probab=91.25  E-value=0.28  Score=47.88  Aligned_cols=101  Identities=17%  Similarity=0.233  Sum_probs=14.7

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHH-------HH
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEER-------LN  100 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~-------i~  100 (287)
                      ....|...+..+-.+|+.|++.|+..+-.+..=...|..+..-|..+...|.+|.+.++++.....+-+..       +.
T Consensus        43 sv~sL~~SVs~lss~iSdLss~L~~l~~sl~~~~s~L~sLsstV~~lq~Sl~~lsssVs~lS~~ls~h~ssIS~Lqs~v~  122 (326)
T PF04582_consen   43 SVASLSDSVSSLSSTISDLSSDLQDLASSLADMTSELNSLSSTVTSLQSSLSSLSSSVSSLSSTLSDHSSSISDLQSSVS  122 (326)
T ss_dssp             ---------------------------------------------------------------------------HHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHhhhhhhhhhhhhHHHHHHhhh
Confidence            34556666777888888888888887777777777777777777777777777777777764444444433       45


Q ss_pred             HHHHHHHHHHHHHhhhhhhhhhHHhhhH
Q 038837          101 ALEEEIRLLWAASRKNNFDIHNLESKAL  128 (287)
Q Consensus       101 eLEkQVe~L~~elekqn~~~~~LEsrA~  128 (287)
                      .|+-.|-.|+.++-.+--.+..||.|.+
T Consensus       123 ~lsTdvsNLksdVSt~aL~ItdLe~RV~  150 (326)
T PF04582_consen  123 ALSTDVSNLKSDVSTQALNITDLESRVK  150 (326)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhhhhhhcchHhhHHHHHH
Confidence            5555555555555554444444443333

It was demonstrated that the sigmaC subunits are not covalently bound via disulphide linkages and the formation of an intrachain disulphide bond between the two cysteine residues of the sigmaC polypeptide may have a negative effect on oligomer stability. The susceptibility of the trimer to pH, temperature, ionic strength, chemical denaturants and detergents indicates that hydrophobic interactions contribute much more to oligomer stability than do ionic interactions and hydrogen bonding [].; PDB: 2VRS_C 2JJL_A 2BSF_A 2BT7_A 2BT8_A.

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

Probab=91.24  E-value=8.4  Score=39.92  Aligned_cols=135  Identities=20%  Similarity=0.276  Sum_probs=70.4

Q ss_pred             ccCcccchHHHHHHH----HHHHHHHHHHHHHHHH---HhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh------
Q 038837           22 SQNQQHSQQHLIAEL----QDAKLKIAGLETMLEE---SIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI------   88 (287)
Q Consensus        22 s~~~~~~~~~l~~eL----~qLk~kIa~LES~i~e---~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL------   88 (287)
                      +.+-+++.++|+.-.    .-+.-.|++|.+..++   ..++...=+..|+.++.--+++..+-.-+++-...+      
T Consensus       248 ~~~~~~~e~Elk~~f~~~~~~i~~~i~~lk~~n~~l~e~i~ea~k~s~~i~~l~ek~r~l~~D~nk~~~~~~~mk~K~~~  327 (622)
T COG5185         248 EDNYEPSEQELKLGFEKFVHIINTDIANLKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKYENYVNAMKQKSQE  327 (622)
T ss_pred             CCccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHh
Confidence            445556666655433    2244445555443322   223333334444444444444444444444444433      


Q ss_pred             --------hccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHH---HHHHHHHHHHHHHhhhhHHHHHHHH
Q 038837           89 --------KDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAE---DRLEEVSLQVEKMSEIVTEQWIQIQ  156 (287)
Q Consensus        89 --------kk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAE---kkv~eL~sklek~~ki~~EQ~~qIq  156 (287)
                              +..-...|++|..|..+.+.|.+-+++|.-..+-.|-.-.+-|   +-++..+.+.+++-|.+-+++.-+|
T Consensus       328 ~~g~l~kl~~eie~kEeei~~L~~~~d~L~~q~~kq~Is~e~fe~mn~Ere~L~reL~~i~~~~~~L~k~V~~~~leaq  406 (622)
T COG5185         328 WPGKLEKLKSEIELKEEEIKALQSNIDELHKQLRKQGISTEQFELMNQEREKLTRELDKINIQSDKLTKSVKSRKLEAQ  406 (622)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHhHHHHHH
Confidence                    1111235677888999999999999988877776665444433   2334444455555555555554443

>TIGR02977 phageshock_pspA phage shock protein A

Probab=91.24  E-value=7.7  Score=35.17  Aligned_cols=105  Identities=14%  Similarity=0.147  Sum_probs=58.6

Q ss_pred             hhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhH-------HHH
Q 038837           61 SNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDA-------EDR  133 (287)
Q Consensus        61 d~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dA-------Ekk  133 (287)
                      .+...-++..|+|+...|......+....-..--.+.++.+++..++.+.+--+.=-..+.  |+.|..|       +..
T Consensus        23 EDP~~~l~q~irem~~~l~~ar~~lA~~~a~~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~--EdLAr~Al~~k~~~~~~  100 (219)
T TIGR02977        23 EDPEKMIRLIIQEMEDTLVEVRTTSARTIADKKELERRVSRLEAQVADWQEKAELALSKGR--EDLARAALIEKQKAQEL  100 (219)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHH
Confidence            3555666777777777776666666555333333444455555555555432222111111  2334444       666


Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 038837          134 LEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAEL  167 (287)
Q Consensus       134 v~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~  167 (287)
                      +..|...++.+...+.+-+.+++.+++-+..++.
T Consensus       101 ~~~l~~~~~~~~~~v~~l~~~l~~L~~ki~~~k~  134 (219)
T TIGR02977       101 AEALERELAAVEETLAKLQEDIAKLQAKLAEARA  134 (219)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666777777777777777777766555443

Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.

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

Probab=91.19  E-value=2.9  Score=40.31  Aligned_cols=49  Identities=20%  Similarity=0.264  Sum_probs=21.9

Q ss_pred             hhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhH
Q 038837           75 TNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNL  123 (287)
Q Consensus        75 s~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~L  123 (287)
                      ...+..++.++..++.......+.+.+||++-+.|.+++++...+...+
T Consensus        42 ~~~~~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l   90 (314)
T PF04111_consen   42 EEDIEELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEEL   90 (314)
T ss_dssp             HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555544433333444444555555555555554444443333

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.

>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules

Probab=91.14  E-value=12  Score=34.37  Aligned_cols=56  Identities=18%  Similarity=0.192  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHH
Q 038837           29 QQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSL   84 (287)
Q Consensus        29 ~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsE   84 (287)
                      +-.+..-+..++..+..-|..+.+..+....+.....++.++|.+-+..|+.+..+
T Consensus         4 ~~d~d~~~~~~~~e~~~~E~e~~~l~~k~~e~~~~~~~m~~i~~e~Ek~i~~~i~e   59 (207)
T PF05010_consen    4 QKDLDAAIKKVQEEVAEKEEEEQELKKKYEELHKENQEMRKIMEEYEKTIAQMIEE   59 (207)
T ss_pred             HHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            34455566667777666666666666666666677777777777777777777766

The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].

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

Probab=91.11  E-value=8.9  Score=36.82  Aligned_cols=8  Identities=13%  Similarity=0.509  Sum_probs=3.0

Q ss_pred             hhHHHHHH
Q 038837           76 NKIHHLQS   83 (287)
Q Consensus        76 ~kI~sLqs   83 (287)
                      ..|..|++
T Consensus       191 ~e~~~Lk~  198 (325)
T PF08317_consen  191 EELENLKQ  198 (325)
T ss_pred             HHHHHHHH
Confidence            33333333

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

Probab=91.10  E-value=1.5  Score=42.30  Aligned_cols=12  Identities=25%  Similarity=0.216  Sum_probs=8.3

Q ss_pred             hhhhhhHHHHHHH
Q 038837          254 ALANEELVFFVAS  266 (287)
Q Consensus       254 ~lAtkeLvWflAs  266 (287)
                      ++.+.+ -|=.|.
T Consensus       283 ~~~~~~-~WT~Al  294 (314)
T PF04111_consen  283 QFNSEE-EWTKAL  294 (314)
T ss_dssp             TTS-HH-HHHHHH
T ss_pred             cCCChh-HHHHHH
Confidence            556666 999888

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.

>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]

Probab=91.00  E-value=9.1  Score=42.05  Aligned_cols=59  Identities=20%  Similarity=0.240  Sum_probs=40.4

Q ss_pred             hhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhchhhH
Q 038837          121 HNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCT  182 (287)
Q Consensus       121 ~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~p~~~~  182 (287)
                      ..|.....+-|..|.+++..|+.+..+.+   .--++.|+|-|+.+.+-||..++----+|-
T Consensus       280 s~L~~ElSqkeelVk~~qeeLd~lkqt~t---~a~gdseqatkylh~enmkltrqkadirc~  338 (1265)
T KOG0976|consen  280 SVLGDELSQKEELVKELQEELDTLKQTRT---RADGDSEQATKYLHLENMKLTRQKADIRCA  338 (1265)
T ss_pred             HHHhhhhhHHHHHHHHHHHHHHHHHHHHH---HhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35666667777778888777777666543   234567888888888888877775544554

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

Probab=90.90  E-value=5.9  Score=41.79  Aligned_cols=108  Identities=17%  Similarity=0.200  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhh-c----cchhHH----HHHHHHHHHHHHH
Q 038837           39 AKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIK-D----DSSRAE----ERLNALEEEIRLL  109 (287)
Q Consensus        39 Lk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLk-k----~s~~ae----e~i~eLEkQVe~L  109 (287)
                      |+...+.+...+.+.+.++..=.......-..|++.+.+|+.|.+.+.... .    |-+..+    ..+..|.++++.|
T Consensus        20 lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eLk~q~~~~~~~~~pa~pse~E~~Lq~E~~~L~kElE~L   99 (617)
T PF15070_consen   20 LKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSELKNQMAEPPPPEPPAGPSEVEQQLQAEAEHLRKELESL   99 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCccccccchHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444443433333223333444557777788888888877551 1    122222    2267788888888


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      ...+..+..+...|--.-.+-|.++.+|...|+..+.
T Consensus       100 ~~qlqaqv~~ne~Ls~L~~EqEerL~ELE~~le~~~e  136 (617)
T PF15070_consen  100 EEQLQAQVENNEQLSRLNQEQEERLAELEEELERLQE  136 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888766666633334555555555555544333

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

Probab=90.75  E-value=8.5  Score=42.31  Aligned_cols=84  Identities=18%  Similarity=0.162  Sum_probs=45.2

Q ss_pred             chhhHHHHhHHhHHHhhhHHHHHHHHhhh--hcc-----chhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHH
Q 038837           60 KSNYIEERDKLVDDMTNKIHHLQSLLSKI--KDD-----SSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAED  132 (287)
Q Consensus        60 Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL--kk~-----s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEk  132 (287)
                      ........++..+.+-.++..|..+-.-|  |-+     ...++.-+.+++++...|-.-+++.....+.+|.+.++-.+
T Consensus       415 ~e~~~l~~e~ry~klkek~t~l~~~h~~lL~K~~di~kQle~~~~s~~~~~~~~~~L~d~le~~~~~~~~~~~K~e~~~~  494 (980)
T KOG0980|consen  415 AENKALAAENRYEKLKEKYTELRQEHADLLRKYDDIQKQLESAEQSIDDVEEENTNLNDQLEELQRAAGRAETKTESQAK  494 (980)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            33444444555555555666665555444  211     11122224455555556666666666666666666666666


Q ss_pred             HHHHHHHHHHH
Q 038837          133 RLEEVSLQVEK  143 (287)
Q Consensus       133 kv~eL~sklek  143 (287)
                      .++.+-.++..
T Consensus       495 ~le~l~~El~~  505 (980)
T KOG0980|consen  495 ALESLRQELAL  505 (980)
T ss_pred             HHHHHHHHHHH
Confidence            66666665544

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

Probab=90.58  E-value=1.8  Score=38.79  Aligned_cols=36  Identities=28%  Similarity=0.419  Sum_probs=15.6

Q ss_pred             hHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Q 038837          127 ALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMA  165 (287)
Q Consensus       127 A~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~a  165 (287)
                      ....++.+..|..++++..+..++   +|+++.+..+.+
T Consensus       112 l~~l~~~~~~l~~el~~~~~~Dp~---~i~~~~~~~~~~  147 (188)
T PF03962_consen  112 LEELKKELKELKKELEKYSENDPE---KIEKLKEEIKIA  147 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCHH---HHHHHHHHHHHH
Confidence            334444444444445544444443   334444444433

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

>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=90.55  E-value=1.5  Score=33.89  Aligned_cols=52  Identities=19%  Similarity=0.240  Sum_probs=34.8

Q ss_pred             hHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHh
Q 038837           63 YIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASR  114 (287)
Q Consensus        63 ~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~ele  114 (287)
                      .+.++|..|...-..|+.|+-|++-|+..+....+...+|..+.++|+.+-.
T Consensus         5 ~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~   56 (72)
T PF06005_consen    5 LLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERN   56 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            4567777777777888888888887755444444556666666666664433

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.

>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=90.54  E-value=9  Score=32.16  Aligned_cols=82  Identities=12%  Similarity=0.136  Sum_probs=37.8

Q ss_pred             HhhhHHHHHHHHhhhhccchhHHHHH-HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHH
Q 038837           74 MTNKIHHLQSLLSKIKDDSSRAEERL-NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQW  152 (287)
Q Consensus        74 ks~kI~sLqsEi~sLkk~s~~aee~i-~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~  152 (287)
                      ...++..++.++.+..+-.-.++.+. .||-+.-+- -..|.+.+.+...+..........++.....|+..+..+.+|+
T Consensus        22 ~~~~~~~~~~dl~~q~~~a~~Aq~~YE~El~~Ha~~-~~~L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~~~e~sw~~qk  100 (132)
T PF07926_consen   22 AEEQLQSLREDLESQAKIAQEAQQKYERELVKHAED-IKELQQLREELQELQQEINELKAEAESAKAELEESEASWEEQK  100 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            33455556666555544444455442 233222222 2223333333334444444444555555555566666666666


Q ss_pred             HHHH
Q 038837          153 IQIQ  156 (287)
Q Consensus       153 ~qIq  156 (287)
                      ..++
T Consensus       101 ~~le  104 (132)
T PF07926_consen  101 EQLE  104 (132)
T ss_pred             HHHH
Confidence            4443

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

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

Probab=90.46  E-value=3.3  Score=41.22  Aligned_cols=25  Identities=24%  Similarity=0.335  Sum_probs=19.2

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHH
Q 038837          256 ANEELVFFVASALITFPILAAWVLL  280 (287)
Q Consensus       256 AtkeLvWflAsALlalP~~~~~~ll  280 (287)
                      .-..+++|++|+-+++.+|.+.++.
T Consensus       472 ~~~~~~~~~~~~~~~~~~~~~~~~~  496 (498)
T TIGR03007       472 RRRRLAAFLASAGLLIAVYGALMAM  496 (498)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3346788889999999999887653

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.

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

Probab=90.25  E-value=4.3  Score=36.44  Aligned_cols=60  Identities=23%  Similarity=0.394  Sum_probs=32.4

Q ss_pred             hhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHH------HHHHHHHHHHHHHHHh
Q 038837           55 RKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEER------LNALEEEIRLLWAASR  114 (287)
Q Consensus        55 qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~------i~eLEkQVe~L~~ele  114 (287)
                      ++...+...+.++.+.+.+...+|..|+.+++..+.|..+.+++      +.+|++++..|++++.
T Consensus        62 ~~~~~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~  127 (188)
T PF03962_consen   62 QAKQKRQNKLEKLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELE  127 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555566666666666666666666665554444333      3555555555555554

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

>PF12795 MscS_porin: Mechanosensitive ion channel porin domain

Probab=90.16  E-value=15  Score=33.63  Aligned_cols=139  Identities=19%  Similarity=0.255  Sum_probs=100.0

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hcc-chhHHHH-------
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDD-SSRAEER-------   98 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~-s~~aee~-------   98 (287)
                      +-..|...|.+..+.+..++..+.+.+..+.+=....+..-..+-+....+..+.+.+.++ ..| +.-.+.+       
T Consensus        79 s~~eLeq~l~~~~~~L~~~q~~l~~~~~~l~~~~~~p~~aq~~l~~~~~~l~ei~~~L~~~~~~~~~~l~~a~~~~l~ae  158 (240)
T PF12795_consen   79 SLEELEQRLSQEQAQLQELQEQLQQENSQLIEIQTRPERAQQQLSEARQRLQEIRNQLQNLPPNGESPLSEAQRWLLQAE  158 (240)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhhHHHHHHHHHH
Confidence            3467778888888888888888887777777666777777777777778888888887777 333 3334444       


Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELR  168 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~  168 (287)
                      ...|+-+++-|..++--++...+-+..+-..+.++++.+...+..++.....+  +-...|+++.-++..
T Consensus       159 ~~~l~~~~~~le~el~s~~~rq~L~~~qrdl~~~~~~~l~~~l~~Lq~~ln~~--R~~eae~~~~~a~~~  226 (240)
T PF12795_consen  159 LAALEAQIEMLEQELLSNNNRQELLQLQRDLLKARIQRLQQQLQALQNLLNQK--RRQEAEQAVEEAEQL  226 (240)
T ss_pred             HHHHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence            46677777777777777777777777777888888888888888887776653  345677777665554

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

Probab=90.11  E-value=6.1  Score=41.25  Aligned_cols=119  Identities=14%  Similarity=0.191  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHH
Q 038837           33 IAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAA  112 (287)
Q Consensus        33 ~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~e  112 (287)
                      ..++..|+-.+..|...+++       +.........-+.+-..-+.+++.|+.-+|..--+.++.+..|-+|..+|+.+
T Consensus       112 e~ei~kl~~e~~elr~~~~~-------~~k~~~~~re~~~~~~~~l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~  184 (546)
T KOG0977|consen  112 EIEITKLREELKELRKKLEK-------AEKERRGAREKLDDYLSRLSELEAEINTLKRRIKALEDELKRLKAENSRLREE  184 (546)
T ss_pred             HHHHHHhHHHHHHHHHHHHH-------HHHHHhhhHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHH
Confidence            34444444444444444444       33344444444555556677777777766666666777788888888888888


Q ss_pred             HhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh-----hhHHHHHHHHHH
Q 038837          113 SRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE-----IVTEQWIQIQHL  158 (287)
Q Consensus       113 lekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k-----i~~EQ~~qIqk~  158 (287)
                      |.......+.==..=.|.+.++++|--+|+-+.-     |.+++.+.-+++
T Consensus       185 l~~~r~~ld~Etllr~d~~n~~q~Lleel~f~~~~h~~eI~e~~~~~~rd~  235 (546)
T KOG0977|consen  185 LARARKQLDDETLLRVDLQNRVQTLLEELAFLKRIHKQEIEEERRKARRDT  235 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHhhcc
Confidence            8777776554434457888899999998887763     344444444433

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

Probab=90.11  E-value=5.3  Score=41.35  Aligned_cols=114  Identities=21%  Similarity=0.271  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhh
Q 038837           37 QDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKN  116 (287)
Q Consensus        37 ~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekq  116 (287)
                      ++|++.+...=-.|-.-+..+++-.+.|.+.=+...+++.+|..|.-.--.|+.++.--+.-+..|+-.-+.--+-+++.
T Consensus       256 ~Elk~~f~~~~~~i~~~i~~lk~~n~~l~e~i~ea~k~s~~i~~l~ek~r~l~~D~nk~~~~~~~mk~K~~~~~g~l~kl  335 (622)
T COG5185         256 QELKLGFEKFVHIINTDIANLKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKYENYVNAMKQKSQEWPGKLEKL  335 (622)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhcchHHHHH
Confidence            45666666666666666666666677777776777777777777777766666665555555555555544444444455


Q ss_pred             hhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHH
Q 038837          117 NFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQ  151 (287)
Q Consensus       117 n~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ  151 (287)
                      ..+++..|........+..+|+-.|++ ++|++||
T Consensus       336 ~~eie~kEeei~~L~~~~d~L~~q~~k-q~Is~e~  369 (622)
T COG5185         336 KSEIELKEEEIKALQSNIDELHKQLRK-QGISTEQ  369 (622)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHh-cCCCHHH
Confidence            555444444444445555566666554 4444444

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

Probab=90.11  E-value=1.4  Score=33.49  Aligned_cols=51  Identities=27%  Similarity=0.371  Sum_probs=38.2

Q ss_pred             HHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038837          123 LESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQ  173 (287)
Q Consensus       123 LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q  173 (287)
                      +|+|..+.|-|+.-..--++.+.+++.+|+.+|..+++.++.-..++-...
T Consensus         2 le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen    2 LEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            567777777777777778888888999999999999999887666655544

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.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.04  E-value=2.9  Score=44.11  Aligned_cols=24  Identities=21%  Similarity=0.440  Sum_probs=12.1

Q ss_pred             HHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           65 EERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        65 ~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      +.++..+.++...|.-|.++++++
T Consensus       439 ~~L~~~~ee~k~eie~L~~~l~~~  462 (652)
T COG2433         439 SELKRELEELKREIEKLESELERF  462 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444445555555555555

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=89.89  E-value=13  Score=32.48  Aligned_cols=31  Identities=19%  Similarity=0.194  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchh
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSN   62 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~   62 (287)
                      .+.+++.+|++...|...+......|+.|++
T Consensus         4 k~~~i~~~Rl~~~~lk~~l~k~~~ql~~ke~   34 (177)
T PF13870_consen    4 KRNEISKLRLKNITLKHQLAKLEEQLRQKEE   34 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566777777777777766666655555554

>PRK11281 hypothetical protein; Provisional

Probab=89.89  E-value=13  Score=41.84  Aligned_cols=153  Identities=16%  Similarity=0.130  Sum_probs=83.0

Q ss_pred             ccchHHHHHHHHHHHHH----------HHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccc---
Q 038837           26 QHSQQHLIAELQDAKLK----------IAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDS---   92 (287)
Q Consensus        26 ~~~~~~l~~eL~qLk~k----------Ia~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s---   92 (287)
                      -++...++++|++++..          +..||.-++-..+-. .-....+++++.+.+-..++...+.+++.+|+..   
T Consensus        35 ~p~~~~iq~~l~~~~~~~~~~~~~k~~~~~l~~tL~~L~qi~-~~~~~~~~L~k~l~~Ap~~l~~a~~~Le~Lk~~~~~~  113 (1113)
T PRK11281         35 LPTEADVQAQLDALNKQKLLEAEDKLVQQDLEQTLALLDKID-RQKEETEQLKQQLAQAPAKLRQAQAELEALKDDNDEE  113 (1113)
T ss_pred             CCCHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcccccc
Confidence            36666688999887642          333444333322222 2223445567777777777888888888775421   


Q ss_pred             ----------hhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhh-------hHhHHHHHHHHHHHHHHHhh----hhHHH
Q 038837           93 ----------SRAEERLNALEEEIRLLWAASRKNNFDIHNLESK-------ALDAEDRLEEVSLQVEKMSE----IVTEQ  151 (287)
Q Consensus        93 ----------~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsr-------A~dAEkkv~eL~sklek~~k----i~~EQ  151 (287)
                                ..-|.++.+++.+.+..++++-.-|+...+++++       ..++-.++++.+..+.....    .++.|
T Consensus       114 ~~~~~~~~Sl~qLEq~L~q~~~~Lq~~Q~~La~~NsqLi~~qT~PERAQ~~lsea~~RlqeI~~~L~~~~~~~~~l~~~~  193 (1113)
T PRK11281        114 TRETLSTLSLRQLESRLAQTLDQLQNAQNDLAEYNSQLVSLQTQPERAQAALYANSQRLQQIRNLLKGGKVGGKALRPSQ  193 (1113)
T ss_pred             ccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcCCHHH
Confidence                      1122334556666666666666666666665553       34444555555554433111    11222


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhchh
Q 038837          152 WIQIQHLEQALHMAELRAANVQRQLMYAR  180 (287)
Q Consensus       152 ~~qIqk~E~Alk~ae~~~~k~q~ea~p~~  180 (287)
                       +.--++|+++--++..+.+-.....+.+
T Consensus       194 -~~~l~ae~~~l~~~~~~~~~~l~~~~~l  221 (1113)
T PRK11281        194 -RVLLQAEQALLNAQNDLQRKSLEGNTQL  221 (1113)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHhcchHH
Confidence             2223567777777666666655555544

>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=89.85  E-value=21  Score=34.89  Aligned_cols=127  Identities=17%  Similarity=0.232  Sum_probs=82.2

Q ss_pred             CcccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCch----------------------------hhHHHHhHHhHHHh
Q 038837           24 NQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKS----------------------------NYIEERDKLVDDMT   75 (287)
Q Consensus        24 ~~~~~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd----------------------------~~l~e~Ek~i~eks   75 (287)
                      +.+.++..+..+|...+..|.+|.-.+.-+..-|+.-.                            ..+..+.+-++..+
T Consensus        94 ~L~~~~~~le~~L~~~~e~v~qLrHeL~~kdeLL~~ys~~~ee~~~~~~~~~~~~~~~~~~~~~~~~~le~Lq~Klk~LE  173 (306)
T PF04849_consen   94 DLSERNEALEEQLGAALEQVEQLRHELSMKDELLQIYSNDDEESEPESSESTPLRRNESSLSSQKCIQLEALQEKLKSLE  173 (306)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHhhhcccccCCCccccccccccccccchhHHHHHHHHHHHH
Confidence            34455566666777777777777655555443322111                            12333444444444


Q ss_pred             hhHHHHHHHHhhhhccchh------------------HHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHH
Q 038837           76 NKIHHLQSLLSKIKDDSSR------------------AEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEV  137 (287)
Q Consensus        76 ~kI~sLqsEi~sLkk~s~~------------------aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL  137 (287)
                      ..-..|.+|.+.|+.....                  |..+|..|.+++-+-..+...|..++..|-++.-|.++|+..+
T Consensus       174 eEN~~LR~Ea~~L~~et~~~EekEqqLv~dcv~QL~~An~qia~LseELa~k~Ee~~rQQEEIt~LlsqivdlQ~r~k~~  253 (306)
T PF04849_consen  174 EENEQLRSEASQLKTETDTYEEKEQQLVLDCVKQLSEANQQIASLSEELARKTEENRRQQEEITSLLSQIVDLQQRCKQL  253 (306)
T ss_pred             HHHHHHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444555555555433222                  3344788888888888999999999999999999999999999


Q ss_pred             HHHHHHHhhhhHH
Q 038837          138 SLQVEKMSEIVTE  150 (287)
Q Consensus       138 ~sklek~~ki~~E  150 (287)
                      +.+-|.+......
T Consensus       254 ~~EnEeL~q~L~~  266 (306)
T PF04849_consen  254 AAENEELQQHLQA  266 (306)
T ss_pred             hhhHHHHHHHHHH
Confidence            9988887766443

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 [].

