Citrus Sinensis ID: 022288

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------30
Protein Sequence
MFCSQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTTDQDLPSGQRKSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKADDLG
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mfcsqknegevkDCAATRKMQKADREKLRRDRLNEHFTElgnaldpdrpkndkatILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPwaamdhsvmmappsypypvpmpmppgaipmhppmqpypmfgnqnpgvipnpcstfvpymapntlVEQQSAQYASavaqpsgrsqgsakedsgnkssgeskieknedsndvttdlelktpgsttdqdlpsgqrkskkslrkensftngssssrcsssrsvqdsssnsvaggrkaddlg
Flexible Loop (DISEMBL)
mfcsqknegevkdcaatrkmqkadreklrrdrLNEHftelgnaldpdrpknDKATILADTVQLLKDLTSQVEKLKTEhaalteesreltqeknDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEQQSAQYASAVAqpsgrsqgsakedsgnkssgeskieknedsndvttdlelktpgsttdqdlpsgqrkskkslrkensftngssssrcsssrsvqdsssnsvaggrkaddlg
Low Complexity Region (SEG)
MFCSQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVmmappsypypvpmpmppgaipmhppmqpYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEqqsaqyasavaqpsGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTTDQDLPSGQRKSKKSLRKENSFTNGssssrcsssrsvqdsssnsVAGGRKADDLG
Disordered region (IsUnstruct)
*******************************************************ILADTVQLLK*****************************************ENLNIQYQQRVRAMVPWAAMDHSV**************************************VIPNPCSTFVPYMAPNT******************************************************************************************************************
Disordered Region (DISOPRED)
***********************************HFTELGNALD********ATILADTVQLLKDLTS************************************************************************PMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTF**************************************************************************************************************************
Disordered Region (DISEMBL)
*************CAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEQQ*****************************************VTTDLELKTPG*********************************************************
Disordered Region (DISPRO)
*************************EKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNT********************************************NDVTTDLELKT***********************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFCSQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxYQQRVRAMVPWAAMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTTDQDLPSGQRKSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKADDLG
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	299	2.2.26 [Sep-21-2011]
Q9LT23	337	Transcription factor bHLH	yes	no	0.939	0.833	0.644	2e-81
Q8W2F2	286	Transcription factor bHLH	no	no	0.739	0.772	0.423	6e-42
Q9FH37	234	Transcription factor ILR3	no	no	0.528	0.675	0.371	4e-17
Q9LTC7	320	Transcription factor bHLH	no	no	0.401	0.375	0.382	1e-16
Q8L467	283	Transcription factor bHLH	no	no	0.391	0.413	0.410	3e-16
Q9SN74	240	Transcription factor bHLH	no	no	0.331	0.412	0.414	3e-15
Q9C682	226	Transcription factor bHLH	no	no	0.347	0.460	0.419	4e-14

>sp|Q9LT23|BH121_ARATH Transcription factor bHLH121 OS=Arabidopsis thaliana GN=BHLH121 PE=2 SV=1

 Score =  302 bits (774), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 190/295 (64%), Positives = 225/295 (76%), Gaps = 14/295 (4%)

Query: 8   EGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDL 67
           E EV D +A RK QKA REKLRR++LNEHF ELGN LDP+RPKNDKATIL DTVQLLK+L
Sbjct: 50  EEEVMDVSA-RKSQKAGREKLRREKLNEHFVELGNVLDPERPKNDKATILTDTVQLLKEL 108

Query: 68  TSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPW-AAM 126
           TS+V KLK+E+ ALT+ESRELTQEKNDLREEK SL+S+IENLN+QYQQR+R+M PW AAM
Sbjct: 109 TSEVNKLKSEYTALTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMSPWGAAM 168

Query: 127 DHSVMMA-PPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNT 185
           DH+VMMA PPS+PYP+P+ MPPG+IPMHP M  Y  FGNQNP +IP PC T++PYM PNT
Sbjct: 169 DHTVMMAPPPSFPYPMPIAMPPGSIPMHPSMPSYTYFGNQNPSMIPAPCPTYMPYMPPNT 228

Query: 186 LVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTT 245
           +VEQQS         P  RS+     +   K S ES+ EK EDSN+V T LELKTPGST+
Sbjct: 229 VVEQQSVHIPQ---NPGNRSR-----EPRAKVSRESRSEKAEDSNEVATQLELKTPGSTS 280

Query: 246 DQDLPSGQRKSKKSLR--KENSFTNGSSSSRCSSSRSVQD-SSSNSVAGGRKADD 297
           D+D      K+K+  R    NS    S SS+CSSS SV+D SSS+SVAGG+K DD
Sbjct: 281 DKDTLQRPEKTKRCKRNNNNNSIEESSHSSKCSSSPSVRDHSSSSSVAGGQKPDD 335

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W2F2|BH011_ARATH Transcription factor bHLH11 OS=Arabidopsis thaliana GN=BHLH11 PE=2 SV=2

 Score =  171 bits (433), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 119/281 (42%), Positives = 155/281 (55%), Gaps = 60/281 (21%)

