Citrus Sinensis ID: 024294

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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-------27
Protein Sequence
MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSVLGSTRMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFNIY
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccEEccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccEEcHcccccEEEEcccccHHHcccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mkkedapdkgrtlsvdpnvprwvcqncrhflcivgvdsyadkylndssrstmhgssihasnsvlgstrmdnsfvvlpkqrpqshgvpprprgssaqseasqsgkamdESFVVIYKsesasdgggphipppeggtngpmqpnnsgfhSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFNIY
Flexible Loop (DISEMBL)
mkkedapdkgrtlsvdpnvprwVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSVLGSTRMDNSFVVLPKQrpqshgvpprprgssAQSEASQSGKAMDESFVVIYKSESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSqtqveqplCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAElkelelkskrfkeleeryffniy
Low Complexity Region (SEG)
MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSVLGSTRMDNSFVVLPKQRPQSHGVPPRPRgssaqseasqsgKAMDESFVVIYKSESASDgggphipppeggTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLkeklkieeeerkleaaieeteKQNAEVNAELKELELKSKRFKELEERYFFNIY
Disordered region (IsUnstruct)
*****************NVPRWVCQNCRHFLCIVGVDSYADKYL******************************************************************VVI********************************HSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVL*****************************************************YFF***
Disordered Region (DISOPRED)
****************PNVPRWVCQNCRHFLCIVGVDSYADKYLN*********************************************************************************************************VLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEAC***************************************KQNAEVNA*************ELEERYFFNIY
Disordered Region (DISEMBL)
************LSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSVLGSTRMDNSFVVLPK***************************MDESFVVIYKSESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFNIY
Disordered Region (DISPRO)
*************SVDPNVPRWVCQNCRHFLCIVGVDSYADKYLN***************************************************************SF****K*****************************FHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFNIY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSVLGSTRMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxYFFNIY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	269	2.2.26 [Sep-21-2011]
Q9M367	517	Beclin-1-like protein OS=	yes	no	0.985	0.512	0.726	1e-103
Q6GP52	445	Beclin-1 OS=Xenopus laevi	N/A	no	0.687	0.415	0.247	2e-07
Q4A1L3	445	Beclin-1 OS=Xenopus tropi	yes	no	0.687	0.415	0.247	3e-07
Q54JI9	855	Beclin-1-like protein B O	yes	no	0.401	0.126	0.324	2e-06
Q5ZKS6	447	Beclin-1 OS=Gallus gallus	yes	no	0.472	0.284	0.25	4e-06
Q02948	557	Vacuolar protein sorting-	yes	no	0.278	0.134	0.266	1e-05
A8MW95	431	Putative beclin-1-like pr	yes	no	0.572	0.357	0.265	3e-05
Q91XJ1	448	Beclin-1 OS=Rattus norveg	no	no	0.460	0.276	0.256	5e-05
O88597	448	Beclin-1 OS=Mus musculus	yes	no	0.460	0.276	0.256	9e-05
P87117	464	Vacuolar protein sorting-	yes	no	0.408	0.237	0.255	0.0001

>sp|Q9M367|BECN1_ARATH Beclin-1-like protein OS=Arabidopsis thaliana GN=At3g61710 PE=2 SV=2

 Score =  375 bits (964), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 194/267 (72%), Positives = 222/267 (83%), Gaps = 2/267 (0%)

Query: 1   MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHAS 60
           M+KE+ PDK RT+ +DPN+P+WVCQNC H L IVGVDSYA K+ ND   S   GSSIH +
Sbjct: 1   MRKEEIPDKSRTIPIDPNLPKWVCQNCHHSLTIVGVDSYAGKFFNDPPPSATQGSSIHGA 60

Query: 61  NSVLGSTRMDNSFVVLPKQRP-QSHGVPPRPRG-SSAQSEASQSGKAMDESFVVIYKSES 118
           NSVLGSTRMDNSFVVLP+ +P QS G+PPRPRG SS Q +A+QSGKAM+ESFVV+YKSE 
Sbjct: 61  NSVLGSTRMDNSFVVLPRHKPPQSQGIPPRPRGASSPQPDATQSGKAMEESFVVVYKSEP 120

Query: 119 ASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLS 178
            SD GG H    E G NGP+  N SGF++TI VL RAF+IA +QTQVEQPLCLECMRVLS
Sbjct: 121 VSDSGGSHNLSLEVGQNGPLHSNTSGFNATINVLTRAFDIARTQTQVEQPLCLECMRVLS 180

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEK 238
           DKL+KEV+DVTRD+EAYEAC+QRLEGE +DVLSEADFLKEK KIEEEERKL AAIEETEK
Sbjct: 181 DKLEKEVEDVTRDVEAYEACVQRLEGETQDVLSEADFLKEKKKIEEEERKLVAAIEETEK 240

Query: 239 QNAEVNAELKELELKSKRFKELEERYF 265
           QNAEVN +LKELE K  RF ELE+RY+
Sbjct: 241 QNAEVNHQLKELEFKGNRFNELEDRYW 267

Arabidopsis thaliana (taxid: 3702)

>sp|Q6GP52|BECN1_XENLA Beclin-1 OS=Xenopus laevis GN=becn1 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 97/214 (45%), Gaps = 29/214 (13%)

Query: 68  RMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGGGPHI 127
           ++D SF +L K   Q    P     +    +  +    ++E+F     +E+ +DG    +
Sbjct: 23  KLDTSFKILDKVTMQELTAPLVTTAAVKPGDIQEVDSNIEETF-----AENRTDGVSRRL 77

Query: 128 PPP----------------EGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCL 171
            PP                E    G M+         + V    F+I + QT V+ PLC 
Sbjct: 78  IPPARMMSTESATSFTLIGEASDGGTME----NLSRRLKVTGDLFDIMSGQTDVDHPLCE 133

Query: 172 ECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLK-IEEEERKLE 230
           EC   L D+LD +++    + + Y+ CL+ LE    D   + + L+ KLK + E+E +L 
Sbjct: 134 ECTDTLLDQLDTQLNITENECQNYKRCLEILERMNED---DKEKLEAKLKELAEDEERLI 190

Query: 231 AAIEETEKQNAEVNAELKELELKSKRFKELEERY 264
             +EE E+    V  +++++  +++R ++ E RY
Sbjct: 191 QELEEVERNRELVAKDIEKVREEAERLEQEEARY 224

Plays a central role in autophagy. Required for the abcission step in cytokinesis. May play a role in antiviral host defense.

Xenopus laevis (taxid: 8355)

>sp|Q4A1L3|BECN1_XENTR Beclin-1 OS=Xenopus tropicalis GN=becn1 PE=2 SV=1

 Score = 55.8 bits (133), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 53/214 (24%), Positives = 97/214 (45%), Gaps = 29/214 (13%)

Query: 68  RMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGGGPHI 127
           ++D SF +L K   Q    P     +    +  +    ++E+F     +E+ +DG    +
Sbjct: 23  KLDTSFKILDKVTMQELTAPLVTTAAVKPGDIQEVDSNIEETF-----AENRTDGVSRRL 77

Query: 128 PPP----------------EGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCL 171
            PP                E    G M+         + V    F+I + QT V+ PLC 
Sbjct: 78  IPPARMMSTESATSFTLIGEASDGGTME----NLSRRLKVTGDLFDIMSGQTDVDHPLCE 133

Query: 172 ECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLK-IEEEERKLE 230
           EC   L D+LD +++    + + Y+ CL+ LE    D   + + L+ KLK + E+E +L 
Sbjct: 134 ECTDTLLDQLDTQLNITENECQNYKRCLEILERMNED---DKEKLEAKLKELAEDEDRLI 190

Query: 231 AAIEETEKQNAEVNAELKELELKSKRFKELEERY 264
             +EE E+    V  +++++  +++R ++ E RY
Sbjct: 191 QELEEVERNRELVAKDIEKVREEAERLEQEEARY 224

Plays a central role in autophagy. Required for the abcission step in cytokinesis. May play a role in antiviral host defense.

Xenopus tropicalis (taxid: 8364)

>sp|Q54JI9|BECNB_DICDI Beclin-1-like protein B OS=Dictyostelium discoideum GN=atg6B PE=3 SV=1

 Score = 52.8 bits (125), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 58/111 (52%), Gaps = 3/111 (2%)

Query: 156 FEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLE-GEARDVLSEAD 214
           F+IAT     + PLCLEC ++   +L+ E   +  ++  Y A L++LE G+  + L E  
Sbjct: 491 FKIATDLINYDLPLCLECTKLTIGELEDEGSILDGEVSIYSAYLKQLEKGKTEEDLEELG 550

Query: 215 FLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYF 265
             KE   + EEE +L   IE T ++  EV     +L+ +    K LE+ Y+
Sbjct: 551 --KEMTLLCEEEEQLRLMIENTHQERKEVEQLTLQLQDRIATLKSLEDSYW 599

Involved in autophagy. May be required to recruit the atg8-phosphatidylinositol conjugate and the atg12-atg5 conjugate to the pre-autophagosomal structure.

Dictyostelium discoideum (taxid: 44689)

>sp|Q5ZKS6|BECN1_CHICK Beclin-1 OS=Gallus gallus GN=BECN1 PE=2 SV=1

 Score = 52.0 bits (123), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 38/152 (25%), Positives = 61/152 (40%), Gaps = 25/152 (16%)

Query: 68  RMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGGGPHI 127
           ++D SF +L +   Q    PP     +   +A +     +E+F     +E   DG     
Sbjct: 25  KLDTSFKILDRLTIQELTAPPLTAAPARPGDAQEESALSEEAF-----TEGRQDGVSRRF 79

Query: 128 PPP----------------EGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCL 171
            PP                E    G M+         + V    F+I + QT V+ PLC 
Sbjct: 80  IPPARMMSTESANSFTLIGEASDGGTME----NLSRRLKVTGDLFDIMSGQTDVDHPLCE 135

Query: 172 ECMRVLSDKLDKEVDDVTRDIEAYEACLQRLE 203
           EC   L D+LD +++    + + Y+ CL+ LE
Sbjct: 136 ECTDTLLDQLDTQLNITENECQNYKRCLEILE 167

Plays a central role in autophagy. Required for the abcission step in cytokinesis. May play a role in antiviral host defense.

Gallus gallus (taxid: 9031)

>sp|Q02948|VPS30_YEAST Vacuolar protein sorting-associated protein 30 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=VPS30 PE=1 SV=1

 Score = 50.8 bits (120), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)

Query: 135 NGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEA 194
           N  +Q N+    + +  +   F I +SQT ++ P+C +C  +L ++L  E DD  ++ + 
Sbjct: 147 NQQIQLNSKTLSTQVNAMTNVFNILSSQTNIDFPICQDCCNILINRLKSEYDDAIKERDT 206

Query: 195 YEACLQRLEGEARDV 209
           Y   L +LE + +++
Sbjct: 207 YAQFLSKLESQNKEI 221

Required for cytoplasm to vacuole transport (Cvt) and autophagy as a part of the autophagy-specific VPS34 PI3-kinase complex I. This complex is essential to recruit the ATG8-phosphatidylinositol conjugate and the ATG12-ATG5 conjugate to the pre-autophagosomal structure. Also involved in endosome-to-Golgi retrograde transport as part of the VPS34 PI3-kinase complex II. This second complex is required for the endosome-to-Golgi retrieval of PEP1 and KEX2, and the recruitment of VPS5 and VPS7, two components of the retromer complex, to endosomal membranes (probably through the synthesis of a specific pool of phosphatidylinositol 3-phosphate recruiting the retromer to the endosomes).

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|A8MW95|BECP1_HUMAN Putative beclin-1-like protein OS=Homo sapiens GN=BECN1P1 PE=5 SV=2

 Score = 49.3 bits (116), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 77/173 (44%), Gaps = 19/173 (10%)

Query: 82  QSHGVPPRPRGSSAQSEASQS---GKAMDESFVVIYKSESASDGGGPHIPPPEGGTNG-- 136
           +S  +P  P  +S Q+E   +   G    E    +  +E   DG     PP +G  +   
Sbjct: 22  ESRSLPAAPAPTSGQAEPGDTREPGVTTRE----VTDAEEQQDGASSRSPPGDGSVSKGH 77

Query: 137 ----PMQPNNSGFHSTITVLKRA---FEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVT 189
                +       H   ++ K A   F+I + Q  V+ PLC EC   L ++LD ++    
Sbjct: 78  ANIFTLLGELGAMHMLSSIQKAAGDIFDIVSGQAVVDHPLCEECTDSLLEQLDIQLALTE 137

Query: 190 RDIEAYEACLQRLEGEARDVLSEADFLKEKLK-IEEEERKLEAAIEETEKQNA 241
            D + Y+ CL+   GE      EA  L+ +L+ +E EE +L   +E+ ++ NA
Sbjct: 138 ADSQNYQRCLE--TGELATSEDEAAALRAELRDLELEEARLVQELEDVDRNNA 188

May play a role in autophagy and antiviral host defense.

Homo sapiens (taxid: 9606)

>sp|Q91XJ1|BECN1_RAT Beclin-1 OS=Rattus norvegicus GN=Becn1 PE=1 SV=1

 Score = 48.5 bits (114), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 40/156 (25%), Positives = 64/156 (41%), Gaps = 32/156 (20%)

Query: 68  RMDNSFVVLPKQRPQSHGVP----PRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGG 123
           ++D SF +L +   Q    P     + +   +Q E + SG   +E F+     E+  DG 
Sbjct: 25  KLDTSFKILDRVTIQELTAPLLTTAQAKPGESQEEEANSG---EEPFI-----ETRQDGV 76

Query: 124 GPHIPPP----------------EGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQ 167
                PP                E    G M+         + V    F+I + QT V+ 
Sbjct: 77  SRRFIPPARMMSTESANSFTLIGEASDGGTME----NLSRRLKVTGDLFDIMSGQTDVDH 132

Query: 168 PLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLE 203
           PLC EC   L D+LD +++    + + Y+ CL+ LE
Sbjct: 133 PLCEECTDTLLDQLDTQLNVTENECQNYKRCLEMLE 168

Plays a central role in autophagy. Required for the abcission step in cytokinesis. May play a role in antiviral host defense.

Rattus norvegicus (taxid: 10116)

>sp|O88597|BECN1_MOUSE Beclin-1 OS=Mus musculus GN=Becn1 PE=1 SV=3

 Score = 47.8 bits (112), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 40/156 (25%), Positives = 63/156 (40%), Gaps = 32/156 (20%)

Query: 68  RMDNSFVVLPKQRPQSHGVP----PRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGG 123
           ++D SF +L +   Q    P     + +    Q E + SG   +E F+     E+  DG 
Sbjct: 25  KLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEEEANSG---EEPFI-----ETRQDGV 76

Query: 124 GPHIPPP----------------EGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQ 167
                PP                E    G M+         + V    F+I + QT V+ 
Sbjct: 77  SRRFIPPARMMSTESANSFTLIGEASDGGTME----NLSRRLKVTGDLFDIMSGQTDVDH 132

Query: 168 PLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLE 203
           PLC EC   L D+LD +++    + + Y+ CL+ LE
Sbjct: 133 PLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILE 168

Plays a central role in autophagy. Required for the abcission step in cytokinesis. May play a role in antiviral host defense.