>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=89.82  E-value=14  Score=33.96  Aligned_cols=19  Identities=16%  Similarity=0.323  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHhhhhHH
Q 038837          132 DRLEEVSLQVEKMSEIVTE  150 (287)
Q Consensus       132 kkv~eL~sklek~~ki~~E  150 (287)
                      +|++.|..-+++-.-...|
T Consensus       131 ~Rl~~L~~~l~~~dv~~~e  149 (251)
T PF11932_consen  131 ERLARLRAMLDDADVSLAE  149 (251)
T ss_pred             HHHHHHHHhhhccCCCHHH
Confidence            4444444444443333333

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.

>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site

Probab=89.76  E-value=15  Score=37.96  Aligned_cols=130  Identities=19%  Similarity=0.296  Sum_probs=72.9

Q ss_pred             HHHHHhhccccCcccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccc
Q 038837           13 ILFWSFTLTSQNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDS   92 (287)
Q Consensus        13 ~~~~~~~~~s~~~~~~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s   92 (287)
                      -++-+|+++-.+-... ..+..++.++..+...+...+++....-..=.+.+++..+.+.+.+.....+...+.+|-++.
T Consensus       331 ~v~~sY~L~~~e~~~~-~~l~~~l~~l~~~~~~~~~~i~~~~~~yS~i~~~l~~~~~~l~~ie~~q~~~~~~l~~L~~dE  409 (560)
T PF06160_consen  331 RVSQSYTLNHNELEIV-RELEKQLKELEKRYEDLEERIEEQQVPYSEIQEELEEIEEQLEEIEEEQEEINESLQSLRKDE  409 (560)
T ss_pred             HHHHhcCCCchHHHHH-HHHHHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555543222111 223344444444444444444443333333333444444555555555555555666666666


Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhhhhhhh--hhHHhhhHhHHHHHHHHHHHHHH
Q 038837           93 SRAEERLNALEEEIRLLWAASRKNNFDI--HNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus        93 ~~aee~i~eLEkQVe~L~~elekqn~~~--~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      ..|.+++..+...+...++-+++.|==+  +.+...-.++.++++.|...|++
T Consensus       410 ~~Ar~~l~~~~~~l~~ikR~lek~nLPGlp~~y~~~~~~~~~~i~~l~~~L~~  462 (560)
T PF06160_consen  410 KEAREKLQKLKQKLREIKRRLEKSNLPGLPEDYLDYFFDVSDEIEELSDELNQ  462 (560)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6777778888888888888888877411  35556677777777777777765

EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane

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

Probab=89.61  E-value=8.1  Score=43.11  Aligned_cols=54  Identities=30%  Similarity=0.364  Sum_probs=46.9

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      .+.+|.-+|..++.||-.|+-.++|       |.+.+.+++..+.++...|..|+.|+...
T Consensus       171 ~~~hL~velAdle~kir~LrqElEE-------K~enll~lr~eLddleae~~klrqe~~e~  224 (1195)
T KOG4643|consen  171 KNLHLEVELADLEKKIRTLRQELEE-------KFENLLRLRNELDDLEAEISKLRQEIEEF  224 (1195)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3478889999999999999888888       55999999999999999999999988755

>KOG1003 consensus Actin filament-coating protein tropomyosin [Cytoskeleton]

Probab=89.58  E-value=17  Score=33.57  Aligned_cols=104  Identities=21%  Similarity=0.311  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWA  111 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~  111 (287)
                      +-+...++..++-.+|.++.+-.       -.-+....--.+-..+.+-..+++++.-.+.-.++.++.+|+.+...+..
T Consensus        51 ~enr~~kdEE~~e~~e~qLkEAk-------~iaE~adrK~eEVarkL~iiE~dLE~~eeraE~~Es~~~eLeEe~~~~~~  123 (205)
T KOG1003|consen   51 IENRAQKLEEKMEAQEAQLKEAK-------HIAEKADRKYEEVARKLVIIEGELERAEERAEAAESQSEELEEDLRILDS  123 (205)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhHh
Confidence            33445555556666666555532       11111133333344455555566665544455556666777777777665


Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHHHHHHH
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEVSLQVE  142 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL~skle  142 (287)
                      .+.-....-+.++-+-..-+..+..++.||.
T Consensus       124 nlk~l~~~ee~~~q~~d~~e~~ik~ltdKLk  154 (205)
T KOG1003|consen  124 NLKSLSAKEEKLEQKEEKYEEELKELTDKLK  154 (205)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHh
Confidence            5554444444444444444455555555543

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

Probab=89.58  E-value=18  Score=33.75  Aligned_cols=127  Identities=16%  Similarity=0.173  Sum_probs=72.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHh
Q 038837           35 ELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASR  114 (287)
Q Consensus        35 eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~ele  114 (287)
                      +..+|..++.++|.......++|....+.+..++       .+...++.+-.       -.+.+..+++...+.|.....
T Consensus         6 ~k~Ele~rL~q~eee~~~a~~~L~e~e~~a~~Le-------ek~k~aeeea~-------~Le~k~~eaee~~~rL~~~~~   71 (246)
T PF00769_consen    6 EKQELEERLRQMEEEMRRAQEALEESEETAEELE-------EKLKQAEEEAE-------ELEQKRQEAEEEKQRLEEEAE   71 (246)
T ss_dssp             HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH
Confidence            3456667777777777766655544444444443       23223333322       234456888899999999999


Q ss_pred             hhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038837          115 KNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQ  175 (287)
Q Consensus       115 kqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~e  175 (287)
                      ++..++..|+.+..+++..+..|....+.-..-...-..++.....++.-|.+++..+-.-
T Consensus        72 ~~~eEk~~Le~e~~e~~~~i~~l~ee~~~ke~Ea~~lq~el~~ar~~~~~ak~~L~~~~~~  132 (246)
T PF00769_consen   72 MQEEEKEQLEQELREAEAEIARLEEESERKEEEAEELQEELEEAREDEEEAKEELLEVMSA  132 (246)
T ss_dssp             ---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999988888887776666665566666777777666666544333

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.

>PRK00736 hypothetical protein; Provisional

Probab=89.54  E-value=1.9  Score=32.83  Aligned_cols=49  Identities=22%  Similarity=0.400  Sum_probs=38.5

Q ss_pred             hHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 038837          122 NLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAA  170 (287)
Q Consensus       122 ~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~  170 (287)
                      ++|+|..+.|-|+.-..--++.+.+++.+|+++|..+.+.++.--.++.
T Consensus         2 ~~e~Ri~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~   50 (68)
T PRK00736          2 DAEERLTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFL   50 (68)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566777777777777777888888999999999999988876655543

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=89.50  E-value=21  Score=40.95  Aligned_cols=18  Identities=17%  Similarity=0.104  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLET   48 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES   48 (287)
                      .++..|+.++.++..|+.
T Consensus       234 ~~~~~le~l~~~~~~l~~  251 (1353)
T TIGR02680       234 EYRDELERLEALERALRN  251 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            334444444444444433

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.

>PF06705 SF-assemblin: SF-assemblin/beta giardin

Probab=89.49  E-value=17  Score=33.41  Aligned_cols=113  Identities=18%  Similarity=0.280  Sum_probs=62.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHH-HHHHHHHHHHHH
Q 038837           33 IAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERL-NALEEEIRLLWA  111 (287)
Q Consensus        33 ~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i-~eLEkQVe~L~~  111 (287)
                      ++-|..+..++..+++.++.-.      ..--...+..+......|..|...|..=.+.-..+.+++ ...+.++..+..
T Consensus         4 ~~KL~~i~e~~~~f~~~le~e~------~~Rr~~ee~r~~~i~e~i~~Le~~l~~E~k~R~E~~~~lq~~~e~~i~~~~~   77 (247)
T PF06705_consen    4 KSKLASINERFSGFESDLENEK------RQRREQEEQRFQDIKEQIQKLEKALEAEVKRRVESNKKLQSKFEEQINNMQE   77 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH------HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3567778888888888876532      122233355666666677777777665533333333332 455555655555


Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQH  157 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk  157 (287)
                      .++.+-..      +.......+..|+.++..+++...+.+.++..
T Consensus        78 ~v~~~~~~------~~~~~~~~l~~L~~ri~~L~~~i~ee~~~r~~  117 (247)
T PF06705_consen   78 RVENQISE------KQEQLQSRLDSLNDRIEALEEEIQEEKEERPQ  117 (247)
T ss_pred             HHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            55443322      33344455566666666666655555544443

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=89.42  E-value=16  Score=36.39  Aligned_cols=24  Identities=25%  Similarity=0.253  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEES   53 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~   53 (287)
                      ..+..++..++.++++|+..++..
T Consensus       100 ~~~~~~~~~~~~~~~rL~a~~~~~  123 (457)
T TIGR01000       100 QLLEQQLDNLKDQKKSLDTLKQSI  123 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            458888888999999888777653

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

>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea

Probab=89.39  E-value=1.6  Score=34.15  Aligned_cols=43  Identities=30%  Similarity=0.333  Sum_probs=34.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHH
Q 038837           94 RAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEE  136 (287)
Q Consensus        94 ~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~e  136 (287)
                      +.++=+.+|+++++.+..++.+.+.....++.+.++.++++.+
T Consensus        59 ~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~  101 (106)
T PF01920_consen   59 DKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYE  101 (106)
T ss_dssp             EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556678899999999999998888888887777777766543

Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=89.36  E-value=9.7  Score=40.17  Aligned_cols=22  Identities=14%  Similarity=0.081  Sum_probs=11.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEE   52 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e   52 (287)
                      ..+.++.+.+.+...+++.+..
T Consensus       248 ~a~~~~~~a~a~~~~l~~~l~~  269 (754)
T TIGR01005       248 RARANRAAAEGTADSVKKALQN  269 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhc
Confidence            3445555555555555555543

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.

>PF08702 Fib_alpha: Fibrinogen alpha/beta chain family; InterPro: IPR012290 Fibrinogen plays key roles in both blood clotting and platelet aggregation

Probab=89.34  E-value=14  Score=32.10  Aligned_cols=37  Identities=19%  Similarity=0.267  Sum_probs=30.8

Q ss_pred             HhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 038837          128 LDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       128 ~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      ..-|.++-.--+.+.-++.+...|..+|++||++..+
T Consensus        93 ~~~e~~i~~~~~~I~~Lq~~~~~~~~ki~~Le~~i~~  129 (146)
T PF08702_consen   93 YILETKIINQPSNIRVLQNILRSNRQKIQRLEQDIDQ  129 (146)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5667777777788888999999999999999997764

During blood clot formation, the conversion of soluble fibrinogen to insoluble fibrin is triggered by thrombin, resulting in the polymerisation of fibrin, which forms a soft clot; this is then converted to a hard clot by factor XIIIA, which cross-links fibrin molecules. Platelet aggregation involves the binding of the platelet protein receptor integrin alpha(IIb)-beta(3) to the C-terminal D domain of fibrinogen []. In addition to platelet aggregation, platelet-fibrinogen interaction mediates both adhesion and fibrin clot retraction. Fibrinogen occurs as a dimer, where each monomer is composed of three non-identical chains, alpha, beta and gamma, linked together by several disulphide bonds []. The N-terminals of all six chains come together to form the centre of the molecule (E domain), from which the monomers extend in opposite directions as coiled coils, followed by C-terminal globular domains (D domains). Therefore, the domain composition is: D-coil-E-coil-D. At each end, the C-terminal of the alpha chain extends beyond the D domain as a protuberance that is important for cross-linking the molecule. During clot formation, the N-terminal fragments of the alpha and beta chains (within the E domain) in fibrinogen are cleaved by thrombin, releasing fibrinopeptides A and B, respectively, and producing fibrin. This cleavage results in the exposure of four binding sites on the E domain, each of which can bind to a D domain from different fibrin molecules. The binding of fibrin molecules produces a polymer consisting of a lattice network of fibrins that form a long, branching, flexible fibre [, ]. Fibrin fibres interact with platelets to increase the size of the clot, as well as with several different proteins and cells, thereby promoting the inflammatory response and concentrating the cells required for wound repair at the site of damage. This entry represents the coiled-coil domain and part of the N-terminal E domain found in all three fibrinogen polypeptides, namely the alpha, beta and gamma chains. More information about these proteins can be found at Protein of the Month: Fibrinogen [].; GO: 0005102 receptor binding, 0030674 protein binding, bridging, 0007165 signal transduction, 0030168 platelet activation, 0051258 protein polymerization, 0005577 fibrinogen complex; PDB: 1LWU_D 1N73_D 1M1J_B 1JY2_R 1JY3_R 1RF0_A 2H43_D 1RE4_D 2XNY_D 2HPC_D ....

>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]

Probab=89.14  E-value=19  Score=33.45  Aligned_cols=102  Identities=19%  Similarity=0.201  Sum_probs=56.1

Q ss_pred             hhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHH----HHhhhh--------hhhhhHHhhhHh
Q 038837           62 NYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWA----ASRKNN--------FDIHNLESKALD  129 (287)
Q Consensus        62 ~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~----elekqn--------~~~~~LEsrA~d  129 (287)
                      +...-++..|+++...+.-+...+..+...-.-.+.++..+..+++++..    .+.+-|        .++.+||..+..
T Consensus        24 Dp~~~l~Q~ird~~~~l~~ar~~~A~~~a~~k~~e~~~~~~~~~~~k~e~~A~~Al~~g~E~LAr~al~~~~~le~~~~~  103 (225)
T COG1842          24 DPEKMLEQAIRDMESELAKARQALAQAIARQKQLERKLEEAQARAEKLEEKAELALQAGNEDLAREALEEKQSLEDLAKA  103 (225)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            44466677788888777777777665533333344445555555544442    122222        234455555555


Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 038837          130 AEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALH  163 (287)
Q Consensus       130 AEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk  163 (287)
                      -+.-+..+...+++|.+-...-..+|.+++.-..
T Consensus       104 ~~~~~~~~~~~~~~l~~~~~~Le~Ki~e~~~~~~  137 (225)
T COG1842         104 LEAELQQAEEQVEKLKKQLAALEQKIAELRAKKE  137 (225)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5556666666666666666555555555554333

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

Probab=89.11  E-value=8.5  Score=40.38  Aligned_cols=83  Identities=14%  Similarity=0.214  Sum_probs=40.5

Q ss_pred             hhhHHHHhHHhHHHhhhHHHHHHHHhhhhcc------chh-HHHH---HHHHHHHHHHHHHHHhhhhhhhhhHHh----h
Q 038837           61 SNYIEERDKLVDDMTNKIHHLQSLLSKIKDD------SSR-AEER---LNALEEEIRLLWAASRKNNFDIHNLES----K  126 (287)
Q Consensus        61 d~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~------s~~-aee~---i~eLEkQVe~L~~elekqn~~~~~LEs----r  126 (287)
                      +..++++...|.+++..|..|+.+.+.||+.      |+. .+..   -.+|...|..++.+++.-.++...++.    .
T Consensus       293 ~~~l~~l~~Eie~kEeE~e~lq~~~d~Lk~~Ie~Q~iS~~dve~mn~Er~~l~r~l~~i~~~~d~l~k~vw~~~l~~~~~  372 (581)
T KOG0995|consen  293 EKKLEMLKSEIEEKEEEIEKLQKENDELKKQIELQGISGEDVERMNLERNKLKRELNKIQSELDRLSKEVWELKLEIEDF  372 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            3445555666666667777777777766332      222 2221   234444444444444444444333332    3


Q ss_pred             hHhHHHHHHHHHHHHHH
Q 038837          127 ALDAEDRLEEVSLQVEK  143 (287)
Q Consensus       127 A~dAEkkv~eL~sklek  143 (287)
                      ...-|+++.++++-.-+
T Consensus       373 f~~le~~~~~~~~l~~~  389 (581)
T KOG0995|consen  373 FKELEKKFIDLNSLIRR  389 (581)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            34445555555554433

>PRK02119 hypothetical protein; Provisional

Probab=89.11  E-value=2.6  Score=32.58  Aligned_cols=52  Identities=17%  Similarity=0.245  Sum_probs=41.5

Q ss_pred             hhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 038837          120 IHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAAN  171 (287)
Q Consensus       120 ~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k  171 (287)
                      ...+|+|..+.|-|+.-..--++.+.+++.+|+++|..+.+.++.--.++..
T Consensus         4 ~~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~~rl~~   55 (73)
T PRK02119          4 QQNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYMANKLKD   55 (73)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3457788888888888888888888999999999999999888766555433

>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein

Probab=89.02  E-value=9.7  Score=37.93  Aligned_cols=21  Identities=24%  Similarity=0.316  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 038837          154 QIQHLEQALHMAELRAANVQR  174 (287)
Q Consensus       154 qIqk~E~Alk~ae~~~~k~q~  174 (287)
                      ++..++..+..++..+..++.
T Consensus       292 ~l~~~~~~l~~~~~~l~~a~~  312 (457)
T TIGR01000       292 EITDLNQKLLELESKIKSLKE  312 (457)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444433

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

>PRK10698 phage shock protein PspA; Provisional

Probab=89.02  E-value=15  Score=33.79  Aligned_cols=106  Identities=12%  Similarity=0.104  Sum_probs=59.3

Q ss_pred             chhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHh-------HHH
Q 038837           60 KSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALD-------AED  132 (287)
Q Consensus        60 Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~d-------AEk  132 (287)
                      -.+..+-++..|++|...+..+...+....-..--.+.++.+++.+++....--+.=-..+.  |+.|..       .+.
T Consensus        22 aEDP~k~l~q~i~em~~~l~~~r~alA~~~A~~k~~er~~~~~~~~~~~~e~kA~~Al~~G~--EdLAr~AL~~K~~~~~   99 (222)
T PRK10698         22 AEDPQKLVRLMIQEMEDTLVEVRSTSARALAEKKQLTRRIEQAEAQQVEWQEKAELALRKEK--EDLARAALIEKQKLTD   99 (222)
T ss_pred             hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHH
Confidence            44566677777788777777776665544322333444455555555554422221111111  233444       566


Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 038837          133 RLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAEL  167 (287)
Q Consensus       133 kv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~  167 (287)
                      ++..|...++......+.-..++++++.-+.-++.
T Consensus       100 ~~~~l~~~~~~~~~~~~~L~~~l~~L~~ki~eak~  134 (222)
T PRK10698        100 LIATLEHEVTLVDETLARMKKEIGELENKLSETRA  134 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66677777777777777767777777665554443

>TIGR03017 EpsF chain length determinant protein EpsF

Probab=88.98  E-value=19  Score=35.18  Aligned_cols=28  Identities=7%  Similarity=0.150  Sum_probs=21.7

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038837           27 HSQQHLIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        27 ~~~~~l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      ....-|..++.+++.++...|..+..-.
T Consensus       171 ~~~~fl~~ql~~~~~~l~~ae~~l~~fr  198 (444)
T TIGR03017       171 KAALWFVQQIAALREDLARAQSKLSAYQ  198 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456678889999999999988887633

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.