Query: 21  QKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAA 80
           QKA+REKLRRD+L E F ELGNALDP+RPK+DKA++L DT+Q+LKD+ +QV++LK E+  
Sbjct: 48  QKAEREKLRRDKLKEQFLELGNALDPNRPKSDKASVLTDTIQMLKDVMNQVDRLKAEYET 107

Query: 81  LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSYPYP 140
           L++ESREL QEK++LREEK +L+S+IE LN QYQ R++ MVPW           P Y Y 
Sbjct: 108 LSQESRELIQEKSELREEKATLKSDIEILNAQYQHRIKTMVPWV----------PHYSYH 157

Query: 141 VPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAP-NTLVEQQSAQYASAVA 199
           +P                           I    S+F+PY A  N L EQQ    AS   
Sbjct: 158 IPFV------------------------AITQGQSSFIPYSASVNPLTEQQ----ASVQQ 189

Query: 200 QPSGRSQGSAKEDSGNK-----------SSGESKIEKNEDSNDVTTDLELKTPGSTTDQD 248
             S  +  S K+DS  K            SG+     N+  +DV   LELK   S+  Q 
Sbjct: 190 HSSSSADASMKQDSKIKPLDLDLMMNSNHSGQG----NDQKDDVRLKLELKIHASSLAQQ 245

Query: 249 LPSGQRKSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSV 289
             SG+ K K SL      T  SSS+  S S++VQDSS  +V
Sbjct: 246 DVSGKEK-KVSLT-----TTASSSNSYSLSQAVQDSSPGTV 280

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FH37|ILR3_ARATH Transcription factor ILR3 OS=Arabidopsis thaliana GN=ILR3 PE=1 SV=1

 Score = 89.0 bits (219), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/183 (37%), Positives = 98/183 (53%), Gaps = 25/183 (13%)

Query: 6   KNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRP-KNDKATILADTVQLL 64
           K  G  +  +AT    KA REK RRDRLN+ F ELG  L+P  P K DKA IL D V+++
Sbjct: 62  KKRGRCESSSATS--SKACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDAVRMV 119

Query: 65  KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA 124
             L  + +KLK  +++L ++ +EL  EKN+LR+EK  L++E E L    +Q+++A     
Sbjct: 120 TQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKL----EQQLKA----- 170

Query: 125 AMDHSVMMAP-PSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAP 183
                 M AP PS+ +P P PM P A        P    GN+   +I  P      +M P
Sbjct: 171 ------MNAPQPSF-FPAP-PMMPTAFASAQGQAP----GNKMVPIISYPGVAMWQFMPP 218

Query: 184 NTL 186
            ++
Sbjct: 219 ASV 221

Transcription factor. Plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. May regulates gene expression in response to metal homeostasis changes.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LTC7|BH034_ARATH Transcription factor bHLH34 OS=Arabidopsis thaliana GN=BHLH34 PE=2 SV=1

 Score = 87.4 bits (215), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 52/136 (38%), Positives = 80/136 (58%), Gaps = 16/136 (11%)

Query: 22  KADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTSQVEKLKTEHAA 80
           KA REKLRR++LN+ F +L + L+P R PK DK+ IL D ++++  L  +  +L+  +  
Sbjct: 167 KACREKLRREKLNDKFMDLSSVLEPGRTPKTDKSAILDDAIRVVNQLRGEAHELQETNQK 226

Query: 81  LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMV-----------PWAAMDHS 129
           L EE + L  +KN+LREEKL L++E E +    +Q++++MV           P A   H 
Sbjct: 227 LLEEIKSLKADKNELREEKLVLKAEKEKM----EQQLKSMVVPSPGFMPSQHPAAFHSHK 282

Query: 130 VMMAPPSYPYPVPMPM 145
           + +A P   YP  MPM
Sbjct: 283 MAVAYPYGYYPPNMPM 298

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L467|BH104_ARATH Transcription factor bHLH104 OS=Arabidopsis thaliana GN=BHLH104 PE=2 SV=1

 Score = 85.9 bits (211), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 55/134 (41%), Positives = 81/134 (60%), Gaps = 17/134 (12%)

Query: 22  KADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTSQVEKLKTEHAA 80
           KA RE+LRR++LNE F +L + L+P R PK DK  IL D +++L  L  +  KL+  +  
Sbjct: 135 KACRERLRREKLNERFMDLSSVLEPGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQK 194

Query: 81  LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM-------VPW--AAMDHSVM 131
           L EE + L  EKN+LREEKL L+++ E    + +Q++++M       +P   AA +H+ M
Sbjct: 195 LLEEIKSLKAEKNELREEKLVLKADKE----KTEQQLKSMTAPSSGFIPHIPAAFNHNKM 250

Query: 132 MAPPSYPYPVPMPM 145
              PSY Y   MPM
Sbjct: 251 AVYPSYGY---MPM 261

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN74|BH047_ARATH Transcription factor bHLH47 OS=Arabidopsis thaliana GN=BHLH47 PE=2 SV=1