Mus musculus (taxid: 10090)

>sp|P87117|YDKA_SCHPO Vacuolar protein sorting-associated protein atg6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=atg6 PE=3 SV=4

 Score = 47.0 bits (110), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/145 (25%), Positives = 64/145 (44%), Gaps = 35/145 (24%)

Query: 115 KSESASDGGGPHIPPPEGGT--------------------NGPMQPNNSGFHSTITVLKR 154
           K+ S  D    ++PPPE  T                    N P + N+  F   I +  R
Sbjct: 69  KTISEGDYNFDNVPPPELRTPTLDSFVVLPAAKDGYEEEKNSPEEVNDL-FSWKIEIYNR 127

Query: 155 AFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEAD 214
            F++ +S+T+V+ PLC+EC  +L++++ K               L+ L+ E +   +  +
Sbjct: 128 IFDLLSSKTKVDHPLCVECAELLTEEMSK--------------TLRALKEEKKMYFNYDN 173

Query: 215 FLKEKLKIEEEERKLEAAIEETEKQ 239
           FL  +   EE    L++ I+E  KQ
Sbjct: 174 FLSSQTVHEENTAALDSEIDELMKQ 198

Required for cytoplasm to vacuole transport (Cvt) and autophagy as a part of the autophagy-specific vps34 PI3-kinase complex I. Also involved in endosome-to-Golgi retrograde transport as part of the vps34 PI3-kinase complex II.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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	269
255564727	523	Beclin-1, putative [Ricinus communis] gi	0.985	0.506	0.814	1e-111
224067974	516	predicted protein [Populus trichocarpa]	0.985	0.513	0.779	1e-110
73587480	505	beclin 1 protein [Malus x domestica]	0.959	0.510	0.731	1e-110
225454518	522	PREDICTED: beclin 1 protein [Vitis vinif	0.988	0.509	0.76	1e-109
73587486	479	beclin 1 protein [Vitis vinifera]	0.973	0.546	0.769	1e-109
73587476	511	beclin 1 protein [Gossypium raimondii]	0.985	0.518	0.788	1e-107
18412104	517	Beclin-1-like protein [Arabidopsis thali	0.985	0.512	0.726	1e-102
42572759	386	Beclin-1-like protein [Arabidopsis thali	0.985	0.686	0.726	1e-101
6850862	443	putative protein [Arabidopsis thaliana]	0.985	0.598	0.726	1e-101
357456733	517	Beclin 1 protein [Medicago truncatula] g	0.973	0.506	0.745	1e-100

>gi|255564727|ref|XP_002523358.1| Beclin-1, putative [Ricinus communis] gi|223537446|gb|EEF39074.1| Beclin-1, putative [Ricinus communis]

 Score =  405 bits (1042), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 220/270 (81%), Positives = 234/270 (86%), Gaps = 5/270 (1%)

Query: 1   MKKEDA-PDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSS-RSTMHGSSIH 58
           M KE    DK RT  VDPN+PRWVCQNCRH LCIVGVDSYADK+LN+SS RS M G S+H
Sbjct: 1   MNKEGTMTDKSRTFPVDPNLPRWVCQNCRHSLCIVGVDSYADKFLNESSSRSAMQGFSMH 60

Query: 59  ASNSVLGSTRMDNSFVVLPKQRP-QSHGVPPRPRGSSAQS-EASQS-GKAMDESFVVIYK 115
            +NSVLGSTRMDNSFVVLPKQRP Q+ GVPPRPRG   Q  E+ QS GKAMDESFVV+Y 
Sbjct: 61  GANSVLGSTRMDNSFVVLPKQRPLQAQGVPPRPRGGPLQPPESGQSCGKAMDESFVVVYN 120

Query: 116 SESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMR 175
           SE ASDGGG H+P  EGG NG +QPNN+GFHSTITVLKRAFEIAT+QTQVEQPLCLECMR
Sbjct: 121 SEPASDGGGTHLPLLEGGHNGLLQPNNNGFHSTITVLKRAFEIATTQTQVEQPLCLECMR 180

Query: 176 VLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEE 235
           VLSDKLDKEV+DV RDIEAY ACLQR EGEARDVLSEADFLKEKLKIEEEERKLEAAIEE
Sbjct: 181 VLSDKLDKEVEDVNRDIEAYVACLQRFEGEARDVLSEADFLKEKLKIEEEERKLEAAIEE 240

Query: 236 TEKQNAEVNAELKELELKSKRFKELEERYF 265
            EKQNAEVNAEL ELELKS RFKELEERY+
Sbjct: 241 IEKQNAEVNAELNELELKSFRFKELEERYW 270

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067974|ref|XP_002302626.1| predicted protein [Populus trichocarpa] gi|222844352|gb|EEE81899.1| predicted protein [Populus trichocarpa]

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 208/267 (77%), Positives = 236/267 (88%), Gaps = 2/267 (0%)

Query: 1   MKKED-APDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSS-RSTMHGSSIH 58
           MK+ED   D+ +T   DPN+PRWVCQNCR+ LCIVGVDS+ADK+LNDSS RS M G S+H
Sbjct: 1   MKEEDPMSDRNQTFQADPNLPRWVCQNCRNPLCIVGVDSFADKFLNDSSSRSGMQGCSVH 60

Query: 59  ASNSVLGSTRMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSES 118
            +NS+LG TRMDNSFVVLPKQ+PQ+ GVPPRPR  + Q +  QSGKAM+ESFVV+YKSE 
Sbjct: 61  GANSILGLTRMDNSFVVLPKQKPQAPGVPPRPRSGAVQPDTGQSGKAMEESFVVVYKSEP 120

Query: 119 ASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLS 178
           +SDGGG H+P  EGG NG + PNN+GF+STITVLKRAFEIAT+QTQVEQPLCLECMRVLS
Sbjct: 121 SSDGGGSHLPSIEGGPNGQLHPNNAGFNSTITVLKRAFEIATTQTQVEQPLCLECMRVLS 180

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEK 238
           DKL+KEV+DV RDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAI+ETEK
Sbjct: 181 DKLNKEVEDVNRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIQETEK 240

Query: 239 QNAEVNAELKELELKSKRFKELEERYF 265
           Q AEVNAELKELE+KS RFK+LEERY+
Sbjct: 241 QYAEVNAELKELEIKSDRFKDLEERYW 267

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|73587480|emb|CAJ27522.1| beclin 1 protein [Malus x domestica]

 Score =  402 bits (1033), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 193/264 (73%), Positives = 227/264 (85%), Gaps = 6/264 (2%)

Query: 8   DKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSVLGST 67
           ++GR+ +VDPNVPR+VCQNCR+ LC+VG DSYA+K+ +D SRS M GSS+H + SVL S 
Sbjct: 3   ERGRSFTVDPNVPRYVCQNCRNSLCVVGADSYAEKFFHDFSRSGMQGSSMHGATSVLSSM 62

Query: 68  RMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESASDGGGPHI 127
           RMDNSFVVLP+QR Q  GVPPRPRG +  +    SG AMDESFVV+ KSES++DGGG H+
Sbjct: 63  RMDNSFVVLPQQRAQ--GVPPRPRGGAVNT--GHSGNAMDESFVVVNKSESSADGGGAHL 118

Query: 128 PPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDD 187
           P P+GG NGP+QPNNSGFHSTI++LKRAFEIA++QTQVEQPLC+ECMRVLSDKLDKEV+D
Sbjct: 119 PSPDGGPNGPLQPNNSGFHSTISLLKRAFEIASTQTQVEQPLCVECMRVLSDKLDKEVED 178

Query: 188 VTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAEL 247
           V RDI+AYEACL+RLEGE R+VLSE DFLKEKLKIEEE+RKLEA IEE EKQNAEVN EL
Sbjct: 179 VNRDIKAYEACLKRLEGETREVLSETDFLKEKLKIEEEQRKLEAEIEEMEKQNAEVNNEL 238

Query: 248 KELELKSKRFKELEERYF--FNIY 269
           K LELKS RFKELEE+Y+  FN +
Sbjct: 239 KGLELKSSRFKELEEQYWHKFNNF 262

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454518|ref|XP_002277370.1| PREDICTED: beclin 1 protein [Vitis vinifera] gi|297745431|emb|CBI40511.3| unnamed protein product [Vitis vinifera]

 Score =  401 bits (1031), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 209/275 (76%), Positives = 236/275 (85%), Gaps = 9/275 (3%)

Query: 4   EDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSV 63
           ED+ +K RT  VDP +PRWVCQNCRH LCIVGVDSYADK+ +DSSRS M GS IH + SV
Sbjct: 3   EDSANKSRTFPVDPTLPRWVCQNCRHNLCIVGVDSYADKFYSDSSRSGMQGSLIHGAGSV 62

Query: 64  LGSTRMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVV-------IYKS 116
           LGST MD+SFVVLPKQR Q+ GVPPRPRG + Q + SQSGKAM+ESFV+       +YK 
Sbjct: 63  LGSTHMDHSFVVLPKQRNQAQGVPPRPRGGAVQPDVSQSGKAMEESFVMLPPAPASVYKC 122

Query: 117 ESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRV 176
           ESA++G G H+P PEGG +G +QPNNSGFH+TITVLKRAF+IAT+Q QVEQPLCLECMRV
Sbjct: 123 ESAAEGSGTHLPSPEGGPSGHLQPNNSGFHTTITVLKRAFDIATTQIQVEQPLCLECMRV 182

Query: 177 LSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEET 236
           LSDKLDKEV+DV RDI+AYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEET
Sbjct: 183 LSDKLDKEVEDVNRDIQAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEET 242

Query: 237 EKQNAEVNAELKELELKSKRFKELEERYF--FNIY 269
           EKQ A+VNAE+KELELKS RFKELEERY+  FN +
Sbjct: 243 EKQCAQVNAEMKELELKSSRFKELEERYWHEFNNF 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|73587486|emb|CAJ27525.1| beclin 1 protein [Vitis vinifera]

 Score =  401 bits (1030), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 207/269 (76%), Positives = 233/269 (86%), Gaps = 7/269 (2%)

Query: 4   EDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHASNSV 63
           ED+ +K RT  VDP +PRWVCQNCRH LCIVGVDSYADK+ +DSSRS M GS IH + SV
Sbjct: 3   EDSANKSRTFPVDPTLPRWVCQNCRHNLCIVGVDSYADKFYSDSSRSGMQGSLIHGAGSV 62

Query: 64  LGSTRMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVV-------IYKS 116
           LGST MD+SFVVLPKQR Q+ GVPPRPRG + Q + SQSGKAM+ESFV+       +YK 
Sbjct: 63  LGSTHMDHSFVVLPKQRNQAQGVPPRPRGGAVQPDVSQSGKAMEESFVMLPPAPASVYKC 122

Query: 117 ESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRV 176
           ESA++G G H+P PEGG +G +QPNNSGFH+TITVLKRAF+IAT+Q QVEQPLCLECMRV
Sbjct: 123 ESAAEGSGTHLPSPEGGPSGHLQPNNSGFHTTITVLKRAFDIATTQIQVEQPLCLECMRV 182

Query: 177 LSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEET 236
           LSDKLDKEV+DV RDI+AYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEET
Sbjct: 183 LSDKLDKEVEDVNRDIQAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEET 242

Query: 237 EKQNAEVNAELKELELKSKRFKELEERYF 265
           EKQ A+VNAE+KELELKS RFKELEERY+
Sbjct: 243 EKQCAQVNAEMKELELKSSRFKELEERYW 271

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|73587476|emb|CAJ27520.1| beclin 1 protein [Gossypium raimondii]

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 209/265 (78%), Positives = 229/265 (86%)

Query: 1   MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHAS 60
           MKKE  PDKGR+L VDPN+P+W+CQNC H LCIVGVDSY DK+ NDSSRS M GSSIH +
Sbjct: 1   MKKEYIPDKGRSLPVDPNLPKWICQNCHHSLCIVGVDSYVDKFPNDSSRSAMQGSSIHGA 60

Query: 61  NSVLGSTRMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESAS 120
           +SVLGSTRMDNSFVVLPKQ+P + G+PPRPRG   Q +  Q+ K M+ESFVV+ KSESAS
Sbjct: 61  SSVLGSTRMDNSFVVLPKQKPLAPGIPPRPRGMPGQPDTGQARKGMEESFVVVDKSESAS 120

Query: 121 DGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDK 180
           DG G  +P  EGG +  +QPNNSGFHSTITVLK AFEIAT+QTQVEQPLCLECMRVLSDK
Sbjct: 121 DGSGTQLPSSEGGPSSSLQPNNSGFHSTITVLKNAFEIATTQTQVEQPLCLECMRVLSDK 180

Query: 181 LDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQN 240
           LDKEV+DVTRDIEAYEACLQRLEGE RDVLSEADF KEKLKIEEEERKLEAAIEE EKQN
Sbjct: 181 LDKEVEDVTRDIEAYEACLQRLEGEPRDVLSEADFRKEKLKIEEEERKLEAAIEEIEKQN 240

Query: 241 AEVNAELKELELKSKRFKELEERYF 265
           A VNAELKELE KS RFKELEERY+
Sbjct: 241 AAVNAELKELEQKSNRFKELEERYW 265

Source: Gossypium raimondii

Species: Gossypium raimondii

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18412104|ref|NP_567116.1| Beclin-1-like protein [Arabidopsis thaliana] gi|148852650|sp|Q9M367.2|BECN1_ARATH RecName: Full=Beclin-1-like protein gi|14517556|gb|AAK62668.1| AT3g61710/F15G16_100 [Arabidopsis thaliana] gi|23308215|gb|AAN18077.1| At3g61710/F15G16_100 [Arabidopsis thaliana] gi|332646723|gb|AEE80244.1| Beclin-1-like protein [Arabidopsis thaliana]

 Score =  375 bits (964), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 194/267 (72%), Positives = 222/267 (83%), Gaps = 2/267 (0%)

Query: 1   MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHAS 60
           M+KE+ PDK RT+ +DPN+P+WVCQNC H L IVGVDSYA K+ ND   S   GSSIH +
Sbjct: 1   MRKEEIPDKSRTIPIDPNLPKWVCQNCHHSLTIVGVDSYAGKFFNDPPPSATQGSSIHGA 60

Query: 61  NSVLGSTRMDNSFVVLPKQRP-QSHGVPPRPRG-SSAQSEASQSGKAMDESFVVIYKSES 118
           NSVLGSTRMDNSFVVLP+ +P QS G+PPRPRG SS Q +A+QSGKAM+ESFVV+YKSE 
Sbjct: 61  NSVLGSTRMDNSFVVLPRHKPPQSQGIPPRPRGASSPQPDATQSGKAMEESFVVVYKSEP 120

Query: 119 ASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLS 178
            SD GG H    E G NGP+  N SGF++TI VL RAF+IA +QTQVEQPLCLECMRVLS
Sbjct: 121 VSDSGGSHNLSLEVGQNGPLHSNTSGFNATINVLTRAFDIARTQTQVEQPLCLECMRVLS 180

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEK 238
           DKL+KEV+DVTRD+EAYEAC+QRLEGE +DVLSEADFLKEK KIEEEERKL AAIEETEK
Sbjct: 181 DKLEKEVEDVTRDVEAYEACVQRLEGETQDVLSEADFLKEKKKIEEEERKLVAAIEETEK 240

Query: 239 QNAEVNAELKELELKSKRFKELEERYF 265
           QNAEVN +LKELE K  RF ELE+RY+
Sbjct: 241 QNAEVNHQLKELEFKGNRFNELEDRYW 267

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42572759|ref|NP_974475.1| Beclin-1-like protein [Arabidopsis thaliana] gi|332646724|gb|AEE80245.1| Beclin-1-like protein [Arabidopsis thaliana]

 Score =  375 bits (962), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 194/267 (72%), Positives = 222/267 (83%), Gaps = 2/267 (0%)

Query: 1   MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHAS 60
           M+KE+ PDK RT+ +DPN+P+WVCQNC H L IVGVDSYA K+ ND   S   GSSIH +
Sbjct: 1   MRKEEIPDKSRTIPIDPNLPKWVCQNCHHSLTIVGVDSYAGKFFNDPPPSATQGSSIHGA 60

Query: 61  NSVLGSTRMDNSFVVLPKQRP-QSHGVPPRPRG-SSAQSEASQSGKAMDESFVVIYKSES 118
           NSVLGSTRMDNSFVVLP+ +P QS G+PPRPRG SS Q +A+QSGKAM+ESFVV+YKSE 
Sbjct: 61  NSVLGSTRMDNSFVVLPRHKPPQSQGIPPRPRGASSPQPDATQSGKAMEESFVVVYKSEP 120

Query: 119 ASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLS 178
            SD GG H    E G NGP+  N SGF++TI VL RAF+IA +QTQVEQPLCLECMRVLS
Sbjct: 121 VSDSGGSHNLSLEVGQNGPLHSNTSGFNATINVLTRAFDIARTQTQVEQPLCLECMRVLS 180

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEK 238
           DKL+KEV+DVTRD+EAYEAC+QRLEGE +DVLSEADFLKEK KIEEEERKL AAIEETEK
Sbjct: 181 DKLEKEVEDVTRDVEAYEACVQRLEGETQDVLSEADFLKEKKKIEEEERKLVAAIEETEK 240

Query: 239 QNAEVNAELKELELKSKRFKELEERYF 265
           QNAEVN +LKELE K  RF ELE+RY+
Sbjct: 241 QNAEVNHQLKELEFKGNRFNELEDRYW 267

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6850862|emb|CAB71101.1| putative protein [Arabidopsis thaliana]

 Score =  374 bits (960), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 194/267 (72%), Positives = 222/267 (83%), Gaps = 2/267 (0%)

Query: 1   MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHAS 60
           M+KE+ PDK RT+ +DPN+P+WVCQNC H L IVGVDSYA K+ ND   S   GSSIH +
Sbjct: 1   MRKEEIPDKSRTIPIDPNLPKWVCQNCHHSLTIVGVDSYAGKFFNDPPPSATQGSSIHGA 60

Query: 61  NSVLGSTRMDNSFVVLPKQRP-QSHGVPPRPRG-SSAQSEASQSGKAMDESFVVIYKSES 118
           NSVLGSTRMDNSFVVLP+ +P QS G+PPRPRG SS Q +A+QSGKAM+ESFVV+YKSE 
Sbjct: 61  NSVLGSTRMDNSFVVLPRHKPPQSQGIPPRPRGASSPQPDATQSGKAMEESFVVVYKSEP 120

Query: 119 ASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLS 178
            SD GG H    E G NGP+  N SGF++TI VL RAF+IA +QTQVEQPLCLECMRVLS
Sbjct: 121 VSDSGGSHNLSLEVGQNGPLHSNTSGFNATINVLTRAFDIARTQTQVEQPLCLECMRVLS 180

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEK 238
           DKL+KEV+DVTRD+EAYEAC+QRLEGE +DVLSEADFLKEK KIEEEERKL AAIEETEK
Sbjct: 181 DKLEKEVEDVTRDVEAYEACVQRLEGETQDVLSEADFLKEKKKIEEEERKLVAAIEETEK 240

