Citrus Sinensis ID: 021632

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310
Protein Sequence
MKKLVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKHHFRNGSSETIITASSSADAESDAESTISYQQQQITTTTATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKKGSSNWWERVKKADFFNCGLPSCS
Secondary Structure (PSIPRED)
cHHHHHcccccccccccHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHcccccccccccccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHcccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEcccccccccccHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHEHccccHHHHHHHHHHHHHHHHccccccccHHHHHHHccEEEccccccc
Coil and Loop (DISEMBL)
MKKLVISgsseeenvgdTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRcrnhkkhhfrngssetiitasssadaesdaesTISYQQQQITTTTATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEYEnswsnsnstsssssyvkeksaqVTLESCFQSFEKIKLKKKKGSSNWWERVKkadffncglpscs
Flexible Loop (DISEMBL)
mkklvisgsseeenvgDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKhhfrngssetiiTASSSADAESDAESTISYQQQQITTTTATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEYEnswsnsnstsssssYVKEKSAQVTLESCFQSFEkiklkkkkgssnwwervkkadffncglpscs
Low Complexity Region (SEG)
MKKLVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKHHFRNGssetiitasssadaesdaestisYQQQQIttttatmaaaaasaNIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRkiellkslmellesermilVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEYEnswsnsnstsssssYVKEKSAQVTLESCFQSFEkiklkkkkGSSNWWERVKKADFFNCGLPSCS
Disordered region (IsUnstruct)
*****************TFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKK**************************************TATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVN*********************************LESCFQSFEKIKLKKKKGSSNWWERVKKADFFNCGL****
Disordered Region (DISOPRED)
*****************TFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRN***********************************************************************************************************************************************************ILSQ********************************************************************************WERVKKADFFNCGLPSC*
Disordered Region (DISEMBL)
MKKLVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKHHFRNGSSETII******************QQQQITTTTATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQV***************************TLESCFQSFEKI*********NWWERVKKADFFNCGLPSCS
Disordered Region (DISPRO)
**************VGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNH*************************************************SANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKK*KGSSNWWERVKKADFFNCGLPSCS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKLVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKHHFRNGSSETIITASSSADAESDAESTISYQQQQITTTTATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVxxxxxxxxxxxxxxxxxxxxxxxxxxxxNVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKKGSSNWWERVKKADFFNCGLPSCS
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	310
225457466	447	PREDICTED: uncharacterized protein LOC10	0.916	0.635	0.476	6e-73
147801789	329	hypothetical protein VITISV_027923 [Viti	0.916	0.863	0.476	1e-72
449439231	356	PREDICTED: uncharacterized protein LOC10	0.903	0.786	0.471	2e-70
449507157	369	PREDICTED: uncharacterized LOC101212854	0.893	0.750	0.470	8e-69
224118072	317	predicted protein [Populus trichocarpa]	0.909	0.889	0.486	1e-64
357500075	327	hypothetical protein MTR_6g081040 [Medic	0.745	0.706	0.552	5e-63
53749473	372	Putative kinase interacting protein, ide	0.880	0.733	0.425	1e-61
224125848	338	predicted protein [Populus trichocarpa]	0.932	0.855	0.479	1e-61
356560047	325	PREDICTED: uncharacterized protein LOC10	0.932	0.889	0.447	2e-60
255646090	325	unknown [Glycine max]	0.932	0.889	0.444	8e-60

>gi|225457466|ref|XP_002264687.1| PREDICTED: uncharacterized protein LOC100246194 [Vitis vinifera]

 Score =  280 bits (716), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 162/340 (47%), Positives = 219/340 (64%), Gaps = 56/340 (16%)

Query: 1   MKKLVISGSS----EEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR------ 50
           MK L ++G++    E  +  DTFA+RAE YYQKRPQLLALL+DLYN Y+TL DR      
Sbjct: 123 MKMLALNGNTKTKVEGGDATDTFAQRAESYYQKRPQLLALLQDLYNAYLTLADRYSQTQT 182

Query: 51  -CRNHKKHHFRNGSSETIITA--------SSSADAE-------SDAESTISYQQQQITTT 94
             + +  HH R  S+ + I A        ++S D E       SD ES++SYQ Q     
Sbjct: 183 LAKQYHHHHRRQSSNLSQIQALHLDGQEDTNSYDEEDDDIGAVSDVESSLSYQPQPPLPK 242

Query: 95  TATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLES 154
            A +       +++ ++AE+V KNVE +IL+++V+ ++    ES RKIEL KSL+E+LES
Sbjct: 243 HAKL-------DVEAMIAEIVMKNVECDILLDEVSMVERRFGESTRKIELQKSLLEVLES 295

Query: 155 ERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKI 214
           ERMIL+NENV+LGY+VSA++EENKGLASE++FM+RKA ELA+CVL+MRED+RVC+LS+KI
Sbjct: 296 ERMILLNENVRLGYKVSALIEENKGLASESLFMKRKAGELARCVLKMREDHRVCMLSRKI 355

Query: 215 EDLQEQIYGLEKRNKEYYQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESC 274
           EDLQ QIYGLEKRNKEYY+ L+ R+Q+V++                  K+K  ++ LE C
Sbjct: 356 EDLQGQIYGLEKRNKEYYEQLMKRDQEVEQL--------------FKSKDKKKKLGLEVC 401

Query: 275 FQSFE-------KIKLKKKKGSS--NWWERVKKADFFNCG 305
           FQ  +        + +K K G     WWERVK  D F CG
Sbjct: 402 FQVHKLKMVENADVNVKGKDGGKVFKWWERVKNLDLFICG 441

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147801789|emb|CAN67913.1| hypothetical protein VITISV_027923 [Vitis vinifera]

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 162/340 (47%), Positives = 219/340 (64%), Gaps = 56/340 (16%)

Query: 1   MKKLVISGSS----EEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR------ 50
           MK L ++G++    E  +  DTFA+RAE YYQKRPQLLALL+DLYN Y+TL DR      
Sbjct: 5   MKMLALNGNTKTKVEGGDATDTFAQRAESYYQKRPQLLALLQDLYNAYLTLADRYSQTQT 64

Query: 51  -CRNHKKHHFRNGSSETIITA--------SSSADAE-------SDAESTISYQQQQITTT 94
             + +  HH R  S+ + I A        ++S D E       SD ES++SYQ Q     
Sbjct: 65  LAKQYHHHHRRQSSNLSQIQALHLDGQEDTNSYDEEDDDIGAVSDVESSLSYQPQPPLPK 124

Query: 95  TATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLES 154
            A +       +++ ++AE+V KNVE +IL+++V+ ++    ES RKIEL KSL+E+LES
Sbjct: 125 HAKL-------DVEAMIAEIVMKNVECDILLDEVSMVERRFGESTRKIELQKSLLEVLES 177

Query: 155 ERMILVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKI 214
           ERMIL+NENV+LGY+VSA++EENKGLASE++FM+RKA ELA+CVL+MRED+RVC+LS+KI
Sbjct: 178 ERMILLNENVRLGYKVSALIEENKGLASESLFMKRKAGELARCVLKMREDHRVCMLSRKI 237

Query: 215 EDLQEQIYGLEKRNKEYYQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESC 274
           EDLQ QIYGLEKRNKEYY+ L+ R+Q+V++                  K+K  ++ LE C
Sbjct: 238 EDLQGQIYGLEKRNKEYYEQLMKRDQEVEQL--------------FKSKDKKKKLGLEVC 283

Query: 275 FQSFE-------KIKLKKKKGSS--NWWERVKKADFFNCG 305
           FQ  +        + +K K G     WWERVK  D F CG
Sbjct: 284 FQVHKLKMVENADVNVKGKDGGKVFKWWERVKNLDLFICG 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439231|ref|XP_004137390.1| PREDICTED: uncharacterized protein LOC101212854 [Cucumis sativus]

 Score =  271 bits (694), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 151/320 (47%), Positives = 208/320 (65%), Gaps = 40/320 (12%)

Query: 4   LVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR-CRNHKKHHFRNG 62
           L+   ++EE+NVGD+FAERAE+YY KRPQLLALL++LY  Y TL DR  +   KHH R  
Sbjct: 53  LLAMKNAEEDNVGDSFAERAEFYYNKRPQLLALLQELYTAYTTLSDRYIQTVAKHHNRQF 112

Query: 63  SSETIITASSSAD------AESDAESTISYQQQQITTTTATMAAAAASANIDDLVAELVA 116
           S  + + +   A+       ESDAES++SYQQ  +T+T           + D  +AELV 
Sbjct: 113 SVTSTLDSFDGAEDSGISQIESDAESSLSYQQVSVTST-----KYYGMVDNDAFIAELVM 167

Query: 117 KNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEE 176
           KNVE +IL N+V  ++  C +S RKIEL KSL+++LESER+IL+NEN +LGY+V ++MEE
Sbjct: 168 KNVEYDILTNEVTTLEKQCCDSSRKIELQKSLLDVLESERLILLNENARLGYRVESLMEE 227