 Score = 82.8 bits (203), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 41/99 (41%), Positives = 65/99 (65%)

Query: 18  RKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTE 77
           +++ KA RE+L+R+ LNE F EL + L+ ++  + KA+IL +  + LKD+  Q+E L+ E
Sbjct: 28  KRINKAVRERLKREHLNELFIELADTLELNQQNSGKASILCEATRFLKDVFGQIESLRKE 87

Query: 78  HAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR 116
           HA+L  ES  +T EKN+L+EE   L +EI  L  + + R
Sbjct: 88  HASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEAR 126

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C682|BH115_ARATH Transcription factor bHLH115 OS=Arabidopsis thaliana GN=BHLH115 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 44/105 (41%), Positives = 67/105 (63%), Gaps = 1/105 (0%)

Query: 11  VKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTS 69
           +K  + T    KA REK RRDRLN+ FTEL + L+P R PK DK  I+ D ++++     
Sbjct: 60  IKTESCTGSNSKACREKQRRDRLNDKFTELSSVLEPGRTPKTDKVAIINDAIRMVNQARD 119

Query: 70  QVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ 114
           + +KLK  +++L E+ +EL  EKN+LR+EK  L+ E E ++ Q +
Sbjct: 120 EAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLK 164

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	299
255576719	316	DNA binding protein, putative [Ricinus c	0.989	0.936	0.729	1e-105
224080584	326	predicted protein [Populus trichocarpa]	0.852	0.782	0.772	1e-105
224103239	283	predicted protein [Populus trichocarpa]	0.946	1.0	0.784	1e-104
356525604	282	PREDICTED: transcription factor bHLH121-	0.866	0.918	0.741	1e-103
147815026	378	hypothetical protein VITISV_018451 [Viti	0.983	0.777	0.714	8e-99
359475051	329	PREDICTED: transcription factor bHLH121-	0.983	0.893	0.714	1e-98
356556676	281	PREDICTED: transcription factor bHLH121-	0.866	0.921	0.703	7e-98
225431132	327	PREDICTED: transcription factor bHLH121-	0.963	0.880	0.631	3e-84
297735012	326	unnamed protein product [Vitis vinifera]	0.963	0.883	0.631	3e-84
449458566	335	PREDICTED: transcription factor bHLH121-	0.979	0.874	0.640	4e-84

>gi|255576719|ref|XP_002529247.1| DNA binding protein, putative [Ricinus communis] gi|223531283|gb|EEF33125.1| DNA binding protein, putative [Ricinus communis]

 Score =  389 bits (999), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 218/299 (72%), Positives = 241/299 (80%), Gaps = 3/299 (1%)

Query: 2   FC--SQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILAD 59
           FC  SQ  E EVKD  A RK +KADREKLRRDRLNEHF ELG+ALDPD+PKNDKATIL D
Sbjct: 17  FCFDSQGLESEVKDSVAVRKSEKADREKLRRDRLNEHFIELGDALDPDKPKNDKATILTD 76

Query: 60  TVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRA 119
           T+QLLKDLTSQV KLK E+A LTEESRELTQEKNDLREEK SL+SEIENLNIQYQQR RA
Sbjct: 77  TIQLLKDLTSQVNKLKVEYATLTEESRELTQEKNDLREEKASLKSEIENLNIQYQQRARA 136

Query: 120 MVPWAAMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVP 179
             PW AMDHSV+MAP SYP+ +PMP+PP  I +HP MQPYP FGNQNP VI NP S FVP
Sbjct: 137 TYPWVAMDHSVVMAPTSYPFLMPMPIPPRPISLHPTMQPYPFFGNQNPTVIHNPYSIFVP 196

Query: 180 YMAPNTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELK 239
           YM P+ LVEQQS Q+A++ A P+  S  S KEDS NKSS ESK  K+ DSNDVTT+LELK
Sbjct: 197 YMTPSALVEQQSTQHATSSALPASGSHVSGKEDSKNKSSRESKTGKSWDSNDVTTELELK 256

Query: 240 TPGSTTDQDLPSGQRKSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKADDL 298
           TPGSTTD DL S QRKSKKSL KENS T+GSS+SRCSS      SSS+S+AG  KADD+
Sbjct: 257 TPGSTTDPDLSSRQRKSKKSLGKENSITDGSSTSRCSSRSVQD-SSSSSIAGSPKADDI 314

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224080584|ref|XP_002306170.1| predicted protein [Populus trichocarpa] gi|222849134|gb|EEE86681.1| predicted protein [Populus trichocarpa]

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 197/255 (77%), Positives = 221/255 (86%)

Query: 8   EGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDL 67
           E E+KD  + RK+QKADREKLRRDRLNEHF ELGN LDPDRPKNDKATILADT+QLLKDL
Sbjct: 32  EAEIKDSVSARKIQKADREKLRRDRLNEHFVELGNTLDPDRPKNDKATILADTIQLLKDL 91