>PRK10884 SH3 domain-containing protein; Provisional

Probab=88.90  E-value=5  Score=36.69  Aligned_cols=16  Identities=13%  Similarity=0.287  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHh
Q 038837           39 AKLKIAGLETMLEESI   54 (287)
Q Consensus        39 Lk~kIa~LES~i~e~~   54 (287)
                      ++.++..||.++++.+
T Consensus        91 ~~~rlp~le~el~~l~  106 (206)
T PRK10884         91 LRTRVPDLENQVKTLT  106 (206)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444444444444433

>PRK00295 hypothetical protein; Provisional

Probab=88.85  E-value=2.3  Score=32.39  Aligned_cols=51  Identities=18%  Similarity=0.249  Sum_probs=39.1

Q ss_pred             hHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 038837          122 NLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANV  172 (287)
Q Consensus       122 ~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~  172 (287)
                      ++|+|..+.|-|+.-..--++.+.+++.+|+++|..+++.++.-..++...
T Consensus         2 ~~e~Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~~   52 (68)
T PRK00295          2 SLEERVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEEM   52 (68)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            366777777777777777788888899999999999998887665554443

>PRK04406 hypothetical protein; Provisional

Probab=88.80  E-value=2.6  Score=32.84  Aligned_cols=49  Identities=16%  Similarity=0.272  Sum_probs=39.7

Q ss_pred             hhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 038837          121 HNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRA  169 (287)
Q Consensus       121 ~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~  169 (287)
                      ..+|+|..+.|-|+.-..--++.+.+++.+|+++|..+.+.++.--.++
T Consensus         7 ~~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl   55 (75)
T PRK04406          7 EQLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKV   55 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3577778888888888888888888999999999999998887655544

>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins

Probab=88.72  E-value=11  Score=33.13  Aligned_cols=23  Identities=17%  Similarity=0.095  Sum_probs=16.1

Q ss_pred             HHhHHhHHHhhhHHHHHHHHhhh
Q 038837           66 ERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        66 e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      +.|+........++.|.+|+.++
T Consensus        48 d~e~~~~~~~a~~~eLr~el~~~   70 (177)
T PF07798_consen   48 DLENQEYLFKAAIAELRSELQNS   70 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            35666667777777788887665

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

Probab=88.71  E-value=51  Score=37.93  Aligned_cols=82  Identities=13%  Similarity=0.062  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhch
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYA  179 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~p~  179 (287)
                      .+-++-++.--.+++.-...++.++.+..-||+.+..-+..+.++++..++-|.++.+--..-+.|+...--|+.+|.-+
T Consensus      1580 ~~a~~ai~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~~eL~~~~e~lk~~~~qns~~A~~a~~~a~sa~~~A~~a 1659 (1758)
T KOG0994|consen 1580 GEAQDAIQGADRDIRLAQQLLAKVQEETAAAEKLATSATQQLGELETRMEELKHKAAQNSAEAKQAEKTAGSAKEQALSA 1659 (1758)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Confidence            44555566666777777778888888888999999999999999999999999998877666666666666666666655


Q ss_pred             hh
Q 038837          180 RC  181 (287)
Q Consensus       180 ~~  181 (287)
                      ..
T Consensus      1660 ~q 1661 (1758)
T KOG0994|consen 1660 EQ 1661 (1758)
T ss_pred             HH
Confidence            43

>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea

Probab=88.62  E-value=11  Score=30.33  Aligned_cols=94  Identities=19%  Similarity=0.243  Sum_probs=49.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      +.|+.+++.+..++..|++.+.|..       ..+.+++.+=  -...|--+.+++--    ..+.++=+..|++.++.+
T Consensus         9 q~l~~~~~~l~~~~~~l~~~~~E~~-------~v~~EL~~l~--~d~~vy~~VG~vfv----~~~~~ea~~~Le~~~e~l   75 (105)
T cd00632           9 QQLQQQLQAYIVQRQKVEAQLNENK-------KALEELEKLA--DDAEVYKLVGNVLV----KQEKEEARTELKERLETI   75 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHcCC--CcchHHHHhhhHHh----hccHHHHHHHHHHHHHHH
Confidence            4466677777777777777777743       3333333211  11122222222100    112333356777777777


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHH
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEE  136 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~e  136 (287)
                      ..++.+.+.+.+.++....+.+.++.+
T Consensus        76 e~~i~~l~~~~~~l~~~~~elk~~l~~  102 (105)
T cd00632          76 ELRIKRLERQEEDLQEKLKELQEKIQQ  102 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777777766555555555544444

Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st

>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=88.49  E-value=1.8  Score=33.41  Aligned_cols=65  Identities=14%  Similarity=0.184  Sum_probs=46.5

Q ss_pred             hhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 038837           55 RKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFD  119 (287)
Q Consensus        55 qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~  119 (287)
                      +.|+.||+.|.++-..-+..|.+...+.+.|-.|.....+.++++.+|-+.++.+..++...+..
T Consensus         5 ~~l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~   69 (74)
T PF12329_consen    5 KKLAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEER   69 (74)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555888888887777777788777888877776667777777777777777766666655443

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.

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

Probab=88.37  E-value=21  Score=38.35  Aligned_cols=67  Identities=21%  Similarity=0.242  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEER   98 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~   98 (287)
                      |--+.+.-..||..||--|++....|+++++.|.+.=-.+.+.+.+--.|..|+++||-.-...|+.
T Consensus       130 LteqVeaQgEKIrDLE~cie~kr~kLnatEEmLQqellsrtsLETqKlDLmaevSeLKLkltalEke  196 (861)
T KOG1899|consen  130 LTEQVEAQGEKIRDLETCIEEKRNKLNATEEMLQQELLSRTSLETQKLDLMAEVSELKLKLTALEKE  196 (861)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHhhhchHHHHHHHHHHhhhhHHHHHhHHHHHHHHhHHHHHHHHHH
Confidence            3344555678899999999999999999999998876666777777778999999997665555533

>PRK00846 hypothetical protein; Provisional

Probab=88.27  E-value=3.1  Score=32.81  Aligned_cols=53  Identities=15%  Similarity=0.191  Sum_probs=40.3

Q ss_pred             hhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038837          121 HNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQ  173 (287)
Q Consensus       121 ~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q  173 (287)
                      +.+|+|..+.|-|+.-..--++.+.+++..||.+|..+.+.++.--+++-.++
T Consensus         9 ~~le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~   61 (77)
T PRK00846          9 QALEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR   61 (77)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45667777777777777777788888899999999999998887666655444

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

Probab=88.08  E-value=1.6  Score=42.95  Aligned_cols=88  Identities=20%  Similarity=0.373  Sum_probs=37.6

Q ss_pred             hHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHH
Q 038837           71 VDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTE  150 (287)
Q Consensus        71 i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~E  150 (287)
                      +.++...+..|..|++++++.-+.....+..+.+.   +.......+...+.+|.|..++|++++++...+..+++-...
T Consensus       100 l~el~~~~~elkkEie~IKk~q~e~~~~i~~~~~~---~~~~~~~l~~Ri~e~Eeris~lEd~~~~i~~~~~~~~k~i~~  176 (370)
T PF02994_consen  100 LNELKKRIKELKKEIENIKKNQSEMKLEIENLKKK---LENIDESLNSRIDELEERISELEDRIEEIEQAIKELEKRIKK  176 (370)
T ss_dssp             ------------------H----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhH---HHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            33455555666777777755433333333333222   222223456778888888888888888888888888887777


Q ss_pred             HHHHHHHHHHH
Q 038837          151 QWIQIQHLEQA  161 (287)
Q Consensus       151 Q~~qIqk~E~A  161 (287)
                      -+.+++++|..
T Consensus       177 l~~kl~DlEnr  187 (370)
T PF02994_consen  177 LEDKLDDLENR  187 (370)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhh
Confidence            78888888883

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.

>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=88.07  E-value=4.4  Score=34.21  Aligned_cols=81  Identities=19%  Similarity=0.223  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHH
Q 038837           33 IAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAA  112 (287)
Q Consensus        33 ~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~e  112 (287)
                      ..|+..++..+++|+..=++.++|+-.    +.......+.....+..|+.++..|...-...=+=++|=.++|+.|+.|
T Consensus        29 E~E~~~l~~el~~l~~~r~~l~~Eiv~----l~~~~e~~~~~~~~~~~L~~el~~l~~ry~t~LellGEK~E~veEL~~D  104 (120)
T PF12325_consen   29 EGELASLQEELARLEAERDELREEIVK----LMEENEELRALKKEVEELEQELEELQQRYQTLLELLGEKSEEVEELRAD  104 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHH
Confidence            344555555555555554444444322    1122223355566677777777666222222223356667777777777


Q ss_pred             Hhhhh
Q 038837          113 SRKNN  117 (287)
Q Consensus       113 lekqn  117 (287)
                      +.+..
T Consensus       105 v~DlK  109 (120)
T PF12325_consen  105 VQDLK  109 (120)
T ss_pred             HHHHH
Confidence            76553

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 [].

>TIGR02680 conserved hypothetical protein TIGR02680

Probab=87.93  E-value=11  Score=43.16  Aligned_cols=45  Identities=11%  Similarity=0.147  Sum_probs=22.5

Q ss_pred             HHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhcc
Q 038837           47 ETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDD   91 (287)
Q Consensus        47 ES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~   91 (287)
                      ...+....+++......+.+.+..+.+.+..+..++.+++.|+.+
T Consensus       282 ~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~~~~l~~~~~~l~~~  326 (1353)
T TIGR02680       282 SRDLGRARDELETAREEERELDARTEALEREADALRTRLEALQGS  326 (1353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            333333333333444455555555555555555566666655433

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.

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

Probab=87.91  E-value=27  Score=39.96  Aligned_cols=77  Identities=25%  Similarity=0.349  Sum_probs=44.7

Q ss_pred             hHHhHHHhhhHHHHHHHHhhhhcc-------chhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHH-------hhhHhHHHH
Q 038837           68 DKLVDDMTNKIHHLQSLLSKIKDD-------SSRAEERLNALEEEIRLLWAASRKNNFDIHNLE-------SKALDAEDR  133 (287)
Q Consensus        68 Ek~i~eks~kI~sLqsEi~sLkk~-------s~~aee~i~eLEkQVe~L~~elekqn~~~~~LE-------srA~dAEkk  133 (287)
                      +..|+.....|..-++-++.+...       ...+-+++.+||.-|+.|+....++..+....|       .+|.+||..
T Consensus      1583 ~~ai~~a~~~~~~a~~~l~kv~~~t~~aE~~~~~a~q~~~eL~~~~e~lk~~~~qns~~A~~a~~~a~sa~~~A~~a~q~ 1662 (1758)
T KOG0994|consen 1583 QDAIQGADRDIRLAQQLLAKVQEETAAAEKLATSATQQLGELETRMEELKHKAAQNSAEAKQAEKTAGSAKEQALSAEQG 1662 (1758)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455555445444444222       223445688999999999988877776655544       345555666


Q ss_pred             HHHHHHHHHHH
Q 038837          134 LEEVSLQVEKM  144 (287)
Q Consensus       134 v~eL~sklek~  144 (287)
                      ++.|..+.+.+
T Consensus      1663 ~~~lq~~~~~~ 1673 (1758)
T KOG0994|consen 1663 LEILQKYYELV 1673 (1758)
T ss_pred             HHHHHHHHHHH
Confidence            65555555443

>PRK04325 hypothetical protein; Provisional

Probab=87.89  E-value=3  Score=32.23  Aligned_cols=48  Identities=15%  Similarity=0.172  Sum_probs=38.0

Q ss_pred             hHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 038837          122 NLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRA  169 (287)
Q Consensus       122 ~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~  169 (287)
                      .+|+|..+.|-|+.-..--++.+.+++.+|+++|..+++.++.--.++
T Consensus         6 ~~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl   53 (74)
T PRK04325          6 EMEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQM   53 (74)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566777777777777777778888999999999999998887654444

>TIGR01005 eps_transp_fam exopolysaccharide transport protein family

Probab=87.70  E-value=41  Score=35.59  Aligned_cols=138  Identities=15%  Similarity=0.183  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchh--hHH-------HHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSN--YIE-------ERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLN  100 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~--~l~-------e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~  100 (287)
                      ..+..+|..++.+..+.++..+.....+..-..  .+.       ..+..|++...+...++.++..+...-.+.--++.
T Consensus       240 ~~l~~ql~~a~~~~~~a~a~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~i~~L~~~l~~l~~~~~~l~~~y~~~hP~v~  319 (754)
T TIGR01005       240 AELNTELSRARANRAAAEGTADSVKKALQNGGSLDVLPEVLSSQLKLEDLIQRLRERQAELRATIADLSTTMLANHPRVV  319 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhhcCcccccHHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHH
Confidence            344455555555555666666655555443211  111       11245666666666666665555221111112245


Q ss_pred             HHHHHHHHHHHHHhhhhhh-hhhHHhhhHhHHHHHHHHHHHHHHHhhh---hHHHHHHHHHHHHHHHHHHH
Q 038837          101 ALEEEIRLLWAASRKNNFD-IHNLESKALDAEDRLEEVSLQVEKMSEI---VTEQWIQIQHLEQALHMAEL  167 (287)
Q Consensus       101 eLEkQVe~L~~elekqn~~-~~~LEsrA~dAEkkv~eL~sklek~~ki---~~EQ~~qIqk~E~Alk~ae~  167 (287)
                      +++.|++.|++.+.....+ ..+++.....+..+.+.|..++++++.-   ...+-.+.+.++|-...++.
T Consensus       320 ~l~~qi~~l~~~i~~e~~~~~~~~~~~~~~a~~~~~~L~~~l~~~~~~~~~~~~~~~e~~~L~Re~~~~~~  390 (754)
T TIGR01005       320 AAKSSLADLDAQIRSELQKITKSLLMQADAAQARESQLVSDVNQLKAASAQAGEQQVDLDALQRDAAAKRQ  390 (754)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcHhHHHHHHHHHHHHHHHH
Confidence            5555555555444332221 2233344444444444454444444322   12223445555555544443

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.

>PRK02793 phi X174 lysis protein; Provisional

Probab=87.69  E-value=3.4  Score=31.78  Aligned_cols=51  Identities=20%  Similarity=0.318  Sum_probs=41.8

Q ss_pred             hHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 038837          122 NLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANV  172 (287)
Q Consensus       122 ~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~  172 (287)
                      .+|+|..+.|-|+.-..--++.+.+++.+|+++|..+.+.++.--.++..+
T Consensus         5 ~~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~   55 (72)
T PRK02793          5 SLEARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLKAS   55 (72)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            477888888888888888889999999999999999999888765555443

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=87.64  E-value=19  Score=37.60  Aligned_cols=133  Identities=13%  Similarity=0.095  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHH-HHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHH
Q 038837           35 ELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIH-HLQSLLSKIKDDSSRAEERLNALEEEIRLLWAAS  113 (287)
Q Consensus        35 eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~-sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~el  113 (287)
                      .++.|+-|+-.+|+.+..    |++|-.-++.-.-...++++..- .+       -|.--|...++..+.++++.+-+++
T Consensus       160 ~~EaL~ekLk~~~een~~----lr~k~~llk~Et~~~~~keq~~y~~~-------~KelrdtN~q~~s~~eel~~kt~el  228 (596)
T KOG4360|consen  160 LLEALQEKLKPLEEENTQ----LRSKAMLLKTETLTYEEKEQQLYGDC-------VKELRDTNTQARSGQEELQSKTKEL  228 (596)
T ss_pred             HHHHHHhhcCChHHHHHH----HHHHHHHHHhhhcchhHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356677776666655443    45555555555555555554422 11       2223345555666666666666666


Q ss_pred             hhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHH--------------HHHHHHHHHHHHHHHHHHHHHhhhhc
Q 038837          114 RKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQW--------------IQIQHLEQALHMAELRAANVQRQLMY  178 (287)
Q Consensus       114 ekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~--------------~qIqk~E~Alk~ae~~~~k~q~ea~p  178 (287)
                      -.+..+.-.|++..-|+.||+..+.-++|-+..+-..=+              .|--..++-+.-||+++-+++....|
T Consensus       229 ~~q~Ee~skLlsql~d~qkk~k~~~~Ekeel~~~Lq~~~da~~ql~aE~~EleDkyAE~m~~~~EaeeELk~lrs~~~p  307 (596)
T KOG4360|consen  229 SRQQEENSKLLSQLVDLQKKIKYLRHEKEELDEHLQAYKDAQRQLTAELEELEDKYAECMQMLHEAEEELKCLRSCDAP  307 (596)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCc
Confidence            666666666666666666666666655554433322111              22223456666677777666655555

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=87.62  E-value=16  Score=37.75  Aligned_cols=26  Identities=19%  Similarity=0.295  Sum_probs=14.7

Q ss_pred             hHhHHHHHHHHHHHHHHHhhhhHHHH
Q 038837          127 ALDAEDRLEEVSLQVEKMSEIVTEQW  152 (287)
Q Consensus       127 A~dAEkkv~eL~sklek~~ki~~EQ~  152 (287)
                      -.+.+....+...+|+++...+.|+-
T Consensus       124 ~~e~~~~~~~~~~~le~~a~lt~~ea  149 (514)
T TIGR03319       124 EEELEELIAEQREELERISGLTQEEA  149 (514)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCHHHH
Confidence            34444555556666666666655544

>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=87.54  E-value=22  Score=32.35  Aligned_cols=23  Identities=17%  Similarity=0.135  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Q 038837           32 LIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      ++..|..++.++..+-...+...
T Consensus        18 ~~~~L~~~~~~l~~~~~~~~~l~   40 (302)
T PF10186_consen   18 VNNRLLELRSELQQLKEENEELR   40 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456666666666644444433

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

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

Probab=87.42  E-value=5.6  Score=35.97  Aligned_cols=37  Identities=19%  Similarity=0.256  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLE  135 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~  135 (287)
                      +.+|+.+...+...-+....++..+++.++..+..+.
T Consensus       140 i~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~  176 (190)
T PF05266_consen  140 ILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEEIE  176 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444444433333

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=87.35  E-value=35  Score=38.33  Aligned_cols=79  Identities=22%  Similarity=0.311  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHH-------HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEV-------SLQVEKMSEIVTEQWIQIQHLEQALHMAELRAAN  171 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL-------~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k  171 (287)
                      ..-|.++++.+.+++++.+.++..|++-.++.+.+++++       +.+++.++..--+-|+.=+++-..+-..+.++.+
T Consensus       413 e~~lq~e~~~~e~~l~~~~e~i~~l~~si~e~~~r~~~~~~~~~~~k~~~del~~~Rk~lWREE~~l~~~i~~~~~dl~~  492 (1200)
T KOG0964|consen  413 ENILQKEIEDLESELKEKLEEIKELESSINETKGRMEEFDAENTELKRELDELQDKRKELWREEKKLRSLIANLEEDLSR  492 (1200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            466777777777888777777777777777666666655       5556667777777887777777777777777777


Q ss_pred             HHhhhh
Q 038837          172 VQRQLM  177 (287)
Q Consensus       172 ~q~ea~  177 (287)
                      ++..-.
T Consensus       493 ~~~~L~  498 (1200)
T KOG0964|consen  493 AEKNLR  498 (1200)
T ss_pred             HHHHHH
Confidence            765443

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

Probab=87.29  E-value=23  Score=39.80  Aligned_cols=115  Identities=17%  Similarity=0.196  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhh
Q 038837           39 AKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNF  118 (287)
Q Consensus        39 Lk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~  118 (287)
                      .+.++-.+-++..+.+-++..+   |+.+.+.+++.-..+..|++.++-+       .+|+..+.-|..++.+-++-...
T Consensus       468 ~~~q~ls~~~Q~~~et~el~~~---iknlnk~L~~r~~elsrl~a~~~el-------keQ~kt~~~qye~~~~k~eeLe~  537 (1195)
T KOG4643|consen  468 ELDQLLSLQDQLEAETEELLNQ---IKNLNKSLNNRDLELSRLHALKNEL-------KEQYKTCDIQYELLSNKLEELEE  537 (1195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444555555555544   6677777777777777776665544       34455555555555555555555


Q ss_pred             hhhhHHhhhHhHHHHHHHHHH---H-------HHHHhhhhHHHHHHHHHHHHHHHH
Q 038837          119 DIHNLESKALDAEDRLEEVSL---Q-------VEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       119 ~~~~LEsrA~dAEkkv~eL~s---k-------lek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      .+.++|.+-...=++|+-|..   +       .+..+-++.||++-|-+++ |++.
T Consensus       538 ~l~~lE~ENa~LlkqI~~Lk~t~qn~~~LEq~~n~lE~~~~elkk~idaL~-alrr  592 (1195)
T KOG4643|consen  538 LLGNLEEENAHLLKQIQSLKTTSQNGALLEQNNNDLELIHNELKKYIDALN-ALRR  592 (1195)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHHHHHHH-HHHH
Confidence            555555555555555555443   1       1223334456666666665 4443

>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]

Probab=87.22  E-value=23  Score=40.32  Aligned_cols=32  Identities=9%  Similarity=0.145  Sum_probs=14.9

Q ss_pred             hcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           57 VNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        57 l~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      .+..++.+++.+...+..+..+..++-+++.+
T Consensus       496 ~ke~~ek~~~~~~~~~~l~~~~~~~~eele~~  527 (1317)
T KOG0612|consen  496 QKEVEEKLSEEEAKKRKLEALVRQLEEELEDA  527 (1317)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444455555555444

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

Probab=87.16  E-value=19  Score=31.26  Aligned_cols=63  Identities=19%  Similarity=0.269  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQA  161 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~A  161 (287)
                      +..|+.+++.+-.++.....+..++=+.-.+..+.++....+|..++..+.+=...|+..|+.
T Consensus        54 ie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~~~~~~~~l~~~E~e  116 (140)
T PF10473_consen   54 IETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKVSELESLNSSLENLLQEKEQE  116 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            455666666655555555555555544444444555555555555555554444444444443

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

>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=87.10  E-value=5.6  Score=34.40  Aligned_cols=57  Identities=18%  Similarity=0.296  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhcC--chhhHHHHhHHhHHHhhhHHHHHHHHhhhh
Q 038837           33 IAELQDAKLKIAGLETMLEESIRKVNG--KSNYIEERDKLVDDMTNKIHHLQSLLSKIK   89 (287)
Q Consensus        33 ~~eL~qLk~kIa~LES~i~e~~qel~~--Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLk   89 (287)
                      ..++.+|+.++..|+..+.....+|++  +.-...++...|.+...+|..|++.+..|+
T Consensus        78 d~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~  136 (169)
T PF07106_consen   78 DAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLR  136 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444333332  223345556666666666666666666663

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 [].

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

Probab=87.05  E-value=29  Score=37.75  Aligned_cols=24  Identities=13%  Similarity=0.141  Sum_probs=12.9

Q ss_pred             hhhcCchhhHHHHhHHhHHHhhhH
Q 038837           55 RKVNGKSNYIEERDKLVDDMTNKI   78 (287)
Q Consensus        55 qel~~Kd~~l~e~Ek~i~eks~kI   78 (287)
                      .+|..||+.|.++-..=...|+++
T Consensus       446 DeLaEkdE~I~~lm~EGEkLSK~q  469 (961)
T KOG4673|consen  446 DELAEKDEIINQLMAEGEKLSKKQ  469 (961)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHH
Confidence            366667777766533333334443

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

Probab=87.02  E-value=6.5  Score=36.00  Aligned_cols=63  Identities=14%  Similarity=0.208  Sum_probs=48.5

Q ss_pred             cCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 038837           58 NGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDI  120 (287)
Q Consensus        58 ~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~  120 (287)
                      .++..++.+++....+.++++.+|..-+++.|.|.-..|+...+|.+...-|+++++.++-+.
T Consensus        77 ~~~ks~~qeLe~~L~~~~qk~~tl~e~~en~K~~~e~tEer~~el~kklnslkk~~e~lr~el  139 (203)
T KOG3433|consen   77 CDRKSVLQELESQLATGSQKKATLGESIENRKAGREETEERTDELTKKLNSLKKILESLRWEL  139 (203)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHhHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457778888888888888888888888888888887888877788777777776655555443

>PF13166 AAA_13: AAA domain

Probab=86.97  E-value=40  Score=35.09  Aligned_cols=15  Identities=0%  Similarity=0.093  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHhc
Q 038837          235 HHELQGFIKQEMVKN  249 (287)
Q Consensus       235 H~qvQ~~I~~~L~~h  249 (287)
                      ..-+.+.+|..|+.+
T Consensus       633 ~~~~~N~~RriLE~y  647 (712)
T PF13166_consen  633 AYNIPNVMRRILEAY  647 (712)
T ss_pred             HHhhHHHhHHHHHHH
Confidence            455667777777776

>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=86.83  E-value=16  Score=34.10  Aligned_cols=45  Identities=18%  Similarity=0.368  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHH
Q 038837           36 LQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSL   84 (287)
Q Consensus        36 L~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsE   84 (287)
                      |..||.|+..||..-++..+++.    .+++.++.|.|-...+..|..|
T Consensus         3 i~~ir~K~~~lek~k~~i~~e~~----~~e~ee~~L~e~~kE~~~L~~E   47 (230)
T PF10146_consen    3 IKEIRNKTLELEKLKNEILQEVE----SLENEEKCLEEYRKEMEELLQE   47 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHH
Confidence            45677777777766666554442    2333444444444444444444

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.