Query: 239 QNAEVNAELKELELKSKRFKELEERYF 265
           QNAEVN +LKELE K  RF ELE+RY+
Sbjct: 241 QNAEVNHQLKELEFKGNRFNELEDRYW 267

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357456733|ref|XP_003598647.1| Beclin 1 protein [Medicago truncatula] gi|355487695|gb|AES68898.1| Beclin 1 protein [Medicago truncatula]

 Score =  371 bits (953), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 199/267 (74%), Positives = 227/267 (85%), Gaps = 5/267 (1%)

Query: 1   MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHAS 60
           M+      + R+L VDPNVPRWVCQNCR+ LCIVGVDSYADKY ND SRS M GSSIH +
Sbjct: 9   MRDSTKKGRNRSLPVDPNVPRWVCQNCRNPLCIVGVDSYADKYFNDPSRSGMQGSSIHGA 68

Query: 61  NSVLGSTRMDNSFVVLPKQRPQSHGVPPRPRGSSAQSEASQSGKAMDESFVVIYKSESAS 120
           +SV+ +T+MDNS+VVLPKQRPQ+ GVPPRPRG     + S  GK M+ESFVV+YKSESAS
Sbjct: 69  SSVMSTTKMDNSYVVLPKQRPQTQGVPPRPRG-----DTSHPGKTMEESFVVVYKSESAS 123

Query: 121 DGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDK 180
           DGGG +   P     G + P+NSGF+STITVL RAFEIAT+QTQVEQPLCL+CMRVLSDK
Sbjct: 124 DGGGGNSLSPGVDHGGHLPPHNSGFNSTITVLTRAFEIATTQTQVEQPLCLDCMRVLSDK 183

Query: 181 LDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQN 240
           LDKEV+DV RDIEAYEACL+RLEGEA+DVLSEADFLKEKLKIEEEER+LEAAIEETE+QN
Sbjct: 184 LDKEVEDVNRDIEAYEACLKRLEGEAKDVLSEADFLKEKLKIEEEERRLEAAIEETERQN 243

Query: 241 AEVNAELKELELKSKRFKELEERYFFN 267
           AEVNAELKELELKS RFKELEER +++
Sbjct: 244 AEVNAELKELELKSTRFKELEERRYWH 270

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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	269
TAIR|locus:2076715	517	ATG6 "AT3G61710" [Arabidopsis	0.992	0.516	0.605	1.3e-82
SGD|S000006041	557	VPS30 "Subunit of phosphatidyl	0.293	0.141	0.275	5.9e-05
UNIPROTKB|G3N106	437	LOC100847722 "Uncharacterized	0.460	0.283	0.233	0.00061
MGI|MGI:1891828	448	Becn1 "beclin 1, autophagy rel	0.394	0.236	0.263	0.00083

TAIR|locus:2076715 ATG6 "AT3G61710" [Arabidopsis thaliana (taxid:3702)]

 Score = 828 (296.5 bits), Expect = 1.3e-82, P = 1.3e-82
 Identities = 164/271 (60%), Positives = 190/271 (70%)

Query:     1 MKKEDAPDKGRTLSVDPNVPRWVCQNCRHFLCIVGVDSYADKYLNDSSRSTMHGSSIHAS 60
             M+KE+ PDK RT+ +DPN+P+WVCQNC H L IVGVDSYA K+ ND   S   GSSIH +
Sbjct:     1 MRKEEIPDKSRTIPIDPNLPKWVCQNCHHSLTIVGVDSYAGKFFNDPPPSATQGSSIHGA 60

Query:    61 NSVLGSTRMDNSFVVLPKQRP-QSHGVPPRPRXXXXXX-XXXXXXKAMDESFVVIYKSES 118
             NSVLGSTRMDNSFVVLP+ +P QS G+PPRPR             KAM+ESFVV+YKSE 
Sbjct:    61 NSVLGSTRMDNSFVVLPRHKPPQSQGIPPRPRGASSPQPDATQSGKAMEESFVVVYKSEP 120

Query:   119 ASDXXXXXXXXXXXXTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLS 178
              SD             NGP+  N SGF++TI VL RAF+IA +QTQVEQPLCLECMRVLS
Sbjct:   121 VSDSGGSHNLSLEVGQNGPLHSNTSGFNATINVLTRAFDIARTQTQVEQPLCLECMRVLS 180

Query:   179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLXXXXXXXXXXXXXXXXXXXXXK 238
             DKL+KEV+DVTRD+EAYEAC+QRLEGE +DVLSEADFL                     K
Sbjct:   181 DKLEKEVEDVTRDVEAYEACVQRLEGETQDVLSEADFLKEKKKIEEEERKLVAAIEETEK 240

Query:   239 QNAEVNAELKELELKSKRFKELEERYF--FN 267
             QNAEVN +LKELE K  RF ELE+RY+  FN
Sbjct:   241 QNAEVNHQLKELEFKGNRFNELEDRYWQEFN 271

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0006914 "autophagy" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0000045 "autophagic vacuole assembly" evidence=IGI

GO:0000407 "pre-autophagosomal structure" evidence=IDA

GO:0006623 "protein targeting to vacuole" evidence=IGI

GO:0009846 "pollen germination" evidence=IMP

GO:0050832 "defense response to fungus" evidence=IEP

SGD|S000006041 VPS30 "Subunit of phosphatidylinositol (PtdIns) 3-kinase complexes I and II" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 122 (48.0 bits), Expect = 5.9e-05, P = 5.9e-05
 Identities = 22/80 (27%), Positives = 45/80 (56%)

Query:   135 NGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEA 194
             N  +Q N+    + +  +   F I +SQT ++ P+C +C  +L ++L  E DD  ++ + 
Sbjct:   147 NQQIQLNSKTLSTQVNAMTNVFNILSSQTNIDFPICQDCCNILINRLKSEYDDAIKERDT 206

Query:   195 YEACLQRLEGEARDVLSEAD 214
             Y   L +LE + +++ SE++
Sbjct:   207 YAQFLSKLESQNKEI-SESN 225

GO:0006914 "autophagy" evidence=IEA

GO:0045324 "late endosome to vacuole transport" evidence=IMP

GO:0005768 "endosome" evidence=IEA

GO:0005774 "vacuolar membrane" evidence=IEA

GO:0010008 "endosome membrane" evidence=IEA

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=IMP

GO:0030433 "ER-associated protein catabolic process" evidence=IMP

GO:0016236 "macroautophagy" evidence=IMP

GO:0005773 "vacuole" evidence=IEA

GO:0032258 "CVT pathway" evidence=IMP

GO:0042147 "retrograde transport, endosome to Golgi" evidence=IGI;IMP

GO:0016303 "1-phosphatidylinositol-3-kinase activity" evidence=IPI

GO:0034272 "phosphatidylinositol 3-kinase complex II" evidence=IDA

GO:0034271 "phosphatidylinositol 3-kinase complex I" evidence=IDA

GO:0034727 "piecemeal microautophagy of nucleus" evidence=IMP

GO:0030242 "peroxisome degradation" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0019898 "extrinsic to membrane" evidence=IDA

GO:0016020 "membrane" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0006810 "transport" evidence=IEA

UNIPROTKB|G3N106 LOC100847722 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 112 (44.5 bits), Expect = 0.00061, P = 0.00061
 Identities = 31/133 (23%), Positives = 63/133 (47%)

Query:   136 GPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAY 195
             G ++P  S  +S    ++ + +I + +T+V+ PLC++C   L + LD E+     D++ Y
Sbjct:    91 GRLEPWRS-LNSIQKTIRDSSDILSGETEVDHPLCVDCTDYLLEVLDVELAITESDVQNY 149

Query:   196 EACLQR---LEGEARDVLSEADFLXXXXXXXXXXXXXXXXXXXXXKQNAEVNAELKELEL 252
             + CL+    L G+ R++L E                         K    V A+L+  + 
Sbjct:   150 KRCLETRKWLSGDDREMLQEK-----LKGLELEEARLLQEVAEVEKNQERVAADLEAAQA 204

Query:   253 KSKRFKELEERYF 265
             ++K  ++ E++Y+
Sbjct:   205 ETKMLEQQEKQYW 217

GO:0006914 "autophagy" evidence=IEA

MGI|MGI:1891828 Becn1 "beclin 1, autophagy related" [Mus musculus (taxid:10090)]

 Score = 111 (44.1 bits), Expect = 0.00083, P = 0.00083
 Identities = 29/110 (26%), Positives = 55/110 (50%)

Query:   156 FEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADF 215
             F+I + QT V+ PLC EC   L D+LD +++    + + Y+ CL+ LE    D   +++ 
Sbjct:   121 FDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILEQMNED---DSEQ 177

Query:   216 LXXXXXXXXXXXXXXXXXXXXXKQNAEVNAE-LKELELKSKRFKELEERY 264
             L                     ++N +V AE L++++ +++R  + E +Y
Sbjct:   178 LQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQY 227


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.131   0.377    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      269       224   0.00099  112 3  11 22  0.42    33
                                                     32  0.40    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  4
  No. of states in DFA:  597 (63 KB)
  Total size of DFA:  173 KB (2101 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  19.25u 0.08s 19.33t   Elapsed:  00:00:01
  Total cpu time:  19.25u 0.08s 19.33t   Elapsed:  00:00:01
  Start:  Tue May 21 03:55:07 2013   End:  Tue May 21 03:55:08 2013

GO:0000045 "autophagic vacuole assembly" evidence=ISO

GO:0000910 "cytokinesis" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO;IDA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0005802 "trans-Golgi network" evidence=IDA

GO:0005856 "cytoskeleton" evidence=ISS

GO:0006914 "autophagy" evidence=ISO;IMP;IDA

GO:0007040 "lysosome organization" evidence=IMP

GO:0007049 "cell cycle" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IDA

GO:0016020 "membrane" evidence=ISS

GO:0016023 "cytoplasmic membrane-bounded vesicle" evidence=IDA

GO:0016239 "positive regulation of macroautophagy" evidence=IGI

GO:0030425 "dendrite" evidence=ISO

GO:0043234 "protein complex" evidence=IDA

GO:0048666 "neuron development" evidence=IMP

GO:0050435 "beta-amyloid metabolic process" evidence=IMP

GO:0051301 "cell division" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0051707 "response to other organism" evidence=IDA

GO:0060548 "negative regulation of cell death" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9M367	BECN1_ARATH	No assigned EC number	0.7265	0.9851	0.5125	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	269
pfam04111	356	pfam04111, APG6, Autophagy protein Apg6	2e-15
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	3e-07
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	8e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	5e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	7e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	8e-04
PRK03918	880	PRK03918, PRK03918, chromosome segregation protein	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.004
TIGR00020	364	TIGR00020, prfB, peptide chain release factor 2	0.004

>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6

 Score = 74.9 bits (184), Expect = 2e-15
 Identities = 33/119 (27%), Positives = 69/119 (57%)

Query: 149 ITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARD 208
           +  +   F+I +SQT ++ PLC EC  +L ++LD E+ D  ++ + Y+  L +LE +  +
Sbjct: 2   VKAMTNLFDILSSQTNIDHPLCEECADILLERLDSELRDAEKERDTYKQYLSKLESQNVE 61

Query: 209 VLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFN 267
           + +      E  ++++EE +L   +EE EK++ +++ EL EL+ + ++ +  E +Y   
Sbjct: 62  ISNYEALDSELDELKKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENEELQYLRE 120

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. Length = 356

>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 51.2 bits (123), Expect = 3e-07
 Identities = 28/84 (33%), Positives = 50/84 (59%), Gaps = 3/84 (3%)

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEK 238
           +++  E+ ++  ++E  E  ++ LE E ++ + E +  KE   +E  +RKLE  I E E+
Sbjct: 210 NEISSELPELREELEKLEKEVKELE-ELKEEIEELE--KELESLEGSKRKLEEKIRELEE 266

Query: 239 QNAEVNAELKELELKSKRFKELEE 262
           +  E+  E++ELE K K  KEL+E
Sbjct: 267 RIEELKKEIEELEEKVKELKELKE 290

Length = 880

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

 Score = 43.5 bits (103), Expect = 8e-05
 Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 8/94 (8%)

Query: 171 LECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLK-IEEEERKL 229
           LE +R   ++L +E+ ++  +IE        LEGE   +    + L+ +L+ +EE   +L
Sbjct: 276 LEELREELEELQEELLELKEEIE-------ELEGEISLLRERLEELENELEELEERLEEL 328

Query: 230 EAAIEETEKQNAEVNAELKELELKSKRFKELEER 263
           +  IE  +++  E    L+ELE      +E +E 
Sbjct: 329 KEKIEALKEELEERETLLEELEQLLAELEEAKEE 362

Length = 1163

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

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 25/103 (24%), Positives = 54/103 (52%), Gaps = 11/103 (10%)

Query: 175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEE----RKLE 230
           R    +L +E+ ++  ++   +  L  L+ E +++  E   L+ +L+  ++E    ++L 
Sbjct: 65  RERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLS 124

Query: 231 AAIEETEKQNAEVNAELKE-------LELKSKRFKELEERYFF 266
           A   E +++N E+  EL E       LE +++R +E E+R +F
Sbjct: 125 ANAIELDEENRELREELAELKQENEALEAENERLQENEQRRWF 167

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

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

 Score = 40.4 bits (95), Expect = 7e-04
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 6/86 (6%)

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKL-KIEEEERKLEAAIEETE 237
            +L+  ++++  D+   E  L  LE  AR   S    ++ +L K+EEE  ++EA + E E
Sbjct: 761 KELEARIEELEEDLHKLEEALNDLE--ARLSHSRIPEIQAELSKLEEEVSRIEARLREIE 818

Query: 238 KQNAEVNAELKELELKSKRFKELEER 263
               ++N    E E   K  +EL+E+
Sbjct: 819 ---QKLNRLTLEKEYLEKEIQELQEQ 841

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|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 40.5 bits (95), Expect = 8e-04
 Identities = 26/99 (26%), Positives = 49/99 (49%), Gaps = 5/99 (5%)

Query: 171 LECMRVLSDKLDKEVDDVTRDIEAYE-----ACLQRLEGEARDVLSEADFLKEKLKIEEE 225
           LE    L ++L+++++ +   +E  E       LQ+L+ E R +      LKE L+    
Sbjct: 521 LELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEELRL 580

Query: 226 ERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERY 264
            R  +  +EE  ++  E+  +LKELE +  + +EL +  
Sbjct: 581 LRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSL 619

Length = 908

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

 Score = 40.4 bits (95), Expect = 8e-04
 Identities = 27/107 (25%), Positives = 47/107 (43%), Gaps = 12/107 (11%)

Query: 171 LECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKL---------- 220
           LE +    ++L KE+++++R I A    L RLE E   +      L ++L          
Sbjct: 707 LEELEEELEQLRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEEL 766

Query: 221 --KIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYF 265
             ++EE E +L  A  E E+  A++    +EL+   +   EL     
Sbjct: 767 EERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELT 813

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|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 28/100 (28%), Positives = 56/100 (56%), Gaps = 6/100 (6%)

Query: 171 LECMRVLSDKLDK-EVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKL 229
            E ++ L +KL K  ++++ +  E YE   ++L     ++ S    L++  +++++  +L
Sbjct: 502 AEQLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAEL 561

Query: 230 EAAIEETEKQNAEVNAELKELELKS-----KRFKELEERY 264
           E  ++E E++ AE+  EL+EL  +S     +R KELE  Y
Sbjct: 562 EKKLDELEEELAELLKELEELGFESVEELEERLKELEPFY 601

Length = 880

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

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 25/84 (29%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 180 KLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEER-KLEAAIEETEK 238
           KL +E++++    +A +  L+ LE E  +     D L+ +L+  E+ R +LE  IEE E+
Sbjct: 776 KLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEE 835

Query: 239 QNAEVNAELKELELKSKRFKELEE 262
           +  E+  +L ELE + +  ++  E
Sbjct: 836 EIEELEEKLDELEEELEELEKELE 859

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 29/88 (32%), Positives = 47/88 (53%), Gaps = 3/88 (3%)

Query: 180 KLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLK--IEEEERKLEAAIEETE 237
             +KE  ++  +IE  E  L+ LE E  ++L   + LKE+L+  +E+ E  LE   E  E
Sbjct: 491 SREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKE 550

Query: 238 KQNAE-VNAELKELELKSKRFKELEERY 264
           K   + +  EL++LE + +  KEL E  
Sbjct: 551 KLQLQQLKEELRQLEDRLQELKELLEEL 578

Length = 908

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

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 24/114 (21%), Positives = 55/114 (48%), Gaps = 11/114 (9%)

Query: 157 EIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFL 216
           E+   + ++E+      +R+   +L++E++++ +++ A    + RLE + + +      L
Sbjct: 261 ELQELEEKLEE------LRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANL 314

Query: 217 KEKLK-----IEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYF 265
           + +L+     +EE E KL+   EE  +   ++    +ELE      +ELE    
Sbjct: 315 ERQLEELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELE 368

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|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 6/92 (6%)