Query: 68  TSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMD 127
           TSQV+KLK E+A L+EES ELTQEKNDLREEK SL+S+IENLNIQ QQR+RA  PW AMD
Sbjct: 92  TSQVDKLKAEYATLSEESLELTQEKNDLREEKASLKSDIENLNIQCQQRLRAPYPWPAMD 151

Query: 128 HSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLV 187
           HS MMAPPSYP+P+P+PMPPGAIP+H  +QPYP FGNQNP VI NPCSTFVP MAPNTLV
Sbjct: 152 HSFMMAPPSYPFPMPVPMPPGAIPLHSSIQPYPFFGNQNPAVIHNPCSTFVPCMAPNTLV 211

Query: 188 EQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTTDQ 247
           +QQSAQ+ S+++QP+ RS  S ++D  NK SGE KIEK+E SNDVTTDLELKTPGST DQ
Sbjct: 212 DQQSAQHVSSLSQPASRSHVSGEQDLKNKPSGECKIEKSEGSNDVTTDLELKTPGSTADQ 271

Query: 248 DLPSGQRKSKKSLRK 262
           DL SGQRKSKKS RK
Sbjct: 272 DLSSGQRKSKKSQRK 286

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224103239|ref|XP_002312979.1| predicted protein [Populus trichocarpa] gi|222849387|gb|EEE86934.1| predicted protein [Populus trichocarpa]

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 222/283 (78%), Positives = 246/283 (86%)

Query: 15  AATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKL 74
            A RK+QKADREKLRRDRLNEHF ELGN LDPDRPKNDKATILADTVQLLKDL S+V+KL
Sbjct: 1   VAARKIQKADREKLRRDRLNEHFVELGNTLDPDRPKNDKATILADTVQLLKDLNSKVDKL 60

Query: 75  KTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAP 134
           K EHAAL+EESRELT EKNDLREEK SL+S++ENLNIQ QQ++RA  PWAAMDHSVMMAP
Sbjct: 61  KAEHAALSEESRELTLEKNDLREEKASLKSDVENLNIQCQQQLRATYPWAAMDHSVMMAP 120

Query: 135 PSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEQQSAQY 194
           PSYP+P+P+PMPPG IPMHP MQPYP +GNQNP VI NPCSTFVPY+APNTL +QQSAQ+
Sbjct: 121 PSYPFPMPVPMPPGPIPMHPSMQPYPFYGNQNPAVIHNPCSTFVPYIAPNTLFDQQSAQH 180

Query: 195 ASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTTDQDLPSGQR 254
            S++AQ + RS  S K+DS NKSSGESK+EK++DSNDVTTDLELKTPGST DQDL S QR
Sbjct: 181 VSSLAQSASRSHVSVKQDSKNKSSGESKVEKSKDSNDVTTDLELKTPGSTADQDLTSVQR 240

Query: 255 KSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKADD 297
           KSKKS  KE+S T  SSSSRCSSS SVQDSSSNSV G  K DD
Sbjct: 241 KSKKSTGKESSVTKESSSSRCSSSHSVQDSSSNSVVGNTKVDD 283

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356525604|ref|XP_003531414.1| PREDICTED: transcription factor bHLH121-like [Glycine max]

 Score =  382 bits (981), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 195/263 (74%), Positives = 214/263 (81%), Gaps = 4/263 (1%)

Query: 13  DCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVE 72
           DC+A RK QKADREKLRRDRLNE F ELGN LDPDRPKNDKATI+ DT+QLLKDLTSQV 
Sbjct: 2   DCSAARKTQKADREKLRRDRLNEQFVELGNILDPDRPKNDKATIIGDTIQLLKDLTSQVS 61

Query: 73  KLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMM 132
           KLK E+A L EESRELTQEKNDLREEK SL+S+I NLN QYQQ++R M PW AMDHSVMM
Sbjct: 62  KLKDEYATLNEESRELTQEKNDLREEKASLKSDIGNLNNQYQQQLRTMFPWTAMDHSVMM 121

Query: 133 APPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEQQSA 192
           APPSYPYPVPM +PPG I    PMQPYP F NQ+P VI NPCST+VPY+APNT+VEQQS 
Sbjct: 122 APPSYPYPVPMAVPPGPI----PMQPYPFFANQHPAVISNPCSTYVPYLAPNTIVEQQST 177

Query: 193 QYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTTDQDLPSG 252
           QY S    P GRS  S K++S +KSS ESK EKNEDSNDVTTDLELKTPGS+ DQDL S 
Sbjct: 178 QYVSPPLHPCGRSNVSGKQESKSKSSRESKAEKNEDSNDVTTDLELKTPGSSADQDLSSR 237

Query: 253 QRKSKKSLRKENSFTNGSSSSRC 275
           QRKS K  R+E+S T GSS  RC
Sbjct: 238 QRKSSKLSRRESSCTEGSSLGRC 260

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147815026|emb|CAN74571.1| hypothetical protein VITISV_018451 [Vitis vinifera]

 Score =  366 bits (939), Expect = 8e-99,   Method: Compositional matrix adjust.
 Identities = 213/298 (71%), Positives = 248/298 (83%), Gaps = 4/298 (1%)