Query: 177 NKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLV 236
           NKGL +E++FM++KA E+A+C+L++R+D+RV +L+QKIEDLQ QIYGLEKRNKEYY  LV
Sbjct: 228 NKGLVAESVFMKQKAGEMARCMLKLRDDHRVYLLNQKIEDLQGQIYGLEKRNKEYYDQLV 287

Query: 237 NREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKKG-------- 288
             ++ +   E+  SN                +VTLE+CFQ   ++K K+  G        
Sbjct: 288 KTDKAM--VESRCSNGK--------------EVTLEACFQ-IGRLKSKRNVGVIGKTKSS 330

Query: 289 ---SSNWWERVKKADFFNCG 305
              S  WW +VK  D F CG
Sbjct: 331 GKKSYKWWAKVKSMDMFLCG 350

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449507157|ref|XP_004162948.1| PREDICTED: uncharacterized LOC101212854 [Cucumis sativus]

 Score =  266 bits (680), Expect = 8e-69,   Method: Compositional matrix adjust.
 Identities = 149/317 (47%), Positives = 206/317 (64%), Gaps = 40/317 (12%)

Query: 4   LVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR-CRNHKKHHFRNG 62
           L+   ++EE+NVGD+FAERAE+YY KRPQLLALL++LY  Y TL DR  +   KHH R  
Sbjct: 53  LLAMKNAEEDNVGDSFAERAEFYYNKRPQLLALLQELYTAYTTLSDRYIQTVAKHHNRQF 112

Query: 63  SSETIITASSSAD------AESDAESTISYQQQQITTTTATMAAAAASANIDDLVAELVA 116
           S  + + +   A+       ESDAES++SYQQ  +T+T           + D  +AELV 
Sbjct: 113 SVTSTLDSFDGAEDSGISQIESDAESSLSYQQVSVTST-----KYYGMVDNDAFIAELVM 167

Query: 117 KNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEE 176
           KNVE +IL N+V  ++  C +S RKIEL KSL+++LESER+IL+NEN +LGY+V ++MEE
Sbjct: 168 KNVEYDILTNEVTTLEKQCCDSSRKIELQKSLLDVLESERLILLNENARLGYRVESLMEE 227

Query: 177 NKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLV 236
           NKGL +E++FM++KA E+A+C+L++R+D+RV +L+QKIEDLQ QIYGLEKRNKEYY  LV
Sbjct: 228 NKGLVAESVFMKQKAGEMARCMLKLRDDHRVYLLNQKIEDLQGQIYGLEKRNKEYYDQLV 287

Query: 237 NREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKKG-------- 288
             ++ +   E+  SN                +VTLE+CFQ   ++K K+  G        
Sbjct: 288 KTDKAM--VESRCSNGK--------------EVTLEACFQ-IGRLKSKRNVGVIGKTKSS 330

Query: 289 ---SSNWWERVKKADFF 302
              S  WW +VK  D F
Sbjct: 331 GKKSYKWWAKVKSMDMF 347

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118072|ref|XP_002317725.1| predicted protein [Populus trichocarpa] gi|222858398|gb|EEE95945.1| predicted protein [Populus trichocarpa]

 Score =  252 bits (644), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 160/329 (48%), Positives = 209/329 (63%), Gaps = 47/329 (14%)

Query: 9   SSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRC-RNHKKHHFRNGSSETI 67
           S E+   GD+FAERAEWYYQKRPQLLALL+DLYNGY  L DRC R  K     N  S  +
Sbjct: 8   SEEDMGCGDSFAERAEWYYQKRPQLLALLRDLYNGYTALADRCSRMEKGKKLSNHFSYPM 67

Query: 68  ITA-------------SSSADAESDAESTISYQQQQITTTTATMAAAAASANIDDLVAEL 114
           + A             SS    + DAES++SYQQ     TT     +     ID++V +L
Sbjct: 68  LMALDDDQDQEGSGGSSSCQFLDWDAESSMSYQQ----PTTPFQDGSDTVLGIDEVVVDL 123

Query: 115 VAKNVESEILVNQVNEMD--HVCNES-RRKIELLKSLMELLESERMILVNENVKLGYQVS 171
           V KNVE++IL +Q++EM+      ES  RK+ELLK L+E+LESER++L+NENV+LGY++ 
Sbjct: 124 VMKNVENDILADQLSEMEKQQQGQESIWRKVELLKKLLEVLESERIVLLNENVRLGYKMQ 183

Query: 172 AVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEY 231
           AV+EENKGL+SEA+F++RKA ELA+CVL+MRED+RV +L++KIEDLQ QIYGLE RNK+Y
Sbjct: 184 AVLEENKGLSSEAVFLKRKAGELARCVLKMREDHRVSMLTRKIEDLQGQIYGLEMRNKDY 243

Query: 232 YQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKKGSS- 290
           Y  L+ +E Q +E  +S              ++      +  CFQ  EK+KLKKK G+S 
Sbjct: 244 YLQLLRKELQGEEKISS--------------RKDDGVAFVGCCFQ-IEKLKLKKKDGASV 288

Query: 291 ---------NWWERVKKADFFNCGLPSCS 310
                     WWE+VK  D F CG   CS
Sbjct: 289 SKGGAKRRPKWWEKVKSMDLFMCGF-QCS 316

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357500075|ref|XP_003620326.1| hypothetical protein MTR_6g081040 [Medicago truncatula] gi|355495341|gb|AES76544.1| hypothetical protein MTR_6g081040 [Medicago truncatula]

 Score =  247 bits (630), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 141/255 (55%), Positives = 178/255 (69%), Gaps = 24/255 (9%)

Query: 1   MKKLVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR---CRNHKKH 57
           MK L I G+SEEE  GDTFAERAE YYQKRPQLL+LL DLYNGY+TL DR        KH
Sbjct: 12  MKMLAI-GTSEEEEEGDTFAERAETYYQKRPQLLSLLHDLYNGYVTLSDRYIQTLAKHKH 70

Query: 58  HFRNGSS-----------ETIITASSSADAESDAESTISYQQQQITTTTATMAAAAASAN 106
           H R+ S            E +I+  S  D  SD ES+ISYQQ  +     +M       +
Sbjct: 71  HSRHSSQVSTLEEGFSDQEEVISGVSQVD--SDMESSISYQQM-LPMVKGSMV------D 121

Query: 107 IDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKL 166
           +D +VAELV KNV  + LV++V  M+    ES RK EL KSL+E+LESER++L+NEN  L
Sbjct: 122 VDAIVAELVMKNVMCDFLVHEVGVMERKYCESSRKSELQKSLLEVLESERLVLLNENAGL 181

Query: 167 GYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEK 226
            Y+V++++EENK LASE++F++RKA ELAKCVL+MRED+RV +L +KIEDLQ QI+GLEK
Sbjct: 182 SYRVNSLVEENKELASESVFIKRKAGELAKCVLKMREDHRVYLLHRKIEDLQGQIHGLEK 241

Query: 227 RNKEYYQMLVNREQQ 241
           RNKEYY+ L+ RE Q
Sbjct: 242 RNKEYYERLLRRESQ 256

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|53749473|gb|AAU90326.1| Putative kinase interacting protein, identical [Solanum demissum]

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 141/331 (42%), Positives = 201/331 (60%), Gaps = 58/331 (17%)

Query: 12  EENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR-CRNHKKHHFRNGSSETIITA 70
           E+   D+FAERA+ YYQKRPQL+ALL++LYN Y+ L DR C+   K+H     S  I   
Sbjct: 55  EKGSPDSFAERADAYYQKRPQLMALLQELYNSYVNLADRYCQALAKNHNHRRYSSPIPPL 114

Query: 71  SSSADA------------ESDAESTISYQQQQITTTTATMAAAAASANIDDLVAELVAKN 118
           S + +             +SDAES++S+Q     +T           +I+ +VA+LV +N
Sbjct: 115 SYNENGYCDEEEYSGEIIDSDAESSLSFQPSFPPSTQDKF-------DIEMIVADLVIRN 167

Query: 119 VESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENK 178
           V+ + +++++N+++   NES RKIEL KSL++++ESER+IL+NEN +LGY+V+ +MEENK
Sbjct: 168 VDYDFVLDELNQVERQNNESSRKIELQKSLLDVMESERLILLNENARLGYKVATLMEENK 227

Query: 179 GLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNR 238
            ++SE++FM+RK +ELA C+L+MRED+RVC+LS+KIEDLQ QIYGLEKRNKEYY  LV  
Sbjct: 228 AVSSESLFMKRKVAELAGCILKMREDHRVCMLSRKIEDLQGQIYGLEKRNKEYYDQLVKH 287