Query: 177 LSDKLDKEVDDVTRDIEAYEA----CLQRLEGEARDVLSEADFLKEKLKI--EEEERKLE 230
           LS+ L + + +    IE  E      L+ +E     +  E   LK+  +I  E+EE +LE
Sbjct: 172 LSELLKEVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEELE 231

Query: 231 AAIEETEKQNAEVNAELKELELKSKRFKELEE 262
             IE  E++ AE+  E + LE    R  E+E 
Sbjct: 232 QEIEALEERLAELEEEKERLEELKARLLEIES 263

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 198 CLQRLEGEARDVL-----SEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELEL 252
           C Q L  E    L      E + L+E+L  E+EE +L   IEE EK+  E+  EL EL  
Sbjct: 463 CGQELPEEHEKELLELYELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLE 522

Query: 253 KSKRFKELEER 263
             +  KE  E 
Sbjct: 523 LEEALKEELEE 533

Length = 908

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

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 180 KLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEER-KLEAAIEETEK 238
            L++E++ +   +E  E  L+ LE E  ++    + L+E+L+  EE   KL+  IEE E+
Sbjct: 727 ALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEE 786

Query: 239 QNAEVNAELKELELKSKRFKE 259
           +   +  EL+ELE + +  + 
Sbjct: 787 KRQALQEELEELEEELEEAER 807

Length = 1163

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

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 5/93 (5%)

Query: 177 LSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEER-----KLEA 231
           L +KL   ++++    EA    L  LE E  ++ +E + LK +++  EE       +LE 
Sbjct: 363 LEEKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLED 422

Query: 232 AIEETEKQNAEVNAELKELELKSKRFKELEERY 264
             EE ++  AE+     ELE  ++  +ELEE+ 
Sbjct: 423 LKEELKELEAELEELQTELEELNEELEELEEQL 455

Length = 1163

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

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 5/91 (5%)

Query: 179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLK-----IEEEERKLEAAI 233
           ++ ++ +D + R++E+ E   +RLE E  ++  E + L+EKL      +EE E++LE   
Sbjct: 803 EEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELK 862

Query: 234 EETEKQNAEVNAELKELELKSKRFKELEERY 264
           EE E+  AE      EL+   +  +ELEE  
Sbjct: 863 EELEELEAEKEELEDELKELEEEKEELEEEL 893

Length = 1163

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 32/97 (32%), Positives = 46/97 (47%), Gaps = 14/97 (14%)

Query: 179 DKLDKEVDDVTRDIEAYEAC------LQRLEGEARDVLSEADFLKEKLK-----IEEEER 227
            +L++ ++++   IE  E        L+      R +L E + L EKLK     +E+ E 
Sbjct: 277 RELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEE 336

Query: 228 KLEAAIEETEKQNAEVNAELKELELKSKRFKELEERY 264
           KLE    E E+   E N   K LE   +R KELEER 
Sbjct: 337 KLEKLESELEELAEEKNELAKLLE---ERLKELEERL 370

Length = 908

>gnl|CDD|232785 TIGR00020, prfB, peptide chain release factor 2

 Score = 37.8 bits (88), Expect = 0.004
 Identities = 34/109 (31%), Positives = 47/109 (43%), Gaps = 26/109 (23%)

Query: 181 LDKEVDDVTR--DIEAYEACLQRLEGE------------ARDVLSEADFLKEKL-KIEEE 225
           L   +D V    D E  +A L+ LE E            A+ V+ E   L+  L  +EE 
Sbjct: 12  LTSRLDTVRGSLDPEKKKARLEELEKEMEDPNFWNDQERAQAVIKERSSLEAVLDTLEEL 71

Query: 226 ERKLE--------AAIEETEKQNAEVNAELKELELKSKRFKELEERYFF 266
           +  LE        A  E+ E+   E++AELK LE   K+  ELE R   
Sbjct: 72  KNSLEDLSELLELAVEEDDEETFNELDAELKALE---KKLAELELRTML 117

In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a PFAM model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc [Protein synthesis, Translation factors]. Length = 364

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	269
KOG2751	447	consensus Beclin-like protein [Signal transduction	100.0
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	99.76
KOG2751	447	consensus Beclin-like protein [Signal transduction	97.22
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.07
PRK11637	428	AmiB activator; Provisional	95.44
PRK10884	206	SH3 domain-containing protein; Provisional	94.97
COG4026	290	Uncharacterized protein containing TOPRIM domain,	94.65
PF15285	25	BH3: Beclin-1 BH3 domain, Bcl-2-interacting; PDB:	94.6
PRK11637	428	AmiB activator; Provisional	94.07
COG4942	420	Membrane-bound metallopeptidase [Cell division and	93.85
PF05700	221	BCAS2: Breast carcinoma amplified sequence 2 (BCAS	93.47
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	93.45
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	92.98
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	92.91
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	92.85
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	92.29
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	91.87
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	91.33
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	91.3
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	90.92
PHA02562	562	46 endonuclease subunit; Provisional	90.15
PF10186	302	Atg14: UV radiation resistance protein and autopha	89.51
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	89.29
TIGR02231	525	conserved hypothetical protein. This family consis	89.04
PF05278	269	PEARLI-4: Arabidopsis phospholipase-like protein (	88.94
KOG2129	552	consensus Uncharacterized conserved protein H4 [Fu	88.83
PHA02562	562	46 endonuclease subunit; Provisional	88.63
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	88.17
PRK03918	880	chromosome segregation protein; Provisional	88.03
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	87.94
COG4026	290	Uncharacterized protein containing TOPRIM domain,	87.82
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	87.41
PRK04863	1486	mukB cell division protein MukB; Provisional	87.23
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	86.9
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	86.82
PRK10884	206	SH3 domain-containing protein; Provisional	86.54
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	86.35
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	86.18
TIGR02473	141	flagell_FliJ flagellar export protein FliJ. Member	85.94
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	85.78
PF11414	84	Suppressor_APC: Adenomatous polyposis coli tumour	85.3
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	85.24
PRK03918	880	chromosome segregation protein; Provisional	84.88
PF03961	451	DUF342: Protein of unknown function (DUF342); Inte	84.27
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	83.28
PRK09039	343	hypothetical protein; Validated	82.6
KOG3119	269	consensus Basic region leucine zipper transcriptio	82.39
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	82.22
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	82.15
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	81.8
PRK03947	140	prefoldin subunit alpha; Reviewed	81.51
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	81.23
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	81.09
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	81.07
PF14662	193	CCDC155: Coiled-coil region of CCDC155	81.0
PRK01156	895	chromosome segregation protein; Provisional	80.95
TIGR03319	514	YmdA_YtgF conserved hypothetical protein YmdA/YtgF	80.91
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	80.9
PRK12704	520	phosphodiesterase; Provisional	80.81
COG5185	622	HEC1 Protein involved in chromosome segregation, i	80.65
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	80.54
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	80.5
COG4942	420	Membrane-bound metallopeptidase [Cell division and	80.31

>KOG2751 consensus Beclin-like protein [Signal transduction mechanisms]

Probab=100.00  E-value=7.8e-37  Score=293.50  Aligned_cols=234  Identities=47%  Similarity=0.705  Sum_probs=211.5

Q ss_pred             eeccccchhhhcccccCCcCCCCccccccccccCCCCCCceeeccCCCC-CCCCCCCCCCCCCCCcccccCCCCCCCceE
Q 024294           33 IVGVDSYADKYLNDSSRSTMHGSSIHASNSVLGSTRMDNSFVVLPKQRP-QSHGVPPRPRGSSAQSEASQSGKAMDESFV  111 (269)
Q Consensus        33 i~g~d~~~~~~~~~~~~~~~~~s~~~~~~s~~~~~~md~s~vvlp~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~eSfV  111 (269)
                      |||+|+|.++|+..|..+--.+.++|+..++.+..+|+++++|+|.+.+ ++.+.++++|++.. .++. ++..+.+|||
T Consensus         1 ~~g~~~s~~~~~q~~~~~~r~~~~i~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~t~~~~a~~-~~~~-~~~~~~~~~~   78 (447)
T KOG2751|consen    1 IVGVDSSANKFFQVPFPCQRCLQPIHLDNSLLGSDRMDISELVLPLHKPPQSQGGPTRPRGASS-GDAT-SGKTPQESSV   78 (447)
T ss_pred             CcccccccccccCCChhhhhccchhhhhhhhccccccchhhccCCCCCCccccCCCccCccccC-cccc-CCcchhhccc
Confidence            5899999999999998888889999999999999999999999999976 99999999988876 5565 8889999999


Q ss_pred             EEeccCCCCCCCCCCCCCCCCCCCCCCCCCCCChhhhHHHHHHHHHHhcCCCCCCCcchHHHHHHHHHHHHHHHHHHHHH
Q 024294          112 VIYKSESASDGGGPHIPPPEGGTNGPMQPNNSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRD  191 (269)
Q Consensus       112 vl~~s~~~~e~~g~~~~~~~~~~~~~~~~~~~~ls~~i~~l~~lFdILS~~s~IDhPLC~ECtd~Lle~Ld~ql~~~~~E  191 (269)
                      +++...+-......|-++...+..+.-..+..+++.++++++++|+|+|++++||||+|.||+|.|++.|+++++.++.|
T Consensus        79 ~~~~~~p~r~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~f~i~~~qt~~d~PlC~eC~d~l~~~ld~e~~~~~~e  158 (447)
T KOG2751|consen   79 VVYFSPPVRDSDTEHNLSFELGENGSDGSNTKTLSATINVLTRLFDILSSQTQVDHPLCEECMDVLLNKLDKEVEDAEDE  158 (447)
T ss_pred             eecccCcccccccccccccccccccchhhhhHHHHHHHHHHHHHHHHhhccCCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            99988765555555544444444445567778999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 024294          192 IEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFNIY  269 (269)
Q Consensus       192 ~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~yWre~~  269 (269)
                      +++|.+||+.|+.+..+ .+++++++|++.++.||.+|.++|++++++.+.++.+|..++.+..++.++|.+||++||
T Consensus       159 ~~~Y~~~l~~Le~~~~~-~~~~~~~~e~~~l~~eE~~L~q~lk~le~~~~~l~~~l~e~~~~~~~~~e~~~~~~~ey~  235 (447)
T KOG2751|consen  159 VDTYKACLQRLEQQNQD-VSEEDLLKELKNLKEEEERLLQQLEELEKEEAELDHQLKELEFKAERLNEEEDQYWREYN  235 (447)
T ss_pred             HHHHHHHHHHHhhcCcc-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999987654 489999999999999999999999999999999999999999999999999999999996

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

Probab=99.76  E-value=1.2e-18  Score=163.73  Aligned_cols=101  Identities=34%  Similarity=0.580  Sum_probs=55.4

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          168 PLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAEL  247 (269)
Q Consensus       168 PLC~ECtd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL  247 (269)
                      |||.||++.|+++|+.+++.+++|+++|..||++++.......+..++.+++.+|++||+++.++|++||++++++++||
T Consensus         1 PlC~eC~~~l~~~l~~~~~~~~~E~~~Y~~fL~~l~~~~~~~~~~~~~~~el~~le~Ee~~l~~eL~~LE~e~~~l~~el   80 (314)
T PF04111_consen    1 PLCQECTDLLLEQLDKQLEQAEKERDTYQEFLKKLEEESDSEEDIEELEEELEKLEQEEEELLQELEELEKEREELDQEL   80 (314)
T ss_dssp             -----------------------------------------HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999853332346788899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhhhc
Q 024294          248 KELELKSKRFKELEERYFFNI  268 (269)
Q Consensus       248 ~~le~E~~~Ld~eEe~yWre~  268 (269)
                      .+++.+.++|+++|++||++|
T Consensus        81 ~~le~e~~~l~~eE~~~~~~~  101 (314)
T PF04111_consen   81 EELEEELEELDEEEEEYWREY  101 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999986

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.

>KOG2751 consensus Beclin-like protein [Signal transduction mechanisms]

Probab=97.22  E-value=0.002  Score=63.64  Aligned_cols=122  Identities=10%  Similarity=-0.040  Sum_probs=80.5

Q ss_pred             CCChhhhHHHHHHHHHHhcCCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHH----HHHhcccc
Q 024294          142 NSGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYE----------ACL----QRLEGEAR  207 (269)
Q Consensus       142 ~~~ls~~i~~l~~lFdILS~~s~IDhPLC~ECtd~Lle~Ld~ql~~~~~E~d~Y~----------~fL----~~L~~e~~  207 (269)
                      ..+++.....-...|+..+.++.+|||.|..|...+...+-+=...+....-.|.          .|.    .++..+..
T Consensus        74 ~~~~~~~~~~~p~r~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~f~i~~~qt~~d~PlC~eC~d~l~~~ld~e~~  153 (447)
T KOG2751|consen   74 QESSVVVYFSPPVRDSDTEHNLSFELGENGSDGSNTKTLSATINVLTRLFDILSSQTQVDHPLCEECMDVLLNKLDKEVE  153 (447)
T ss_pred             hhccceecccCcccccccccccccccccccchhhhhHHHHHHHHHHHHHHHHhhccCCcccchHHHHHHHHHHHHHHHHH
Confidence            3456666777788999999999999999999999887776555444444433332          222    22222211


Q ss_pred             cc----CCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          208 DV----LSEADFLKEKLKI--EEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEER  263 (269)
Q Consensus       208 ~~----~seeel~~El~~L--e~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~  263 (269)
                      ..    ...+.+...++.-  ..++..+..+++.+..+..++-++|+.++++...++.++.+
T Consensus       154 ~~~~e~~~Y~~~l~~Le~~~~~~~~~~~~~e~~~l~~eE~~L~q~lk~le~~~~~l~~~l~e  215 (447)
T KOG2751|consen  154 DAEDEVDTYKACLQRLEQQNQDVSEEDLLKELKNLKEEEERLLQQLEELEKEEAELDHQLKE  215 (447)
T ss_pred             HHHHHHHHHHHHHHHHhhcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            10    1111122222221  22678899999999999999999999999999888876654

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=96.07  E-value=0.14  Score=44.96  Aligned_cols=80  Identities=16%  Similarity=0.245  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHHHHHHH------------HHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          176 VLSDKLDKEVDDVTRDI------------EAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEV  243 (269)
Q Consensus       176 ~Lle~Ld~ql~~~~~E~------------d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l  243 (269)
                      .+-.++...++.+.++|            +.-..||+.++..   .+....+..|...|+.+-..|.++++.|+++...+
T Consensus        54 ~VRkqY~~~i~~AKkqRk~~~~~~~~ltl~~vI~fLq~l~~~---~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L  130 (161)
T TIGR02894        54 YVRKQYEEAIELAKKQRKELKREAGSLTLQDVISFLQNLKTT---NPSDQALQKENERLKNQNESLQKRNEELEKELEKL  130 (161)
T ss_pred             HHHHHHHHHHHHHHHHHhccccCcccCCHHHHHHHHHHHHhc---chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677888888888887            4567888888754   34567778888888888888999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q 024294          244 NAELKELELKSKRFK  258 (269)
Q Consensus       244 ~~EL~~le~E~~~Ld  258 (269)
                      ..++..++++.+.|-
T Consensus       131 ~~~~~~~~eDY~~L~  145 (161)
T TIGR02894       131 RQRLSTIEEDYQTLI  145 (161)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            888888888877664

In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.