>PF13166 AAA_13: AAA domain

Probab=86.43  E-value=11  Score=39.14  Aligned_cols=31  Identities=19%  Similarity=0.364  Sum_probs=22.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 038837           29 QQHLIAELQDAKLKIAGLETMLEESIRKVNG   59 (287)
Q Consensus        29 ~~~l~~eL~qLk~kIa~LES~i~e~~qel~~   59 (287)
                      ...+...++.++..+..+...|+.+......
T Consensus       324 ~~~~~~~~~~l~~~l~~l~~~L~~K~~~~~~  354 (712)
T PF13166_consen  324 KEELKSAIEALKEELEELKKALEKKIKNPSS  354 (712)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            5667778888888888887777776655544

>TIGR02473 flagell_FliJ flagellar export protein FliJ

Probab=86.41  E-value=17  Score=29.76  Aligned_cols=64  Identities=14%  Similarity=0.175  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 038837           98 RLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQA  161 (287)
Q Consensus        98 ~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~A  161 (287)
                      .......-+..|...+..+......++.....+...+.+-+.+++.+++.-+-+...-+..+..
T Consensus        62 ~l~~~~~f~~~l~~~i~~q~~~l~~~~~~~e~~r~~l~~a~~~~k~lekL~ek~~~~~~~~~~r  125 (141)
T TIGR02473        62 ELSNYQRFIRQLDQRIQQQQQELALLQQEVEAKRERLLEARRELKALEKLKEKKQKEYRAEEAK  125 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556666777777788888888888888888888888999999999888877666555544443

Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems.

>KOG0243 consensus Kinesin-like protein [Cytoskeleton]

Probab=86.18  E-value=17  Score=40.63  Aligned_cols=121  Identities=14%  Similarity=0.183  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhcCch----hhHHHHh---HHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEESIRKVNGKS----NYIEERD---KLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALE  103 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd----~~l~e~E---k~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLE  103 (287)
                      +....|+++..+|..++++|.+.+.-+-.=.    .--++++   ..++.+...+.+++.|+       ..+..++.+.|
T Consensus       445 ~~~~~ieele~el~~~~~~l~~~~e~~~~~~~~~~~l~~~~~~~k~~L~~~~~el~~~~ee~-------~~~~~~l~~~e  517 (1041)
T KOG0243|consen  445 EMAEQIEELEEELENLEKQLKDLTELYMNQLEIKELLKEEKEKLKSKLQNKNKELESLKEEL-------QQAKATLKEEE  517 (1041)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHH
Confidence            4446678888888888888877664443211    1112222   22222222222223332       22222333333


Q ss_pred             HHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 038837          104 EEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHL  158 (287)
Q Consensus       104 kQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~  158 (287)
                      .=|+.+..--.+.......|..-...+-+.+..|..++....+.+++....|.++
T Consensus       518 ~ii~~~~~se~~l~~~a~~l~~~~~~s~~d~s~l~~kld~~~~~~d~n~~~~~~~  572 (1041)
T KOG0243|consen  518 EIISQQEKSEEKLVDRATKLRRSLEESQDDLSSLFEKLDRKDRLDDDNQEVIDDF  572 (1041)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccccccHHHHHHH
Confidence            2232222211111122334445566777777788888877777777666666554

>PF06008 Laminin_I: Laminin Domain I; InterPro: IPR009254 Laminins are glycoproteins that are major constituents of the basement membrane of cells

Probab=86.16  E-value=28  Score=32.18  Aligned_cols=55  Identities=15%  Similarity=0.351  Sum_probs=31.2

Q ss_pred             HHHhHHhHHHhhhHHHHHHHHhhh-hccchhHHHHHHHHHHHHHHHHHHHhhhhhh
Q 038837           65 EERDKLVDDMTNKIHHLQSLLSKI-KDDSSRAEERLNALEEEIRLLWAASRKNNFD  119 (287)
Q Consensus        65 ~e~Ek~i~eks~kI~sLqsEi~sL-kk~s~~aee~i~eLEkQVe~L~~elekqn~~  119 (287)
                      ..++..|+.....|..+...+.++ ..+...+.+.+..+-++++.+=+++|+-++.
T Consensus        90 ~~L~~~i~~l~~~i~~l~~~~~~l~~~~~~~~~~~l~~~l~ea~~mL~emr~r~f~  145 (264)
T PF06008_consen   90 QDLEQFIQNLQDNIQELIEQVESLNENGDQLPSEDLQRALAEAQRMLEEMRKRDFT  145 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHHHHHHHHHHhccch
Confidence            334555555666666666666666 3344445555555556666666666555544

Laminins are trimeric molecules; laminin-1 is an alpha1 beta1 gamma1 trimer. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure []. Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components.; GO: 0005102 receptor binding, 0030155 regulation of cell adhesion, 0030334 regulation of cell migration, 0045995 regulation of embryonic development, 0005606 laminin-1 complex

>TIGR00634 recN DNA repair protein RecN

Probab=86.08  E-value=28  Score=35.84  Aligned_cols=124  Identities=17%  Similarity=0.183  Sum_probs=72.4

Q ss_pred             hhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHH
Q 038837           62 NYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQV  141 (287)
Q Consensus        62 ~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skl  141 (287)
                      ..+.+....+++....+..+..++.....+-..+.+.+.+++.....+.+-.+|-......+-.+..+.+++++.+..--
T Consensus       266 ~~~~~~~~~l~~~~~~l~d~~~~l~~~~~~l~~dp~~L~ele~RL~~l~~LkrKyg~s~e~l~~~~~~l~~eL~~l~~~~  345 (563)
T TIGR00634       266 GSLRELAEQVGNALTEVEEATRELQNYLDELEFDPERLNEIEERLAQIKRLKRKYGASVEEVLEYAEKIKEELDQLDDSD  345 (563)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCH
Confidence            34444444455555555555555555433334445667888888888888888877777766666666666666544322


Q ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhchhh-HHHHHHHH
Q 038837          142 EKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARC-TFLKFVKD  189 (287)
Q Consensus       142 ek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~p~~~-~f~k~~~~  189 (287)
                      +    ...+-..++.+++..+...-..+++....+.|..+ .+..++++
T Consensus       346 ~----~le~L~~el~~l~~~l~~~a~~Ls~~R~~~a~~l~~~v~~~l~~  390 (563)
T TIGR00634       346 E----SLEALEEEVDKLEEELDKAAVALSLIRRKAAERLAKRVEQELKA  390 (563)
T ss_pred             H----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            2    23334455666666666666666666666666443 23444444

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

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=85.91  E-value=4.9  Score=31.95  Aligned_cols=67  Identities=10%  Similarity=0.135  Sum_probs=42.7

Q ss_pred             hhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhH
Q 038837           62 NYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKAL  128 (287)
Q Consensus        62 ~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~  128 (287)
                      +.+.++|.-|+..-+.|+.|+=||+-||..+....+.+..+-..-+.|..+-.+...+-++++.|.+
T Consensus         4 EvleqLE~KIqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~WqerLr   70 (79)
T PRK15422          4 EVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQ   70 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4578889899999999999999999996554444444433333333344444444455556665543

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

Probab=85.73  E-value=26  Score=31.33  Aligned_cols=109  Identities=15%  Similarity=0.205  Sum_probs=60.0

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhh-hhccchh----HHHHHHHH
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSK-IKDDSSR----AEERLNAL  102 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~s-Lkk~s~~----aee~i~eL  102 (287)
                      |+--|...|.++...|..++..+....       ..-..+++.+.+-...|..++..... |+.|.-+    +-.+...+
T Consensus        24 P~~~l~q~ird~e~~l~~a~~~~a~~~-------a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~   96 (221)
T PF04012_consen   24 PEKMLEQAIRDMEEQLRKARQALARVM-------ANQKRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADL   96 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            335556666666666666666655544       33344455555555555555555442 3555322    22334556


Q ss_pred             HHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH
Q 038837          103 EEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus       103 EkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      +.++..|+..+..+......|.......+.|+.++.++.+.
T Consensus        97 e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~  137 (221)
T PF04012_consen   97 EEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREE  137 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666666666666665555555555666666666555544

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 [].

>COG1340 Uncharacterized archaeal coiled-coil protein [Function unknown]

Probab=85.69  E-value=37  Score=33.06  Aligned_cols=68  Identities=21%  Similarity=0.273  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhh--------------hHhHHHHHHHHHHHHHHHhhhhHHH-------HHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESK--------------ALDAEDRLEEVSLQVEKMSEIVTEQ-------WIQIQH  157 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsr--------------A~dAEkkv~eL~sklek~~ki~~EQ-------~~qIqk  157 (287)
                      +.+|-.+++.|+...+..+.++..|-..              |.+.-++..++|.++.+..+-..+.       ...|++
T Consensus       160 ~~el~aei~~lk~~~~e~~eki~~la~eaqe~he~m~k~~~~~De~Rkeade~he~~ve~~~~~~e~~ee~~~~~~elre  239 (294)
T COG1340         160 LKELKAEIDELKKKAREIHEKIQELANEAQEYHEEMIKLFEEADELRKEADELHEEFVELSKKIDELHEEFRNLQNELRE  239 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            5666677777776666666666555332              3333444445555544444443333       345556


Q ss_pred             HHHHHHHHH
Q 038837          158 LEQALHMAE  166 (287)
Q Consensus       158 ~E~Alk~ae  166 (287)
                      ++..++--.
T Consensus       240 ~~k~ik~l~  248 (294)
T COG1340         240 LEKKIKALR  248 (294)
T ss_pred             HHHHHHHHH
Confidence            666555333

>KOG0979 consensus Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=85.49  E-value=46  Score=37.41  Aligned_cols=109  Identities=18%  Similarity=0.209  Sum_probs=60.9

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHH------HHHHHHhhh--hccchh---H
Q 038837           27 HSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIH------HLQSLLSKI--KDDSSR---A   95 (287)
Q Consensus        27 ~~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~------sLqsEi~sL--kk~s~~---a   95 (287)
                      -..++  .+|-.|+..-.+||...+..+       +.|..++..++....+..      -..+.|+.+  |+.-..   -
T Consensus       176 ll~~h--~eL~~lr~~e~~Le~~~~~~~-------~~l~~L~~~~~~l~kdVE~~rer~~~~~~Ie~l~~k~~~v~y~~~  246 (1072)
T KOG0979|consen  176 LLQYH--IELMDLREDEKSLEDKLTTKT-------EKLNRLEDEIDKLEKDVERVRERERKKSKIELLEKKKKWVEYKKH  246 (1072)
T ss_pred             hHHHH--HHHHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccchHhh
Confidence            44555  788888888888887777755       444444444444333332      245666666  222221   1


Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837           96 EERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus        96 ee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      .....+.-+.++++++++|+.+++...++++-.+.|+.+.++.++...+
T Consensus       247 ~~ey~~~k~~~~r~k~~~r~l~k~~~pi~~~~eeLe~~~~et~~~~s~~  295 (1072)
T KOG0979|consen  247 DREYNAYKQAKDRAKKELRKLEKEIKPIEDKKEELESEKKETRSKISQK  295 (1072)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHhHHHhHHHHHHHH
Confidence            1224455555666666666666666555555555555555555544443

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

Probab=85.46  E-value=25  Score=36.88  Aligned_cols=50  Identities=10%  Similarity=0.165  Sum_probs=32.1

Q ss_pred             hhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Q 038837          117 NFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAE  166 (287)
Q Consensus       117 n~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae  166 (287)
                      +.+...++.++++.|..+.-+..+.+.+++-..+-+..+-.+...|.-+.
T Consensus       140 re~~~~~~~~l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r  189 (546)
T KOG0977|consen  140 REKLDDYLSRLSELEAEINTLKRRIKALEDELKRLKAENSRLREELARAR  189 (546)
T ss_pred             HHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence            45555566677777777777777777777776666666655555554443

>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]

Probab=85.28  E-value=25  Score=30.75  Aligned_cols=45  Identities=18%  Similarity=0.184  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHH
Q 038837           97 ERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQV  141 (287)
Q Consensus        97 e~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skl  141 (287)
                      +=+.-|.++++.|.+.+++.+.++..|..++..-+..++.+..+.
T Consensus        94 eAie~l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~~~q~~  138 (145)
T COG1730          94 EAIEFLKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQQKQ  138 (145)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            447888888888888888888888888777777777776666554

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=85.24  E-value=20  Score=39.31  Aligned_cols=19  Identities=32%  Similarity=0.410  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETML   50 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i   50 (287)
                      |..||.-|+-|+.+|+-.|
T Consensus       442 l~~eletLn~k~qqls~kl  460 (1118)
T KOG1029|consen  442 LQQELETLNFKLQQLSGKL  460 (1118)
T ss_pred             HHHHHHHHHHHHHHHhhhh
Confidence            3345555666666664443

>PF05622 HOOK: HOOK protein; InterPro: IPR008636 This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organisms

Probab=85.17  E-value=0.27  Score=51.81  Aligned_cols=132  Identities=20%  Similarity=0.296  Sum_probs=0.0

Q ss_pred             cchHHHHHHHH--HHHHHHHHHHHHHHHHhhhhcCc-----hhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHH
Q 038837           27 HSQQHLIAELQ--DAKLKIAGLETMLEESIRKVNGK-----SNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERL   99 (287)
Q Consensus        27 ~~~~~l~~eL~--qLk~kIa~LES~i~e~~qel~~K-----d~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i   99 (287)
                      .+.+.|..|+.  .++.+|.+||..-    +.|+.+     .+.+..+...+.+.......|+.+.       -.+.+++
T Consensus       443 ~~~~~l~~El~~~~l~erl~rLe~EN----k~Lk~~~e~~~~e~~~~L~~~Leda~~~~~~Le~~~-------~~~~~~~  511 (713)
T PF05622_consen  443 SSGDNLSAELNPAELRERLLRLEHEN----KRLKEKQEESEEEKLEELQSQLEDANRRKEKLEEEN-------REANEKI  511 (713)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccchhhhccchHHHHHHHHHHHHH----HHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHH
Confidence            34456666664  5778888887543    233222     1223333333333333333333331       1233456


Q ss_pred             HHHHHHHHHHHHHHhhhhhhhh---hHHhhhHhHHHHHHHHHHHHHH-------HhhhhHHH-HHHHHHHHHHHHHHHHH
Q 038837          100 NALEEEIRLLWAASRKNNFDIH---NLESKALDAEDRLEEVSLQVEK-------MSEIVTEQ-WIQIQHLEQALHMAELR  168 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~---~LEsrA~dAEkkv~eL~sklek-------~~ki~~EQ-~~qIqk~E~Alk~ae~~  168 (287)
                      .+|+.||+.|.+.+..++....   .+..+....-+++.+++..+.+       ++.-.... ..+|..++.+|+-.+.+
T Consensus       512 ~~lq~qle~lq~~l~~~~~~~~d~~~lk~~le~~~~~l~e~~~e~~~~~~~le~l~~~~~~~~~~ki~~Le~~L~~k~~e  591 (713)
T PF05622_consen  512 LELQSQLEELQKSLQEQGSKSEDSSELKQKLEEHLEKLRELKDELQKKREQLEELEQELNQSLSQKIEELEEALQKKEEE  591 (713)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhHHH
Confidence            7777777777777666655544   2222222222333333333333       22112222 45567777777765544


Q ss_pred             H
Q 038837          169 A  169 (287)
Q Consensus       169 ~  169 (287)
                      |
T Consensus       592 ~  592 (713)
T PF05622_consen  592 M  592 (713)
T ss_dssp             -
T ss_pred             H
Confidence            3

The different members of the Homo sapiens gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three Homo sapiens HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas the central coiled-coil motif mediates homodimerisation and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes [], whereas both HOOK1 and HOOK2 are localised to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head [].; GO: 0008017 microtubule binding, 0000226 microtubule cytoskeleton organization, 0005737 cytoplasm; PDB: 1WIX_A.

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

Probab=85.10  E-value=54  Score=34.96  Aligned_cols=36  Identities=19%  Similarity=0.242  Sum_probs=17.4

Q ss_pred             HHHHHHHhhccccCc-ccchHHHHHHHHHHHHHHHHH
Q 038837           11 LVILFWSFTLTSQNQ-QHSQQHLIAELQDAKLKIAGL   46 (287)
Q Consensus        11 ~~~~~~~~~~~s~~~-~~~~~~l~~eL~qLk~kIa~L   46 (287)
                      |++.|.-=-++++.+ +..+..|+.++...+..++.+
T Consensus       104 pll~sa~~~l~k~~~~~~e~~~lk~~lee~~~el~~~  140 (629)
T KOG0963|consen  104 PLLASAAELLNKQQKASEENEELKEELEEVNNELADL  140 (629)
T ss_pred             hHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHhhh
Confidence            344444444455544 555555555555544444433

>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=85.06  E-value=13  Score=32.78  Aligned_cols=24  Identities=29%  Similarity=0.328  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q 038837           31 HLIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      .+..++..++.++.++..+.+..+
T Consensus       122 ~li~~l~~~~~~~~~~~kq~~~~~  145 (192)
T PF05529_consen  122 SLIKELIKLEEKLEALKKQAESAS  145 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhh
Confidence            455666666666666666555443

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

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

Probab=85.01  E-value=26  Score=32.37  Aligned_cols=83  Identities=20%  Similarity=0.240  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHH
Q 038837           34 AELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAAS  113 (287)
Q Consensus        34 ~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~el  113 (287)
                      +|+.+=-..|-+|-..+.+..-++++++..+..+....+.++..+...++|+...+.....-.++++.|+.++..|+.++
T Consensus        24 ~E~~~K~~Eiv~Lr~ql~e~~~~l~~~~~~~~~l~~~~~~K~~ELE~ce~ELqr~~~Ea~lLrekl~~le~El~~Lr~~l  103 (202)
T PF06818_consen   24 AEVNQKDSEIVSLRAQLRELRAELRNKESQIQELQDSLRTKQLELEVCENELQRKKNEAELLREKLGQLEAELAELREEL  103 (202)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhHhHHHhHHHHHHHhCHHHHhhhhhhhhHHHHHHHHHHH
Confidence            56666667788899999999999999999999999999999999999999988776656666688999999999999888


Q ss_pred             hhh
Q 038837          114 RKN  116 (287)
Q Consensus       114 ekq  116 (287)
                      ...
T Consensus       104 ~~~  106 (202)
T PF06818_consen  104 ACA  106 (202)
T ss_pred             Hhh
Confidence            875

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

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

Probab=84.78  E-value=20  Score=32.50  Aligned_cols=25  Identities=28%  Similarity=0.306  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNL  123 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~L  123 (287)
                      +..++.+|..|++.+..-.+++..|
T Consensus        64 L~~a~~e~~eL~k~L~~y~kdK~~L   88 (201)
T PF13851_consen   64 LKKAEEEVEELRKQLKNYEKDKQSL   88 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566667777777776666666554

>PRK12704 phosphodiesterase; Provisional

Probab=84.65  E-value=20  Score=36.96  Aligned_cols=30  Identities=30%  Similarity=0.416  Sum_probs=19.2

Q ss_pred             HHhhhHhHHHHHHHHHHHHHHHhhhhHHHH
Q 038837          123 LESKALDAEDRLEEVSLQVEKMSEIVTEQW  152 (287)
Q Consensus       123 LEsrA~dAEkkv~eL~sklek~~ki~~EQ~  152 (287)
                      |+.+-.+.++..++...+|+++...+.|+-
T Consensus       126 Le~~~~~~~~~~~~~~~~l~~~a~lt~~ea  155 (520)
T PRK12704        126 LEKKEEELEELIEEQLQELERISGLTAEEA  155 (520)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHH
Confidence            334445566667777777777777766654

>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=84.55  E-value=28  Score=32.05  Aligned_cols=16  Identities=6%  Similarity=0.324  Sum_probs=6.9

Q ss_pred             HHhhhHHHHHHHHhhh
Q 038837           73 DMTNKIHHLQSLLSKI   88 (287)
Q Consensus        73 eks~kI~sLqsEi~sL   88 (287)
                      ++...|..|..++++|
T Consensus        53 ~L~~e~~~l~~e~e~L   68 (251)
T PF11932_consen   53 ELLAEYRQLEREIENL   68 (251)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3334444444444433

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.