Query: 4   SQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQL 63
           S+++EGE KD    RK+QKADREKLRRDRLNE F ELGNALDPDRPKNDKATIL+DT+QL
Sbjct: 81  SKRSEGEFKDFVTARKVQKADREKLRRDRLNEQFIELGNALDPDRPKNDKATILSDTIQL 140

Query: 64  LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPW 123
           LKDLT+QVEKLK E+A+L EESRELTQEKNDLREEK SL+S  ENLN+QYQQR+RAM PW
Sbjct: 141 LKDLTAQVEKLKAENASLNEESRELTQEKNDLREEKASLKSATENLNVQYQQRLRAMFPW 200

Query: 124 AAMDHSVMMAPPSYPYPVPMPMPP--GAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYM 181
           +A+D SV+++PPSYP+PVP+P+P   G+IPMHP MQPYP FG+QN G+IPNPCSTFVPY 
Sbjct: 201 SAIDPSVVVSPPSYPFPVPVPVPIPTGSIPMHPSMQPYPFFGSQNTGIIPNPCSTFVPYF 260

Query: 182 APNTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTP 241
            PNTL+E QS Q+ S   QP   S  S+K+DS N+S GESK EK EDS DV TDL+LKTP
Sbjct: 261 TPNTLIEPQSTQHVSPPMQPGSTSNISSKQDSKNESPGESKSEKGEDSTDVATDLQLKTP 320

Query: 242 GSTTDQDLPSGQR--KSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKADD 297
           GS +DQ++ SGQ+  K K+SL KE + T GSSSSRCSSS SVQDSSSNSV GGRKADD
Sbjct: 321 GSKSDQEVSSGQQQHKPKRSLSKEKNSTEGSSSSRCSSSPSVQDSSSNSVVGGRKADD 378

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359475051|ref|XP_002277206.2| PREDICTED: transcription factor bHLH121-like [Vitis vinifera] gi|297744660|emb|CBI37922.3| unnamed protein product [Vitis vinifera]

 Score =  365 bits (938), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 213/298 (71%), Positives = 248/298 (83%), Gaps = 4/298 (1%)

Query: 4   SQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQL 63
           S+++EGE KD    RK+QKADREKLRRDRLNE F ELGNALDPDRPKNDKATIL+DT+QL
Sbjct: 32  SKRSEGEFKDFVTARKVQKADREKLRRDRLNEQFIELGNALDPDRPKNDKATILSDTIQL 91

Query: 64  LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPW 123
           LKDLT+QVEKLK E+A+L EESRELTQEKNDLREEK SL+S  ENLN+QYQQR+RAM PW
Sbjct: 92  LKDLTAQVEKLKAENASLNEESRELTQEKNDLREEKASLKSATENLNVQYQQRLRAMFPW 151

Query: 124 AAMDHSVMMAPPSYPYPVPMPMPP--GAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYM 181
           +A+D SV+++PPSYP+PVP+P+P   G+IPMHP MQPYP FG+QN G+IPNPCSTFVPY 
Sbjct: 152 SAIDPSVVVSPPSYPFPVPVPVPIPTGSIPMHPSMQPYPFFGSQNTGIIPNPCSTFVPYF 211

Query: 182 APNTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTP 241
            PNTL+E QS Q+ S   QP   S  S+K+DS N+S GESK EK EDS DV TDL+LKTP
Sbjct: 212 TPNTLIEPQSTQHVSPPMQPGSTSNISSKQDSKNESPGESKSEKGEDSTDVATDLQLKTP 271

Query: 242 GSTTDQDLPSGQR--KSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKADD 297
           GS +DQ++ SGQ+  K K+SL KE + T GSSSSRCSSS SVQDSSSNSV GGRKADD
Sbjct: 272 GSKSDQEVSSGQQQHKPKRSLSKEKNSTEGSSSSRCSSSPSVQDSSSNSVVGGRKADD 329

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556676|ref|XP_003546649.1| PREDICTED: transcription factor bHLH121-like [Glycine max]

 Score =  362 bits (930), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 185/263 (70%), Positives = 207/263 (78%), Gaps = 4/263 (1%)

Query: 13  DCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVE 72
           DC+A RK QKADREKLRRDR+NE F ELGN LDPDRPKNDKATIL DT+QLLKDL SQV 
Sbjct: 2   DCSAARKTQKADREKLRRDRINEQFVELGNILDPDRPKNDKATILCDTIQLLKDLISQVS 61

Query: 73  KLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMM 132
           KLK E+A L EESRELT EK DLREEK SL+S+I+NLN QYQQ++R M PW AM+HSVMM
Sbjct: 62  KLKDEYAMLNEESRELTLEKTDLREEKASLKSDIDNLNNQYQQQLRTMFPWTAMEHSVMM 121

Query: 133 APPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAPNTLVEQQSA 192
           AP SYPYPVPM +PPG I    PMQPYP F NQ+P VI NPCST+VPY+APNT+VEQQS 
Sbjct: 122 APSSYPYPVPMAVPPGPI----PMQPYPFFANQHPAVISNPCSTYVPYLAPNTIVEQQST 177