>PRK11637 AmiB activator; Provisional

Probab=95.44  E-value=0.23  Score=48.52  Aligned_cols=85  Identities=15%  Similarity=0.198  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcccccc-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDV-LSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRF  257 (269)
Q Consensus       179 e~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~-~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~L  257 (269)
                      +.++++++.++++++....-++.++....+. .....+..++..+..+-..+.++|..++++...+..+|..++.+...+
T Consensus        43 ~~~~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~  122 (428)
T PRK11637         43 SDNRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQ  122 (428)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666666666666666665554432110 123444555566666666666666666666666666666666665555


Q ss_pred             HHHHHH
Q 024294          258 KELEER  263 (269)
Q Consensus       258 d~eEe~  263 (269)
                      ...-.+
T Consensus       123 ~~~l~~  128 (428)
T PRK11637        123 ERLLAA  128 (428)
T ss_pred             HHHHHH
Confidence            444433

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.97  E-value=0.67  Score=41.91  Aligned_cols=81  Identities=9%  Similarity=0.090  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          176 VLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSK  255 (269)
Q Consensus       176 ~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~  255 (269)
                      ..+..|++|+..++.+.+.-..=++         ....++++++...+....+|.++.++|.++.+.+..++..++.+..
T Consensus        93 ~rlp~le~el~~l~~~l~~~~~~~~---------~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~  163 (206)
T PRK10884         93 TRVPDLENQVKTLTDKLNNIDNTWN---------QRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLD  163 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455777777777655444221111         1234455666667777777888888888888888888888888888


Q ss_pred             HHHHHHHHhh
Q 024294          256 RFKELEERYF  265 (269)
Q Consensus       256 ~Ld~eEe~yW  265 (269)
                      .++......|
T Consensus       164 ~~~~~~~~~w  173 (206)
T PRK10884        164 DKQRTIIMQW  173 (206)
T ss_pred             HHHHHHHHHH
Confidence            8888777766

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

Probab=94.65  E-value=0.51  Score=43.93  Aligned_cols=106  Identities=20%  Similarity=0.296  Sum_probs=61.8

Q ss_pred             HHHHHHHHHhcC--------CCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc--c-cCCHHHHHHH
Q 024294          150 TVLKRAFEIATS--------QTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEAR--D-VLSEADFLKE  218 (269)
Q Consensus       150 ~~l~~lFdILS~--------~s~IDhPLC~ECtd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~--~-~~seeel~~E  218 (269)
                      +...++|+-|++        +.+|-|-+         +.+|-+|-.-+-+...-++=|+.|+.-..  + ...-+++...
T Consensus        73 eLA~kf~eeLrg~VGhiERmK~PiGHDv---------EhiD~elvrkEl~nAlvRAGLktL~~v~~~~d~ke~~ee~kek  143 (290)
T COG4026          73 ELAEKFFEELRGMVGHIERMKIPIGHDV---------EHIDVELVRKELKNALVRAGLKTLQRVPEYMDLKEDYEELKEK  143 (290)
T ss_pred             HHHHHHHHHHHHhhhhhheeccCCCCCc---------cccCHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHH
Confidence            456688888886        34555543         22222222222222234455665553210  0 0122344455


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024294          219 KLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERY  264 (269)
Q Consensus       219 l~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~y  264 (269)
                      ++.+.+|...|+.+|++++.+.++++..|+.++.|..+|.+.-.+.
T Consensus       144 l~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l  189 (290)
T COG4026         144 LEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKL  189 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6667777778888888888888888888888888877776654443

>PF15285 BH3: Beclin-1 BH3 domain, Bcl-2-interacting; PDB: 3BL2_C 2P1L_H 3DVU_C 2PON_A

Probab=94.60  E-value=0.012  Score=36.61  Aligned_cols=20  Identities=20%  Similarity=0.368  Sum_probs=16.9

Q ss_pred             CChhhhHHHHHHHHHHhcCC
Q 024294          143 SGFHSTITVLKRAFEIATSQ  162 (269)
Q Consensus       143 ~~ls~~i~~l~~lFdILS~~  162 (269)
                      .++|+++++...+|||+||+
T Consensus         6 e~ls~rlkvtg~lfdimsGq   25 (25)
T PF15285_consen    6 ENLSRRLKVTGDLFDIMSGQ   25 (25)
T ss_dssp             HHHHHHHHHHHHHHCCTT--
T ss_pred             cccchhheecccccccccCC
Confidence            46999999999999999985

>PRK11637 AmiB activator; Provisional

Probab=94.07  E-value=0.85  Score=44.62  Aligned_cols=83  Identities=8%  Similarity=0.068  Sum_probs=49.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccc-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDV-LSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELK  253 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~-~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E  253 (269)
                      ..=++.+++++...+.+......-++.+..+-... .....+..++..++.+...+..+|..++++.+.+.++|..++..
T Consensus        46 ~~~l~~l~~qi~~~~~~i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~  125 (428)
T PRK11637         46 RDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERL  125 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455666666666666666555555554432211 13445556666677777777777777777777777776666655


Q ss_pred             HHHH
Q 024294          254 SKRF  257 (269)
Q Consensus       254 ~~~L  257 (269)
                      ...+
T Consensus       126 l~~r  129 (428)
T PRK11637        126 LAAQ  129 (428)
T ss_pred             HHHH
Confidence            5443

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

Probab=93.85  E-value=0.97  Score=45.11  Aligned_cols=96  Identities=17%  Similarity=0.199  Sum_probs=68.5

Q ss_pred             HHHHHHHhcCCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHH
Q 024294          152 LKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEA  231 (269)
Q Consensus       152 l~~lFdILS~~s~IDhPLC~ECtd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~  231 (269)
                      ..-++-+|++    -+|.|..|    ....++++..+.+|...-..-+.....      .-..|++++..++.+-+.+..
T Consensus        15 ~~~~~~~l~~----~~~~~s~s----~~a~~~~l~q~q~ei~~~~~~i~~~~~------~~~kL~~~lk~~e~~i~~~~~   80 (420)
T COG4942          15 TILLASLLSA----AVLAAAFS----AAADDKQLKQIQKEIAALEKKIREQQD------QRAKLEKQLKSLETEIASLEA   80 (420)
T ss_pred             HHHHHHHHHh----cccccchh----HHhHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHH
Confidence            3345556654    35677777    444457777777766555555444332      345677888888999899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          232 AIEETEKQNAEVNAELKELELKSKRFKELE  261 (269)
Q Consensus       232 eLeeLEkE~~~l~~EL~~le~E~~~Ld~eE  261 (269)
                      +|.+.+..+.++++.|..++..+..|..++
T Consensus        81 ql~~s~~~l~~~~~~I~~~~~~l~~l~~q~  110 (420)
T COG4942          81 QLIETADDLKKLRKQIADLNARLNALEVQE  110 (420)
T ss_pred             HHHHHHhHHHHHHhhHHHHHHHHHHHHHHH
Confidence            999999888888888888888888887776

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

Probab=93.47  E-value=0.8  Score=41.35  Aligned_cols=110  Identities=18%  Similarity=0.217  Sum_probs=73.9

Q ss_pred             CChhhhHHHHHHHHHHhcCCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHH
Q 024294          143 SGFHSTITVLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKI  222 (269)
Q Consensus       143 ~~ls~~i~~l~~lFdILS~~s~IDhPLC~ECtd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~L  222 (269)
                      ..+.|.-.++.+| ++|+.-..--.=+..+.-..++..|++++..+.++.+.=...-+.-+         .+...+|..|
T Consensus       111 a~lehq~~R~~NL-eLl~~~g~naW~~~n~~Le~~~~~le~~l~~~k~~ie~vN~~RK~~Q---------~~~~~~L~~L  180 (221)
T PF05700_consen  111 AQLEHQRLRLENL-ELLSKYGENAWLIHNEQLEAMLKRLEKELAKLKKEIEEVNRERKRRQ---------EEAGEELRYL  180 (221)
T ss_pred             HHHHHHHHHHHHH-HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHhHHHHHHH
Confidence            3455555556666 56654222222344556666666666666666666665444433332         2345678889


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          223 EEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEE  262 (269)
Q Consensus       223 e~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe  262 (269)
                      +..=..+...--+++.....|++||.+++++..++++..+
T Consensus       181 e~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~~~~~~  220 (221)
T PF05700_consen  181 EQRWKELVSKNLEIEVACEELEQEIEQLKRKAAELKENQQ  220 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999999999999888876543

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

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

Probab=93.45  E-value=0.91  Score=43.26  Aligned_cols=44  Identities=27%  Similarity=0.398  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          212 EADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSK  255 (269)
Q Consensus       212 eeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~  255 (269)
                      ++.+.+++..|+.|..++.++|..++.+.++++.+....-.+..
T Consensus        59 e~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~~~n  102 (314)
T PF04111_consen   59 EEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWREYN  102 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555666666666666666666666666655555444443333

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.

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

Probab=92.98  E-value=2  Score=39.61  Aligned_cols=74  Identities=15%  Similarity=0.168  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          174 MRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELK  253 (269)
Q Consensus       174 td~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E  253 (269)
                      .+.+|..+.++.+.+..|+..+..-|+.+..      +...++..+..++.|-.+....+..+..+...+..++..+..+
T Consensus        30 ee~~L~e~~kE~~~L~~Er~~h~eeLrqI~~------DIn~lE~iIkqa~~er~~~~~~i~r~~eey~~Lk~~in~~R~e  103 (230)
T PF10146_consen   30 EEKCLEEYRKEMEELLQERMAHVEELRQINQ------DINTLENIIKQAESERNKRQEKIQRLYEEYKPLKDEINELRKE  103 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456666666666666666666666665553      2334455555555555555555555555555555555555544

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.

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

Probab=92.91  E-value=4.1  Score=35.18  Aligned_cols=31  Identities=23%  Similarity=0.439  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 024294          174 MRVLSDKLDKEVDDVTRDIEAYEACLQRLEG  204 (269)
Q Consensus       174 td~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~  204 (269)
                      ....+..+++++++..+........+..++.
T Consensus        86 ~~~~l~~l~~el~~l~~~~~~~~~~l~~~~~  116 (191)
T PF04156_consen   86 LQQQLQQLQEELDQLQERIQELESELEKLKE  116 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555666666666666666666555543

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 [].

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

Probab=92.85  E-value=1.8  Score=41.07  Aligned_cols=84  Identities=15%  Similarity=0.229  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc---------------------c--c---CCHHHHHHHHHHHHHHHHH
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGEAR---------------------D--V---LSEADFLKEKLKIEEEERK  228 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~---------------------~--~---~seeel~~El~~Le~EE~~  228 (269)
                      +.|.+.|+..++.+..+.......+..+..-..                     +  .   ...+.+..+|..+..+-+.
T Consensus       148 ~gl~~~L~~~~~~L~~D~~~L~~~~~~l~~~~~~l~~~~~~L~~e~~~Lk~~~~e~~~~D~~eL~~lr~eL~~~~~~i~~  227 (325)
T PF08317_consen  148 EGLKEGLEENLELLQEDYAKLDKQLEQLDELLPKLRERKAELEEELENLKQLVEEIESCDQEELEALRQELAEQKEEIEA  227 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCHHHHHHHHHHHHHHHHHHHH
Confidence            566777777777777777776666665543211                     0  0   1123333455555555555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          229 LEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       229 L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      ..++|.+++.++..+..+++++.++..++.
T Consensus       228 ~k~~l~el~~el~~l~~~i~~~~~~k~~l~  257 (325)
T PF08317_consen  228 KKKELAELQEELEELEEKIEELEEQKQELL  257 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555666666666666655555554443

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

Probab=92.29  E-value=1.6  Score=40.54  Aligned_cols=29  Identities=28%  Similarity=0.367  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 024294          177 LSDKLDKEVDDVTRDIEAYEACLQRLEGE  205 (269)
Q Consensus       177 Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e  205 (269)
                      .|..||.++......++.|..+|++++.+
T Consensus        11 ~iq~lD~e~~rl~~~~~~~~~~l~k~~~e   39 (239)
T COG1579          11 AIQKLDLEKDRLEPRIKEIRKALKKAKAE   39 (239)
T ss_pred             HHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            35567777777777777777777766554

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

Probab=91.87  E-value=2.8  Score=38.64  Aligned_cols=46  Identities=13%  Similarity=0.203  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          214 DFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKE  259 (269)
Q Consensus       214 el~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~  259 (269)
                      ++.+|...|..|.....++|..+......|+..|++++.+..+..+
T Consensus        36 e~~kE~~~L~~Er~~h~eeLrqI~~DIn~lE~iIkqa~~er~~~~~   81 (230)
T PF10146_consen   36 EYRKEMEELLQERMAHVEELRQINQDINTLENIIKQAESERNKRQE   81 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555555555555555555555444444333

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.

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

Probab=91.33  E-value=4.2  Score=37.78  Aligned_cols=80  Identities=18%  Similarity=0.262  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccccccC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          178 SDKLDKEVDDVTRDIEAYEACLQRLEGEARDVL---SEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKS  254 (269)
Q Consensus       178 le~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~---seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~  254 (269)
                      ++.|++|+...+.|.+.-..=+++++..-..+.   .-.+|..|+..++.....|..+|..+..+.+.+..++..+..+.
T Consensus        54 ~e~le~qv~~~e~ei~~~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~  133 (239)
T COG1579          54 LEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERL  133 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555554444444432211111   22444566666666666666666666666666666666665544


Q ss_pred             HHH
Q 024294          255 KRF  257 (269)
Q Consensus       255 ~~L  257 (269)
                      ..+
T Consensus       134 ~~~  136 (239)
T COG1579         134 ERL  136 (239)
T ss_pred             HHH
Confidence            443

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

Probab=91.30  E-value=3.1  Score=34.78  Aligned_cols=32  Identities=22%  Similarity=0.401  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGEA  206 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~  206 (269)
                      -.+++.|..++...+.|...+..-+.+|....
T Consensus        15 ~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r   46 (120)
T PF12325_consen   15 VQLVERLQSQLRRLEGELASLQEELARLEAER   46 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36889999999999999999999999998754

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 [].

>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=90.92  E-value=3  Score=35.73  Aligned_cols=70  Identities=19%  Similarity=0.225  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc---ccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          170 CLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEAR---DVLSEADFLKEKLKIEEEERKLEAAIEETEKQ  239 (269)
Q Consensus       170 C~ECtd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~---~~~seeel~~El~~Le~EE~~L~~eLeeLEkE  239 (269)
                      +..|+.-=+..|+.++..+..+........+.|+.+-.   ..++.+++...+..|+.+-..+...|..|...
T Consensus        66 ~~~~s~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~  138 (169)
T PF07106_consen   66 LEVPSPEELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSG  138 (169)
T ss_pred             cCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            44455555556666666655555555555555443321   24788899999999999999999999888864

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 [].

>PHA02562 46 endonuclease subunit; Provisional

Probab=90.15  E-value=2.1  Score=42.56  Aligned_cols=12  Identities=17%  Similarity=0.645  Sum_probs=7.1

Q ss_pred             CCcchHHHHHHH
Q 024294          166 EQPLCLECMRVL  177 (269)
Q Consensus       166 DhPLC~ECtd~L  177 (269)
                      .+..|.-|...+
T Consensus       283 ~~~~Cp~C~~~~  294 (562)
T PHA02562        283 KGGVCPTCTQQI  294 (562)
T ss_pred             CCCCCCCCCCcC
Confidence            356777775444

>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=89.51  E-value=13  Score=33.61  Aligned_cols=37  Identities=14%  Similarity=0.321  Sum_probs=30.9

Q ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          166 EQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRL  202 (269)
Q Consensus       166 DhPLC~ECtd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L  202 (269)
                      -...|..|+..=+-.+...+..+..+++....=+..+
T Consensus        10 ~~~~C~~C~~~~L~~~~~~l~~~~~~~~~l~~~i~~~   46 (302)
T PF10186_consen   10 RRFYCANCVNNRLLELRSELQQLKEENEELRRRIEEI   46 (302)
T ss_pred             CCeECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4568999999999999999999999998877755544

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

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=89.29  E-value=11  Score=33.48  Aligned_cols=92  Identities=20%  Similarity=0.303  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---hcc----ccccCCHHHHHHHHHHHHHHHHH----------HHHHHHHHH
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRL---EGE----ARDVLSEADFLKEKLKIEEEERK----------LEAAIEETE  237 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L---~~e----~~~~~seeel~~El~~Le~EE~~----------L~~eLeeLE  237 (269)
                      ..|+..|+.++.+-.+-|..+..-+..-   ...    ..+.....++..-+.+|++|..+          |...|+..-
T Consensus        15 a~Lv~~LQ~KV~qYr~rc~ele~~l~~~~~l~~~~~~~~~~~e~s~dLe~~l~rLeEEqqR~~~L~qvN~lLReQLEq~~   94 (182)
T PF15035_consen   15 AQLVQRLQAKVLQYRKRCAELEQQLSASQVLESPSQRRRSEEEHSPDLEEALIRLEEEQQRSEELAQVNALLREQLEQAR   94 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcccCcCcccccccccccCcccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            3578889999888888888777777311   000    00111123344445555554433          666777778


Q ss_pred             HHHHHHHHHHHHHHHHHHH----HHHHHHHhhh
Q 024294          238 KQNAEVNAELKELELKSKR----FKELEERYFF  266 (269)
Q Consensus       238 kE~~~l~~EL~~le~E~~~----Ld~eEe~yWr  266 (269)
                      .....|..+|..+..+...    |...|..||.
T Consensus        95 ~~N~~L~~dl~klt~~~~~l~~eL~~ke~~~~~  127 (182)
T PF15035_consen   95 KANEALQEDLQKLTQDWERLRDELEQKEAEWRE  127 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888888887766655    4444444443

>TIGR02231 conserved hypothetical protein

Probab=89.04  E-value=5.8  Score=39.83  Aligned_cols=82  Identities=18%  Similarity=0.203  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH---HHHHHhccc---------cccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          178 SDKLDKEVDDVTRDIEAYEA---CLQRLEGEA---------RDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNA  245 (269)
Q Consensus       178 le~Ld~ql~~~~~E~d~Y~~---fL~~L~~e~---------~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~  245 (269)
                      |+.++.++..++.++++...   ||+.+....         ....+.+++.+-+..+.++-.++..++.+++++++++++
T Consensus        80 l~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (525)
T TIGR02231        80 IRELEAELRDLEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTEDREAERRIRELEK  159 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555444   444443211         012255666666777777888888888888888888888


Q ss_pred             HHHHHHHHHHHHHH
Q 024294          246 ELKELELKSKRFKE  259 (269)
Q Consensus       246 EL~~le~E~~~Ld~  259 (269)
                      +|..++.+...+..
T Consensus       160 ~l~~l~~~l~~l~~  173 (525)
T TIGR02231       160 QLSELQNELNALLT  173 (525)
T ss_pred             HHHHHHHHHHhhcc
Confidence            88888888777653

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

>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=88.94  E-value=6.6  Score=37.19  Aligned_cols=39  Identities=26%  Similarity=0.497  Sum_probs=22.0