>COG3206 GumC Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]

Probab=84.54  E-value=27  Score=34.72  Aligned_cols=83  Identities=14%  Similarity=0.144  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hccchhHHHHHHHHHHHHHHHHHHHh
Q 038837           36 LQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDDSSRAEERLNALEEEIRLLWAASR  114 (287)
Q Consensus        36 L~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~s~~aee~i~eLEkQVe~L~~ele  114 (287)
                      ++.||.+...+...+.+.+.++..+-..+..++..+.+-...|..--..+-.- ...--..+.+...|++++..+++.+.
T Consensus       287 i~~Lr~~~~~~~~~~~~l~~~~~~~~p~~~~~~~q~~~~~~~~~~e~~~~~~~~~~~~~~l~~~~~~L~~~~~~l~~~~~  366 (458)
T COG3206         287 IQDLRQQYAQVRQQIADLSTELGAKHPQLVALEAQLAELRQQIAAELRQILASLPNELALLEQQEAALEKELAQLKGRLS  366 (458)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcccChHHHhHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            67777777777777777777777777777777777777766644322222111 11112244555666666666665555


Q ss_pred             hhhh
Q 038837          115 KNNF  118 (287)
Q Consensus       115 kqn~  118 (287)
                      +.+.
T Consensus       367 ~~~~  370 (458)
T COG3206         367 KLPK  370 (458)
T ss_pred             hchH
Confidence            4443

>PF05483 SCP-1: Synaptonemal complex protein 1 (SCP-1); InterPro: IPR008827 Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex

Probab=84.14  E-value=24  Score=38.15  Aligned_cols=78  Identities=10%  Similarity=0.131  Sum_probs=51.7

Q ss_pred             hhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHH
Q 038837           62 NYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSL  139 (287)
Q Consensus        62 ~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~s  139 (287)
                      ++-+-.+..+-.+..+|..|.+.+.+|++.--.-...+.+|+.+...|++.+-+-+.+...+|-+.+..+..++.+..
T Consensus       573 en~r~~e~e~~~k~kq~k~lenk~~~LrKqvEnk~K~ieeLqqeNk~LKKk~~aE~kq~~~~eikVn~L~~E~e~~kk  650 (786)
T PF05483_consen  573 ENARSIECEILKKEKQMKILENKCNNLRKQVENKNKNIEELQQENKALKKKITAESKQSNVYEIKVNKLQEELENLKK  650 (786)
T ss_pred             HhhHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            333444666777888899999999988664333345578888888888888888777766665444444433333333

Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase [].; GO: 0007130 synaptonemal complex assembly, 0000795 synaptonemal complex

>PF14992 TMCO5: TMCO5 family

Probab=83.94  E-value=9.5  Score=36.75  Aligned_cols=91  Identities=20%  Similarity=0.246  Sum_probs=44.4

Q ss_pred             HhHHHhhhHHHHHHHHhhh-h-ccchhHHHH--------HHHHHHHHHHHHHHHhhhhhhhhhHHhhh-----------H
Q 038837           70 LVDDMTNKIHHLQSLLSKI-K-DDSSRAEER--------LNALEEEIRLLWAASRKNNFDIHNLESKA-----------L  128 (287)
Q Consensus        70 ~i~eks~kI~sLqsEi~sL-k-k~s~~aee~--------i~eLEkQVe~L~~elekqn~~~~~LEsrA-----------~  128 (287)
                      -|++++..|++|.+||.-. . .+-.+.+..        .++||.+-.+|.+.-+.-..+...|..+-           .
T Consensus        26 ki~~~E~~iq~Le~Eit~~~~~~~~~e~e~~~~~~~e~~l~~le~e~~~LE~~ne~l~~~~~elq~k~~e~~~~~~~e~~  105 (280)
T PF14992_consen   26 KIQEKEGAIQSLEREITKMDHIADRSEEEDIISEERETDLQELELETAKLEKENEHLSKSVQELQRKQDEQETNVQCEDP  105 (280)
T ss_pred             HHHHHHHHHHHHHHHHHHHccccCchhHHhhhhhchHHHHHHHHhhhHHHhhhhHhhhhhhhhhhhhhccccCCCCCCcc
Confidence            4667777777777777755 1 222222211        34444444444433333322222222221           1


Q ss_pred             hHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 038837          129 DAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQ  160 (287)
Q Consensus       129 dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~  160 (287)
                      .+..++++.-.+++++..-...|..+|-+.|.
T Consensus       106 ~~~~~lq~sk~~lqql~~~~~~qE~ei~kve~  137 (280)
T PF14992_consen  106 QLSQSLQFSKNKLQQLLESCASQEKEIAKVED  137 (280)
T ss_pred             chhcccHHhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            23344555555556666666666666666653

>PF01576 Myosin_tail_1: Myosin tail; InterPro: IPR002928 Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril

Probab=83.87  E-value=0.33  Score=52.53  Aligned_cols=74  Identities=20%  Similarity=0.234  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 038837          104 EEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLM  177 (287)
Q Consensus       104 kQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~ea~  177 (287)
                      .+++.|.++......+++-+-+.-.++.+.|++|......++.-..|+..++..+|.+++.+|...++++.+-.
T Consensus       426 e~~e~lere~k~L~~El~dl~~q~~~~~k~v~eLek~kr~LE~e~~El~~~leE~E~~l~~~E~~~lRl~~el~  499 (859)
T PF01576_consen  426 EQLEELERENKQLQDELEDLTSQLDDAGKSVHELEKAKRRLEQEKEELQEQLEEAEDALEAEEQKKLRLQVELQ  499 (859)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHhhccchhhhhhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333344444444445567777788888777788888889999999999999998888887766655

Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains [], 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family []. Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy []. The 3-D structure of the head portion of myosin has been determined [] and a model for actin-myosin complex has been constructed []. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament []. The coiled-coil region provides the structural backbone of the thick filament [].; GO: 0003774 motor activity, 0016459 myosin complex; PDB: 2LNK_C 3ZWH_Q.

>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=83.84  E-value=4.1  Score=30.77  Aligned_cols=44  Identities=23%  Similarity=0.251  Sum_probs=33.6

Q ss_pred             HHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHH
Q 038837          107 RLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTE  150 (287)
Q Consensus       107 e~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~E  150 (287)
                      +.+..+|.+....--..|++..|||++-.+|..+++.+.+-.+|
T Consensus        14 Q~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee   57 (61)
T PF08826_consen   14 QAIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEE   57 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35667777777777778888888888888888888887765544

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

>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []

Probab=83.79  E-value=9.5  Score=36.93  Aligned_cols=78  Identities=19%  Similarity=0.300  Sum_probs=56.3

Q ss_pred             hcc-chhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhh-------HHHHHHHHHHHH
Q 038837           89 KDD-SSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIV-------TEQWIQIQHLEQ  160 (287)
Q Consensus        89 kk~-s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~-------~EQ~~qIqk~E~  160 (287)
                      |.| +..+=.+|.+||.|+++|++|--.-.+..++||+-......|+++-..+.-.+..-|       +..-+.-+++.+
T Consensus         9 KeGL~~~aLqKIqelE~QldkLkKE~qQrQfQleSlEAaLqKQKqK~e~ek~e~s~LkREnq~l~e~c~~lek~rqKlsh   88 (307)
T PF10481_consen    9 KEGLPTRALQKIQELEQQLDKLKKERQQRQFQLESLEAALQKQKQKVEEEKNEYSALKRENQSLMESCENLEKTRQKLSH   88 (307)
T ss_pred             hccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHHHHHHHHHhhH
Confidence            555 555678899999999999999999999999999999988888887766655544332       222334445555


Q ss_pred             HHHHHH
Q 038837          161 ALHMAE  166 (287)
Q Consensus       161 Alk~ae  166 (287)
                      -|++-|
T Consensus        89 dlq~Ke   94 (307)
T PF10481_consen   89 DLQVKE   94 (307)
T ss_pred             HHhhhH
Confidence            555433

Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].

>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=83.64  E-value=17  Score=30.26  Aligned_cols=68  Identities=15%  Similarity=0.218  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGL-ETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLW  110 (287)
Q Consensus        32 l~~eL~qLk~kIa~L-ES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~  110 (287)
                      |..|-..||++.+-| ...|+|..+.        ..+...++.++..|-.+++|++||.-       +..-|++-|+.|+
T Consensus         3 la~eYsKLraQ~~vLKKaVieEQ~k~--------~~L~e~Lk~ke~~LRk~eqE~dSL~F-------rN~QL~kRV~~LQ   67 (102)
T PF10205_consen    3 LAQEYSKLRAQNQVLKKAVIEEQAKN--------AELKEQLKEKEQALRKLEQENDSLTF-------RNQQLTKRVEVLQ   67 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHH
Confidence            456677777777777 4556664422        23445566677777778888877722       2345666666666


Q ss_pred             HHHh
Q 038837          111 AASR  114 (287)
Q Consensus       111 ~ele  114 (287)
                      .|++
T Consensus        68 ~El~   71 (102)
T PF10205_consen   68 EELE   71 (102)
T ss_pred             HHHH
Confidence            6665

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.

>PF10212 TTKRSYEDQ: Predicted coiled-coil domain-containing protein; InterPro: IPR019348 This entry represents a C-terminal 500 residue region, which contains a conserved TTKRSYEDQ motif

Probab=83.24  E-value=12  Score=38.79  Aligned_cols=52  Identities=23%  Similarity=0.261  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQ  160 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~  160 (287)
                      +.++...+..|++|++..+.+          =|+-+..++-.|..|.+-...|...|+.+-+
T Consensus       464 L~~a~~~i~~LqDEL~TTr~N----------YE~QLs~MSEHLasmNeqL~~Q~eeI~~LK~  515 (518)
T PF10212_consen  464 LKEANQNISRLQDELETTRRN----------YEEQLSMMSEHLASMNEQLAKQREEIQTLKL  515 (518)
T ss_pred             HHHHHHHHHHHHHHHHHHHhh----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            555556666666666666554          3456677777777777777777777776643

It is found in a family of coiled-coil domain-containing proteins that are conserved from nematodes to humans. These proteins also contain an N-terminal domain with a KLRAQ motif (IPR019343 from INTERPRO). The function of these proteins is not known.

>KOG0239 consensus Kinesin (KAR3 subfamily) [Cytoskeleton]

Probab=83.24  E-value=12  Score=39.84  Aligned_cols=44  Identities=20%  Similarity=0.234  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVE  142 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skle  142 (287)
                      +..|..++..|++++...+.....+...-.++-+.+..+-..|+
T Consensus       243 i~~l~~~l~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~L~  286 (670)
T KOG0239|consen  243 IQALQQELEELKAELKELNDQVSLLTREVQEALKESNTLQSDLE  286 (670)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444333333333333333333333333333

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=83.12  E-value=19  Score=40.33  Aligned_cols=57  Identities=16%  Similarity=0.190  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 038837          102 LEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHL  158 (287)
Q Consensus       102 LEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~  158 (287)
                      +-+++..|..-+-..+.....+.....++|.-+.+...+++.+.....|++-++-++
T Consensus       395 ir~ei~~l~~~i~~~ke~e~~lq~e~~~~e~~l~~~~e~i~~l~~si~e~~~r~~~~  451 (1200)
T KOG0964|consen  395 IRSEIEKLKRGINDTKEQENILQKEIEDLESELKEKLEEIKELESSINETKGRMEEF  451 (1200)
T ss_pred             HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHH
Confidence            344556666666556666666666666666666666666666666666666666555

>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family []

Probab=83.09  E-value=1.5  Score=27.27  Aligned_cols=19  Identities=32%  Similarity=0.483  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 038837           35 ELQDAKLKIAGLETMLEES   53 (287)
Q Consensus        35 eL~qLk~kIa~LES~i~e~   53 (287)
                      |++++|.+|..||+++++=
T Consensus         2 E~~rlr~rI~dLer~L~~C   20 (23)
T PF04508_consen    2 EMNRLRNRISDLERQLSEC   20 (23)
T ss_pred             hHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999873

; GO: 0016032 viral reproduction

>PRK11281 hypothetical protein; Provisional

Probab=82.90  E-value=51  Score=37.41  Aligned_cols=132  Identities=13%  Similarity=0.115  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhh-ccchhHHHH-------HHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIK-DDSSRAEER-------LNALE  103 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLk-k~s~~aee~-------i~eLE  103 (287)
                      |.+.|.++.....+.+..+.+-+..+-+=..-.+.....+.+....++.+.+.+.+.. .+..-.+.+       ...++
T Consensus       126 LEq~L~q~~~~Lq~~Q~~La~~NsqLi~~qT~PERAQ~~lsea~~RlqeI~~~L~~~~~~~~~l~~~~~~~l~ae~~~l~  205 (1113)
T PRK11281        126 LESRLAQTLDQLQNAQNDLAEYNSQLVSLQTQPERAQAALYANSQRLQQIRNLLKGGKVGGKALRPSQRVLLQAEQALLN  205 (1113)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444444455555566666677777777666652 221122222       46677


Q ss_pred             HHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Q 038837          104 EEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMA  165 (287)
Q Consensus       104 kQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~a  165 (287)
                      -|++.++.++..++...+-+..+......+++.+...++.++....+++  .+++|++.+-|
T Consensus       206 ~~~~~~~~~l~~~~~l~~l~~~q~d~~~~~~~~~~~~~~~lq~~in~kr--~~~se~~~~~a  265 (1113)
T PRK11281        206 AQNDLQRKSLEGNTQLQDLLQKQRDYLTARIQRLEHQLQLLQEAINSKR--LTLSEKTVQEA  265 (1113)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH
Confidence            7777888888888888888888888888888888888888888777633  34455544433

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=82.74  E-value=8.2  Score=31.64  Aligned_cols=14  Identities=21%  Similarity=0.491  Sum_probs=6.5

Q ss_pred             HHHHHHHHHhhccc
Q 038837            9 LLLVILFWSFTLTS   22 (287)
Q Consensus         9 ~~~~~~~~~~~~~s   22 (287)
                      ++.+++++.+.+-.
T Consensus         8 ll~ll~~l~y~l~~   21 (105)
T PRK00888          8 LLALLVWLQYSLWF   21 (105)
T ss_pred             HHHHHHHHHHHHhc
Confidence            33444455555533

>PF05557 MAD: Mitotic checkpoint protein; InterPro: IPR008672 This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins

Probab=82.70  E-value=0.39  Score=50.60  Aligned_cols=13  Identities=31%  Similarity=0.435  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHH
Q 038837           99 LNALEEEIRLLWA  111 (287)
Q Consensus        99 i~eLEkQVe~L~~  111 (287)
                      +..|+.+++.++.
T Consensus       187 ~~~l~~e~~~l~~  199 (722)
T PF05557_consen  187 IQSLESELEELKE  199 (722)
T ss_dssp             -------------
T ss_pred             HHHHHHHHHHHHH
Confidence            3333333333333

The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in Saccharomyces cerevisiae and higher eukaryotes. In Saccharomyces cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated [].; PDB: 1GO4_F 4DZO_A.

>PF05557 MAD: Mitotic checkpoint protein; InterPro: IPR008672 This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins

Probab=82.70  E-value=0.39  Score=50.60  Aligned_cols=41  Identities=24%  Similarity=0.421  Sum_probs=0.0

Q ss_pred             hhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Q 038837          119 DIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLE  159 (287)
Q Consensus       119 ~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E  159 (287)
                      +...++..+..++..+..+..+++.+....+++..+.+..|
T Consensus       172 ~~~~l~~~~~~~e~~~~~l~~e~~~l~~~le~~~~~~~e~e  212 (722)
T PF05557_consen  172 ELSELERQAENAESQIQSLESELEELKEQLEELQSELQEAE  212 (722)
T ss_dssp             -----------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444555555555565555555555555554444333

The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in Saccharomyces cerevisiae and higher eukaryotes. In Saccharomyces cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated [].; PDB: 1GO4_F 4DZO_A.

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

Probab=82.47  E-value=25  Score=35.98  Aligned_cols=128  Identities=16%  Similarity=0.153  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHH----HhHHhHHHhhhHH----------HHHHHHhhh----hcc
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEE----RDKLVDDMTNKIH----------HLQSLLSKI----KDD   91 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e----~Ek~i~eks~kI~----------sLqsEi~sL----kk~   91 (287)
                      ..|+.|.+.++..|..|+.+|+...-++...+.....    .++..++.+..+.          .+..|+..+    ...
T Consensus       277 ~~l~~E~~~~~ee~~~l~~Qi~~l~~e~~d~e~~~~~~~~~~~~~~~~~~~~~~~~~~~e~e~~l~~~el~~~~ee~~~~  356 (511)
T PF09787_consen  277 EELKQERDHLQEEIQLLERQIEQLRAELQDLEAQLEGEQESFREQPQELSQQLEPELTTEAELRLYYQELYHYREELSRQ  356 (511)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHh
Confidence            4455666666666666666664443333333332222    2333334443333          333444333    222


Q ss_pred             chhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHH----HHHhhhhHHHHHHHHHHHHHH
Q 038837           92 SSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQV----EKMSEIVTEQWIQIQHLEQAL  162 (287)
Q Consensus        92 s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skl----ek~~ki~~EQ~~qIqk~E~Al  162 (287)
                      .+...-++.+-+.|+++|+..+..-- ..    +.-.|.|+++..|+.-|    ..++....|-+.-.=++|+..
T Consensus       357 ~s~~~~k~~~ke~E~q~lr~~l~~~~-~~----s~~~elE~rl~~lt~~Li~KQ~~lE~l~~ek~al~lqlErl~  426 (511)
T PF09787_consen  357 KSPLQLKLKEKESEIQKLRNQLSARA-SS----SSWNELESRLTQLTESLIQKQTQLESLGSEKNALRLQLERLE  426 (511)
T ss_pred             cChHHHHHHHHHHHHHHHHHHHHHHh-cc----CCcHhHHHHHhhccHHHHHHHHHHHHHHhhhhhccccHHHHH
Confidence            44455567888999999998876633 11    12358899999988433    445555555442222444433

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 [].

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=82.47  E-value=13  Score=30.25  Aligned_cols=41  Identities=15%  Similarity=0.215  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHH
Q 038837           97 ERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEV  137 (287)
Q Consensus        97 e~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL  137 (287)
                      +=+..|++.++.+...+.+.+.+...++....+.++++.++
T Consensus        67 e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~~  107 (110)
T TIGR02338        67 EAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQEA  107 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33577777777777777777777777776666666666654

Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.

>PF14073 Cep57_CLD: Centrosome localisation domain of Cep57

Probab=82.41  E-value=38  Score=30.70  Aligned_cols=71  Identities=20%  Similarity=0.311  Sum_probs=46.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHH----HHHHHHHHHHHhhhhHHHH----------HHHHHH
Q 038837           93 SRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDR----LEEVSLQVEKMSEIVTEQW----------IQIQHL  158 (287)
Q Consensus        93 ~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkk----v~eL~sklek~~ki~~EQ~----------~qIqk~  158 (287)
                      +.||.+-.-||+|.+-..+-++.-+.+...+-.+...+++-    ..++.++++++++.-.|..          .+|+.+
T Consensus        67 ~aAEtRCslLEKQLeyMRkmv~~ae~er~~~le~q~~l~~e~~~~~~~~~~klekLe~LE~E~~rLt~~Q~~ae~Ki~~L  146 (178)
T PF14073_consen   67 SAAETRCSLLEKQLEYMRKMVESAEKERNAVLEQQVSLQRERQQDQSELQAKLEKLEKLEKEYLRLTATQSLAETKIKEL  146 (178)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677788899999998888877666655554444444443    5567777777766643322          567777


Q ss_pred             HHHHH
Q 038837          159 EQALH  163 (287)
Q Consensus       159 E~Alk  163 (287)
                      |.-|+
T Consensus       147 E~KL~  151 (178)
T PF14073_consen  147 EEKLQ  151 (178)
T ss_pred             HHHHH
Confidence            66554

>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles

Probab=82.38  E-value=6.1  Score=29.79  Aligned_cols=74  Identities=12%  Similarity=0.276  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hccchhHHHHHHHHHHHHHHHHHHHh
Q 038837           36 LQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDDSSRAEERLNALEEEIRLLWAASR  114 (287)
Q Consensus        36 L~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~s~~aee~i~eLEkQVe~L~~ele  114 (287)
                      +++++.+|..+...-.      ..|...|.+.+..+.|...-|..|+-|+.++ .........++.....+...|+++++
T Consensus         5 ~~~i~~~l~~~~~~~~------~~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk~~l~   78 (79)
T PF05008_consen    5 TAEIKSKLERIKNLSG------EQRKSLIREIERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLKKELK   78 (79)
T ss_dssp             HHHHHHHHHHGGGS-C------HHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccCh------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4556666766642211      2466778888888888888888888888777 33344445557777777777777665


Q ss_pred             h
Q 038837          115 K  115 (287)
Q Consensus       115 k  115 (287)
                      +
T Consensus        79 ~   79 (79)
T PF05008_consen   79 K   79 (79)
T ss_dssp             H
T ss_pred             C
Confidence            3

The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.

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

Probab=82.29  E-value=50  Score=36.00  Aligned_cols=21  Identities=19%  Similarity=0.036  Sum_probs=11.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHH
Q 038837          148 VTEQWIQIQHLEQALHMAELR  168 (287)
Q Consensus       148 ~~EQ~~qIqk~E~Alk~ae~~  168 (287)
                      +.+-+..++++||++..-|.+
T Consensus       589 v~dLR~~L~~~Eq~aarrEd~  609 (961)
T KOG4673|consen  589 VEDLRQTLSKKEQQAARREDM  609 (961)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            344555666666666655443

>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function

Probab=82.25  E-value=10  Score=32.36  Aligned_cols=40  Identities=10%  Similarity=0.240  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVS  138 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~  138 (287)
                      .....++|..++.++...+.+.+.+.......|-|+.++.
T Consensus        84 ~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~Le~ki~~ie  123 (126)
T PF07889_consen   84 SKQIKDEVTEVREDVSQIGDDVDSVQQMVEGLEGKIDEIE  123 (126)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4666777888888888888887777766666666665553

The region featured in this family is approximately 100 amino acids long.

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

Probab=81.94  E-value=19  Score=32.52  Aligned_cols=94  Identities=23%  Similarity=0.273  Sum_probs=53.1

Q ss_pred             hhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh---hccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhH
Q 038837           54 IRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI---KDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDA  130 (287)
Q Consensus        54 ~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL---kk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dA  130 (287)
                      .-.+.++...+..+|+    ..=++..|++-|+.|   |.+....-+..+.+|+++..-       .-+...+|+...+.
T Consensus        68 ~~~f~~~~~tl~~LE~----~GFnV~~l~~RL~kLL~lk~~~~~~~e~~k~le~~~~~~-------~~~~~~~e~~i~~L  136 (190)
T PF05266_consen   68 RSSFESLMKTLSELEE----HGFNVKFLRSRLNKLLSLKDDQEKLLEERKKLEKKIEEK-------EAELKELESEIKEL  136 (190)
T ss_pred             HHHHHHHHHHHHHHHH----cCCccHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH-------HHhhhhHHHHHHHH
Confidence            3344445555655553    445677777777755   666666666666666666554       22334555556666


Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 038837          131 EDRLEEVSLQVEKMSEIVTEQWIQIQHL  158 (287)
Q Consensus       131 Ekkv~eL~sklek~~ki~~EQ~~qIqk~  158 (287)
                      |.++.+|..+...+.+...+-...|-.+
T Consensus       137 e~ki~el~~~~~~~~~~ke~~~~ei~~l  164 (190)
T PF05266_consen  137 EMKILELQRQAAKLKEKKEAKDKEISRL  164 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666666555554444444444433

>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]

Probab=81.67  E-value=30  Score=39.52  Aligned_cols=93  Identities=19%  Similarity=0.282  Sum_probs=49.5

Q ss_pred             HHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhH---Hh
Q 038837           50 LEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNL---ES  125 (287)
Q Consensus        50 i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~L---Es  125 (287)
                      ++++.+.++.+++..++++..|.........|+.+-..| ...-..+++++.+.+++.+.|.+.++....+...+   .+
T Consensus       453 ~~~~~~~~~~~~~~~keL~e~i~~lk~~~~el~~~q~~l~q~~~ke~~ek~~~~~~~~~~l~~~~~~~~eele~~q~~~~  532 (1317)
T KOG0612|consen  453 LDEKCQAVAELEEMDKELEETIEKLKSEESELQREQKALLQHEQKEVEEKLSEEEAKKRKLEALVRQLEEELEDAQKKND  532 (1317)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555566666666666666666655555555422222 33334455566666666666665555444443333   33


Q ss_pred             hhHhHHHHHHHHHHHHH
Q 038837          126 KALDAEDRLEEVSLQVE  142 (287)
Q Consensus       126 rA~dAEkkv~eL~skle  142 (287)
                      .+.+...+|..+-.+|+
T Consensus       533 ~~~~~~~kv~~~rk~le  549 (1317)
T KOG0612|consen  533 NAADSLEKVNSLRKQLE  549 (1317)
T ss_pred             HHHHHHhhHHHHHHHHH
Confidence            44455556655555554

>PF13747 DUF4164: Domain of unknown function (DUF4164)

Probab=81.58  E-value=22  Score=28.41  Aligned_cols=44  Identities=30%  Similarity=0.339  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      .+++.+|+.|..+--....+.+..++|++..|.--.+++.+|..
T Consensus        35 ~~~e~ei~~l~~dr~rLa~eLD~~~ar~~~Le~~~~Evs~rL~~   78 (89)
T PF13747_consen   35 DELEEEIQRLDADRSRLAQELDQAEARANRLEEANREVSRRLDS   78 (89)
T ss_pred             hhHHHHHHHHHhhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            55666666666666666666666666666666666666666654

>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]

Probab=81.35  E-value=72  Score=35.51  Aligned_cols=34  Identities=24%  Similarity=0.046  Sum_probs=22.4

Q ss_pred             HHHHHHHhhhhHHHHHHHHHHHHH----------HHHHHHHHHH
Q 038837          138 SLQVEKMSEIVTEQWIQIQHLEQA----------LHMAELRAAN  171 (287)
Q Consensus       138 ~sklek~~ki~~EQ~~qIqk~E~A----------lk~ae~~~~k  171 (287)
                      ...-++.+.-.++||..|=-+|+.          |+-|.+.+-.
T Consensus       385 ~~l~aerqeQidelKn~if~~e~~~~dhe~~kneL~~a~ekld~  428 (1265)
T KOG0976|consen  385 LELQAERQEQIDELKNHIFRLEQGKKDHEAAKNELQEALEKLDL  428 (1265)
T ss_pred             HHHHHHHHHHHHHHHHhhhhhhhccchhHHHHHHHHHHHHHHHH
Confidence            333344555577888888888888          7766665433

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)

Probab=81.18  E-value=31  Score=28.91  Aligned_cols=65  Identities=22%  Similarity=0.336  Sum_probs=32.5

Q ss_pred             HHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHH
Q 038837           72 DDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEE  136 (287)
Q Consensus        72 ~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~e  136 (287)
                      .++..+.++|+.+++..|-+-.--..+-.+|+..++.|+..-...+..+.-|+++..|+.+-++.
T Consensus        12 ~el~n~La~Le~slE~~K~S~~eL~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~   76 (107)
T PF09304_consen   12 NELQNRLASLERSLEDEKTSQGELAKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLED   76 (107)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556667777777666433222233334455555555555555555555555555555444443

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.