Query: 239 EQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQ-----------SFEKIKLKK-- 285
           E++            +  S S  VK    +V ++ CF+           SF    LKK  
Sbjct: 288 EEE-----------KTRRSKSMKVK---GEVNMKYCFKVPEDVVAGITRSFSFGNLKKGG 333

Query: 286 -----------KKGSSNWWERVKKADFFNCG 305
                      KK     W+RVKK D F CG
Sbjct: 334 GEQKVNANAEVKKKVPKLWDRVKKFDIFFCG 364

Source: Solanum demissum

Species: Solanum demissum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125848|ref|XP_002329732.1| predicted protein [Populus trichocarpa] gi|222870640|gb|EEF07771.1| predicted protein [Populus trichocarpa]

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 153/319 (47%), Positives = 202/319 (63%), Gaps = 30/319 (9%)

Query: 9   SSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKHH--FRNGSSET 66
           S E+   GD+FAERAEWYYQKRPQLLA L+DLYNGY  LLDRC   +K     ++ SS  
Sbjct: 32  SEEDMGCGDSFAERAEWYYQKRPQLLASLQDLYNGYTILLDRCNRMEKGKRLSKHLSSPM 91

Query: 67  IIT------------ASSSADAESDAESTISYQQQQITTTTATMAAAAASANIDDLVAEL 114
            IT            +SS    + DAES++SYQQ      T     +     ID++VA+L
Sbjct: 92  SITSDDDQDQEDSRGSSSCQFLDWDAESSLSYQQ----PPTPFQDGSNTILGIDEIVADL 147

Query: 115 VAKNVESEILVNQVNEMD--HVCNES-RRKIELLKSLMELLESERMILVNENVKLGYQVS 171
           V KNV ++IL +Q+++M+   +  ES  RK+ELLK L+E+LESER++L+NENV+LGY++ 
Sbjct: 148 VMKNVGNDILADQLSDMEKQQLGQESIWRKVELLKKLLEVLESERIVLLNENVRLGYKMQ 207

Query: 172 AVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEY 231
           A++EENKGL+SEAMFM+RKA ELA+CVL+MRED+RVC+L++KIEDLQ QIYGLE RNKEY
Sbjct: 208 ALLEENKGLSSEAMFMKRKAGELARCVLKMREDHRVCMLTRKIEDLQGQIYGLEMRNKEY 267

Query: 232 YQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKKGSSN 291
           YQ L+ +E+  ++          +SS    V        LE      +        G S 
Sbjct: 268 YQQLLKKEEHQED--------KISSSKDGGVAFVGCCFQLEKLKLKKKNEAYVGNGGWSK 319

Query: 292 WWERVKKADFFNCGLPSCS 310
           WW +VK  D F CG   CS
Sbjct: 320 WWSKVKNMDMFLCGF-QCS 337

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560047|ref|XP_003548307.1| PREDICTED: uncharacterized protein LOC100776808 [Glycine max]

 Score =  238 bits (607), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 150/335 (44%), Positives = 202/335 (60%), Gaps = 46/335 (13%)

Query: 1   MKKLVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR---CRNHKKH 57
           MK L +S ++EEE +GDTFAERAE YYQKRPQLL+LL+DLYNGYITL DR        KH
Sbjct: 12  MKVLAMS-TTEEEEMGDTFAERAETYYQKRPQLLSLLQDLYNGYITLSDRYIQTLAKHKH 70

Query: 58  HFRNGSSETIITASSSADAESDAES--------TISYQQQQITTTTATMAAAAASA--NI 107
           H R+ S  + +    S   E+   S        +ISYQ              ++S   ++
Sbjct: 71  HSRHSSQVSTVDEGFSDQEEASGVSHSDSDIESSISYQHPPPMMMMPIGLPRSSSMLLDV 130

Query: 108 DDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLG 167
           D + AELV +NVE ++LV++V  M+    ES RK EL KSL+E+LESER++L+NEN  L 
Sbjct: 131 DAIYAELVMRNVEYDLLVHEVGVMERRYCESSRKSELQKSLLEVLESERIVLLNENASLS 190

Query: 168 YQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKR 227
           Y+V+ ++EENK LASE++F++RKA ELAKCVL+MRED+RV +L +KIEDLQ QI+GLEKR
Sbjct: 191 YRVNTLVEENKELASESVFIKRKAGELAKCVLKMREDHRVYLLHRKIEDLQAQIHGLEKR 250

Query: 228 NKEYYQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKK 287
           NKEYY+ L+ R+ Q                    V +K   V LE C Q  +  + K K 
Sbjct: 251 NKEYYEKLLRRDVQ------------------EDVGKKG--VALEVCVQLDKHKRFKWKD 290

Query: 288 G-----------SSNWWERVKKADFFNCGL-PSCS 310
           G           S + W+++K  D   CG  P+C+
Sbjct: 291 GNTSGKKFHGKKSPSLWKKLKNMDLLLCGANPTCA 325

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255646090|gb|ACU23532.1| unknown [Glycine max]

 Score =  236 bits (603), Expect = 8e-60,   Method: Compositional matrix adjust.
 Identities = 149/335 (44%), Positives = 202/335 (60%), Gaps = 46/335 (13%)

Query: 1   MKKLVISGSSEEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR---CRNHKKH 57
           MK L +S ++EEE +GDTFAERAE YYQKRPQLL+LL+DLYNGYITL DR        KH
Sbjct: 12  MKVLAMS-TTEEEEMGDTFAERAETYYQKRPQLLSLLQDLYNGYITLSDRYIQTLAKHKH 70

Query: 58  HFRNGSSETIITASSSADAESDAES--------TISYQQQQITTTTATMAAAAASA--NI 107
           H R+ S  + +    S   E+   S        +ISYQ              ++S   ++
Sbjct: 71  HSRHSSQVSTVDEGFSDQEEASGVSHSDSDIESSISYQHPPPMMMMPIGLPRSSSMLLDV 130

Query: 108 DDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLG 167
           D + AELV +NVE ++LV++V  M+    ES RK EL KSL+E+LESER++L+NEN  L 
Sbjct: 131 DAIYAELVMRNVEYDLLVHEVGVMERRYCESSRKSELQKSLLEVLESERIVLLNENASLS 190

Query: 168 YQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKR 227
           Y+V+ ++EENK LASE++F++R+A ELAKCVL+MRED+RV +L +KIEDLQ QI+GLEKR
Sbjct: 191 YRVNTLVEENKELASESVFIKREAGELAKCVLKMREDHRVYLLHRKIEDLQAQIHGLEKR 250

Query: 228 NKEYYQMLVNREQQVKEYENSWSNSNSTSSSSSYVKEKSAQVTLESCFQSFEKIKLKKKK 287
           NKEYY+ L+ R+ Q                    V +K   V LE C Q  +  + K K 
Sbjct: 251 NKEYYEKLLRRDVQED------------------VGKKG--VALEVCVQLDKHKRFKWKD 290

Query: 288 G-----------SSNWWERVKKADFFNCGL-PSCS 310
           G           S + W+++K  D   CG  P+C+
Sbjct: 291 GNTSGKKFHGKKSPSLWKKLKNMDLLLCGANPTCA 325

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	310
TAIR|locus:504956328	297	AT1G48405 "AT1G48405" [Arabido	0.703	0.734	0.288	3.3e-24
TAIR|locus:2041203	947	NET2D "AT2G22560" [Arabidopsis	0.112	0.036	0.485	0.00084

TAIR|locus:504956328 AT1G48405 "AT1G48405" [Arabidopsis thaliana (taxid:3702)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 69/239 (28%), Positives = 122/239 (51%)

Query:    11 EEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKHHFRNGXXXXXXXX 70
             ++   G+TF++RAEW+YQ+ P LL+L +DLY+GY TLLDR   + K    +         
Sbjct:    30 DDNQTGETFSQRAEWFYQRSPLLLSLCQDLYDGYATLLDRFNQNPKQVIPHDNDTDTDIT 89

Query:    71 XXXXXXXXXXXXXXXYQQQQIXXXXXXXXXXXXXXNIDDLVAELVAKNVESEILVNQVNE 130
                            +QQ ++              NI+DLV++LV  N+E +   + +  
Sbjct:    90 SEVESILS-------FQQMEVSTCDMQK-------NIEDLVSQLVTANLEKDTAKHILQR 135

Query:   131 MDHVCNESRRXXXXXXXXXXXXXXXXXXXVNENVKLGYQVSAVMEENKGLASEAMFMRRK 190
              +    E+ +                   V E   LG+++++++EEN+ LASEA+FM+ +
Sbjct:   136 REQTLQEACKTIGLLKKLVMLLDMEKEVAVEETANLGHKLTSLLEENRELASEALFMKNE 195