Query: 193 QYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGSTTDQDLPSG 252
            Y S    P  R   S K++S +KSS ES  EKNE+SNDVTTDLELKTPGS+ DQDL SG
Sbjct: 178 LYVSPPLHPGARPNVSGKQESKSKSSRESMAEKNEESNDVTTDLELKTPGSSADQDLSSG 237

Query: 253 QRKSKKSLRKENSFTNGSSSSRC 275
           QRKS K  R+E+S T  SS  RC
Sbjct: 238 QRKSSKLSRRESSCTEWSSLGRC 260

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431132|ref|XP_002265960.1| PREDICTED: transcription factor bHLH121-like [Vitis vinifera]

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 185/293 (63%), Positives = 224/293 (76%), Gaps = 5/293 (1%)

Query: 5   QKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLL 64
           Q+ E E KD  A RK+QKADREKLRRDRLNEHF ELGN LDPDRPKNDKATILADT+Q+L
Sbjct: 38  QRTEVEAKDSIAARKVQKADREKLRRDRLNEHFLELGNTLDPDRPKNDKATILADTIQML 97

Query: 65  KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA 124
           KDLT++V +LK E AAL+EESREL QEKN+LREEK++L+S+I+NLN+QYQQR+R M PWA
Sbjct: 98  KDLTAEVNRLKVECAALSEESRELVQEKNELREEKVALKSDIDNLNVQYQQRLRVMFPWA 157

Query: 125 AMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAP- 183
            +D SV+M P  Y YPVP+P+P G IPMHP +QP+P FGNQNP  IPNPCSTF+PY  P 
Sbjct: 158 PIDPSVVMGPSPYSYPVPVPVPSGPIPMHPSLQPFPFFGNQNPSGIPNPCSTFIPYQTPA 217

Query: 184 NTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGS 243
           N   E  SAQYASA    S  S     +   +     S  EK ++SNDV TDLELKTPGS
Sbjct: 218 NPPTEVPSAQYASA----SHVSSKPDSKSKSSDRERSSNTEKCDESNDVATDLELKTPGS 273

Query: 244 TTDQDLPSGQRKSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKAD 296
           ++ QDL +G++K K+S RKE S T+GS SS+ SSS+++QDSSSNSV    K+D
Sbjct: 274 SSQQDLLTGEKKGKQSQRKERSATDGSCSSKYSSSQALQDSSSNSVGDLPKSD 326

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735012|emb|CBI17374.3| unnamed protein product [Vitis vinifera]

 Score =  317 bits (813), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 185/293 (63%), Positives = 224/293 (76%), Gaps = 5/293 (1%)

Query: 5   QKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLL 64
           Q+ E E KD  A RK+QKADREKLRRDRLNEHF ELGN LDPDRPKNDKATILADT+Q+L
Sbjct: 37  QRTEVEAKDSIAARKVQKADREKLRRDRLNEHFLELGNTLDPDRPKNDKATILADTIQML 96

Query: 65  KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA 124
           KDLT++V +LK E AAL+EESREL QEKN+LREEK++L+S+I+NLN+QYQQR+R M PWA
Sbjct: 97  KDLTAEVNRLKVECAALSEESRELVQEKNELREEKVALKSDIDNLNVQYQQRLRVMFPWA 156

Query: 125 AMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAP- 183
            +D SV+M P  Y YPVP+P+P G IPMHP +QP+P FGNQNP  IPNPCSTF+PY  P 
Sbjct: 157 PIDPSVVMGPSPYSYPVPVPVPSGPIPMHPSLQPFPFFGNQNPSGIPNPCSTFIPYQTPA 216

Query: 184 NTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGS 243
           N   E  SAQYASA    S  S     +   +     S  EK ++SNDV TDLELKTPGS
Sbjct: 217 NPPTEVPSAQYASA----SHVSSKPDSKSKSSDRERSSNTEKCDESNDVATDLELKTPGS 272

Query: 244 TTDQDLPSGQRKSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKAD 296
           ++ QDL +G++K K+S RKE S T+GS SS+ SSS+++QDSSSNSV    K+D
Sbjct: 273 SSQQDLLTGEKKGKQSQRKERSATDGSCSSKYSSSQALQDSSSNSVGDLPKSD 325

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449458566|ref|XP_004147018.1| PREDICTED: transcription factor bHLH121-like [Cucumis sativus]

 Score =  317 bits (812), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 189/295 (64%), Positives = 232/295 (78%), Gaps = 2/295 (0%)

Query: 4   SQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQL 63
           S ++EGE KD AA R++QKADREKLRR RLNE F ELGN LDPDRPKNDKATIL DT+QL
Sbjct: 39  SSRSEGEFKDSAAARRVQKADREKLRRGRLNEQFVELGNILDPDRPKNDKATILMDTIQL 98