>COG4372 Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

Probab=81.17  E-value=68  Score=32.79  Aligned_cols=73  Identities=22%  Similarity=0.295  Sum_probs=49.5

Q ss_pred             hHHHhhhHHHHHHHHhhh--hc-------cchhHHHH-----HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHH
Q 038837           71 VDDMTNKIHHLQSLLSKI--KD-------DSSRAEER-----LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEE  136 (287)
Q Consensus        71 i~eks~kI~sLqsEi~sL--kk-------~s~~aee~-----i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~e  136 (287)
                      ..-.+.+-+.|++++..|  ..       .|+.++.+     +.-|..||..|+...++...+..+|..+++-++.+-++
T Consensus       139 lar~t~Q~q~lqtrl~~l~~qr~ql~aq~qsl~a~~k~LQ~s~~Qlk~~~~~L~~r~~~ieQ~~~~la~r~~a~q~r~~e  218 (499)
T COG4372         139 LARLTKQAQDLQTRLKTLAEQRRQLEAQAQSLQASQKQLQASATQLKSQVLDLKLRSAQIEQEAQNLATRANAAQARTEE  218 (499)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333445556666666655  11       13333322     46677888899988888888888899999999988888


Q ss_pred             HHHHHHH
Q 038837          137 VSLQVEK  143 (287)
Q Consensus       137 L~sklek  143 (287)
                      |.+.-..
T Consensus       219 la~r~aa  225 (499)
T COG4372         219 LARRAAA  225 (499)
T ss_pred             HHHHHHH
Confidence            8765543

>PF15450 DUF4631: Domain of unknown function (DUF4631)

Probab=81.15  E-value=65  Score=33.75  Aligned_cols=29  Identities=14%  Similarity=0.077  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhhhhhhHHh
Q 038837           97 ERLNALEEEIRLLWAASRKNNFDIHNLES  125 (287)
Q Consensus        97 e~i~eLEkQVe~L~~elekqn~~~~~LEs  125 (287)
                      ..+.++.+-|+.|..+|+..|.+..++.+
T Consensus       412 ~~l~~v~eKVd~LpqqI~~vs~Kc~~~Ks  440 (531)
T PF15450_consen  412 KHLKEVQEKVDSLPQQIEEVSDKCDLHKS  440 (531)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHh
Confidence            33677777777777777777776665543

>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function

Probab=80.84  E-value=16  Score=36.35  Aligned_cols=80  Identities=11%  Similarity=0.108  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh--hccchhHHHH--HHHHHHHHHHHHHH
Q 038837           37 QDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI--KDDSSRAEER--LNALEEEIRLLWAA  112 (287)
Q Consensus        37 ~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL--kk~s~~aee~--i~eLEkQVe~L~~e  112 (287)
                      .+++.+=.+||-++++..++.+.|.+.-.++.....|.-.-++.|-+|....  .-.+.-.-.|  |++||..|+-|.-|
T Consensus       137 ~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~layqq~L~~eyQatf~eq~~ml~kRQ~yI~~LEsKVqDLm~E  216 (401)
T PF06785_consen  137 RHLREENQCLQLQLDALQQECGEKEEESQTLNRELAEALAYQQELNDEYQATFVEQHSMLDKRQAYIGKLESKVQDLMYE  216 (401)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhHHHHHHHHHHHHHHHHHHHH
Confidence            3344445556777888888888888888888888888888888888887755  3334444444  89999999999988


Q ss_pred             Hhhh
Q 038837          113 SRKN  116 (287)
Q Consensus       113 lekq  116 (287)
                      ++..
T Consensus       217 irnL  220 (401)
T PF06785_consen  217 IRNL  220 (401)
T ss_pred             HHHH
Confidence            8764

>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=80.76  E-value=92  Score=34.00  Aligned_cols=19  Identities=37%  Similarity=0.181  Sum_probs=8.6

Q ss_pred             HHHHHHHHHHHHHHHhhhh
Q 038837           99 LNALEEEIRLLWAASRKNN  117 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn  117 (287)
                      ..+++...+.|....++.+
T Consensus       625 ~~e~~~~~~~l~~~~~~l~  643 (908)
T COG0419         625 ENELEEAEEELESELEKLN  643 (908)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444

>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=80.74  E-value=29  Score=37.34  Aligned_cols=20  Identities=25%  Similarity=0.283  Sum_probs=11.2

Q ss_pred             hHHHHHHHHHH--HHHHHHHHH
Q 038837          148 VTEQWIQIQHL--EQALHMAEL  167 (287)
Q Consensus       148 ~~EQ~~qIqk~--E~Alk~ae~  167 (287)
                      ++.|+..|+.+  +++-+++++
T Consensus       683 ~~~Q~~~I~~iL~~~~~~I~~~  704 (717)
T PF10168_consen  683 SESQKRTIKEILKQQGEEIDEL  704 (717)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Confidence            55666666654  555555443

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 [].

>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site

Probab=80.67  E-value=75  Score=32.95  Aligned_cols=21  Identities=10%  Similarity=0.259  Sum_probs=11.1

Q ss_pred             hHHhHHHhhhHHHHHHHHhhh
Q 038837           68 DKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        68 Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      ...+......-..|..|++.+
T Consensus       312 ~~~l~~~~~~~~~l~~e~~~v  332 (560)
T PF06160_consen  312 YEYLEHAKEQNKELKEELERV  332 (560)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            344444455555566666655

EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane

>PRK00106 hypothetical protein; Provisional

Probab=80.65  E-value=33  Score=35.84  Aligned_cols=31  Identities=10%  Similarity=0.198  Sum_probs=20.4

Q ss_pred             HHhhhHhHHHHHHHHHHHHHHHhhhhHHHHH
Q 038837          123 LESKALDAEDRLEEVSLQVEKMSEIVTEQWI  153 (287)
Q Consensus       123 LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~  153 (287)
                      ++.+-.+.++..++...+|+++.+.+.||-+
T Consensus       141 Lee~~~~~~~~~~~~~~~Le~~a~lt~~eak  171 (535)
T PRK00106        141 IDEREEQVEKLEEQKKAELERVAALSQAEAR  171 (535)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHH
Confidence            4444555666677777788887777776653

>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=80.44  E-value=42  Score=32.79  Aligned_cols=83  Identities=13%  Similarity=0.246  Sum_probs=62.4

Q ss_pred             hHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhh
Q 038837           68 DKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEI  147 (287)
Q Consensus        68 Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki  147 (287)
                      =+...+-+.+|+.|..|+..-......-.+.|..|-.||=.|++.....-.+.+.|-.....+...=..|..+|..+++-
T Consensus       205 v~QL~~An~qia~LseELa~k~Ee~~rQQEEIt~LlsqivdlQ~r~k~~~~EnEeL~q~L~~ske~Q~~L~aEL~elqdk  284 (306)
T PF04849_consen  205 VKQLSEANQQIASLSEELARKTEENRRQQEEITSLLSQIVDLQQRCKQLAAENEELQQHLQASKESQRQLQAELQELQDK  284 (306)
T ss_pred             HHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566778889999999876666666777778888888888888888887777777777777777777777777666554


Q ss_pred             hHH
Q 038837          148 VTE  150 (287)
Q Consensus       148 ~~E  150 (287)
                      ..|
T Consensus       285 Y~E  287 (306)
T PF04849_consen  285 YAE  287 (306)
T ss_pred             HHH
Confidence            443

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 [].

>PF05739 SNARE: SNARE domain; InterPro: IPR000727 The process of vesicular fusion with target membranes depends on a set of SNAREs (SNAP-Receptors), which are associated with the fusing membranes [, ]

Probab=80.43  E-value=12  Score=26.64  Aligned_cols=47  Identities=13%  Similarity=0.161  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      .+|-.-...+..+++.|+.-++.++..+..|..++..-+.+|.++.+
T Consensus        14 ~~l~~~~~~i~~ev~~Q~~~ld~i~~~vd~~~~~l~~~~~~l~ka~~   60 (63)
T PF05739_consen   14 QELKQMFQDIGEEVEEQNEMLDRIEDNVDRANENLKKGNKKLKKALK   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334445556889999999999999999999999988888887654

Target SNAREs (t-SNAREs) are localised on the target membrane and belong to two different families, the syntaxin-like family and the SNAP-25 like family. One member of each family, together with a v-SNARE localised on the vesicular membrane, are required for fusion. The Syntaxins are type-I transmembrane proteins that contain several regions with coiled-coil propensity in their cytosolic part, the SNARE motif. SNAP-25 (IPR000928 from INTERPRO) is a protein consisting of two coiled-coil regions, which is associated with the membrane by lipid anchors. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in alpha-helical secondary structure []. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Recently, it was shown that the two coiled-coil regions of SNAP-25 and one of the coiled-coil regions of the syntaxins are related []. This domain is found in both Syntaxin and SNAP-25 families as well as in other proteins.; GO: 0005515 protein binding; PDB: 1URQ_B 3RL0_R 1HVV_B 1SFC_B 1N7S_B 3IPD_B 3C98_B 3HD7_F 3RK2_B 1KIL_B ....

>PRK10929 putative mechanosensitive channel protein; Provisional

Probab=80.38  E-value=60  Score=36.88  Aligned_cols=67  Identities=19%  Similarity=0.133  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELR  168 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~  168 (287)
                      ..++-|++.|..++...+...+-+..+...+.++++.+...++.++....+++  -+++|++++-|+..
T Consensus       183 ~~l~~~~~~l~~~l~s~~~~~~L~~~q~dl~~~~~~~l~~~~~~Lq~~in~kR--~~~se~~~~~~~~~  249 (1109)
T PRK10929        183 AALKALVDELELAQLSANNRQELARLRSELAKKRSQQLDAYLQALRNQLNSQR--QREAERALESTELL  249 (1109)
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHh
Confidence            55777888888888888888888888888888999999998888888887754  35666666655543

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

Probab=80.31  E-value=12  Score=34.86  Aligned_cols=15  Identities=20%  Similarity=0.348  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHHHH
Q 038837           96 EERLNALEEEIRLLW  110 (287)
Q Consensus        96 ee~i~eLEkQVe~L~  110 (287)
                      ++++.+|.||.+.+.
T Consensus       178 ~~~~~al~Kq~e~~~  192 (216)
T KOG1962|consen  178 QKKVDALKKQSEGLQ  192 (216)
T ss_pred             HHHHHHHHHHHHHcc
Confidence            333344444444333

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=80.25  E-value=25  Score=28.54  Aligned_cols=19  Identities=21%  Similarity=0.364  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 038837           33 IAELQDAKLKIAGLETMLE   51 (287)
Q Consensus        33 ~~eL~qLk~kIa~LES~i~   51 (287)
                      ..++++++.++..+-+.+.
T Consensus         9 ~~~~q~~q~~~~~l~~q~~   27 (110)
T TIGR02338         9 LAQLQQLQQQLQAVATQKQ   27 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3444444444444433333

Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.

>KOG0018 consensus Structural maintenance of chromosome protein 1 (sister chromatid cohesion complex Cohesin, subunit SMC1) [Cell cycle control, cell division, chromosome partitioning]

Probab=80.09  E-value=18  Score=40.62  Aligned_cols=52  Identities=17%  Similarity=0.182  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhh
Q 038837           34 AELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIK   89 (287)
Q Consensus        34 ~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLk   89 (287)
                      -++++|+.+=-+|.-+|.+...  +.+  .+++-+.-|.-.+..|..+..++++++
T Consensus       652 k~~~~L~~~k~rl~eel~ei~~--~~~--e~~~v~~~i~~le~~~~~~~~~~~~~k  703 (1141)
T KOG0018|consen  652 KEVDQLKEKKERLLEELKEIQK--RRK--EVSSVESKIHGLEMRLKYSKLDLEQLK  703 (1141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH--hhh--hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4677888887788777777665  333  555555555555555555555555665

---

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	287
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-06
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	4e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.2 bits (124), Expect = 1e-07
 Identities = 49/271 (18%), Positives = 89/271 (32%), Gaps = 76/271 (28%)

Query: 59  GKSNYIEE--RD-KLVDDMTNKIH---------------HLQSLLSKIK-------DDSS 93
           GK+    +     K+   M  KI                 LQ LL +I        D SS
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221

Query: 94  RAEERLNALEEEIRLLWAASRKNNF-----DIHNLESKALDAED---------RLEEV-- 137
             + R+++++ E+R L  +    N      ++ N  +KA +A +         R ++V  
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN--AKAWNAFNLSCKILLTTRFKQVTD 279

Query: 138 SLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQLMYARCTFLKFVKDFSEKHLPK 197
            L     + I  +      H    L   E+++              LK++ D   + LP+
Sbjct: 280 FLSAATTTHISLD------HHSMTLTPDEVKSL------------LLKYL-DCRPQDLPR 320

Query: 198 LTGMLVPYLPGKGSILISFMSQVQHQFKRF-FLAFKKFHHELQGFIKQEMVKNKLTAALA 256
                 P      SI+   +      +  +  +   K    ++  +      N L  A  
Sbjct: 321 EVLTTNPRRL---SIIAESIRDGLATWDNWKHVNCDKLTTIIESSL------NVLEPAEY 371

Query: 257 N---EELVFFVASALITFPILAA-WVLLSSQ 283
               + L  F  SA I   +L+  W  +   
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 46.0 bits (109), Expect = 9e-06
 Identities = 24/153 (15%), Positives = 58/153 (37%)

Query: 23   QNQQHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQ 82
               +     L  E +  + +++ L T L E   K    +    + + ++ ++  ++   +
Sbjct: 993  LIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEE 1052

Query: 83   SLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVE 142
                +++    + E   + L E+I  L A   +    +   E +   A  RLE+ + Q  
Sbjct: 1053 KSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKN 1112

Query: 143  KMSEIVTEQWIQIQHLEQALHMAELRAANVQRQ 175
               + + E    I  L++ L   +      ++Q
Sbjct: 1113 NALKKIRELESHISDLQEDLESEKAARNKAEKQ 1145

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

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 22/137 (16%), Positives = 55/137 (40%), Gaps = 2/137 (1%)

Query: 26   QHSQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLL 85
            Q   + ++A+ +  KLKI      +E   +   G  N I +  + +D+   +   L   +
Sbjct: 894  QCCYRRMMAKRELKKLKIE--ARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKM 951

Query: 86   SKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMS 145
            + ++   S   E+L +  E +R+    ++     + +L+ +       L +   + + + 
Sbjct: 952  NNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIE 1011

Query: 146  EIVTEQWIQIQHLEQAL 162
            E   +   + + L   L
Sbjct: 1012 EWADKYKHETEQLVSEL 1028

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

 Score = 40.5 bits (95), Expect = 5e-04
 Identities = 20/150 (13%), Positives = 56/150 (37%), Gaps = 3/150 (2%)

Query: 28   SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSK 87
            S +         + KI  L+  ++E  ++       +   +      T K+      L  
Sbjct: 915  SVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRM 974

Query: 88   IKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEI 147
             ++++  A  R+ +L+EEI  L     +   +   +E  A   +   E++  ++++ + +
Sbjct: 975  SEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTL 1034

Query: 148  VTEQWIQIQHLEQALHMAELRAANVQRQLM 177
            +     + + L + +H           + +
Sbjct: 1035 LKT---EKEELNRRIHDQAKEITETMEKKL 1061

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	287
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	97.82
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	97.46
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	97.31
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	97.13
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	96.83
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	96.71
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	96.66
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	96.46
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	96.25
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	96.21
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	96.11
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	96.11
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	95.7
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	95.48
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	95.13
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	95.12
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	94.73
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	94.71
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	94.68
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	94.36
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	94.32
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	94.2
2b9c_A	147	Striated-muscle alpha tropomyosin; alpha-helix, co	93.97
3u0c_A	201	Invasin IPAB, 62 kDa antigen; translocator, type t	93.67
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	93.4
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	93.04
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	92.99
3swk_A	86	Vimentin; cytoskeleton, intermediate filament, alp	92.86
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	92.84
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	92.42
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	92.34
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	92.34
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	92.27
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	91.69
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	91.65
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	91.33
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	91.31
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	91.01
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	90.95
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	89.89
2efr_A	155	General control protein GCN4 and tropomyosin 1 Al;	89.71
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	89.34
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	88.85
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	88.37
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	88.18
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	87.9
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	87.61
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	87.58
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	87.41
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	87.07
1m1j_A	491	Fibrinogen alpha subunit; coiled coils, disulfide	85.9
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	85.69
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	85.53
2b9c_A	147	Striated-muscle alpha tropomyosin; alpha-helix, co	84.95
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	84.84
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	84.25
1zxa_A	67	CGMP-dependent protein kinase 1, alpha isozyme; pa	83.5
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	83.08
3a7o_A	75	Autophagy protein 16; coiled-coil, coiled coil, cy	83.06
1l8d_A	112	DNA double-strand break repair RAD50 ATPase; zinc	81.66
2oto_A	155	M protein; helical coiled coil, fibrinogen-binding	80.87
1fxk_A	107	Prefoldin; archaeal protein, chaperone; 2.30A {Met	80.64
3s84_A	273	Apolipoprotein A-IV; four helix bundle, transport	80.11
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	80.03

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

Probab=97.82  E-value=0.0026  Score=53.54  Aligned_cols=51  Identities=8%  Similarity=0.056  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQ   82 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLq   82 (287)
                      +..+++.+..++..|+..+.+...++..-...+.+.+..+......+..+.
T Consensus        11 l~~~~~~~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   61 (284)
T 1c1g_A           11 LKLDKENALDRADEAEADKKAAEDRSKQLEDELVSLQKKLKATEDELDKYS   61 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444433333333333333333333333333

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

Probab=97.46  E-value=0.0078  Score=54.19  Aligned_cols=109  Identities=17%  Similarity=0.209  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWA  111 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~  111 (287)
                      +..+++.|...++.++..+.....+++.-+..+..++..|.+...+|...+..+.+.+     ..+...+|+++++.++.
T Consensus        30 lp~el~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~~v~-----~~kE~~aL~kEie~~~~  104 (256)
T 3na7_A           30 KRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIK-----SERELRSLNIEEDIAKE  104 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-----SSSHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccC-----CHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444444444444444444444444444444333321     22224445555554444


Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHh
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMS  145 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~  145 (287)
                      .+...+.++-.+..+....++.+.++..+++.++
T Consensus       105 ~i~~lE~eile~~e~ie~~~~~l~~~~~~l~~~~  138 (256)
T 3na7_A          105 RSNQANREIENLQNEIKRKSEKQEDLKKEMLELE  138 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444444444443333

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

Probab=97.31  E-value=0.019  Score=51.59  Aligned_cols=53  Identities=11%  Similarity=0.035  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 038837          104 EEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQ  156 (287)
Q Consensus       104 kQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIq  156 (287)
                      ++.+.|.++++....++..+|....+...+++++...++.++....+....+.
T Consensus        90 kE~~aL~kEie~~~~~i~~lE~eile~~e~ie~~~~~l~~~~~~l~~~~~~l~  142 (256)
T 3na7_A           90 RELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQEDLKKEMLELEKLAL  142 (256)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555566666666666666666666666666666665555555554444443

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

Probab=97.13  E-value=0.0033  Score=67.49  Aligned_cols=118  Identities=19%  Similarity=0.180  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHh----HHHhhhHHHHHHHHhhhhc---cchhHHHHHHHHHHHHHHHHH
Q 038837           39 AKLKIAGLETMLEESIRKVNGKSNYIEERDKLV----DDMTNKIHHLQSLLSKIKD---DSSRAEERLNALEEEIRLLWA  111 (287)
Q Consensus        39 Lk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i----~eks~kI~sLqsEi~sLkk---~s~~aee~i~eLEkQVe~L~~  111 (287)
                      ++.....||+.|.+.++.+..+.....++...+    ..+...+..|+.+++.+..   ..-..+.++..|+++++.|..
T Consensus       919 l~~~~~~LE~kl~eLq~rL~~~e~~n~~L~~~~~~~~~~~~~e~~~L~~~l~~le~~~~e~~~~~~~v~~L~~e~~~l~~  998 (1080)
T 2dfs_A          919 YKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRK  998 (1080)
T ss_dssp             --------------------------------CHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455666666666666655444444332222    2334455555555444411   122345668999999999999


Q ss_pred             HHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Q 038837          112 ASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLE  159 (287)
Q Consensus       112 elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E  159 (287)
                      ++.+.++++..+|.+......   +|..+|.+|++.+..-..++.++|
T Consensus       999 ~~~~~~ke~~~lee~~~~~~~---~L~~kv~~L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A          999 ELHQTQTEKKTIEEWADKYKH---ETEQLVSELKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999988877764   666888888888888888888887

>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=96.83  E-value=0.0021  Score=69.15  Aligned_cols=24  Identities=29%  Similarity=0.124  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q 038837           31 HLIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      .+..++.+++.++..++..+.+..
T Consensus       861 ~L~~eL~el~~~L~~le~~l~ele  884 (1184)
T 1i84_S          861 AKDEELQRTKERQQKAEAELKELE  884 (1184)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555544444433

>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=96.71  E-value=0.0024  Score=68.68  Aligned_cols=16  Identities=13%  Similarity=0.115  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q 038837           35 ELQDAKLKIAGLETML   50 (287)
Q Consensus        35 eL~qLk~kIa~LES~i   50 (287)
                      ++.+++.++..|+..+
T Consensus       858 El~~L~~eL~el~~~L  873 (1184)
T 1i84_S          858 EMQAKDEELQRTKERQ  873 (1184)
T ss_dssp             HCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333333333333333

>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=96.66  E-value=0.0073  Score=58.81  Aligned_cols=26  Identities=12%  Similarity=0.183  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHH
Q 038837          135 EEVSLQVEKMSEIVTEQWIQIQHLEQ  160 (287)
Q Consensus       135 ~eL~sklek~~ki~~EQ~~qIqk~E~  160 (287)
                      +.+..+++.+++...+++.+++.+.+
T Consensus       540 ~~~~~~~~~le~~~~~~~~~~~~l~~  565 (597)
T 3oja_B          540 EDLEQENIALEKQLDNKRAKQAELRQ  565 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHhhhHHHHHHHhhhhhHHHHHHH
Confidence            33333344444444444444443333