Query:   191 ASELAKCVLRMREDY--RVCILSQKIEDLQ---EQIYGLEKRNKEYYQMLVNREQQVKE 244
             A +LA+CVL+MR+++  ++C L  +I +LQ   E +Y  E  + +    L N +++ K+
Sbjct:   196 AVKLARCVLKMRDEHFHKMCHLQNQIYELQSSREPVY--ENESSQSCFGLENSKKKSKK 252

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2041203 NET2D "AT2G22560" [Arabidopsis thaliana (taxid:3702)]

 Score = 101 (40.6 bits), Expect = 0.00084, Sum P(2) = 0.00084
 Identities = 17/35 (48%), Positives = 27/35 (77%)

Query:    16 GDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR 50
             GD+FA+RAE YY+KRP+L++ +++ Y  Y  L +R
Sbjct:    48 GDSFAKRAEMYYKKRPELISFVEESYRAYRALAER 82

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005886 "plasma 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: eugene3.00120068 hypothetical protein (317 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	310
pfam07765	74	pfam07765, KIP1, KIP1-like protein	4e-07

>gnl|CDD|116379 pfam07765, KIP1, KIP1-like protein

 Score = 46.3 bits (110), Expect = 4e-07
 Identities = 20/40 (50%), Positives = 30/40 (75%), Gaps = 2/40 (5%)

Query: 11 EEENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDR 50
          EE+   D+FA+RAE YY+KRP+L+AL+++ Y  Y  L +R
Sbjct: 35 EED--ADSFAKRAEMYYKKRPELIALVEEFYRAYRALAER 72

This is a family of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions. It has also been suggested that the protein's coiled- coils allow it to dimerise in vivo. Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	310
PF07765	74	KIP1: KIP1-like protein; InterPro: IPR011684 This	99.84
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	94.58
PF04849	306	HAP1_N: HAP1 N-terminal conserved region; InterPro	94.0
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	92.08
PF10174	775	Cast: RIM-binding protein of the cytomatrix active	91.98
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	91.69
COG2433	652	Uncharacterized conserved protein [Function unknow	91.24
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	91.12
PF05701	522	WEMBL: Weak chloroplast movement under blue light;	90.92
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	90.59
TIGR02168	1179	SMC_prok_B chromosome segregation protein SMC, com	90.34
PF00038	312	Filament: Intermediate filament protein; InterPro:	89.34
PRK09039	343	hypothetical protein; Validated	89.01
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	88.94
PHA02562	562	46 endonuclease subunit; Provisional	88.65
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	87.12
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	85.99
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	85.82
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	85.37
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	83.8
PF11221	144	Med21: Subunit 21 of Mediator complex; InterPro: I	83.61
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	83.16
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	83.16
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	82.36
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	81.87
KOG0996	1293	consensus Structural maintenance of chromosome pro	80.77
PRK09039	343	hypothetical protein; Validated	80.64
KOG4643	1195	consensus Uncharacterized coiled-coil protein [Fun	80.32

>PF07765 KIP1: KIP1-like protein; InterPro: IPR011684 This is a group of sequences found exclusively in plants

Probab=99.84  E-value=1.1e-21  Score=153.38  Aligned_cols=40  Identities=48%  Similarity=0.944  Sum_probs=38.5

Q ss_pred             ccccccHHHHHHHhhhhcHHHHHHHHHHHHHHHHHHHHhh
Q 021632           13 ENVGDTFAERAEWYYQKRPQLLALLKDLYNGYITLLDRCR   52 (310)
Q Consensus        13 eedgDSFAkRAEmYYqkRPeLi~~vee~yr~YraLAeRYd   52 (310)
                      ++||||||+||||||+|||+||++||||||+||+||||||
T Consensus        35 eedgdSfakrAEmyy~kRp~Li~~vee~yr~YrsLAerYD   74 (74)
T PF07765_consen   35 EEDGDSFAKRAEMYYKKRPELISLVEEFYRSYRSLAERYD   74 (74)
T ss_pred             ccCcchHHHhhHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence            4589999999999999999999999999999999999996

They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase []. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions []. It has also been suggested that the coiled-coils of the protein allow it to dimerise in vivo [].

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

Probab=94.58  E-value=0.41  Score=42.28  Aligned_cols=80  Identities=21%  Similarity=0.214  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhhhhHHHHHHhhhhhhhh--------------hhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHH
Q 021632          109 DLVAELVAKNVESEILVNQVNEMDHVC--------------NESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVM  174 (310)
Q Consensus       109 elvaelVa~nve~d~l~del~~~er~~--------------~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~  174 (310)
                      ++...++..+.+...+..++...++.+              ..-...|+-+...++.|..|-.+|--++-.+.-++..++
T Consensus        92 el~~~L~~~~~~l~~l~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~  171 (194)
T PF08614_consen   92 ELAQQLVELNDELQELEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLE  171 (194)
T ss_dssp             ----------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444455555555554444444433333              333445666667888888888888778888888999999


Q ss_pred             HHhhhhhHHHHHHH
Q 021632          175 EENKGLASEAMFMR  188 (310)
Q Consensus       175 eEnk~~asEa~fmk  188 (310)
                      .||+.|-.-.|-.|
T Consensus       172 ~En~~Lv~Rwm~~k  185 (194)
T PF08614_consen  172 EENRELVERWMQRK  185 (194)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99998765444333

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.

>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=94.00  E-value=3.2  Score=40.62  Aligned_cols=126  Identities=20%  Similarity=0.245  Sum_probs=77.2

Q ss_pred             hcChhHHHHHHHHHhhhhHHHHHHhhhhh------------------hhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 021632          104 SANIDDLVAELVAKNVESEILVNQVNEMD------------------HVCNESRRKIELLKSLMELLESERMILVNENVK  165 (310)
Q Consensus       104 ~~~idelvaelVa~nve~d~l~del~~~e------------------r~~~Es~rkieLlk~ll~vLesEr~vll~Ena~  165 (310)
                      ....+.++-.+=..--|...|+.|+++.-                  +++.+|..+|.-|.+.|..-..|-..+=+|+.+
T Consensus       159 ~~~le~Lq~Klk~LEeEN~~LR~Ea~~L~~et~~~EekEqqLv~dcv~QL~~An~qia~LseELa~k~Ee~~rQQEEIt~  238 (306)
T PF04849_consen  159 CIQLEALQEKLKSLEEENEQLRSEASQLKTETDTYEEKEQQLVLDCVKQLSEANQQIASLSEELARKTEENRRQQEEITS  238 (306)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555445555556666555443                  344444555555555555544454555566666


Q ss_pred             hhhhhhhHHHHhhhhhHHHHHHHHhhHHHHHHHHHhhcchhhhHhhhhHHHHHHHHHHHHhhcHHHHHHHHHHHHHHHhh
Q 021632          166 LGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEY  245 (310)
Q Consensus       166 Lg~~~s~~~eEnk~~asEa~fmkr~a~ELArcvlkmredhrvc~l~rKIe~Lq~qIy~lE~rnre~yeql~~~E~e~~~~  245 (310)
                      |=.++..++...|..+.|---|.       ..+...++-|+         .|++++..|+.+..+|...|.-+..|++..
T Consensus       239 LlsqivdlQ~r~k~~~~EnEeL~-------q~L~~ske~Q~---------~L~aEL~elqdkY~E~~~mL~EaQEElk~l  302 (306)
T PF04849_consen  239 LLSQIVDLQQRCKQLAAENEELQ-------QHLQASKESQR---------QLQAELQELQDKYAECMAMLHEAQEELKTL  302 (306)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHH-------HHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            66666666666666666644333       33444444443         368999999999999999999999998866

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 [].

>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function

Probab=92.08  E-value=5.9  Score=39.99  Aligned_cols=74  Identities=20%  Similarity=0.272  Sum_probs=55.4

Q ss_pred             HHhhhhhhhhhhhhHHHHhhhhhHHHHHHHHhhHHHHHHHHHhhcchhhhHhh--hhHHHHHHHHHHHHhhcHHHH
Q 021632          159 LVNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILS--QKIEDLQEQIYGLEKRNKEYY  232 (310)
Q Consensus       159 ll~Ena~Lg~~~s~~~eEnk~~asEa~fmkr~a~ELArcvlkmredhrvc~l~--rKIe~Lq~qIy~lE~rnre~y  232 (310)
                      +-+||++|.-++.+++-|.++-.-|+--+-|+++|.-+-.....+.|.+-+.-  -=|..=|+.|-.||.+.+.+.
T Consensus       139 ~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~layqq~L~~eyQatf~eq~~ml~kRQ~yI~~LEsKVqDLm  214 (401)
T PF06785_consen  139 LREENQCLQLQLDALQQECGEKEEESQTLNRELAEALAYQQELNDEYQATFVEQHSMLDKRQAYIGKLESKVQDLM  214 (401)
T ss_pred             HHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchhhhHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999998888777777777755322110  013445788888888877753

>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=91.98  E-value=8.8  Score=41.69  Aligned_cols=129  Identities=22%  Similarity=0.266  Sum_probs=94.2