Query: 64  LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPW 123
           LKDLTSQV KLK E+A LTEES+EL QEK+DLREEK  L+S+IENLN QYQQ++RA  PW
Sbjct: 99  LKDLTSQVNKLKAEYATLTEESQELAQEKSDLREEKALLKSDIENLNTQYQQKLRATYPW 158

Query: 124 AAMDHSVMMAPPSYPYPVPMPMPPGAIPMHPPMQPYPMFGNQNPGVIPNPCSTFVPYMAP 183
           AAMDHSV+MAP  +P+P+PM MPPG  P+HP +QP+  FGN +P VI NPCSTFVPY+ P
Sbjct: 159 AAMDHSVVMAPAPFPFPMPMQMPPGPYPLHPSLQPFTFFGNPDPRVIANPCSTFVPYIPP 218

Query: 184 NTLVEQQSAQYASAVAQPSGRSQGSAKEDSGNKSSGESKIEKNEDSNDVTTDLELKTPGS 243
           N+L EQQS+Q A    Q   RS+  +++++ +KSS ESKIEK+EDSN+V T LELKTPGS
Sbjct: 219 NSLTEQQSSQNAPPFIQSDNRSRNLSEQNTRSKSSIESKIEKSEDSNEVATCLELKTPGS 278

Query: 244 TTDQDLPSGQRKSKKSLRKENSFTNGSSSSRCSSSRSVQDSSSNSVAGGRKADDL 298
           +TDQD    Q   K   RKE++ +  SSSSRCSS RS++ +SS+S+  GRK+ D+
Sbjct: 279 STDQDTSYEQTNGKN--RKESNLSVESSSSRCSSPRSLEANSSSSMPNGRKSTDI 331

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	299
TAIR|locus:2092216	337	bHLH121 "AT3G19860" [Arabidops	0.408	0.362	0.766	1.8e-68
UNIPROTKB|Q67U21	343	OSJNBa0065F08.2 "Basic helix-l	0.424	0.370	0.661	1.1e-56
TAIR|locus:2135169	286	bHLH11 "AT4G36060" [Arabidopsi	0.344	0.360	0.650	6.5e-39
UNIPROTKB|Q69V10	265	P0506F02.119 "cDNA clone:J0230	0.374	0.422	0.419	1.7e-20
UNIPROTKB|Q2R1K8	278	Os11g0601700 "Helix-loop-helix	0.317	0.341	0.473	4e-19
TAIR|locus:2157538	234	ILR3 "AT5G54680" [Arabidopsis	0.364	0.465	0.439	2.2e-18
UNIPROTKB|Q6ZGM4	236	OJ1442_E05.19 "cDNA clone:006-	0.351	0.444	0.435	5.8e-18
UNIPROTKB|Q6ZKI8	253	OJ1119_D01.9 "BHLH transcripti	0.384	0.454	0.386	3.2e-17
TAIR|locus:2079102	240	PYE "AT3G47640" [Arabidopsis t	0.351	0.437	0.4	1.1e-16
TAIR|locus:2086198	320	bHLH34 "AT3G23210" [Arabidopsi	0.374	0.35	0.383	9e-16

TAIR|locus:2092216 bHLH121 "AT3G19860" [Arabidopsis thaliana (taxid:3702)]

 Score = 477 (173.0 bits), Expect = 1.8e-68, Sum P(2) = 1.8e-68
 Identities = 95/124 (76%), Positives = 110/124 (88%)

Query:     8 EGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDL 67
             E EV D +A RK QKA REKLRR++LNEHF ELGN LDP+RPKNDKATIL DTVQLLK+L
Sbjct:    50 EEEVMDVSA-RKSQKAGREKLRREKLNEHFVELGNVLDPERPKNDKATILTDTVQLLKEL 108

Query:    68 TSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPW-AAM 126
             TS+V KLK+E+ ALT+ESRELTQEKNDLREEK SL+S+IENLN+QYQQR+R+M PW AAM
Sbjct:   109 TSEVNKLKSEYTALTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMSPWGAAM 168

Query:   127 DHSV 130
             DH+V
Sbjct:   169 DHTV 172

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0016558 "protein import into peroxisome matrix" evidence=RCA

UNIPROTKB|Q67U21 OSJNBa0065F08.2 "Basic helix-loop-helix-like protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 447 (162.4 bits), Expect = 1.1e-56, Sum P(2) = 1.1e-56
 Identities = 84/127 (66%), Positives = 106/127 (83%)

Query:     4 SQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQL 63
             S K E + +   ATRK+QKADREK+RRDRLNE F ELG+ LDPDRP+NDKATIL+D +Q+
Sbjct:    26 SGKTECKTQGSIATRKVQKADREKMRRDRLNEQFQELGSTLDPDRPRNDKATILSDAIQM 85

Query:    64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPW 123
             LKDLTSQV KLK E+ +L+EE+RELTQEKN+LR+EK+SL+ E++NLN QYQQR+R + PW
Sbjct:    86 LKDLTSQVNKLKAEYTSLSEEARELTQEKNELRDEKVSLKFEVDNLNTQYQQRMRVLYPW 145