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

Probab=96.46  E-value=0.094  Score=45.54  Aligned_cols=106  Identities=19%  Similarity=0.196  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhh
Q 038837           39 AKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNF  118 (287)
Q Consensus        39 Lk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~  118 (287)
                      .+.||.+||-+++|.+..|+.=.+.-..+.|...|++..+++++.-..-|..-..-.+..-.+||+++-.|+..++.-+.
T Consensus         4 ~neKi~~LekQL~E~n~kLk~EsE~~~rlkK~~tEl~k~~~~~E~~~rELq~~~~~L~~~k~~Leke~~~LQa~L~qEr~   83 (168)
T 3o0z_A            4 ANEKLSQLQKQLEEANDLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQLQAILEAERR   83 (168)
T ss_dssp             ------CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45689999999999999999988888888899999998888888877666544555566668888999999988888888


Q ss_pred             hhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837          119 DIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus       119 ~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      +..--..+..|.+-|+..|..+|+.+
T Consensus        84 ~r~q~se~~~elq~ri~~L~~El~~~  109 (168)
T 3o0z_A           84 DRGHDSEMIGDLQARITSLQEEVKHL  109 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            87777778888888888888888764

>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=96.25  E-value=0.062  Score=52.21  Aligned_cols=62  Identities=11%  Similarity=0.164  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQA  161 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~A  161 (287)
                      ..++.+.+.+++++.+.+.+...++......|+++++-..+++.+..-++..+.+|+++++.
T Consensus       519 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~  580 (597)
T 3oja_B          519 AFKLRETQARRTEADAKQKETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAK  580 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hhhHHHHHHHHHhhhhhhcchhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444444444444444444445555555553

>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=96.21  E-value=0.21  Score=42.70  Aligned_cols=51  Identities=10%  Similarity=0.167  Sum_probs=32.9

Q ss_pred             hhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Q 038837          115 KNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMA  165 (287)
Q Consensus       115 kqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~a  165 (287)
                      ....+..--|.||..||.+|..|...++++++-....+.+...+.+-|..+
T Consensus        81 ~L~~kLKEAE~RAE~AERsv~kLEk~id~lEd~L~~~Kek~~~i~~eLd~t  131 (155)
T 2efr_A           81 VLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEEMKQL  131 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344456677777777777777777777777666666666665555433

>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=96.11  E-value=0.14  Score=41.88  Aligned_cols=115  Identities=19%  Similarity=0.212  Sum_probs=68.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHH
Q 038837           34 AELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAAS  113 (287)
Q Consensus        34 ~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~el  113 (287)
                      .++..+..++..|+..+....   ..+.+.=.+..++..++..-...|++|-++           ..+.|+....|...-
T Consensus        13 ~E~~~~~eel~~lke~l~k~e---~~r~ele~~~~~l~~Ek~~L~~qL~~E~~~-----------l~e~EE~~~~L~~~k   78 (129)
T 2fxo_A           13 KEMASMKEEFTRLKEALEKSE---ARRKELEEKMVSLLQEKNDLQLQVQAEQDN-----------LADAEERCDQLIKNK   78 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHhHHHHHHHHHHHH
Confidence            344445555555544443211   112222222344444444444445544322           344444555555444


Q ss_pred             hhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 038837          114 RKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQAL  162 (287)
Q Consensus       114 ekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Al  162 (287)
                      .......+-+++|..+-|.+..+|+.+-.+++..+.+-+.+|..+|.++
T Consensus        79 ~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~led~e~~l  127 (129)
T 2fxo_A           79 IQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDIDDLELTL  127 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4445566667788888999999999999999999999999999888654

>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=96.11  E-value=0.0069  Score=46.03  Aligned_cols=46  Identities=26%  Similarity=0.369  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           43 IAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        43 Ia~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      |..|+-.+..+..+|..||..|+++|+.+.++...|..|+++++.+
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKf   66 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKY   66 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7788889999999999999999999999999999999999999876

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

Probab=95.70  E-value=0.31  Score=43.00  Aligned_cols=112  Identities=13%  Similarity=0.126  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhh---hhcC-chhhHHHHhHHhHHHhhhHHHHHHHHhhhhcc--ch--hHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIR---KVNG-KSNYIEERDKLVDDMTNKIHHLQSLLSKIKDD--SS--RAEERLNALE  103 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~q---el~~-Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~--s~--~aee~i~eLE  103 (287)
                      .+....+.+.++..|+..+++-..   +|.. =+..|.++|+.+++...++..|..|++++|..  .+  .+..++..|+
T Consensus        15 wk~~~~~~~q~~~~le~El~EFqesSrELE~ELE~eL~~~Ek~~~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq   94 (189)
T 2v71_A           15 WKELSMKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLE   94 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345556666666666666554322   1111 12356677777777778888888888877322  22  2334466666


Q ss_pred             HHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH
Q 038837          104 EEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus       104 kQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      +++..|....+.....+-.||-.--|-|.+.....+.++.
T Consensus        95 ~el~~l~~~~~~l~~~ireLEq~NDdlEr~~R~~~~SleD  134 (189)
T 2v71_A           95 DDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIMSLED  134 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhhHHH
Confidence            6666666555555555444444444444444444444333

>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=95.48  E-value=0.064  Score=40.68  Aligned_cols=73  Identities=16%  Similarity=0.112  Sum_probs=57.5

Q ss_pred             hhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhh
Q 038837           75 TNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEI  147 (287)
Q Consensus        75 s~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki  147 (287)
                      -++|+.|..+.++-......++.++.+.++....+..++...+.++..||.-...++.++.+.+.+|+...+.
T Consensus         5 kkKm~~lk~e~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kLeeaek~   77 (81)
T 1ic2_A            5 KKKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKLELADKK   77 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4677778888777766666677778888888888888888888888888888888888888888888877664

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

Probab=95.13  E-value=0.099  Score=44.74  Aligned_cols=68  Identities=13%  Similarity=0.137  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEI  106 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQV  106 (287)
                      +.+..+++...|..|++.+....       ..|..++..+++|.+.++.|+.|+.+|.-.-...+++...|+++=
T Consensus        59 ~vs~~~~~~~~I~~L~~El~~l~-------~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~kLq~EN  126 (152)
T 3a7p_A           59 IVSHDDALLNTLAILQKELKSKE-------QEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSDLKKEH  126 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56677777777777777777744       556666666777777777777777777444445555555555544

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

Probab=95.12  E-value=0.45  Score=37.50  Aligned_cols=44  Identities=14%  Similarity=0.151  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837          101 ALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus       101 eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      -+|.+++.+...+..-+.+...-+-.+.+||.-|..||.++.-+
T Consensus        55 ~lE~eld~~ee~L~ea~~kLee~ek~~~~aE~ev~~L~Rriqll   98 (101)
T 3u1c_A           55 VTEDSRDQVLEELHKSEDSLLFAEENAAKAESEVASLNRRIQLV   98 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555555555555555556666666666555443

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

Probab=94.73  E-value=0.56  Score=50.42  Aligned_cols=60  Identities=10%  Similarity=0.080  Sum_probs=29.8

Q ss_pred             HHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHh
Q 038837           83 SLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMS  145 (287)
Q Consensus        83 sEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~  145 (287)
                      .|..+++..-...++.+.+|+++++++.++.+....+...+..   +.+.+|..|.....+++
T Consensus       977 ~e~~~~~~~v~~L~~e~~~l~~~~~~~~ke~~~lee~~~~~~~---~L~~kv~~L~~e~~~L~ 1036 (1080)
T 2dfs_A          977 EEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKH---ETEQLVSELKEQNTLLK 1036 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH
Confidence            3333333333445566677777777777666665554443332   33344444444433333

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

Probab=94.71  E-value=1.1  Score=35.01  Aligned_cols=44  Identities=18%  Similarity=0.289  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837          101 ALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus       101 eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      -+|.+++.....+..-+.+.+.-+-.+.+||.-|..||.++.-+
T Consensus        55 ~lE~eld~~~e~l~~a~~kLe~~ek~~~~AE~evasLnRriqll   98 (101)
T 3u59_A           55 GTEDEVEKYSESVKEAQEKLEQAEKKATDAEAEVASLNRRIQLV   98 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444555556666666666555443

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

Probab=94.68  E-value=0.88  Score=40.07  Aligned_cols=110  Identities=16%  Similarity=0.153  Sum_probs=68.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      ..|..+|+++..++..|.+.+.....++.+=.   ...+..-.+-...|.+|+.+++.|....-....++.+||-.=+-|
T Consensus        45 ~ELE~eL~~~Ek~~~~L~~~~~~L~~E~e~~k---~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ireLEq~NDdl  121 (189)
T 2v71_A           45 AELEAQLVQAEQRNRDLQADNQRLKYEVEALK---EKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDL  121 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            45667777777777777777776665543211   222444455566788888887777544444445566666666666


Q ss_pred             HHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHH
Q 038837          110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVE  142 (287)
Q Consensus       110 ~~elekqn~~~~~LEsrA~dAEkkv~eL~skle  142 (287)
                      .+..|....-..-+|++.+.|=.+..-|.+.|+
T Consensus       122 Er~~R~~~~SleD~e~kln~aiEr~alLE~El~  154 (189)
T 2v71_A          122 ERAKRATIMSLEDFEQRLNQAIERNAFLESELD  154 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666666666666666666554

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

Probab=94.36  E-value=0.61  Score=36.56  Aligned_cols=73  Identities=14%  Similarity=0.145  Sum_probs=37.6

Q ss_pred             hhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhh
Q 038837           75 TNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEI  147 (287)
Q Consensus        75 s~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki  147 (287)
                      -.||+.|.-+-++.....-.++.+++.++..-..+..++...+.+...+|.-+..++.++.+.+.+|+...+.
T Consensus         8 KkKm~~lk~e~e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~e~l~~a~~kLe~~ek~   80 (101)
T 3u59_A            8 KKKMQMLKLDKENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYSESVKEAQEKLEQAEKK   80 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555544433333344445555555555555555555555555555555555555555555554444

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=94.32  E-value=0.11  Score=40.15  Aligned_cols=58  Identities=24%  Similarity=0.294  Sum_probs=54.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHh
Q 038837           29 QQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLS   86 (287)
Q Consensus        29 ~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~   86 (287)
                      ...|..|+..||.||..+|+.=..-.+.|++..+.|..+......+...|..|++++.
T Consensus        21 ~E~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~   78 (81)
T 3qh9_A           21 AEELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLS   78 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence            3579999999999999999999999999999999999999999999999999999874

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

Probab=94.20  E-value=0.83  Score=35.96  Aligned_cols=71  Identities=17%  Similarity=0.070  Sum_probs=32.9

Q ss_pred             hhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhh
Q 038837           76 NKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSE  146 (287)
Q Consensus        76 ~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~k  146 (287)
                      .||+.|..+-++-....-.++.+++.++..-..+..++...+.+...+|.-...++.++.+.+.+++.-++
T Consensus         9 kKm~~lk~e~e~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~ee~L~ea~~kLee~ek   79 (101)
T 3u1c_A            9 KKMQMLKLDKENALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQVLEELHKSEDSLLFAEE   79 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555544432222233344444444444444444444444444444444445555554444444433

>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=93.97  E-value=0.72  Score=38.87  Aligned_cols=106  Identities=20%  Similarity=0.228  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhh
Q 038837           39 AKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNF  118 (287)
Q Consensus        39 Lk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~  118 (287)
                      |+.+|.-||..++.....|..-...|.+.++.-.+-......|++.       +..+++++..||.|+..-+.-      
T Consensus         1 l~Rri~llEeeLer~eerl~~a~~kLeeaek~adE~eR~~k~lE~r-------~~~deEr~~~lE~qLkeak~~------   67 (147)
T 2b9c_A            1 MNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESR-------AQKDEEKMEIQEIQLKEAKHI------   67 (147)
T ss_dssp             ----------CCGGGGTTTTHHHHHHHHHHHHHHHHTHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH------
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-------hcccHHHHHHHHHHHHHHHHH------
Confidence            4567777777777777777777777777777777777776666665       556777888888887755432      


Q ss_pred             hhhhHHhhhHhHHHHHHHHHHHHHH-------HhhhhHHHHHHHHHHHHHHHHH
Q 038837          119 DIHNLESKALDAEDRLEEVSLQVEK-------MSEIVTEQWIQIQHLEQALHMA  165 (287)
Q Consensus       119 ~~~~LEsrA~dAEkkv~eL~sklek-------~~ki~~EQ~~qIqk~E~Alk~a  165 (287)
                              |.+|+.|+++.+.|+.-       .+.-...--.+|..+|.-|+++
T Consensus        68 --------aeeadrKyeE~~RKl~~~E~dLeraeeRae~aE~k~~eLEeeL~~~  113 (147)
T 2b9c_A           68 --------AEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTV  113 (147)
T ss_dssp             --------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --------HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                    33444444444444433       3333333345555666555543

>3u0c_A Invasin IPAB, 62 kDa antigen; translocator, type three secretion system, coiled-coil, VIRU cell invasion; 2.05A {Shigella flexneri} PDB: 3gz1_P

Probab=93.67  E-value=0.77  Score=40.19  Aligned_cols=93  Identities=17%  Similarity=0.197  Sum_probs=68.0

Q ss_pred             HHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhh
Q 038837           43 IAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHN  122 (287)
Q Consensus        43 Ia~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~  122 (287)
                      +++|+|.|+..-       ..-+..++..+|.|++|++.-++                     -+.+-+..++.+.+..+
T Consensus        70 lTqL~nrL~~wl-------sQ~em~~qks~EFSD~~qTaL~e---------------------AQ~AtD~y~~Ainny~~  121 (201)
T 3u0c_A           70 LTALTNKITAWK-------SQQQARQQKNLEFSDKINTLLSE---------------------TEGLTRDYEKQINKLKN  121 (201)
T ss_dssp             GHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHhhhhH
Confidence            456777777643       44455588889999998877665                     56677888888999999


Q ss_pred             HHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 038837          123 LESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       123 LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      ..+++.++|+|++.+..+|..|+--.++ +.++-.-|--|-+
T Consensus       122 Ads~~~~lekKvn~aq~kLs~L~P~dP~-Y~K~~~~~~~~~~  162 (201)
T 3u0c_A          122 ADSKIKDLENKINQIQTRLSELDPESPE-KKKLSREEIQLTI  162 (201)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSCSSCTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCCCc-cccccHHHHhhhh
Confidence            9999999999999999999988765544 4443333333333

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

Probab=93.40  E-value=0.58  Score=39.03  Aligned_cols=54  Identities=20%  Similarity=0.238  Sum_probs=25.3

Q ss_pred             hHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHH
Q 038837           71 VDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLE  124 (287)
Q Consensus        71 i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LE  124 (287)
                      +.....+|..+..|+++||.....+..++.+++++++.|++++.....++..||
T Consensus        77 ~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le  130 (138)
T 3hnw_A           77 ADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLE  130 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444444444444444444444444444

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

Probab=93.04  E-value=1.8  Score=51.57  Aligned_cols=22  Identities=5%  Similarity=0.096  Sum_probs=8.1

Q ss_pred             HhhhhcCchhhHHHHhHHhHHH
Q 038837           53 SIRKVNGKSNYIEERDKLVDDM   74 (287)
Q Consensus        53 ~~qel~~Kd~~l~e~Ek~i~ek   74 (287)
                      ..++|..+.-.|+++.+..+++
T Consensus      1939 l~~~L~~~~~~L~~k~~ea~~~ 1960 (3245)
T 3vkg_A         1939 LQVSLAQKNRELDVKNEQANQK 1960 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333

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

Probab=92.99  E-value=1.9  Score=51.43  Aligned_cols=39  Identities=13%  Similarity=0.131  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHH
Q 038837          104 EEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVE  142 (287)
Q Consensus       104 kQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skle  142 (287)
                      +++..+.+++++.+.+....+++..+.|++++.|..+.+
T Consensus      2014 ~~l~~ae~~l~~~~~~L~~~~~~L~~le~~l~~L~~~~~ 2052 (3245)
T 3vkg_A         2014 EEVEQLENAANELKLKQDEIVATITALEKSIATYKEEYA 2052 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444444444443

>3swk_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural; 1.70A {Homo sapiens}

Probab=92.86  E-value=1.6  Score=33.61  Aligned_cols=79  Identities=13%  Similarity=0.068  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLL  109 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L  109 (287)
                      ..||.+|+.+...=++|++.++..-.       .+.....-..+=-..-++.++++..|++.--++-=.-.+||.+|+.|
T Consensus         3 ~eLr~qi~~l~~e~~~l~~e~dn~~~-------~~edfk~KyE~E~~~R~~~E~d~~~LrkdvD~a~l~r~dLE~kvesL   75 (86)
T 3swk_A            3 RELRRQVDQLTNDKARVEVERDNLAE-------DIMRLREKLQEEMLQREEAENTLQSFRQDVDNASLARLDLERKVESL   75 (86)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            36888888888888899988887542       22222222222223446788888888777544444457888888888


Q ss_pred             HHHHhh
Q 038837          110 WAASRK  115 (287)
Q Consensus       110 ~~elek  115 (287)
                      +.|+.=
T Consensus        76 ~eEl~f   81 (86)
T 3swk_A           76 QEEIAF   81 (86)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            888753

>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine exchange factor, coiled-coil, endocytosis/exocytosis complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=92.84  E-value=1.1  Score=38.43  Aligned_cols=18  Identities=11%  Similarity=0.198  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLET   48 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES   48 (287)
                      ++|.+|...+.+|..||+
T Consensus        24 ~~R~el~~~~~ri~~lE~   41 (154)
T 2ocy_A           24 KSLKTIASQKAAIENYNQ   41 (154)
T ss_dssp             HHHHHHHHHHHHHHTTHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            344455555555555554

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=92.42  E-value=0.5  Score=36.53  Aligned_cols=67  Identities=10%  Similarity=0.135  Sum_probs=49.4

Q ss_pred             hhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhH
Q 038837           62 NYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKAL  128 (287)
Q Consensus        62 ~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~  128 (287)
                      +.+.++|.-|+..-..|+.|+-|++-||..+......+.++....+.|..+.+....+...+++|..
T Consensus         6 ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~   72 (81)
T 2jee_A            6 EVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQ   72 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            5678889999999999999999999997666666666666666666666666666666666665543

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

Probab=92.34  E-value=3.7  Score=33.26  Aligned_cols=84  Identities=15%  Similarity=0.110  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhh
Q 038837           37 QDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKN  116 (287)
Q Consensus        37 ~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekq  116 (287)
                      ..|+.++.+|+..+++-.          ...+..-.+-...|.+||.|++.|.              ..-+.|+..+|+.
T Consensus         6 rdL~~~~~~L~~E~e~~k----------~K~~~~~~e~~~~~~~Lq~El~~lr--------------~~~~~l~~~iReL   61 (111)
T 2v66_B            6 RDLQADNQRLKYEVEALK----------EKLEHQYAQSYKQVSVLEDDLSQTR--------------AIKEQLHKYVREL   61 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHH
Confidence            455666666655555522          1122333444455666666655542              2333334444444


Q ss_pred             hhhhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837          117 NFDIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus       117 n~~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      -..-+.||-.+.-+--.++++.+|+.+.
T Consensus        62 Eq~NDDLER~~R~t~~SLeD~E~k~n~a   89 (111)
T 2v66_B           62 EQANDDLERAKRATIVSLEDFEQRLNQA   89 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhchHHHHHHHHHHhhHHHHHHHHHHH
Confidence            4444445555555555555555555543

>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=92.34  E-value=0.66  Score=46.64  Aligned_cols=42  Identities=17%  Similarity=0.273  Sum_probs=28.9

Q ss_pred             HHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 038837          123 LESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       123 LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      ||-+....+.+|+.-=+.+.-++.+.++|..+||+||=+..+
T Consensus       115 LRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDIdi  156 (562)
T 3ghg_A          115 LRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDI  156 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444455444455666888889999999999988774

>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=92.27  E-value=1.1  Score=33.79  Aligned_cols=60  Identities=13%  Similarity=0.118  Sum_probs=42.5

Q ss_pred             hhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038837          116 NNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQ  175 (287)
Q Consensus       116 qn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~e  175 (287)
                      ...++++...+|..++.++.+.....++.+.-...-.++|+.+|.=|..+++++..++..
T Consensus        11 lk~e~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~k   70 (81)
T 1ic2_A           11 LKLDKENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEK   70 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444555556666666666666666666677777889999999999888888877654

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

Probab=91.65  E-value=1.2  Score=37.07  Aligned_cols=56  Identities=7%  Similarity=0.075  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHH
Q 038837           95 AEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTE  150 (287)
Q Consensus        95 aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~E  150 (287)
                      .+.++.++++++..|+.++....-+.+.++....+..+++.+|..++.+++.-..+
T Consensus        80 L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~~  135 (138)
T 3hnw_A           80 LSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELND  135 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34556667777777777777777777777777777777777777777766654443

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

Probab=91.31  E-value=1.5  Score=35.52  Aligned_cols=79  Identities=14%  Similarity=0.220  Sum_probs=57.2

Q ss_pred             hHHhHHHhhhHHHHHHHHhhhhcc--ch--hHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHH
Q 038837           68 DKLVDDMTNKIHHLQSLLSKIKDD--SS--RAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK  143 (287)
Q Consensus        68 Ek~i~eks~kI~sLqsEi~sLkk~--s~--~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek  143 (287)
                      ||.+++.-.+...|..|++++|..  .+  .+...+..|++++..|...-+.....+--||-.--|-|..-...++-|+.
T Consensus         2 Ek~~rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R~t~~SLeD   81 (111)
T 2v66_B            2 EQRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATIVSLED   81 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHhhHHH
Confidence            566777778888888888888332  22  23345788888888888888888888777777777777777777777776


Q ss_pred             Hhh
Q 038837          144 MSE  146 (287)
Q Consensus       144 ~~k  146 (287)
                      ++.
T Consensus        82 ~E~   84 (111)
T 2v66_B           82 FEQ   84 (111)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

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

Probab=91.01  E-value=7.2  Score=33.74  Aligned_cols=80  Identities=16%  Similarity=0.210  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhh
Q 038837           38 DAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNN  117 (287)
Q Consensus        38 qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn  117 (287)
                      ++...++++|....|.-       +.+..++.--.........||+.++.=+.+-....+-+.+|+-.|..|..|++...
T Consensus        38 El~k~~~~~E~~~rELq-------~~~~~L~~~k~~Leke~~~LQa~L~qEr~~r~q~se~~~elq~ri~~L~~El~~~k  110 (168)
T 3o0z_A           38 EMSKSISQLESLNRELQ-------ERNRILENSKSQTDKDYYQLQAILEAERRDRGHDSEMIGDLQARITSLQEEVKHLK  110 (168)
T ss_dssp             HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444444444443322       33344444444455666666666665555555666667888888888888887777


Q ss_pred             hhhhhHH
Q 038837          118 FDIHNLE  124 (287)
Q Consensus       118 ~~~~~LE  124 (287)
                      .....++
T Consensus       111 ~~~~k~~  117 (168)
T 3o0z_A          111 HNLEKVE  117 (168)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6644443

>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=90.95  E-value=5.5  Score=32.29  Aligned_cols=46  Identities=17%  Similarity=0.221  Sum_probs=30.5

Q ss_pred             hhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 038837          117 NFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQAL  162 (287)
Q Consensus       117 n~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Al  162 (287)
                      -.....|-++=.+.|.++.+++.+++..+..|.+--..-+++|+=.
T Consensus        68 EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~  113 (129)
T 2fxo_A           68 EERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDEC  113 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334455555567778888888888888887776666666665533