Q ss_pred             hcChhHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHhhhhhHH
Q 021632          104 SANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASE  183 (310)
Q Consensus       104 ~~~idelvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eEnk~~asE  183 (310)
                      ...+|.+-.+|--+.-|-..+.-++...+.+..+...-|+++|..|.-.+.+...|..++=+|.|++-......-....=
T Consensus       286 K~k~d~~~~eL~rk~~E~~~~qt~l~~~~~~~~d~r~hi~~lkesl~~ke~~~~~Lqsdve~Lr~rle~k~~~l~kk~~~  365 (775)
T PF10174_consen  286 KSKMDRLKLELSRKKSELEALQTRLETLEEQDSDMRQHIEVLKESLRAKEQEAEMLQSDVEALRFRLEEKNSQLEKKQAQ  365 (775)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            44477777777777777777777777777777888779999999999999999999999999999987544332221111


Q ss_pred             HHHHHHhhHHHHHH---HHHhhcchhhhHhhhhHHHHHHHHHHHHhhcHHHHHHHHH
Q 021632          184 AMFMRRKASELAKC---VLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVN  237 (310)
Q Consensus       184 a~fmkr~a~ELArc---vlkmredhrvc~l~rKIe~Lq~qIy~lE~rnre~yeql~~  237 (310)
                      +.-+..   |+++.   +-+|++.|.++=  +||..||++|-.||.-.++=..++..
T Consensus       366 ~~~~qe---E~~~~~~Ei~~l~d~~d~~e--~ki~~Lq~kie~Lee~l~ekd~ql~~  417 (775)
T PF10174_consen  366 IEKLQE---EKSRLQGEIEDLRDMLDKKE--RKINVLQKKIENLEEQLREKDRQLDE  417 (775)
T ss_pred             HHHHHH---HHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            222334   45554   667788888874  49999999999999888775554443

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 [].

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=91.69  E-value=13  Score=39.34  Aligned_cols=26  Identities=38%  Similarity=0.326  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHhhcHHHHHHHHHHH
Q 021632          214 IEDLQEQIYGLEKRNKEYYQMLVNRE  239 (310)
Q Consensus       214 Ie~Lq~qIy~lE~rnre~yeql~~~E  239 (310)
                      +..++.+|..++.+-..+-..+....
T Consensus       905 ~~~l~~~~~~~~~~~~~l~~~~~~~~  930 (1164)
T TIGR02169       905 IEELEAQIEKKRKRLSELKAKLEALE  930 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444433333333333333

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.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=91.24  E-value=5.2  Score=42.74  Aligned_cols=130  Identities=20%  Similarity=0.196  Sum_probs=88.3

Q ss_pred             HHHHhhhhHHHHHHhhhhhhhhhhh-------HHHHHHH-----HHHHHHHHHHHH----------------HHHhhhhh
Q 021632          114 LVAKNVESEILVNQVNEMDHVCNES-------RRKIELL-----KSLMELLESERM----------------ILVNENVK  165 (310)
Q Consensus       114 lVa~nve~d~l~del~~~er~~~Es-------~rkieLl-----k~ll~vLesEr~----------------vll~Ena~  165 (310)
                      |-|+---|.-....+.++|+.+-+.       .+|..++     ...|+..+.++.                +..++.-.
T Consensus       347 LAAA~kAY~~yk~kl~~vEr~~~~~g~~~d~~rika~VIrG~~l~eal~~~~e~~~p~e~~~~~~~e~~ei~~~~~~i~~  426 (652)
T COG2433         347 LAAAYKAYLAYKPKLEKVERKLPELGIWKDVERIKALVIRGYPLAEALSKVKEEERPREKEGTEEEERREITVYEKRIKK  426 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHeecCCcHHHHHHHHHhhhccccccccccccccchhHHHHHHHH
Confidence            4455556777888888888888655       2344443     255555554443                25788899


Q ss_pred             hhhhhhhHHHHhhhhhHHHHHHHHhhHHHHHHHHHhhcchh-hhHhhhhHHHHHHHHHHHHhhcHHHHHHHHHHHHHHH
Q 021632          166 LGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYR-VCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVK  243 (310)
Q Consensus       166 Lg~~~s~~~eEnk~~asEa~fmkr~a~ELArcvlkmredhr-vc~l~rKIe~Lq~qIy~lE~rnre~yeql~~~E~e~~  243 (310)
                      ++-++..+.+||+.|..+..-||+.--+|=.-+-.+|...+ --...|+|+.++..|+.|+..-.+=+......+....
T Consensus       427 ~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~~~~~~~rei~~~~~~I~~L~~~L~e~~~~ve~L~~~l~  505 (652)
T COG2433         427 LEETVERLEEENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLA  505 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999966555444444444222 2234688999999999999766665554444444433

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=91.12  E-value=16  Score=38.33  Aligned_cols=24  Identities=21%  Similarity=0.404  Sum_probs=9.9

Q ss_pred             hHHHHHHHHHHHHhhcHHHHHHHH
Q 021632          213 KIEDLQEQIYGLEKRNKEYYQMLV  236 (310)
Q Consensus       213 KIe~Lq~qIy~lE~rnre~yeql~  236 (310)
                      .+..|+.++..++.+....-.++.
T Consensus       825 ~~~~l~~~~~~l~~~~~~~~~~l~  848 (1179)
T TIGR02168       825 RLESLERRIAATERRLEDLEEQIE  848 (1179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444333333333

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.

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

Probab=90.92  E-value=21  Score=36.57  Aligned_cols=165  Identities=22%  Similarity=0.197  Sum_probs=76.7

Q ss_pred             hhHHHHHHHHHhhhhHHHHHHhh-------hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHhhh
Q 021632          107 IDDLVAELVAKNVESEILVNQVN-------EMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKG  179 (310)
Q Consensus       107 idelvaelVa~nve~d~l~del~-------~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eEnk~  179 (310)
                      ++.+-.++-..+...+.|..||.       .+-.+...+...|.-|..-+..+.+|-.++..+-.+....++.+......
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            33334444444444444555443       33333334444555555555555555555444334433444444445555


Q ss_pred             hhHHHHHHHHhhHHHHHHHHHhhcchhhhHhhhhHHHHHHHHHHHHhhcHHHHHHHHH---HHHHHHhhhhccCCCCCCC
Q 021632          180 LASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVN---REQQVKEYENSWSNSNSTS  256 (310)
Q Consensus       180 ~asEa~fmkr~a~ELArcvlkmredhrvc~l~rKIe~Lq~qIy~lE~rnre~yeql~~---~E~e~~~~~~~~~~~~~~~  256 (310)
                      +.+|+--+|+.+..+-.=+.+.+.+         |+.....|..+|.|-...-..++.   .|.---..+..++.+.+++
T Consensus       377 l~~Eae~Ak~ea~~~~~E~~~~k~E---------~e~~ka~i~t~E~rL~aa~ke~eaaKasEa~Ala~ik~l~e~~~~~  447 (522)
T PF05701_consen  377 LSSEAEEAKKEAEEAKEEVEKAKEE---------AEQTKAAIKTAEERLEAALKEAEAAKASEALALAEIKALSESESSS  447 (522)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            6666666666554443344444442         444455555555554443333322   2222223334444444333


Q ss_pred             CCccccccccccccchhhhhhhhhHHHh
Q 021632          257 SSSSYVKEKSAQVTLESCFQSFEKIKLK  284 (310)
Q Consensus       257 ~s~sksk~~~~~v~~~~cfq~~~k~k~~  284 (310)
                      +.+.  .+.+++|+| +-|- ++.|.++
T Consensus       448 ~~~~--~~~~~~Vtl-s~eE-y~~L~~k  471 (522)
T PF05701_consen  448 RASD--SESSSKVTL-SLEE-YESLSKK  471 (522)
T ss_pred             cccc--cCCCCCeee-cHHH-HHHHHHH
Confidence            2222  126677887 4344 5556544

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

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

Probab=90.59  E-value=9.9  Score=32.78  Aligned_cols=72  Identities=18%  Similarity=0.186  Sum_probs=43.2

Q ss_pred             HHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHhhhhhHHHHHHH
Q 021632          110 LVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMR  188 (310)
Q Consensus       110 lvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eEnk~~asEa~fmk  188 (310)
                      +..++...+-....+.+|+.++++..++....+.-++.....+.       +.....+-++.++.+..+.+..|..-+.
T Consensus        79 ~~~e~~~~~~~l~~l~~el~~l~~~~~~~~~~l~~~~~~~~~~~-------~~~~~~~~~l~~l~~~~~~~~~e~~~l~  150 (191)
T PF04156_consen   79 LQGELSELQQQLQQLQEELDQLQERIQELESELEKLKEDLQELR-------ELLKSVEERLDSLDESIKELEKEIRELQ  150 (191)
T ss_pred             hhhhHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455566666666677777777777666666665555555444       4444555556666666666555555555

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 [].