Q ss_pred             hhhhHHHHHHHH----HHhcC---CCCCCCcchHHHHHHHHHHHHH
Q 024294          145 FHSTITVLKRAF----EIATS---QTQVEQPLCLECMRVLSDKLDK  183 (269)
Q Consensus       145 ls~~i~~l~~lF----dILS~---~s~IDhPLC~ECtd~Lle~Ld~  183 (269)
                      ..+.+..+..||    ||.++   ++..=.-.+.+|-=.++..|+.
T Consensus        95 k~S~~silq~If~KHGDIAsNc~lkS~~~RS~yLe~Lc~IIqeLq~  140 (269)
T PF05278_consen   95 KPSQVSILQKIFEKHGDIASNCKLKSQQFRSYYLECLCDIIQELQS  140 (269)
T ss_pred             cHhHHHHHHHHHHhCccHhhccccCcHHHHHHHHHHHHHHHHHHhc
Confidence            345556666777    45544   2333334466776667777755

>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]

Probab=88.83  E-value=4.6  Score=40.71  Aligned_cols=80  Identities=16%  Similarity=0.194  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH
Q 024294          180 KLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETE----KQNAEVNAELKELELKSK  255 (269)
Q Consensus       180 ~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLE----kE~~~l~~EL~~le~E~~  255 (269)
                      .+...++.++.|...|+.+|.+-+++.         ..++.++.+||...+.++..+.    .+.++-++--+.+.+...
T Consensus       250 ~~~~hi~~l~~EveRlrt~l~~Aqk~~---------~ek~~qy~~Ee~~~reen~rlQrkL~~e~erRealcr~lsEses  320 (552)
T KOG2129|consen  250 AEKLHIDKLQAEVERLRTYLSRAQKSY---------QEKLMQYRAEEVDHREENERLQRKLINELERREALCRMLSESES  320 (552)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence            455667777888888999998776643         2344445555544444443332    222333333345566667


Q ss_pred             HHHHHHHHhhhhc
Q 024294          256 RFKELEERYFFNI  268 (269)
Q Consensus       256 ~Ld~eEe~yWre~  268 (269)
                      -|+-.|++|+.+|
T Consensus       321 slemdeery~Ne~  333 (552)
T KOG2129|consen  321 SLEMDEERYLNEF  333 (552)
T ss_pred             HHHHHHHHHHhhh
Confidence            8888999999887

>PHA02562 46 endonuclease subunit; Provisional

Probab=88.63  E-value=4.7  Score=40.05  Aligned_cols=85  Identities=20%  Similarity=0.313  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHH
Q 024294          178 SDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEV-------NAELKEL  250 (269)
Q Consensus       178 le~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l-------~~EL~~l  250 (269)
                      ++.++.++.....+.+.|..++..++....  ...+++++++..+..+-..+..++..++.+...+       ++.|..+
T Consensus       183 i~~l~~~i~~l~~~i~~~~~~i~~~~~~~~--~~i~~l~~e~~~l~~~~~~l~~~l~~l~~~i~~l~~~i~~~~~~L~~l  260 (562)
T PHA02562        183 IQTLDMKIDHIQQQIKTYNKNIEEQRKKNG--ENIARKQNKYDELVEEAKTIKAEIEELTDELLNLVMDIEDPSAALNKL  260 (562)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHH
Confidence            334455555555566666666666654322  2344555555555444444444444444443333       3344445


Q ss_pred             HHHHHHHHHHHHHh
Q 024294          251 ELKSKRFKELEERY  264 (269)
Q Consensus       251 e~E~~~Ld~eEe~y  264 (269)
                      +.+...++..-..+
T Consensus       261 ~~~~~~~~~~l~~~  274 (562)
T PHA02562        261 NTAAAKIKSKIEQF  274 (562)
T ss_pred             HHHHHHHHHHHHHH
Confidence            55554444443333

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

Probab=88.17  E-value=8.6  Score=42.52  Aligned_cols=50  Identities=20%  Similarity=0.284  Sum_probs=27.2

Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024294          217 KEKLKIEEEE-RKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFF  266 (269)
Q Consensus       217 ~El~~Le~EE-~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~yWr  266 (269)
                      +.+..++++. ..+..++.+++.+.+.|..|++.++.....|.++.+.+-.
T Consensus       379 k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~~~~~~  429 (1074)
T KOG0250|consen  379 KQIADLEKQTNNELGSELEERENKLEQLKKEVEKLEEQINSLREELNEVKE  429 (1074)
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444 4444555555555666666666666655566555555443

>PRK03918 chromosome segregation protein; Provisional

Probab=88.03  E-value=6.1  Score=41.56  Aligned_cols=16  Identities=6%  Similarity=0.366  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHHHH
Q 024294          177 LSDKLDKEVDDVTRDI  192 (269)
Q Consensus       177 Lle~Ld~ql~~~~~E~  192 (269)
                      ++..++.++..+....
T Consensus       170 ~~~~~~~~~~~l~~~l  185 (880)
T PRK03918        170 VIKEIKRRIERLEKFI  185 (880)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444444444433333

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

Probab=87.94  E-value=7.7  Score=37.54  Aligned_cols=87  Identities=16%  Similarity=0.272  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccc------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          174 MRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDV------LSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAEL  247 (269)
Q Consensus       174 td~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~------~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL  247 (269)
                      ...-++.|.++|.++..|++.++.=+.+.+......      ..-+++..+++++.+.-..|...+..+-.|++++..|.
T Consensus        84 L~~Ev~~Lrqkl~E~qGD~KlLR~~la~~r~~~~~~~~~~~~~ere~lV~qLEk~~~q~~qLe~d~qs~lDEkeEl~~ER  163 (319)
T PF09789_consen   84 LKEEVEELRQKLNEAQGDIKLLREKLARQRVGDEGIGARHFPHEREDLVEQLEKLREQIEQLERDLQSLLDEKEELVTER  163 (319)
T ss_pred             HHHHHHHHHHHHHHHhchHHHHHHHHHhhhhhhccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344577899999999999999998888765543221      23466677888888888888888888889999999999


Q ss_pred             HHHHHHHHHHHHH
Q 024294          248 KELELKSKRFKEL  260 (269)
Q Consensus       248 ~~le~E~~~Ld~e  260 (269)
                      .....+..+|..|
T Consensus       164 D~yk~K~~RLN~E  176 (319)
T PF09789_consen  164 DAYKCKAHRLNHE  176 (319)
T ss_pred             HHHHHHHHHHHHH
Confidence            9998888888765

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

Probab=87.82  E-value=3  Score=38.94  Aligned_cols=45  Identities=22%  Similarity=0.324  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          213 ADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRF  257 (269)
Q Consensus       213 eel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~L  257 (269)
                      ++|.+++..|+.+-.....+|+.|+.++..+++.++.+.-+...|
T Consensus       152 eeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l~~ev~~L  196 (290)
T COG4026         152 EELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDL  196 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHH
Confidence            445566666666666666666666666666666666555444333

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

Probab=87.41  E-value=11  Score=33.39  Aligned_cols=23  Identities=22%  Similarity=0.479  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 024294          180 KLDKEVDDVTRDIEAYEACLQRL  202 (269)
Q Consensus       180 ~Ld~ql~~~~~E~d~Y~~fL~~L  202 (269)
                      .++.+++.+.++.+....-+..|
T Consensus        66 ~~~~~~~~l~~~~~~~~~~i~~l   88 (188)
T PF03962_consen   66 KRQNKLEKLQKEIEELEKKIEEL   88 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444433

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

>PRK04863 mukB cell division protein MukB; Provisional

Probab=87.23  E-value=6.9  Score=44.82  Aligned_cols=27  Identities=19%  Similarity=0.254  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024294          177 LSDKLDKEVDDVTRDIEAYEACLQRLE  203 (269)
Q Consensus       177 Lle~Ld~ql~~~~~E~d~Y~~fL~~L~  203 (269)
                      ++.++..++..++++...+..|+....
T Consensus       315 iL~ELe~rL~kLEkQaEkA~kyleL~e  341 (1486)
T PRK04863        315 ELAELNEAESDLEQDYQAASDHLNLVQ  341 (1486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            348899999999999999999887543

>smart00787 Spc7 Spc7 kinetochore protein

Probab=86.90  E-value=12  Score=35.93  Aligned_cols=85  Identities=16%  Similarity=0.190  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc---------------------c--cCC---HHHHHHHHHHHHHHHH
Q 024294          174 MRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEAR---------------------D--VLS---EADFLKEKLKIEEEER  227 (269)
Q Consensus       174 td~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~---------------------~--~~s---eeel~~El~~Le~EE~  227 (269)
                      .+.|.+.|+..++.++.|...-...+..+..-..                     +  .-+   ...+..++..+..+-.
T Consensus       142 legLk~~L~~~~~~l~~D~~~L~~~~~~l~~~~~~l~~~~~~L~~e~~~L~~~~~e~~~~d~~eL~~lk~~l~~~~~ei~  221 (312)
T smart00787      142 LEGLKEGLDENLEGLKEDYKLLMKELELLNSIKPKLRDRKDALEEELRQLKQLEDELEDCDPTELDRAKEKLKKLLQEIM  221 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            5677777777777777777665555444432110                     0  001   1222234444555555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          228 KLEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       228 ~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      ....+|.+++.++.++...|++..++..++.
T Consensus       222 ~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~  252 (312)
T smart00787      222 IKVKKLEELEEELQELESKIEDLTNKKSELN  252 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555666666666666666665555554443

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

>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=86.82  E-value=5.7  Score=29.60  Aligned_cols=45  Identities=22%  Similarity=0.418  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          214 DFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       214 el~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      .+..||.+.+..--.+...|++.++...++..+|..|+.+.+++.
T Consensus        15 ~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r   59 (61)
T PF08826_consen   15 AIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEELR   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            345567777777777778888888888888888888887776654

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

>PRK10884 SH3 domain-containing protein; Provisional

Probab=86.54  E-value=16  Score=33.14  Aligned_cols=68  Identities=16%  Similarity=0.170  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          178 SDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKS  254 (269)
Q Consensus       178 le~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~  254 (269)
                      ++.++.++..+..+.+.-..=++.-         .+...+.+.+|+++-++|.++|..+.++...+++++..++...
T Consensus       102 l~~l~~~l~~~~~~~~~~~~~l~~~---------~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~~  169 (206)
T PRK10884        102 VKTLTDKLNNIDNTWNQRTAEMQQK---------VAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRTI  169 (206)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666776666655444433321         1223444555777777777788888888877777777777544

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

Probab=86.35  E-value=22  Score=31.40  Aligned_cols=109  Identities=22%  Similarity=0.381  Sum_probs=62.9

Q ss_pred             HHHHHHHhcCC-----CCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccc----------------cC
Q 024294          152 LKRAFEIATSQ-----TQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARD----------------VL  210 (269)
Q Consensus       152 l~~lFdILS~~-----s~IDhPLC~ECtd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~----------------~~  210 (269)
                      +++||+|+.++     ..+.-|-  .=.+..|..|+..|..+....-....--++++..-..                ..
T Consensus         3 f~Rl~~~~~a~~~~~ld~~EDP~--~~l~q~ird~e~~l~~a~~~~a~~~a~~~~le~~~~~~~~~~~~~~~~A~~Al~~   80 (221)
T PF04012_consen    3 FKRLKTLVKANINELLDKAEDPE--KMLEQAIRDMEEQLRKARQALARVMANQKRLERKLDEAEEEAEKWEKQAELALAA   80 (221)
T ss_pred             HHHHHHHHHHHHHHHHHhhcCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            34455555432     2355576  6667777778888777777666655555555433110                00


Q ss_pred             CHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          211 SEADF----LKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEE  262 (269)
Q Consensus       211 seeel----~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe  262 (269)
                      ..++|    ..++..++.+-..+.+.+..+......+...|..++.+...+...-.
T Consensus        81 g~edLAr~al~~k~~~e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~  136 (221)
T PF04012_consen   81 GREDLAREALQRKADLEEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKRE  136 (221)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            11222    23445566666666777777777777777777777776666665543

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 [].

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

Probab=86.18  E-value=19  Score=30.96  Aligned_cols=27  Identities=15%  Similarity=0.432  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 024294          178 SDKLDKEVDDVTRDIEAYEACLQRLEG  204 (269)
Q Consensus       178 le~Ld~ql~~~~~E~d~Y~~fL~~L~~  204 (269)
                      +...++++..+.+|.+....++..+..
T Consensus        83 ~~~~~~~l~~l~~el~~l~~~~~~~~~  109 (191)
T PF04156_consen   83 LSELQQQLQQLQEELDQLQERIQELES  109 (191)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566666666666666655555543

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 [].

>TIGR02473 flagell_FliJ flagellar export protein FliJ

Probab=85.94  E-value=17  Score=29.42  Aligned_cols=41  Identities=12%  Similarity=0.210  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          222 IEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEE  262 (269)
Q Consensus       222 Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe  262 (269)
                      |..........|..++.+.+.....+.....+.+.++..-+
T Consensus        73 l~~~i~~q~~~l~~~~~~~e~~r~~l~~a~~~~k~lekL~e  113 (141)
T TIGR02473        73 LDQRIQQQQQELALLQQEVEAKRERLLEARRELKALEKLKE  113 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444444444444444444444333

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.

>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=85.78  E-value=16  Score=31.36  Aligned_cols=48  Identities=17%  Similarity=0.286  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          213 ADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKEL  260 (269)
Q Consensus       213 eel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~e  260 (269)
                      ..+..++..+..+-+.|..+|..+-.++..|..++...+.+...|+..
T Consensus        55 e~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~eLE~~  102 (140)
T PF10473_consen   55 ETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKVSELESL  102 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455555666666666666666666666666666666666665543

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

>PF11414 Suppressor_APC: Adenomatous polyposis coli tumour suppressor protein; PDB: 1M5I_A

Probab=85.30  E-value=3.2  Score=32.73  Aligned_cols=53  Identities=15%  Similarity=0.288  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--Hhhhhc
Q 024294          216 LKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEE--RYFFNI  268 (269)
Q Consensus       216 ~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe--~yWre~  268 (269)
                      .+-++.|++|...|.+.|+.+|++++=...+|..+++....|-.-..  .||.|+
T Consensus         6 lk~mkeLEqEkd~LLqgLe~~Er~r~Wy~~qL~~vq~rq~~Lg~~~~~~~~~~d~   60 (84)
T PF11414_consen    6 LKRMKELEQEKDVLLQGLEMEERERDWYQQQLQSVQERQRHLGRNGTQFDFQMDL   60 (84)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------HHHHH
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCccccccCccccc
Confidence            45677899999999999999999999999999999999998888777  777764

>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=85.24  E-value=7.5  Score=32.47  Aligned_cols=45  Identities=16%  Similarity=0.262  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          213 ADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRF  257 (269)
Q Consensus       213 eel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~L  257 (269)
                      +.+...+..++.|-..+..+|..+++++..+.+||-.+-.+...+
T Consensus        19 e~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~   63 (120)
T PF12325_consen   19 ERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEEL   63 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444556666666666666666666666666666666665555444

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 [].

>PRK03918 chromosome segregation protein; Provisional

Probab=84.88  E-value=11  Score=39.72  Aligned_cols=23  Identities=26%  Similarity=0.537  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 024294          179 DKLDKEVDDVTRDIEAYEACLQR  201 (269)
Q Consensus       179 e~Ld~ql~~~~~E~d~Y~~fL~~  201 (269)
                      +.+......+......+...+..
T Consensus       165 ~~~~~~~~~~~~~~~~l~~~l~~  187 (880)
T PRK03918        165 KNLGEVIKEIKRRIERLEKFIKR  187 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444444433

>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function

Probab=84.27  E-value=11  Score=37.23  Aligned_cols=78  Identities=15%  Similarity=0.312  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          173 CMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKEL  250 (269)
Q Consensus       173 Ctd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~l  250 (269)
                      -....++.|..++.....+.......|..+...........+..+.+.++.+.-..+.++|++++.+...+.+++...
T Consensus       331 ~l~~~~~~l~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~l~~~l~~~  408 (451)
T PF03961_consen  331 ELKEKLEELEEELEELKEELEKLKKNLKKLKKLKKQGKLPPEKKEQLKKLKEKKKELKEELKELKEELKELKEELERS  408 (451)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            345566777777777777777777777766653221112344455566666666666666666666666666665544

The proteins are in the region of 500-600 amino acid residues in length.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=83.28  E-value=15  Score=27.80  Aligned_cols=32  Identities=25%  Similarity=0.229  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGEA  206 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~  206 (269)
                      +..+..|..+++.+.+....|..-++.|..+.
T Consensus         4 ea~~~~Lr~rLd~~~rk~~~~~~~~k~L~~ER   35 (69)
T PF14197_consen    4 EAEIATLRNRLDSLTRKNSVHEIENKRLRRER   35 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677889999999999999998888887653

>PRK09039 hypothetical protein; Validated

Probab=82.60  E-value=23  Score=34.24  Aligned_cols=84  Identities=17%  Similarity=0.220  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc----------------------ccCCHHHHHHHHHHHHHHHHHHHH
Q 024294          174 MRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEAR----------------------DVLSEADFLKEKLKIEEEERKLEA  231 (269)
Q Consensus       174 td~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~----------------------~~~seeel~~El~~Le~EE~~L~~  231 (269)
                      .+.-+..|..+++.++.+|..=...+........                      ..+...-|..++..|+.+-+.+..
T Consensus        79 l~~~l~~l~~~l~~a~~~r~~Le~~~~~~~~~~~~~~~~~~~l~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~  158 (343)
T PRK09039         79 LQDSVANLRASLSAAEAERSRLQALLAELAGAGAAAEGRAGELAQELDSEKQVSARALAQVELLNQQIAALRRQLAALEA  158 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcchHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456677777777777777655544332211000                      012234444555555555566666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          232 AIEETEKQNAEVNAELKELELKSKRF  257 (269)
Q Consensus       232 eLeeLEkE~~~l~~EL~~le~E~~~L  257 (269)
                      +|..+|+..++...+|..++.+....
T Consensus       159 ~L~~ae~~~~~~~~~i~~L~~~L~~a  184 (343)
T PRK09039        159 ALDASEKRDRESQAKIADLGRRLNVA  184 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666666666666666665555544

>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]

Probab=82.39  E-value=9.2  Score=35.76  Aligned_cols=54  Identities=17%  Similarity=0.217  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 024294          214 DFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFN  267 (269)
Q Consensus       214 el~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~yWre  267 (269)
                      ..++...+-+..+.+....+..|++|.+.+..++.+++.+...|.....+||..
T Consensus       205 A~~kSR~~~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~~~  258 (269)
T KOG3119|consen  205 AVRKSRDKRKQKEDEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQLPKP  258 (269)
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            344444455556677778899999999999999999999999999999999975

>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=82.22  E-value=29  Score=31.58  Aligned_cols=44  Identities=32%  Similarity=0.370  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          215 FLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       215 l~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      +..++..|+.|...|....+.+++..+..++++..++.+.+.++
T Consensus        54 L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~   97 (251)
T PF11932_consen   54 LLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIE   97 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444444444333

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.