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.89  E-value=1.4  Score=34.99  Aligned_cols=23  Identities=17%  Similarity=0.137  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 038837           31 HLIAELQDAKLKIAGLETMLEES   53 (287)
Q Consensus        31 ~l~~eL~qLk~kIa~LES~i~e~   53 (287)
                      .|+.+++.||-+|.+||+.....
T Consensus         2 ~~~~~~e~lre~l~~le~~~~~~   24 (97)
T 2eqb_B            2 PLGSNYNQLKEDYNTLKRELSDR   24 (97)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHH
T ss_pred             cHhHHHHHHHHHHHHHHHHHHhh
Confidence            35667888888888888877773

>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=89.71  E-value=8.7  Score=32.67  Aligned_cols=93  Identities=15%  Similarity=0.126  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccch-------hHHHHHHHHHH
Q 038837           32 LIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSS-------RAEERLNALEE  104 (287)
Q Consensus        32 l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~-------~aee~i~eLEk  104 (287)
                      +..+|+..-.+...-|+.+.+...+|+.=+.+++-+|-.-..-+.+-..++..|..|...--       .++.++.-||+
T Consensus        26 ~E~dLEraEERae~aE~k~~eLEeeL~~v~~nlKsLE~seekasqrEd~yEeqIk~L~~kLKEAE~RAE~AERsv~kLEk  105 (155)
T 2efr_A           26 LKKLLERAEERAELSEGKSAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSVTKLEK  105 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555555555555566666655555555555556666655522222       24444666666


Q ss_pred             HHHHHHHHHhhhhhhhhhHH
Q 038837          105 EIRLLWAASRKNNFDIHNLE  124 (287)
Q Consensus       105 QVe~L~~elekqn~~~~~LE  124 (287)
                      .|+.|..++.....+...+.
T Consensus       106 ~id~lEd~L~~~Kek~~~i~  125 (155)
T 2efr_A          106 SIDDLEDELYAQKLKYKAIS  125 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            66666666665554444443

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.34  E-value=4.8  Score=31.99  Aligned_cols=66  Identities=15%  Similarity=0.209  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHH-HHHhhhhHHHHHHHHHHHH
Q 038837           95 AEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQV-EKMSEIVTEQWIQIQHLEQ  160 (287)
Q Consensus        95 aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skl-ek~~ki~~EQ~~qIqk~E~  160 (287)
                      .+.+....+.++..|..++...+......|+.....+.-|++|+..| +...+++.+-++.--.+|.
T Consensus        17 le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTasLFeEAN~MVa~ar~e~~~~e~   83 (97)
T 2eqb_B           17 LKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEI   83 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445557778888888888888888888888888888888888888 6677777665544434443

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

Probab=88.85  E-value=1.3  Score=36.00  Aligned_cols=26  Identities=15%  Similarity=0.138  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhh
Q 038837           96 EERLNALEEEIRLLWAASRKNNFDIH  121 (287)
Q Consensus        96 ee~i~eLEkQVe~L~~elekqn~~~~  121 (287)
                      ...+..||.++..++.+...|..+-.
T Consensus        81 q~~i~~lE~eL~~~r~e~~~ql~EYq  106 (129)
T 3tnu_B           81 RNKLAELEEALQKAKQDMARLLREYQ  106 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            34467777777777777777766644

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=88.37  E-value=4  Score=38.76  Aligned_cols=17  Identities=12%  Similarity=0.122  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHHh
Q 038837           38 DAKLKIAGLETMLEESI   54 (287)
Q Consensus        38 qLk~kIa~LES~i~e~~   54 (287)
                      ++..|-..||-.++..-
T Consensus       364 ~l~~~~~~le~~~~~~~  380 (487)
T 3oja_A          364 TLEQKKKALDEQVSNGR  380 (487)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            44444444544444443

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=88.18  E-value=1.1  Score=30.87  Aligned_cols=44  Identities=20%  Similarity=0.274  Sum_probs=33.0

Q ss_pred             hHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHh
Q 038837           71 VDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASR  114 (287)
Q Consensus        71 i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~ele  114 (287)
                      +...+..++||++|-+.||+...+-..-|.-||+++-.|.+.++
T Consensus         5 vaqlenevaslenenetlkkknlhkkdliaylekeianlrkkie   48 (49)
T 3he5_A            5 VAQLENEVASLENENETLKKKNLHKKDLIAYLEKEIANLRKKIE   48 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhhcccHHHHHhcccHHHHHHHHHHHHHHHHHHhc
Confidence            34444677888888888877777777778888888888877654

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}

Probab=87.90  E-value=0.78  Score=32.51  Aligned_cols=38  Identities=16%  Similarity=0.091  Sum_probs=29.0

Q ss_pred             cccCcc-cchHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 038837           21 TSQNQQ-HSQQHLIAELQDAKLKIAGLETMLEESIRKVN   58 (287)
Q Consensus        21 ~s~~~~-~~~~~l~~eL~qLk~kIa~LES~i~e~~qel~   58 (287)
                      ++..|+ +.-.+|+.|+++|+.|+..|...+++...+|.
T Consensus        12 G~~~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el~~~l~   50 (53)
T 2yy0_A           12 GAATPENPEIELLRLELAEMKEKYEAIVEENKKLKAKLA   50 (53)
T ss_dssp             ----CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444455 45599999999999999999999999876654

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

Probab=87.61  E-value=1.2  Score=36.24  Aligned_cols=26  Identities=19%  Similarity=0.349  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhh
Q 038837           96 EERLNALEEEIRLLWAASRKNNFDIH  121 (287)
Q Consensus        96 ee~i~eLEkQVe~L~~elekqn~~~~  121 (287)
                      ...+..||.++..++.++..|..+-.
T Consensus        83 q~~i~~lE~eL~~~r~em~~ql~EYq  108 (131)
T 3tnu_A           83 QEMIGSVEEQLAQLRCEMEQQNQEYK  108 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34467777777777777777766644

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

Probab=87.58  E-value=4.6  Score=32.62  Aligned_cols=41  Identities=24%  Similarity=0.270  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHH
Q 038837           95 AEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLE  135 (287)
Q Consensus        95 aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~  135 (287)
                      +.+.+.+|--+|+.|..+++.+...+.+||....|+|.+..
T Consensus        34 ~k~Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~   74 (129)
T 3tnu_B           34 TKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGE   74 (129)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            34446777777777777777777777777777777777653

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=87.41  E-value=2.8  Score=42.21  Aligned_cols=22  Identities=32%  Similarity=0.425  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHhhhhhhhhhHHh
Q 038837          104 EEIRLLWAASRKNNFDIHNLES  125 (287)
Q Consensus       104 kQVe~L~~elekqn~~~~~LEs  125 (287)
                      .+++.|++-|++|..++..||.
T Consensus       131 snIrvLQsnLedq~~kIQRLEv  152 (562)
T 3ghg_A          131 QHIQLLQKNVRAQLVDMKRLEV  152 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            4566667777777777777764

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=87.07  E-value=1.4  Score=33.44  Aligned_cols=51  Identities=14%  Similarity=0.139  Sum_probs=42.9

Q ss_pred             hhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 038837          119 DIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRA  169 (287)
Q Consensus       119 ~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~  169 (287)
                      +-..+|+|..+.|-|+.-..--++.+.+++.+||.+|..+.+.++.-..++
T Consensus         8 ~~~~le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~rl   58 (78)
T 3efg_A            8 RDQELEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDL   58 (78)
T ss_dssp             CCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345788888899999999999999999999999999999999887655544

>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: h.1.8.1 PDB: 1ei3_A

Probab=85.90  E-value=11  Score=37.35  Aligned_cols=42  Identities=14%  Similarity=0.358  Sum_probs=30.0

Q ss_pred             HHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 038837          123 LESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       123 LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      ||.+-.....+|.+-=..+.-++.+..+|..+||+||-+..+
T Consensus       116 Le~ri~yIK~kVd~qi~~IrvLq~~l~~q~skIQRLE~dI~~  157 (491)
T 1m1j_A          116 LRRRIVTLKQRVATQVNRIKALQNSIQEQVVEMKRLEVDIDI  157 (491)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444445555554466677889999999999999998874

>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=85.69  E-value=11  Score=37.15  Aligned_cols=24  Identities=21%  Similarity=0.372  Sum_probs=14.1

Q ss_pred             HHHHHhhhhHHHHHHHHHHHHHHH
Q 038837          140 QVEKMSEIVTEQWIQIQHLEQALH  163 (287)
Q Consensus       140 klek~~ki~~EQ~~qIqk~E~Alk  163 (287)
                      .+..++.+.+....+|+++|.++.
T Consensus       169 ~i~~L~~~~~~l~~ki~~l~~~~~  192 (464)
T 1m1j_B          169 SLRVLRAVIDSLHKKIQKLENAIA  192 (464)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444456677888877765

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

Probab=85.53  E-value=3.8  Score=33.29  Aligned_cols=39  Identities=13%  Similarity=0.117  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHH
Q 038837           96 EERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRL  134 (287)
Q Consensus        96 ee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv  134 (287)
                      .+.+.+|--+|+.|..+++.+...+.+||....|+|.+.
T Consensus        37 k~Ei~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~   75 (131)
T 3tnu_A           37 KSEISELRRTMQNLEIELQSQLSMKASLENSLEETKGRY   75 (131)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            344666666666666666666666677777777776654

>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=84.95  E-value=3.6  Score=34.55  Aligned_cols=83  Identities=11%  Similarity=0.151  Sum_probs=36.0

Q ss_pred             hhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHH
Q 038837           62 NYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQV  141 (287)
Q Consensus        62 ~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~skl  141 (287)
                      ...+-+|+.-..-..+|..|+..+.-.+.-.-+++.+..+....+-.+..+++.-.......|++..+.|..+..++..+
T Consensus        38 R~~k~lE~r~~~deEr~~~lE~qLkeak~~aeeadrKyeE~~RKl~~~E~dLeraeeRae~aE~k~~eLEeeL~~~~~nl  117 (147)
T 2b9c_A           38 RGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNL  117 (147)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcccHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444444433333333444444444444444445544444444444444444444444444444


Q ss_pred             HHH
Q 038837          142 EKM  144 (287)
Q Consensus       142 ek~  144 (287)
                      ..+
T Consensus       118 KsL  120 (147)
T 2b9c_A          118 KSL  120 (147)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            333

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=84.84  E-value=5  Score=31.00  Aligned_cols=96  Identities=10%  Similarity=0.120  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh-hcc----chhHHHHHHHHHH
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI-KDD----SSRAEERLNALEE  104 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL-kk~----s~~aee~i~eLEk  104 (287)
                      +.+.+++++++.++..|.+.+.....+++.=+..+.+++.+           -..-... ..|    ..+.++=+..|++
T Consensus         9 Q~~i~~~~~l~~~~~~l~~q~~~l~~~~~e~~~~~~eL~~l-----------~~d~~vy~~iG~vfv~~~~~ea~~~L~~   77 (117)
T 2zqm_A            9 QAMLGQLESYQQQLQLVVQQKQKVQLELTEAKKALDEIESL-----------PDDAVVYKTVGTLIVKTTKDKAVAELKE   77 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-----------CTTCCEEEEETTEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-----------CCCcHhHHHhhHHHhhccHHHHHHHHHH
Confidence            45666777777777777776666443332222333332211           1110011 223    2234555677777


Q ss_pred             HHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHH
Q 038837          105 EIRLLWAASRKNNFDIHNLESKALDAEDRLEE  136 (287)
Q Consensus       105 QVe~L~~elekqn~~~~~LEsrA~dAEkkv~e  136 (287)
                      .++.+..++.+...+...++....+.++++.+
T Consensus        78 ~~e~ie~~i~~le~~~~~l~~~l~~lk~~l~~  109 (117)
T 2zqm_A           78 KIETLEVRLNALERQEKKLNEKLKELTAQIQS  109 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777776666666555555555544443

>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=84.25  E-value=8.6  Score=37.96  Aligned_cols=23  Identities=9%  Similarity=0.264  Sum_probs=12.0

Q ss_pred             hHHHHHHHHHHHHHHHhhhhHHH
Q 038837          129 DAEDRLEEVSLQVEKMSEIVTEQ  151 (287)
Q Consensus       129 dAEkkv~eL~sklek~~ki~~EQ  151 (287)
                      ..+..++.++.|+.+++.....|
T Consensus       172 ~L~~~~~~l~~ki~~l~~~~~~~  194 (464)
T 1m1j_B          172 VLRAVIDSLHKKIQKLENAIATQ  194 (464)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444555666666655554443

>1zxa_A CGMP-dependent protein kinase 1, alpha isozyme; parallel coiled coil dimer, transferase; NMR {Homo sapiens}

Probab=83.50  E-value=0.66  Score=34.66  Aligned_cols=39  Identities=23%  Similarity=0.248  Sum_probs=29.5

Q ss_pred             HHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           50 LEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        50 i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      .++..+.++.||+-|.++|..++++...|..|+++++..
T Consensus        13 ~e~~~~~i~~Kde~I~eLE~~L~~kd~eI~eLr~~LdK~   51 (67)
T 1zxa_A           13 EEDFAKILMLKEERIKELEKRLSEKEEEIQELKRKLHKC   51 (67)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455667778899999999999999999999888887644

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

Probab=83.08  E-value=6.7  Score=31.98  Aligned_cols=97  Identities=15%  Similarity=0.206  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhhhccchhHHHHHHHHHHHHHHHHHHH
Q 038837           34 AELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSRAEERLNALEEEIRLLWAAS  113 (287)
Q Consensus        34 ~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sLkk~s~~aee~i~eLEkQVe~L~~el  113 (287)
                      ..|++|+..|..|-..++..          ..+....|..+...|..|++|++--+.-.   ++-..+.+ +++.-..++
T Consensus        15 ~~Ie~Lkreie~lk~ele~l----------~~E~q~~v~ql~~~i~~Le~eL~e~r~~~---q~a~~e~e-~Lr~e~~~l   80 (120)
T 3i00_A           15 HLIERLYREISGLKAQLENM----------KTESQRVVLQLKGHVSELEADLAEQQHLR---QQAADDCE-FLRAELDEL   80 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHH-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHH-HHHHHHHHH
Confidence            45677777777776666553          34556777777778888888765332110   00011111 122222345


Q ss_pred             hhhhhhhhhHHhhhHhHHHHHHHHHHHHHHH
Q 038837          114 RKNNFDIHNLESKALDAEDRLEEVSLQVEKM  144 (287)
Q Consensus       114 ekqn~~~~~LEsrA~dAEkkv~eL~sklek~  144 (287)
                      ++.+.+.+....++.++|+|-+.-..+..||
T Consensus        81 ~~~~~~~~~~q~~~~e~E~kAqa~Eerf~KL  111 (120)
T 3i00_A           81 RRQREDTEKAQRSLSEIERKAQANEQRYSKL  111 (120)
T ss_dssp             HTTCC--------------------------
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5666666666666667777665544444443

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

Probab=83.06  E-value=1.6  Score=33.07  Aligned_cols=46  Identities=13%  Similarity=0.065  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           36 LQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        36 L~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      =+.++..++.|.+       +|++||..|..++..+.-+++.-..|-.||=|+
T Consensus        13 ~~~~~~~l~~Lr~-------eL~~Ke~eI~~L~e~i~lk~kd~ErLNDEiisl   58 (75)
T 3a7o_A           13 DDALLNTLAILQK-------ELKSKEQEIRRLKEVIALKNKNTERLNDELISG   58 (75)
T ss_dssp             HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhcccHHHhhHHHHHh
Confidence            3455556666654       455588999999988888888877777777665

>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=81.66  E-value=13  Score=28.56  Aligned_cols=25  Identities=12%  Similarity=-0.102  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhH
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNL  123 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~L  123 (287)
                      +...+.++..+...+...+.+...+
T Consensus        66 i~~~~~~l~~l~~~i~~l~~~i~~l   90 (112)
T 1l8d_A           66 LSKYHLDLNNSKNTLAKLIDRKSEL   90 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555554444444433

>2oto_A M protein; helical coiled coil, fibrinogen-binding, virulence factor, S active protein, toxin; 3.04A {Streptococcus pyogenes serotype M1} PDB: 2xny_M

Probab=80.87  E-value=22  Score=29.29  Aligned_cols=54  Identities=17%  Similarity=0.231  Sum_probs=29.6

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCchhhHHHHhHHhHHHhhhHHHHHHHHhhh
Q 038837           28 SQQHLIAELQDAKLKIAGLETMLEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKI   88 (287)
Q Consensus        28 ~~~~l~~eL~qLk~kIa~LES~i~e~~qel~~Kd~~l~e~Ek~i~eks~kI~sLqsEi~sL   88 (287)
                      ++..++.+-+.|+.+.-.|...+....       ....+++..+++++.+...|+..+..+
T Consensus        23 ~n~~l~~eN~~Lk~e~e~l~~~~~~~~-------~~~~eL~~~~~~Le~~n~~L~~~lke~   76 (155)
T 2oto_A           23 QNIRLRHENKDLKARLENAMEVAGRDF-------KRAEELEKAKQALEDQRKDLETKLKEL   76 (155)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHH-------HhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344666666666666666654444322       223445555566666666666655554

>1fxk_A Prefoldin; archaeal protein, chaperone; 2.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.2.5.1 PDB: 1fxk_B

Probab=80.64  E-value=8.1  Score=29.37  Aligned_cols=40  Identities=13%  Similarity=0.137  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHH
Q 038837           95 AEERLNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRL  134 (287)
Q Consensus        95 aee~i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv  134 (287)
                      .++=...|++.++.+..++.+...+...++....+.++++
T Consensus        63 ~~e~~~~L~~~~e~i~~~i~~le~~~~~~~~~l~~lk~~l  102 (107)
T 1fxk_A           63 KDELTEELQEKLETLQLREKTIERQEERVMKKLQEMQVNI  102 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444667777777777666666666655555555544444

>3s84_A Apolipoprotein A-IV; four helix bundle, transport protein; 2.40A {Homo sapiens}

Probab=80.11  E-value=13  Score=33.83  Aligned_cols=24  Identities=21%  Similarity=0.286  Sum_probs=14.2

Q ss_pred             HHhhcccccchhcccCCcccCCcc
Q 038837          188 KDFSEKHLPKLTGMLVPYLPGKGS  211 (287)
Q Consensus       188 ~~~~~ph~~kv~~~~~py~~~~~~  211 (287)
                      ++-+..|+..+.+.+.||.+..+.
T Consensus       127 r~k~~~~leeLr~~l~P~ae~~~~  150 (273)
T 3s84_A          127 KVKIDQTVEELRRSLAPYAQDTQE  150 (273)
T ss_dssp             HHHHHHHHHHHHHHHGGGCSSCHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHH
Confidence            445556666666666676655443

---

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	287
d2efka1	279	CDC42-interacting protein 4, CIP4 {Human (Homo sap	93.8
d2efla1	288	Formin-binding protein 1, FNBP1 {Human (Homo sapie	92.12
d1fxka_	107	Prefoldin beta subunit {Archaeon Methanobacterium	90.66
d1fxkc_	133	Prefoldin alpha subunit {Archaeon Methanobacterium	86.44
d2ap3a1	185	Hypothetical protein MW0975 (SA0943) {Staphylococc	83.16

>d2efka1 a.238.1.4 (A:10-288) CDC42-interacting protein 4, CIP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: BAR/IMD domain-like
superfamily: BAR/IMD domain-like
family: FCH domain
domain: CDC42-interacting protein 4, CIP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.80  E-value=1.1  Score=36.35  Aligned_cols=23  Identities=13%  Similarity=0.254  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhh
Q 038837          153 IQIQHLEQALHMAELRAANVQRQ  175 (287)
Q Consensus       153 ~qIqk~E~Alk~ae~~~~k~q~e  175 (287)
                      .+++++.+..+.+...+.+++.+
T Consensus       158 ~~~~K~~~~~~~~~~~~~~~~~~  180 (279)
T d2efka1         158 ADVEKAKQQAHLRSHMAEESKNE  180 (279)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555444

>d2efla1 a.238.1.4 (A:1-288) Formin-binding protein 1, FNBP1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: BAR/IMD domain-like
superfamily: BAR/IMD domain-like
family: FCH domain
domain: Formin-binding protein 1, FNBP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.12  E-value=1.9  Score=34.86  Aligned_cols=77  Identities=8%  Similarity=-0.021  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038837           99 LNALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHMAELRAANVQRQ  175 (287)
Q Consensus        99 i~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~ae~~~~k~q~e  175 (287)
                      .+.+..++.++.+++.+...+....-.+-..+.+.++.+..++++...-..--..+++++...++.+...+-+++.+
T Consensus       113 ~K~~~~~~~k~~k~~~~~~~~l~k~k~~Y~~~~~e~e~~~~~~~~~~~~~~~~~~~~~K~~~k~~~~~~~~~~a~~~  189 (288)
T d2efla1         113 RKSNFHDGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDADINVTKADVEKARQQAQIRHQMAEDSKAD  189 (288)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444433333333333333333333343333222212234444444444444444444333

>d1fxka_ a.2.5.1 (A:) Prefoldin beta subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin beta subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=90.66  E-value=0.68  Score=34.43  Aligned_cols=25  Identities=20%  Similarity=0.250  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Q 038837           30 QHLIAELQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        30 ~~l~~eL~qLk~kIa~LES~i~e~~   54 (287)
                      ..+..+++.+..++..||..+.|..
T Consensus        11 q~lq~el~~~~~q~~~le~q~~E~~   35 (107)
T d1fxka_          11 QQLQQQAQAISVQKQTVEMQINETQ   35 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456666777777777777666644

>d1fxkc_ a.2.5.1 (C:) Prefoldin alpha subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin alpha subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=86.44  E-value=5.1  Score=29.93  Aligned_cols=19  Identities=11%  Similarity=0.062  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHHHHh
Q 038837           36 LQDAKLKIAGLETMLEESI   54 (287)
Q Consensus        36 L~qLk~kIa~LES~i~e~~   54 (287)
                      |++|...+..|+..|+...
T Consensus         3 L~eL~~~~~~l~~~l~~l~   21 (133)
T d1fxkc_           3 LAEIVAQLNIYQSQVELIQ   21 (133)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444433

>d2ap3a1 a.24.27.1 (A:12-196) Hypothetical protein MW0975 (SA0943) {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: Four-helical up-and-down bundle
superfamily: MW0975(SA0943)-like
family: MW0975(SA0943)-like
domain: Hypothetical protein MW0975 (SA0943)
species: Staphylococcus aureus [TaxId: 1280]

Probab=83.16  E-value=6.2  Score=28.19  Aligned_cols=65  Identities=8%  Similarity=-0.100  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHhhhhhhhhhHHhhhHhHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 038837          100 NALEEEIRLLWAASRKNNFDIHNLESKALDAEDRLEEVSLQVEKMSEIVTEQWIQIQHLEQALHM  164 (287)
Q Consensus       100 ~eLEkQVe~L~~elekqn~~~~~LEsrA~dAEkkv~eL~sklek~~ki~~EQ~~qIqk~E~Alk~  164 (287)
                      ..+.+..+.+...+.........+.......+.++..+..++..+.+...+....+..++..++-
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~  176 (185)
T d2ap3a1         112 KEKYKLHSDYAKAYKKAVNSEKTLFKYLNQNDATQQGVNEKSKAIEQNYKKLKEVSDKYTKVLNK  176 (185)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444555555555555555555666666666666666666666666666666666665553