>TIGR02168 SMC_prok_B chromosome segregation protein SMC, common bacterial type

Probab=90.34  E-value=22  Score=37.37  Aligned_cols=28  Identities=25%  Similarity=0.336  Sum_probs=11.2

Q ss_pred             hHHHHHHHHHHHHhhcHHHHHHHHHHHH
Q 021632          213 KIEDLQEQIYGLEKRNKEYYQMLVNREQ  240 (310)
Q Consensus       213 KIe~Lq~qIy~lE~rnre~yeql~~~E~  240 (310)
                      ++..++.++..++.....+-+++...+.
T Consensus       818 ~l~~~~~~~~~l~~~~~~l~~~~~~~~~  845 (1179)
T TIGR02168       818 EAANLRERLESLERRIAATERRLEDLEE  845 (1179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444443333333333333

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.

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

Probab=89.34  E-value=18  Score=33.38  Aligned_cols=74  Identities=22%  Similarity=0.211  Sum_probs=54.2

Q ss_pred             hcChhHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHh
Q 021632          104 SANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEEN  177 (310)
Q Consensus       104 ~~~idelvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eEn  177 (310)
                      -.-+|++..+....-++.+.+..++..+.+++.+......-+..-+..|..+.+..--.++.|.-++.++.+|.
T Consensus        60 r~~id~~~~eka~l~~e~~~l~~e~~~~r~k~e~e~~~~~~le~el~~lrk~ld~~~~~r~~le~~i~~L~eEl  133 (312)
T PF00038_consen   60 RRQIDDLSKEKARLELEIDNLKEELEDLRRKYEEELAERKDLEEELESLRKDLDEETLARVDLENQIQSLKEEL  133 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhhHHHHhhHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHhHHHHHHHHHHHHH
Confidence            45677888888888899999999998888888777666666666666666666665555666666666666643

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 ....

>PRK09039 hypothetical protein; Validated

Probab=89.01  E-value=14  Score=36.00  Aligned_cols=41  Identities=24%  Similarity=0.327  Sum_probs=25.4

Q ss_pred             hhhHhhhhHHHHHHH-------HHHHHhhcHHHHHHHHHHHHHHHhhh
Q 021632          206 RVCILSQKIEDLQEQ-------IYGLEKRNKEYYQMLVNREQQVKEYE  246 (310)
Q Consensus       206 rvc~l~rKIe~Lq~q-------Iy~lE~rnre~yeql~~~E~e~~~~~  246 (310)
                      .|=.|.+-|+.|++|       |..+|.+.++...++...+.++...+
T Consensus       138 ~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~  185 (343)
T PRK09039        138 QVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVAL  185 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455555555555554       55566777777777777666655543

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=88.94  E-value=30  Score=36.65  Aligned_cols=11  Identities=9%  Similarity=-0.022  Sum_probs=5.8

Q ss_pred             HHHHHHHHHhh
Q 021632           42 NGYITLLDRCR   52 (310)
Q Consensus        42 r~YraLAeRYd   52 (310)
                      ..|+.++++|.
T Consensus       204 ~~~~e~~~~~~  214 (1164)
T TIGR02169       204 RREREKAERYQ  214 (1164)
T ss_pred             HHHHHHHHHHH
Confidence            34555555553

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.

>PHA02562 46 endonuclease subunit; Provisional

Probab=88.65  E-value=23  Score=35.01  Aligned_cols=34  Identities=12%  Similarity=0.180  Sum_probs=24.6

Q ss_pred             hhHHHHHHHHHHHHhhcHHHHHHHHHHHHHHHhh
Q 021632          212 QKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEY  245 (310)
Q Consensus       212 rKIe~Lq~qIy~lE~rnre~yeql~~~E~e~~~~  245 (310)
                      +++..|++.|-.||.++.+..+.+.+.+.+.+..
T Consensus       358 ~~~~~l~~ei~~l~~~~~~~~~~l~~l~~~l~~~  391 (562)
T PHA02562        358 DKAKKVKAAIEELQAEFVDNAEELAKLQDELDKI  391 (562)
T ss_pred             HHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHH
Confidence            4677888888888888887777776666555443

>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=87.12  E-value=44  Score=35.36  Aligned_cols=72  Identities=24%  Similarity=0.258  Sum_probs=41.9

Q ss_pred             HHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHH-------HHHHHHHHHHHHHHhhhhhhhhhhhhHHHHhhhh
Q 021632          109 DLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLK-------SLMELLESERMILVNENVKLGYQVSAVMEENKGL  180 (310)
Q Consensus       109 elvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk-------~ll~vLesEr~vll~Ena~Lg~~~s~~~eEnk~~  180 (310)
                      +|........-++..|..++.+++..++....+.+-|+       ...+.|..|++.|..+++.+.-++..+.++++.+
T Consensus       154 eL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e~L~~~~kel~~~~e~l~~E~~~L~~q~~e~~~ri~~LEedi~~l  232 (546)
T PF07888_consen  154 ELLKENEQLEEEVEQLREEVERLEAELEQEEEEMEQLKQQQKELTESSEELKEERESLKEQLAEARQRIRELEEDIKTL  232 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444455556666677777777766544433333       3445566666666666666666666666665543

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 [].

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

Probab=85.99  E-value=23  Score=31.42  Aligned_cols=68  Identities=18%  Similarity=0.206  Sum_probs=48.0

Q ss_pred             HHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHhhh-hhHHHHHHHH
Q 021632          122 EILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKG-LASEAMFMRR  189 (310)
Q Consensus       122 d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eEnk~-~asEa~fmkr  189 (310)
                      .+|...|-+|+..+.++..-+.-....-..|+-+...+..+...+.-++-.++.-..+ ||.++.--|.
T Consensus        26 ~~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~   94 (221)
T PF04012_consen   26 KMLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKA   94 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4555566677777777777666666777777777777888888888888777665443 6666665555

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 [].

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

Probab=85.82  E-value=12  Score=38.98  Aligned_cols=12  Identities=67%  Similarity=0.830  Sum_probs=7.8

Q ss_pred             hHHHHHHHHHHH
Q 021632          213 KIEDLQEQIYGL  224 (310)
Q Consensus       213 KIe~Lq~qIy~l  224 (310)
                      +|.+||.|++.|
T Consensus       436 ~I~dLqEQlrDl  447 (493)
T KOG0804|consen  436 KITDLQEQLRDL  447 (493)
T ss_pred             HHHHHHHHHHhH
Confidence            666666666654

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

Probab=85.37  E-value=35  Score=32.62  Aligned_cols=32  Identities=22%  Similarity=0.310  Sum_probs=18.5

Q ss_pred             hHHHHHHHHHHHHhhcHHHHHHHHHHHHHHHh
Q 021632          213 KIEDLQEQIYGLEKRNKEYYQMLVNREQQVKE  244 (310)
Q Consensus       213 KIe~Lq~qIy~lE~rnre~yeql~~~E~e~~~  244 (310)
                      ++..|+.+...++....+..++......++.+
T Consensus       231 ~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e  262 (325)
T PF08317_consen  231 ELAELQEELEELEEKIEELEEQKQELLAEIAE  262 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566666666666666666555555555544

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

Probab=83.80  E-value=41  Score=32.03  Aligned_cols=124  Identities=23%  Similarity=0.249  Sum_probs=85.0

Q ss_pred             HhhcChhHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHH---------HHHHHHHHHHHHHHhhhhhhhhhhhh
Q 021632          102 AASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLK---------SLMELLESERMILVNENVKLGYQVSA  172 (310)
Q Consensus       102 ~~~~~idelvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk---------~ll~vLesEr~vll~Ena~Lg~~~s~  172 (310)
                      .+....+.+--.+++...+.+.+..+++..+..+++...++.-..         .-..-|..|..++-...+.|.+.++.
T Consensus        35 k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~le~el~~  114 (239)
T COG1579          35 KAKAELEALNKALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAE  114 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            335566677777888888888889999888888888876665444         33456777777788888889999999


Q ss_pred             HHHHhhhhhHHHHHHHHhhHHHHHHHHHhhc--chhhhHhhhhHHHHHHHHHHHH
Q 021632          173 VMEENKGLASEAMFMRRKASELAKCVLRMRE--DYRVCILSQKIEDLQEQIYGLE  225 (310)
Q Consensus       173 ~~eEnk~~asEa~fmkr~a~ELArcvlkmre--dhrvc~l~rKIe~Lq~qIy~lE  225 (310)
                      ++++-.++..+..-++.+-..+=+++..-+.  +-.+--..++...+..|+..|.
T Consensus       115 l~~~~~~l~~~i~~l~~~~~~~e~~~~e~~~~~e~e~~~i~e~~~~~~~~~~~L~  169 (239)
T COG1579         115 LMEEIEKLEKEIEDLKERLERLEKNLAEAEARLEEEVAEIREEGQELSSKREELK  169 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9998888888888888755555555555444  2233333333444444444443

>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=83.61  E-value=14  Score=31.63  Aligned_cols=75  Identities=24%  Similarity=0.286  Sum_probs=54.5

Q ss_pred             HhhcChhHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHH
Q 021632          102 AASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEE  176 (310)
Q Consensus       102 ~~~~~idelvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eE  176 (310)
                      .....++++..+++.+.=+-+.|.+-|=-++.--.+-..+|.=|..-+...+.|+...+.|.-.|.-+|..+..+
T Consensus        66 ~~~~~~~elA~dIi~kakqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~i~~  140 (144)
T PF11221_consen   66 EFEENIKELATDIIRKAKQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELLKQVQELIRE  140 (144)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            447778899999999999999999988766554444456666666677777777777777776766666665554

Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.