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

Probab=82.15  E-value=32  Score=29.69  Aligned_cols=87  Identities=17%  Similarity=0.293  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc---cc--cc----------------------------CCHHHHHHHHHH
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGE---AR--DV----------------------------LSEADFLKEKLK  221 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e---~~--~~----------------------------~seeel~~El~~  221 (269)
                      +..++.|+.++..++.-+..+..+++.|+.-   ..  +.                            --+.++.+.+..
T Consensus        19 ~~qie~L~~~i~~l~~~~~e~~~~~~tl~~lk~~~~g~E~LVpvGag~fv~~kv~~~~kviV~iGsg~~ae~~~~eAie~   98 (145)
T COG1730          19 QSQIESLQAQIAALNAAISELQTAIETLENLKGAGEGKEVLVPVGAGLFVKAKVKDMDKVIVSIGSGYYAEKSADEAIEF   98 (145)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEEEcCCCceEEEEeccCceEEEEcCCceeeeecHHHHHHH
Confidence            3467778888777777777777776655431   10  10                            012344445555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          222 IEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELE  261 (269)
Q Consensus       222 Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eE  261 (269)
                      |++....|...++.++...+++...+..++.+.+++.+.+
T Consensus        99 l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~~~q~~  138 (145)
T COG1730          99 LKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQQKQ  138 (145)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555666666666666666666666666666555544

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=81.80  E-value=22  Score=38.08  Aligned_cols=13  Identities=23%  Similarity=0.542  Sum_probs=5.1

Q ss_pred             HHHHHHHHHHHHH
Q 024294          180 KLDKEVDDVTRDI  192 (269)
Q Consensus       180 ~Ld~ql~~~~~E~  192 (269)
                      .+..++..++.+.
T Consensus       354 ~~~~~l~~~~~~~  366 (1164)
T TIGR02169       354 KLTEEYAELKEEL  366 (1164)
T ss_pred             HHHHHHHHHHHHH
Confidence            3344444433333

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.

>PRK03947 prefoldin subunit alpha; Reviewed

Probab=81.51  E-value=29  Score=28.71  Aligned_cols=86  Identities=15%  Similarity=0.283  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc---c----------------c--------------CCHHHHHHHHHHH
Q 024294          176 VLSDKLDKEVDDVTRDIEAYEACLQRLEGEAR---D----------------V--------------LSEADFLKEKLKI  222 (269)
Q Consensus       176 ~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~---~----------------~--------------~seeel~~El~~L  222 (269)
                      ..++.|..++..+......|...+..|+.-..   .                +              --+..+.+.+..|
T Consensus        20 ~~~~~l~~~~~~l~~~~~e~~~~~e~l~~l~~~~~~~e~lvplg~~~yv~~~v~~~~kV~v~lG~g~~vE~~~~eA~~~l   99 (140)
T PRK03947         20 AQIEALQQQLEELQASINELDTAKETLEELKSKGEGKETLVPIGAGSFVKAKVKDKDKVIVSLGAGYSAEKDLDEAIEIL   99 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCeEEEEcCCCcEEEEEecCCCeEEEEcCCCEEEEecHHHHHHHH
Confidence            34667777777777777778777765543210   0                0              0012455556667


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          223 EEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELE  261 (269)
Q Consensus       223 e~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eE  261 (269)
                      +.....+...++.++++...+..++..+.....++..+.
T Consensus       100 ~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~l~~~~  138 (140)
T PRK03947        100 DKRKEELEKALEKLEEALQKLASRIAQLAQELQQLQQEA  138 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            777777777777777777777777777777777766554

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=81.23  E-value=24  Score=37.86  Aligned_cols=20  Identities=15%  Similarity=0.415  Sum_probs=8.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 024294          178 SDKLDKEVDDVTRDIEAYEA  197 (269)
Q Consensus       178 le~Ld~ql~~~~~E~d~Y~~  197 (269)
                      +..+..++..++.+......
T Consensus       260 l~~~~~~~~~~~~~~~~~~~  279 (1164)
T TIGR02169       260 ISELEKRLEEIEQLLEELNK  279 (1164)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444333

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.

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=81.09  E-value=24  Score=31.15  Aligned_cols=58  Identities=14%  Similarity=0.165  Sum_probs=34.2

Q ss_pred             CHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 024294          211 SEADFLKEKLKIEE---EERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFNI  268 (269)
Q Consensus       211 seeel~~El~~Le~---EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~yWre~  268 (269)
                      +.++.-.=|+.|+.   ....+..+.+.++.+.+++..+++.|+.|...|.++=..|-.||
T Consensus        81 tl~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY  141 (161)
T TIGR02894        81 TLQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDY  141 (161)
T ss_pred             CHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444433444433   35556666777777777777777777777777766554444443

In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.

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

Probab=81.07  E-value=21  Score=39.71  Aligned_cols=41  Identities=34%  Similarity=0.518  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          219 KLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKE  259 (269)
Q Consensus       219 l~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~  259 (269)
                      +..++.+...+...|..++.++..++.+|..++.+..++..
T Consensus       865 l~~~~~~~~~l~~~l~~~~~~~~~l~~~l~~~~~~~~~~~~  905 (1163)
T COG1196         865 LEELEAEKEELEDELKELEEEKEELEEELRELESELAELKE  905 (1163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444455555555555555555555555554444443

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=81.00  E-value=42  Score=30.44  Aligned_cols=49  Identities=24%  Similarity=0.286  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          212 EADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKEL  260 (269)
Q Consensus       212 eeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~e  260 (269)
                      .+++...+..|+++-+.|..+.+.+|+|...|-++|..|+++...+..+
T Consensus        69 ledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e  117 (193)
T PF14662_consen   69 LEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAE  117 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHh
Confidence            4555555666777777777777777777777777777777766655443

>PRK01156 chromosome segregation protein; Provisional

Probab=80.95  E-value=11  Score=40.23  Aligned_cols=19  Identities=21%  Similarity=0.545  Sum_probs=12.7

Q ss_pred             CcchHHHHHHHHHHHHHHH
Q 024294          167 QPLCLECMRVLSDKLDKEV  185 (269)
Q Consensus       167 hPLC~ECtd~Lle~Ld~ql  185 (269)
                      .|+|.-|-+-+-+.+..++
T Consensus       452 ~~~Cp~c~~~~~~e~~~e~  470 (895)
T PRK01156        452 QSVCPVCGTTLGEEKSNHI  470 (895)
T ss_pred             CCCCCCCCCcCChhhHHHH
Confidence            7999999665555544444

>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF

Probab=80.91  E-value=28  Score=35.61  Aligned_cols=43  Identities=28%  Similarity=0.414  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024294          222 IEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERY  264 (269)
Q Consensus       222 Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~y  264 (269)
                      |.+.+..|....+.|++....|+...+.++...+.|++.++++
T Consensus        85 L~qRee~Lekr~e~Lekre~~Le~ke~~L~~re~eLee~~~e~  127 (514)
T TIGR03319        85 LLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEEL  127 (514)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444444444444444444444444444444444433

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

Probab=80.90  E-value=34  Score=29.10  Aligned_cols=84  Identities=17%  Similarity=0.244  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccc----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          176 VLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDV----LSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELE  251 (269)
Q Consensus       176 ~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~----~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le  251 (269)
                      .=|..|+.++..++.+.+.+...|..+.......    ..-+.|...+..|+++-......|..+......++.....++
T Consensus        35 ~EI~sL~~K~~~lE~eld~~~~~l~~~k~~lee~~~~~~~~E~l~rriq~LEeele~ae~~L~e~~ekl~e~d~~ae~~e  114 (143)
T PF12718_consen   35 QEITSLQKKNQQLEEELDKLEEQLKEAKEKLEESEKRKSNAEQLNRRIQLLEEELEEAEKKLKETTEKLREADVKAEHFE  114 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence            3466788888888888888888888775432211    123456666666777666666666666655555555555555


Q ss_pred             HHHHHHHH
Q 024294          252 LKSKRFKE  259 (269)
Q Consensus       252 ~E~~~Ld~  259 (269)
                      .....|+.
T Consensus       115 Rkv~~le~  122 (143)
T PF12718_consen  115 RKVKALEQ  122 (143)
T ss_pred             HHHHHHHh
Confidence            55444443

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 [].

>PRK12704 phosphodiesterase; Provisional

Probab=80.81  E-value=27  Score=35.76  Aligned_cols=16  Identities=31%  Similarity=0.491  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHHHH
Q 024294          229 LEAAIEETEKQNAEVN  244 (269)
Q Consensus       229 L~~eLeeLEkE~~~l~  244 (269)
                      |.++.+.|++...+|+
T Consensus        98 Le~r~e~Lekke~eL~  113 (520)
T PRK12704         98 LDRKLELLEKREEELE  113 (520)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333333333333333

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

Probab=80.65  E-value=27  Score=35.96  Aligned_cols=71  Identities=18%  Similarity=0.214  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHhccccccCCHHHHHHH----HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024294          192 IEAYEACLQRLEGEARDVLSEADFLKE----KLKIEEEERKLEAAIEETE---KQNAEVNAELKELELKSKRFKELEERY  264 (269)
Q Consensus       192 ~d~Y~~fL~~L~~e~~~~~seeel~~E----l~~Le~EE~~L~~eLeeLE---kE~~~l~~EL~~le~E~~~Ld~eEe~y  264 (269)
                      ++.|..||+   .+....+.+++|..-    ...+-.+-++|..++++|+   ++-.++.+-++.++++.+.|...+..|
T Consensus       238 ~~~Y~~fl~---~~~~~~~~e~Elk~~f~~~~~~i~~~i~~lk~~n~~l~e~i~ea~k~s~~i~~l~ek~r~l~~D~nk~  314 (622)
T COG5185         238 TESYKSFLK---LEDNYEPSEQELKLGFEKFVHIINTDIANLKTQNDNLYEKIQEAMKISQKIKTLREKWRALKSDSNKY  314 (622)
T ss_pred             HHHHHHHhc---CCCccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            578899987   332234566666532    2224445555555555444   555667888888888888888888877


Q ss_pred             h
Q 024294          265 F  265 (269)
Q Consensus       265 W  265 (269)
                      -
T Consensus       315 ~  315 (622)
T COG5185         315 E  315 (622)
T ss_pred             H
Confidence            4

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

Probab=80.54  E-value=41  Score=31.98  Aligned_cols=37  Identities=43%  Similarity=0.468  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          215 FLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELE  251 (269)
Q Consensus       215 l~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le  251 (269)
                      +.+++..++.+-..+..+++++..++.++.++|.+++
T Consensus       228 ~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI~e~~  264 (325)
T PF08317_consen  228 KKKELAELQEELEELEEKIEELEEQKQELLAEIAEAE  264 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555555555555555555444

>TIGR01069 mutS2 MutS2 family protein

Probab=80.50  E-value=8.1  Score=41.24  Aligned_cols=20  Identities=25%  Similarity=0.305  Sum_probs=13.7

Q ss_pred             ceecccCCccee----eeccccch
Q 024294           21 RWVCQNCRHFLC----IVGVDSYA   40 (269)
Q Consensus        21 ~~~Cq~C~~~l~----i~g~d~~~   40 (269)
                      .+...+-+|||.    +|..|..+
T Consensus       295 ~i~l~~~rhPll~~~~~vp~di~l  318 (771)
T TIGR01069       295 KIILENARHPLLKEPKVVPFTLNL  318 (771)
T ss_pred             CEEEccccCceecCCceEeceeEe
Confidence            577888888876    45555554

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

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

Probab=80.31  E-value=30  Score=34.81  Aligned_cols=74  Identities=20%  Similarity=0.267  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKS  254 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~  254 (269)
                      +.=+++++++++..+++...=..-..+|+.      ...+++.++..++.+-.+....|.++++..+.++..|.+++.+.
T Consensus        37 ~~~l~q~q~ei~~~~~~i~~~~~~~~kL~~------~lk~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~l~~l~~q~  110 (420)
T COG4942          37 DKQLKQIQKEIAALEKKIREQQDQRAKLEK------QLKSLETEIASLEAQLIETADDLKKLRKQIADLNARLNALEVQE  110 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHH
Confidence            355677777777777777776666666654      24556666666777766677777777777777777777776555

---

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	269
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-08
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-07
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
1g8x_A	1010	Myosin II heavy chain fused to alpha-actinin 3; mo	8e-07
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	7e-06
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	8e-04

>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 = 51.8 bits (124), Expect = 9e-08
 Identities = 18/86 (20%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 180  KLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLK-IEEEERKLEAAIEETEK 238
            K+ +++ D+   +E  EA  Q+L+ E      +   +++ +  +E++  KL    +  E+
Sbjct: 952  KMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEE 1011

Query: 239  QNAEVNAELKELELKSKRFKELEERY 264
            + +++   L E E K+K   +L+ ++
Sbjct: 1012 RVSDLTTNLAEEEEKAKNLTKLKNKH 1037

>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 = 41.4 bits (97), Expect = 2e-04
 Identities = 19/99 (19%), Positives = 41/99 (41%), Gaps = 21/99 (21%)

Query: 180  KLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQ 239
            K ++E+      +E   +       + R++ S    L+E L+ E+  R       + EKQ
Sbjct: 1092 KKEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAAR------NKAEKQ 1145

Query: 240  NAEVNAELKEL---------------ELKSKRFKELEER 263
              +++ EL+ L               EL+   +K+ +++
Sbjct: 1146 KRDLSEELEALKTELEDTLDTTATQQELRGSDYKDDDDK 1184

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 49.0 bits (117), Expect = 7e-07
 Identities = 18/102 (17%), Positives = 43/102 (42%), Gaps = 8/102 (7%)

Query: 171  LECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLK--------I 222
            +E  + L   L+ ++  + R I+      + L  +  ++        EKL+         
Sbjct: 916  VERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMS 975

Query: 223  EEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERY 264
            EEE +     +   +++ A++  EL + + + K  +E  ++Y
Sbjct: 976  EEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKY 1017

>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 179  DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEK 238
             KL KE+     + +  E    + + E   ++SE    ++   ++ E+ +L   I +  K
Sbjct: 994  AKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELK--EQNTLLKTEKEELNRRIHDQAK 1051

Query: 239  QNAEVNAELKELELKSKRFKELEE 262
            +  E   +    E K     +L +
Sbjct: 1052 EITETMEKKLVEETKQLE-LDLND 1074

>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM, protein engineering, structural protein; HET: ADP; 2.80A {Dictyostelium discoideum} SCOP: k.1.1.1 Length = 1010

 Score = 48.9 bits (117), Expect = 8e-07
 Identities = 16/113 (14%), Positives = 37/113 (32%), Gaps = 3/113 (2%)

Query: 151 VLKRAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVL 210
            L+    +   +  V             D     ++   ++         + + +   +L
Sbjct: 832 SLQTKLRLIKREPFVAP---AGLTPNEIDSTWSALEKAEQEHAEALRIELKRQKKIAVLL 888

Query: 211 SEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEER 263
            + + + +KL+     + +     ET      V A+LK LE      + LE +
Sbjct: 889 QKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQ 941

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus} Length = 96

 Score = 43.0 bits (101), Expect = 7e-06
 Identities = 12/54 (22%), Positives = 27/54 (50%)