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

Probab=83.16  E-value=17  Score=34.96  Aligned_cols=86  Identities=22%  Similarity=0.297  Sum_probs=55.7

Q ss_pred             hcChhHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHhhhhhHH
Q 021632          104 SANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASE  183 (310)
Q Consensus       104 ~~~idelvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eEnk~~asE  183 (310)
                      ..+++++..++-..-.|...+..||..+|+...+...+++-++.-.+.|+.+......+.-.+-..+...+++...+..-
T Consensus        42 ~~~~~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q  121 (314)
T PF04111_consen   42 EEDIEELEEELEKLEQEEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQ  121 (314)
T ss_dssp             HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556677777777777778888888777777777777777777777776666666666666666666555555444444


Q ss_pred             HHHHHH
Q 021632          184 AMFMRR  189 (310)
Q Consensus       184 a~fmkr  189 (310)
                      ..++.+
T Consensus       122 ~~~~~~  127 (314)
T PF04111_consen  122 YEYASN  127 (314)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444444

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.

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

Probab=83.16  E-value=30  Score=29.95  Aligned_cols=30  Identities=30%  Similarity=0.336  Sum_probs=14.1

Q ss_pred             HhhhhHHHHHHHHHHHHhhcHHHHHHHHHH
Q 021632          209 ILSQKIEDLQEQIYGLEKRNKEYYQMLVNR  238 (310)
Q Consensus       209 ~l~rKIe~Lq~qIy~lE~rnre~yeql~~~  238 (310)
                      -+.|||..|+.++-.++.+-++--+.|..+
T Consensus        77 ~l~rriq~LEeele~ae~~L~e~~ekl~e~  106 (143)
T PF12718_consen   77 QLNRRIQLLEEELEEAEKKLKETTEKLREA  106 (143)
T ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555554444444444433

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 [].

>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=82.36  E-value=34  Score=30.09  Aligned_cols=68  Identities=22%  Similarity=0.246  Sum_probs=41.9

Q ss_pred             HhhhhhhhhhhhhHHHHhhhhhHHHHHHHHhhHHHHHHHHHhhcchhhhHhhhhHHHHHHHHHHHHhhcHHHHHHHHHHH
Q 021632          160 VNENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNRE  239 (310)
Q Consensus       160 l~Ena~Lg~~~s~~~eEnk~~asEa~fmkr~a~ELArcvlkmredhrvc~l~rKIe~Lq~qIy~lE~rnre~yeql~~~E  239 (310)
                      -.++-.|...++.+-.+...+..|+..++..=..|.                +.....|++|-.||.+|..+-..|...|
T Consensus        51 k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~----------------k~lq~~q~kv~eLE~~~~~~~~~l~~~E  114 (140)
T PF10473_consen   51 KAEIETLEEELEELTSELNQLELELDTLRSEKENLD----------------KELQKKQEKVSELESLNSSLENLLQEKE  114 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            444445555555555555555666655555222222                2445668888888888888888887777


Q ss_pred             HHHH
Q 021632          240 QQVK  243 (310)
Q Consensus       240 ~e~~  243 (310)
                      .+..
T Consensus       115 ~ek~  118 (140)
T PF10473_consen  115 QEKV  118 (140)
T ss_pred             HHHH
Confidence            7743

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

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

Probab=81.87  E-value=19  Score=31.82  Aligned_cols=48  Identities=21%  Similarity=0.304  Sum_probs=31.0

Q ss_pred             HHHHhhcchhhhHhhhhHHHHHHHHHHHHhhcHHHHHHHHHHHHHHHhhh
Q 021632          197 CVLRMREDYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEYE  246 (310)
Q Consensus       197 cvlkmredhrvc~l~rKIe~Lq~qIy~lE~rnre~yeql~~~E~e~~~~~  246 (310)
                      .+--..+.|-..=+  -...|+.++..|+.-|+++-+..+..-.+.-+..
T Consensus       145 ~~e~l~DE~~~L~l--~~~~~e~k~~~l~~En~~Lv~Rwm~~k~~eAe~m  192 (194)
T PF08614_consen  145 ANEILQDELQALQL--QLNMLEEKLRKLEEENRELVERWMQRKAQEAERM  192 (194)
T ss_dssp             HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33334444433323  3567899999999999999887776665554444

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.

>KOG0996 consensus Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning]

Probab=80.77  E-value=32  Score=39.58  Aligned_cols=70  Identities=17%  Similarity=0.184  Sum_probs=42.8

Q ss_pred             ChhHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHH
Q 021632          106 NIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVME  175 (310)
Q Consensus       106 ~idelvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~e  175 (310)
                      ..+.+...+--.+...+.+.+++..|+.+..+..+.|..++.-+..|.++-..+..+.+-|..++..++.
T Consensus       779 ~v~~le~~l~~~~~~~~~~~~~~~~~ee~~~~lr~~~~~l~~~l~~~~~~~k~~~~~~~~l~~~i~~~E~  848 (1293)
T KOG0996|consen  779 SVEKLERALSKMSDKARQHQEQLHELEERVRKLRERIPELENRLEKLTASVKRLAELIEYLESQIAELEA  848 (1293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555556666677777777777777777777766666666666655555555555554444333

>PRK09039 hypothetical protein; Validated

Probab=80.64  E-value=59  Score=31.72  Aligned_cols=21  Identities=14%  Similarity=0.271  Sum_probs=11.8

Q ss_pred             HHHHHhhhhhhhhhhhHHHHH
Q 021632          123 ILVNQVNEMDHVCNESRRKIE  143 (310)
Q Consensus       123 ~l~del~~~er~~~Es~rkie  143 (310)
                      +|.++|+.++..+.+...+|-
T Consensus        43 fLs~~i~~~~~eL~~L~~qIa   63 (343)
T PRK09039         43 FLSREISGKDSALDRLNSQIA   63 (343)
T ss_pred             HHHHHHhhHHHHHHHHHHHHH
Confidence            355566666666655555443

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

Probab=80.32  E-value=37  Score=38.66  Aligned_cols=84  Identities=18%  Similarity=0.193  Sum_probs=59.5

Q ss_pred             hhhhhhhhhhhhHHHHhhhhhHHHHHHHHhhHHHHHHHHHhhc---chhhhHhhhhHHHHHHHHHHHHhhcHHHHHHHHH
Q 021632          161 NENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMRE---DYRVCILSQKIEDLQEQIYGLEKRNKEYYQMLVN  237 (310)
Q Consensus       161 ~Ena~Lg~~~s~~~eEnk~~asEa~fmkr~a~ELArcvlkmre---dhrvc~l~rKIe~Lq~qIy~lE~rnre~yeql~~  237 (310)
                      +|.-.|...++.+..|+-+.-+|+..|++-++||+-++-+|-.   .|+--+-  -+.-+-.++-.|++.|+.+-+--.=
T Consensus       205 ~eLddleae~~klrqe~~e~l~ea~ra~~yrdeldalre~aer~d~~ykerlm--Ds~fykdRveelkedN~vLleekeM  282 (1195)
T KOG4643|consen  205 NELDDLEAEISKLRQEIEEFLDEAHRADRYRDELDALREQAERPDTTYKERLM--DSDFYKDRVEELKEDNRVLLEEKEM  282 (1195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHhhhcCCCccchhhh--hhHHHHHHHHHHHhhhHHHHHHHHH
Confidence            4444555566667777777888899999999999988887765   5665433  3444678888888888888776555


Q ss_pred             HHHHHHhhh
Q 021632          238 REQQVKEYE  246 (310)
Q Consensus       238 ~E~e~~~~~  246 (310)
                      .+.|+..+-
T Consensus       283 LeeQLq~lr  291 (1195)
T KOG4643|consen  283 LEEQLQKLR  291 (1195)
T ss_pred             HHHHHHHHH
Confidence            666665554

---

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	310
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-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 = 53.7 bits (128), Expect = 3e-08
 Identities = 50/322 (15%), Positives = 113/322 (35%), Gaps = 62/322 (19%)

Query: 22  RAEWYYQKRPQLLALLKDLYNGYITLLDRCRNHKKH--HFRNGSSETIITA--SSSADAE 77
           R      +  +LL   K   N  + LL+    + K    F N S + ++T       D  
Sbjct: 226 RIHSIQAELRRLLKS-KPYENCLLVLLNVQ--NAKAWNAF-NLSCKILLTTRFKQVTDFL 281

Query: 78  SDAEST-ISYQQQQITTT---TATMAAAAASANIDDLVAE----------LVAKNVESEI 123
           S A +T IS     +T T     ++          DL  E          ++A+++   +
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL 341

Query: 124 LVNQVNEMDHVCNESRRKIELLKSLMELLES-------ERMILVNENVKLGYQVSAVMEE 176
                +   HV  +  +   +++S + +LE        +R+ +   +  +   + +++  
Sbjct: 342 --ATWDNWKHVNCD--KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397

Query: 177 NKGLASEAMFMRRKASELAK--CVLRMREDYRVCI--LSQKIEDLQEQIYGLEKRNKEYY 232
           +  + S+ M +    ++L K   V +  ++  + I  +  +++   E  Y L +      
Sbjct: 398 DV-IKSDVMVV---VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS----- 448

Query: 233 QMLVNREQQVKEYENSWSNSNSTSSSSSYV----------KEKSAQVTL-ESCFQSFEKI 281
             +V+     K +++   +         Y            E   ++TL    F  F  +
Sbjct: 449 --IVDHYNIPKTFDS---DDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFL 503

Query: 282 KLKKKKGSSNWWERVKKADFFN 303
           + K +  S+ W       +   
Sbjct: 504 EQKIRHDSTAWNASGSILNTLQ 525

>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 = 40.2 bits (93), Expect = 7e-04
 Identities = 25/155 (16%), Positives = 58/155 (37%), Gaps = 41/155 (26%)

Query: 36  LLKDLYNGYITLLDRCRNHKKHHFRNGSSETIITASSSADAESDAESTISYQ-----QQQ 90
           L+    + Y        +H  HH +N               E      + +      +Q+
Sbjct: 464 LIPPYLDQYFY------SHIGHHLKNIEH-----------PERMTLFRMVFLDFRFLEQK 506

Query: 91  ITTTTATMAAAAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLME 150
           I   +    A  AS +I + + +L  K  +            ++C+   +   L+ ++++
Sbjct: 507 IRHDST---AWNASGSILNTLQQL--KFYK-----------PYICDNDPKYERLVNAILD 550

Query: 151 LLES-ERMILVNENVKLGYQVSAVMEENKGLASEA 184
            L   E  ++ ++   L  ++ A+M E++ +  EA
Sbjct: 551 FLPKIEENLICSKYTDL-LRI-ALMAEDEAIFEEA 583

>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 = 41.7 bits (98), Expect = 3e-04
 Identities = 24/147 (16%), Positives = 61/147 (41%), Gaps = 4/147 (2%)

Query: 101  AAASANIDDLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILV 160
                  + DL   L  +  +++ L    N+ + + +E   +++  +   + LE  +  L 
Sbjct: 1007 KLLEERVSDLTTNLAEEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIKRKLE 1066

Query: 161  NENVKLGYQVSAVMEENKGLASEAMFMRRKASELAKCVLRMREDYRVC-ILSQKIEDLQE 219
             E+  L  Q++ +  +   L ++   + +K  EL   + R+ ++        +KI +L+ 
Sbjct: 1067 GESSDLHEQIAELQAQIAELKAQ---LAKKEEELQAALARLEDETSQKNNALKKIRELES 1123

Query: 220  QIYGLEKRNKEYYQMLVNREQQVKEYE 246
             I  L++  +         E+Q ++  
Sbjct: 1124 HISDLQEDLESEKAARNKAEKQKRDLS 1150

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	310
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	93.89
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	88.39
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	87.93
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	87.55
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	81.84
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	81.4

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

Probab=93.89  E-value=2.1  Score=37.89  Aligned_cols=16  Identities=13%  Similarity=0.459  Sum_probs=10.6

Q ss_pred             CchHHHhhhccc-cccc
Q 021632          289 SSNWWERVKKAD-FFNC  304 (310)
Q Consensus       289 ~~~~w~~vk~~d-~f~c  304 (310)
                      +|..+..|+..| +++|
T Consensus       209 ppq~~~~i~~~~~Iv~C  225 (256)
T 3na7_A          209 NDKIYTEVLTSGDMITC  225 (256)
T ss_dssp             CHHHHHHHHHSSSCEEC
T ss_pred             CHHHHHHHHCCCCEEEC
Confidence            567777777654 5555

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

Probab=88.39  E-value=13  Score=32.85  Aligned_cols=84  Identities=12%  Similarity=0.056  Sum_probs=34.8

Q ss_pred             HHHHHHHHHhhhhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHH--HHhhhhhHHHHH
Q 021632          109 DLVAELVAKNVESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVM--EENKGLASEAMF  186 (310)
Q Consensus       109 elvaelVa~nve~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~--eEnk~~asEa~f  186 (310)
                      .+...+-..-.+.+.+.+++.....++......++=++..+..++.+...+-....+..-++..+-  .|..++..|.-+
T Consensus        22 ~l~~~~~~lp~el~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~~v~~~kE~~aL~kEie~  101 (256)
T 3na7_A           22 SLEPLIREKRKDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMSEIKSERELRSLNIEEDI  101 (256)
T ss_dssp             HTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHH
Confidence            333333333344444444444444444444444444444444444444444333333333332221  122235555556


Q ss_pred             HHHhhH
Q 021632          187 MRRKAS  192 (310)
Q Consensus       187 mkr~a~  192 (310)
                      ++++-.
T Consensus       102 ~~~~i~  107 (256)
T 3na7_A          102 AKERSN  107 (256)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555333

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

Probab=87.93  E-value=9.2  Score=30.68  Aligned_cols=26  Identities=8%  Similarity=0.156  Sum_probs=11.0

Q ss_pred             HHHHHHhhhhHHHHHHhhhhhhhhhh
Q 021632          112 AELVAKNVESEILVNQVNEMDHVCNE  137 (310)
Q Consensus       112 aelVa~nve~d~l~del~~~er~~~E  137 (310)
                      ....+...+.+.+..++...+..+.+
T Consensus         6 ~~~~~l~~~~~~~~~~~~~l~~~l~~   31 (284)
T 1c1g_A            6 KKMQMLKLDKENALDRADEAEADKKA   31 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444433

>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=87.55  E-value=9  Score=36.26  Aligned_cols=35  Identities=23%  Similarity=0.215  Sum_probs=24.8

Q ss_pred             hHHHHHHHHHHHHhhcHHHHHHHHHHHHHHHhhhh
Q 021632          213 KIEDLQEQIYGLEKRNKEYYQMLVNREQQVKEYEN  247 (310)
Q Consensus       213 KIe~Lq~qIy~lE~rnre~yeql~~~E~e~~~~~~  247 (310)
                      +++.|+.+|....++-.+..+++..+.+++++...
T Consensus       545 ~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~  579 (597)
T 3oja_B          545 ENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEA  579 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            55566666666666777777777778777777764

>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=81.84  E-value=3.5  Score=43.79  Aligned_cols=23  Identities=13%  Similarity=0.160  Sum_probs=14.4

Q ss_pred             HhhhhcHHHHHHHHHHHHHHHHH
Q 021632           25 WYYQKRPQLLALLKDLYNGYITL   47 (310)
Q Consensus        25 mYYqkRPeLi~~vee~yr~YraL   47 (310)
                      +-..+...++..++-.+|+|.+-
T Consensus       786 ~r~~~l~~~~~~iQ~~~Rg~l~R  808 (1184)
T 1i84_S          786 ERDLKITDVIIAFQAQCRGYLAR  808 (1184)
T ss_dssp             HHHHHTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445556777777777777543

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

Probab=81.40  E-value=9.9  Score=31.71  Aligned_cols=78  Identities=10%  Similarity=0.018  Sum_probs=53.7

Q ss_pred             HHHHHHHhh--hhHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHhhhhhHHHHHHH
Q 021632          111 VAELVAKNV--ESEILVNQVNEMDHVCNESRRKIELLKSLMELLESERMILVNENVKLGYQVSAVMEENKGLASEAMFMR  188 (310)
Q Consensus       111 vaelVa~nv--e~d~l~del~~~er~~~Es~rkieLlk~ll~vLesEr~vll~Ena~Lg~~~s~~~eEnk~~asEa~fmk  188 (310)
                      ++=+.|.|+  |+-.+..+...+++++.+-.++|.-+|.-+..+..+-+.+-.++..|--.+..++.+++.+.+|+.+-+
T Consensus        58 ~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~~~~  137 (138)
T 3hnw_A           58 RTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELNDSK  137 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            344555554  455556666666777777677777777777777777777777777777778888888777777766543

---

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

No hit with probability above 80.00