Query: 211 SEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERY 264
                 +E  ++  EE +L   +E+ EK    V   L++++ +++R  + E +Y
Sbjct: 5   DSEQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQY 58

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 38.6 bits (89), Expect = 8e-04
 Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 10/58 (17%)

Query: 210 LSEADFLK---EKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERY 264
           +++AD L    E ++   EE++    ++E +  +        E E + K  K+LEE  
Sbjct: 74  IAQADRLTQEPESIRKWREEQRKR--LQELDAASKV-----MEQEWREKAKKDLEEWN 124

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	269
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	99.04
2p1l_B	31	Beclin 1; apoptosis, autophagy, BH3 domain, BCL; 2	98.66
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	90.77
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	90.11
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	89.99
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	89.42
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	88.89
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	88.61
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	87.77
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	87.56
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	87.33
3ajw_A	150	Flagellar FLIJ protein; flagellum, type III secret	86.99
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	86.29
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	85.65
3mq9_A	471	Bone marrow stromal antigen 2 fused to maltose-BI	85.28
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	84.67
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	83.77
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	83.04
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	82.04
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	81.66
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	81.28
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	81.12
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	81.05
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	81.01

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=99.04  E-value=8.6e-10  Score=86.96  Aligned_cols=58  Identities=21%  Similarity=0.351  Sum_probs=55.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 024294          211 SEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFNI  268 (269)
Q Consensus       211 seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~yWre~  268 (269)
                      +.+.+.++|..|+.+|++|+++|+.||++++.|+.+|.+++.++++|+.+|++||++|
T Consensus         5 ~~~~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~eE~~~w~ey   62 (96)
T 3q8t_A            5 DSEQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQREY   62 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            3577889999999999999999999999999999999999999999999999999997

>2p1l_B Beclin 1; apoptosis, autophagy, BH3 domain, BCL; 2.50A {Homo sapiens} PDB: 3dvu_C 2pon_A

Probab=98.66  E-value=6.4e-09  Score=66.63  Aligned_cols=26  Identities=27%  Similarity=0.517  Sum_probs=18.1

Q ss_pred             CChhhhHHHHHHHHHHhcCCCCCCCc
Q 024294          143 SGFHSTITVLKRAFEIATSQTQVEQP  168 (269)
Q Consensus       143 ~~ls~~i~~l~~lFdILS~~s~IDhP  168 (269)
                      .+||++++++++||||||++++||||
T Consensus         6 ~~ls~~~~~~~~lFdILS~~sdIDhP   31 (31)
T 2p1l_B            6 ENLSRRLKVTGDLFDIMSGQTDVDHP   31 (31)
T ss_dssp             HHHHHHHHHHHHHHHHTTC-------
T ss_pred             ccHHHHHHHHHHHHHHHhCCCcCCCC
Confidence            57999999999999999999999999

>3q8t_A Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90A {Rattus norvegicus}

Probab=90.77  E-value=3.3  Score=32.02  Aligned_cols=42  Identities=12%  Similarity=0.302  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          212 EADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELK  253 (269)
Q Consensus       212 eeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E  253 (269)
                      +..+..+|..|+.+++.+..+|..++.+...++.+-...-.+
T Consensus        20 E~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~eE~~~w~e   61 (96)
T 3q8t_A           20 EERLIQELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQRE   61 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            455666666677777666666666666666665554443333

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

Probab=90.11  E-value=5  Score=32.11  Aligned_cols=69  Identities=12%  Similarity=0.185  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKE  249 (269)
Q Consensus       179 e~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~  249 (269)
                      ..|..+...+..|++.|+.=++....+...  ....|+.++..|......+...|.+||.....++..-+.
T Consensus         6 rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~--~~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDLER~~R~   74 (111)
T 2v66_B            6 RDLQADNQRLKYEVEALKEKLEHQYAQSYK--QVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRA   74 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHH
Confidence            457777788888888888777766554322  356677788888777777777888887777776655443

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

Probab=89.99  E-value=4.4  Score=35.72  Aligned_cols=8  Identities=13%  Similarity=-0.214  Sum_probs=3.1

Q ss_pred             HHHHHHHH
Q 024294          215 FLKEKLKI  222 (269)
Q Consensus       215 l~~El~~L  222 (269)
                      +.+|+..+
T Consensus        95 L~kEie~~  102 (256)
T 3na7_A           95 LNIEEDIA  102 (256)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            33343333

>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=89.42  E-value=2.6  Score=40.44  Aligned_cols=22  Identities=18%  Similarity=0.353  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 024294          230 EAAIEETEKQNAEVNAELKELE  251 (269)
Q Consensus       230 ~~eLeeLEkE~~~l~~EL~~le  251 (269)
                      .++++.++++..+++..++..+
T Consensus       536 ~~~~~~~~~~~~~le~~~~~~~  557 (597)
T 3oja_B          536 QKETEDLEQENIALEKQLDNKR  557 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcchhhHHhhhHHHHHHHhhhh
Confidence            3334434444444444333333

>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=88.89  E-value=4.2  Score=39.00  Aligned_cols=29  Identities=14%  Similarity=0.069  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLE  203 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~  203 (269)
                      +..+..++.++...++........++...
T Consensus       462 ~~~i~~l~~~~~~~~~~l~~~~~~i~~~~  490 (597)
T 3oja_B          462 RAEVQQLTNEQIQQEQLLQGLHAEIDTNL  490 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            36777777777777777776666666543

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

Probab=88.61  E-value=0.91  Score=48.40  Aligned_cols=13  Identities=15%  Similarity=0.621  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHH
Q 024294          181 LDKEVDDVTRDIE  193 (269)
Q Consensus       181 Ld~ql~~~~~E~d  193 (269)
                      |+.+++..++++.
T Consensus       933 Lq~rL~~~e~~n~  945 (1080)
T 2dfs_A          933 LQRKIDEQNKEYK  945 (1080)
T ss_dssp             -------------
T ss_pred             HHHHHHHHHHHHH
Confidence            3444444333433

>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=87.77  E-value=6.1  Score=29.23  Aligned_cols=71  Identities=18%  Similarity=0.215  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSK  255 (269)
Q Consensus       179 e~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~  255 (269)
                      +.+++++..+..|.+.+..=+..++..      ..+..+...+++.+-..|...+..||.+...+...+.....++.
T Consensus         2 ~~ikkKm~~lk~e~d~a~~~~~~~e~~------l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kLe   72 (81)
T 1ic2_A            2 DAIKKKMQMLKLDKENALDRAEQAEAD------KKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKLE   72 (81)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346677777777777776666655432      23344455566677777777777777777777666666654443

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

Probab=87.56  E-value=11  Score=32.67  Aligned_cols=31  Identities=19%  Similarity=0.352  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 024294          175 RVLSDKLDKEVDDVTRDIEAYEACLQRLEGE  205 (269)
Q Consensus       175 d~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e  205 (269)
                      ..+...+..++.+++.|-+-|..+=+.|+.+
T Consensus        16 k~~~~~~~q~~~~le~El~EFqesSrELE~E   46 (189)
T 2v71_A           16 KELSMKYKQSFQEARDELVEFQEGSRELEAE   46 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467778889999999988888888877653

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

Probab=87.33  E-value=7.3  Score=31.92  Aligned_cols=43  Identities=16%  Similarity=0.216  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          216 LKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       216 ~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      .+|+..|+.+-..+..+++.+.++.+++..++..++.+..+|+
T Consensus        88 ~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le  130 (138)
T 3hnw_A           88 DKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLE  130 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444445555555555555555555555555555555555553

>3ajw_A Flagellar FLIJ protein; flagellum, type III secretion, coiled-coil, protein transpor; 2.10A {Salmonella typhimurium}

Probab=86.99  E-value=7.6  Score=30.64  Aligned_cols=49  Identities=8%  Similarity=0.083  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 024294          219 KLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKELEERYFFN  267 (269)
Q Consensus       219 l~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~eEe~yWre  267 (269)
                      +..|..........|..++.+.+....++.+...+.+.++...++.+.+
T Consensus        76 i~~L~~~I~~q~~~l~~~~~~~e~~r~~l~~a~~~~k~~e~L~er~~~~  124 (150)
T 3ajw_A           76 IQTLEKAIEQHRLQLTQWTQKVDLALKSWREKKQRLQAWQTLQDRQTAA  124 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555556666666666666666666666666665555555443

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

Probab=86.29  E-value=8.9  Score=33.26  Aligned_cols=68  Identities=10%  Similarity=0.148  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          182 DKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELE  251 (269)
Q Consensus       182 d~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le  251 (269)
                      ..++..+..|.+.|+.=++.+..+...  ....|+.++..|...-..+...|.+||.....++...+...
T Consensus        62 ~~~~~~L~~E~e~~k~K~~~~~~e~~~--~~~~Lq~el~~l~~~~~~l~~~ireLEq~NDdlEr~~R~~~  129 (189)
T 2v71_A           62 QADNQRLKYEVEALKEKLEHQYAQSYK--QVSVLEDDLSQTRAIKEQLHKYVRELEQANDDLERAKRATI  129 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            333334444444444444433332111  24555666666766666677777777766666665555444

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

Probab=85.65  E-value=13  Score=30.51  Aligned_cols=40  Identities=13%  Similarity=0.154  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          215 FLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKS  254 (269)
Q Consensus       215 l~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~  254 (269)
                      +..++..+..+...+.++++++.++...+..++..|+.+.
T Consensus        94 lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~  133 (138)
T 3hnw_A           94 LKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETEL  133 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444455555555555555555555555444

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

Probab=85.28  E-value=8.2  Score=36.09  Aligned_cols=100  Identities=14%  Similarity=0.218  Sum_probs=54.9

Q ss_pred             HHHHHhcCCCCCCCcchHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH-Hhccccc-------cCCHHHHHHH-HHHH
Q 024294          154 RAFEIATSQTQVEQPLCLECMRVLSDKLDKEVDDVTRD--IEAYEACLQR-LEGEARD-------VLSEADFLKE-KLKI  222 (269)
Q Consensus       154 ~lFdILS~~s~IDhPLC~ECtd~Lle~Ld~ql~~~~~E--~d~Y~~fL~~-L~~e~~~-------~~seeel~~E-l~~L  222 (269)
                      .+-.+++|+..+     .+-.+.+.+.+++.|.....+  +..|...|++ |......       .-+.---... ...|
T Consensus       360 ~~~~vl~G~~t~-----eeal~~~~~~i~~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  434 (471)
T 3mq9_A          360 AVINAASGRQTV-----DEALKDAQTRITAARDGLRAVMEARNVTHLLQQELTEAQKGFQDVEAQAATANHTVMALMASL  434 (471)
T ss_dssp             HHHHHHHSSSCH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCH-----HHHHHHHHHHHHHHHHhhHHHHHhhhHHHHHHHHHHHHhhhHHHHHHHhhhcchhHHHHHHHH
Confidence            345677776543     455666666666666655443  4455555552 2111000       0000000011 1235


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          223 EEEERKLEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       223 e~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      +++-....+.++++|.|...++.+|+.++++.+++.
T Consensus       435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  470 (471)
T 3mq9_A          435 DAEKAQGQKKVEELEGEITTLNHKLQDASAEVERLR  470 (471)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            566666667788888888888888888888877764

>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=84.67  E-value=3.3  Score=30.88  Aligned_cols=47  Identities=21%  Similarity=0.197  Sum_probs=31.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          211 SEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRF  257 (269)
Q Consensus       211 seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~L  257 (269)
                      +..+|+..+++-.+|-+.....|+++|++..+.+++|+.|+.+...|
T Consensus        20 ti~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKf   66 (72)
T 3nmd_A           20 SLRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKY   66 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34555655555555556666667888888888888888777766554

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

Probab=83.77  E-value=13  Score=28.64  Aligned_cols=26  Identities=19%  Similarity=0.164  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024294          178 SDKLDKEVDDVTRDIEAYEACLQRLE  203 (269)
Q Consensus       178 le~Ld~ql~~~~~E~d~Y~~fL~~L~  203 (269)
                      ++.+++++..+..|.+.+..-...++
T Consensus         4 MdaIKkKm~~lk~e~e~a~drae~~e   29 (101)
T 3u1c_A            4 MDAIKKKMQMLKLDKENALDRAEQAE   29 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56666777777777776665555444

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

Probab=83.04  E-value=12  Score=32.77  Aligned_cols=39  Identities=15%  Similarity=0.183  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          218 EKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKR  256 (269)
Q Consensus       218 El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~  256 (269)
                      ++..|..|...+..++..+|.+..++..++..++.+...
T Consensus        91 E~~aL~kEie~~~~~i~~lE~eile~~e~ie~~~~~l~~  129 (256)
T 3na7_A           91 ELRSLNIEEDIAKERSNQANREIENLQNEIKRKSEKQED  129 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666666666666665555555555544433

>1wt6_A Myotonin-protein kinase; coiled-coil, kinase activation, DMPK, molecular replacement, transferase; 1.60A {Homo sapiens}

Probab=82.04  E-value=6.4  Score=29.95  Aligned_cols=44  Identities=16%  Similarity=0.388  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          215 FLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       215 l~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      +..||.++...--.+..+|++.++....|..||+.++.+.+.|.
T Consensus        29 i~EELs~vr~~ni~~eskL~eae~rn~eL~~e~~~l~~~~eelq   72 (81)
T 1wt6_A           29 LSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMELLQ   72 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555667777888888888888888887777764

>2w83_C C-JUN-amino-terminal kinase-interacting protein 4; golgi apparatus, protein transport, ER-golgi transport, ARF, GTPase, effector, myristate; HET: GTP; 1.93A {Homo sapiens}

Probab=81.66  E-value=11  Score=28.37  Aligned_cols=72  Identities=14%  Similarity=0.235  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          179 DKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKR  256 (269)
Q Consensus       179 e~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~  256 (269)
                      ..|-++++.+..|...-..--..|+-.      -.+|-..+..|-.|-..|..||..+..-+.+++..++.+++|+++
T Consensus         5 ~gmgkevEnLi~EN~eLl~TKNaLnvv------k~DLI~rvdELt~E~e~l~~El~s~~~~~~r~~~ri~elEeElkr   76 (77)
T 2w83_C            5 EFMGREVENLILENTQLLETKNALNIV------KNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRELEEELRK   76 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---------
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            355666666666654433333333321      245667777788888888888888888888888888888877664

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

Probab=81.28  E-value=14  Score=39.34  Aligned_cols=18  Identities=33%  Similarity=0.438  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 024294          234 EETEKQNAEVNAELKELE  251 (269)
Q Consensus       234 eeLEkE~~~l~~EL~~le  251 (269)
                      ..|+++...|++++.+++
T Consensus      1026 ~~L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A         1026 SELKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            334444444444444443

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1

Probab=81.12  E-value=6.5  Score=27.99  Aligned_cols=37  Identities=22%  Similarity=0.326  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          223 EEEERKLEAAIEETEKQNAEVNAELKELELKSKRFKE  259 (269)
Q Consensus       223 e~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld~  259 (269)
                      ..+...|..+++.|+++..+|..++..|+.|...|.+
T Consensus        22 k~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~   58 (63)
T 1ci6_A           22 RAEQEALTGECKELEKKNEALKERADSLAKEIQYLKD   58 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455567778888888888888888888877776654

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

Probab=81.05  E-value=19  Score=28.67  Aligned_cols=70  Identities=14%  Similarity=0.105  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          173 CMRVLSDKLDKEVDDVTRDIEAYEACLQRLEGEARDVLSEADFLKEKLKIEEEERKLEAAIEETEKQNAEVNAELKELEL  252 (269)
Q Consensus       173 Ctd~Lle~Ld~ql~~~~~E~d~Y~~fL~~L~~e~~~~~seeel~~El~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~  252 (269)
                      .....+..|++++..+...++.|..+++.|+...             .+|+..++....-|+.+|.-....-+...=|+.
T Consensus        32 e~~~~~~~Lq~El~~lr~~~~~l~~~iReLEq~N-------------DDLER~~R~t~~SLeD~E~k~n~aiErnalLE~   98 (111)
T 2v66_B           32 QSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQAN-------------DDLERAKRATIVSLEDFEQRLNQAIERNAFLES   98 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------------hHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence            3456788899999999999999999999987643             234444444444555555444444333334444


Q ss_pred             HHH
Q 024294          253 KSK  255 (269)
Q Consensus       253 E~~  255 (269)
                      |..
T Consensus        99 El~  101 (111)
T 2v66_B           99 ELD  101 (111)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            333

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

Probab=81.01  E-value=17  Score=28.00  Aligned_cols=39  Identities=21%  Similarity=0.218  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024294          220 LKIEEEERKLEAAIEETEKQNAEVNAELKELELKSKRFK  258 (269)
Q Consensus       220 ~~Le~EE~~L~~eLeeLEkE~~~l~~EL~~le~E~~~Ld  258 (269)
                      .+++..-..+...|+..++.....+.++..|......|.
T Consensus        61 d~~ee~L~ea~~kLee~ek~~~~aE~ev~~L~RriqllE   99 (101)
T 3u1c_A           61 DQVLEELHKSEDSLLFAEENAAKAESEVASLNRRIQLVE   99 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            333333344445555555555666666666666555543

---

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