Query:   124 AAMDHSV 130
               M+ SV
Sbjct:   146 TGMEPSV 152

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2135169 bHLH11 "AT4G36060" [Arabidopsis thaliana (taxid:3702)]

 Score = 368 (134.6 bits), Expect = 6.5e-39, Sum P(2) = 6.5e-39
 Identities = 67/103 (65%), Positives = 89/103 (86%)

Query:    21 QKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAA 80
             QKA+REKLRRD+L E F ELGNALDP+RPK+DKA++L DT+Q+LKD+ +QV++LK E+  
Sbjct:    48 QKAEREKLRRDKLKEQFLELGNALDPNRPKSDKASVLTDTIQMLKDVMNQVDRLKAEYET 107

Query:    81 LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPW 123
             L++ESREL QEK++LREEK +L+S+IE LN QYQ R++ MVPW
Sbjct:   108 LSQESRELIQEKSELREEKATLKSDIEILNAQYQHRIKTMVPW 150

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|Q69V10 P0506F02.119 "cDNA clone:J023068N18, full insert sequence" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 242 (90.2 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 47/112 (41%), Positives = 74/112 (66%)

Query:    13 DCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVE 72
             D  A +++ K++REKL+RD+ N+ F ELGN L+PDR  N KA +L +T ++LKDL SQVE
Sbjct:    31 DKKAPKRIHKSEREKLKRDKQNDLFNELGNLLEPDRQNNGKACVLGETTRILKDLLSQVE 90

Query:    73 KLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA 124
              L+ E+++L  ES  +  E+N+L ++   LR+EI  L  + + R+     W+
Sbjct:    91 SLRKENSSLKNESHYVALERNELHDDNSMLRTEILELQNELRTRMEGNPVWS 142

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q2R1K8 Os11g0601700 "Helix-loop-helix DNA-binding domain containing protein, expressed" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 229 (85.7 bits), Expect = 4.0e-19, P = 4.0e-19
 Identities = 45/95 (47%), Positives = 67/95 (70%)

Query:    16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLK 75
             A +K  KA+REKL+RD+LN+ F EL + LDP+R  + KAT+L D  ++L+DL SQVE L+
Sbjct:    45 APKKTHKAEREKLKRDQLNDLFVELSSMLDPERQNSGKATVLGDAARVLRDLVSQVESLR 104

Query:    76 TEHAALTEESRELTQEKNDLREEKLSLRSEIENLN 110
              E +AL  E + +  E N+L+EE + LR++I  L+
Sbjct:   105 KEQSALLTERQYVGSENNELQEENIMLRAQILELH 139

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2157538 ILR3 "AT5G54680" [Arabidopsis thaliana (taxid:3702)]

 Score = 222 (83.2 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 51/116 (43%), Positives = 74/116 (63%)

Query:     6 KNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRP-KNDKATILADTVQLL 64
             K  G  +  +AT    KA REK RRDRLN+ F ELG  L+P  P K DKA IL D V+++
Sbjct:    62 KKRGRCESSSATSS--KACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDAVRMV 119

Query:    65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM 120
               L  + +KLK  +++L ++ +EL  EKN+LR+EK  L++E E L    +Q+++AM
Sbjct:   120 TQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKL----EQQLKAM 171

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

UNIPROTKB|Q6ZGM4 OJ1442_E05.19 "cDNA clone:006-303-B03, full insert sequence" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 218 (81.8 bits), Expect = 5.8e-18, P = 5.8e-18
 Identities = 47/108 (43%), Positives = 71/108 (65%)

Query:    22 KADREKLRRDRLNEHFTELGNALDPDRP-KNDKATILADTVQLLKDLTSQVEKLKTEHAA 80
             KA REK+RRDRLN+ F EL + ++PD+  K DKA IL+D  +LL +L  + EKLK  +  
Sbjct:    71 KACREKIRRDRLNDRFLELSSVINPDKQAKLDKANILSDAARLLAELRGEAEKLKESNEK 130

Query:    81 LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDH 128
             L E  ++L  EKN+LR+EK++L++E E L  + Q +  ++ P   + H
Sbjct:   131 LRETIKDLKVEKNELRDEKVTLKAEKERL--EQQVKALSVAPTGFVPH 176

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q6ZKI8 OJ1119_D01.9 "BHLH transcription factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 211 (79.3 bits), Expect = 3.2e-17, P = 3.2e-17
 Identities = 46/119 (38%), Positives = 75/119 (63%)

Query:    11 VKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRP-KNDKATILADTVQLLKDLTS 69
             V+  +  R   KA REK+RRD++N+ F ELG  L+P +P K+DKA IL+D  +++  L +
Sbjct:    76 VRSGSCGRPTSKASREKIRRDKMNDRFLELGTTLEPGKPVKSDKAAILSDATRMVIQLRA 135

Query:    70 QVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDH 128
             + ++LK  + +L ++ +EL  EK++LR+EK  L+ E E L  + Q ++    P A M H
Sbjct:   136 EAKQLKDTNESLEDKIKELKAEKDELRDEKQKLKVEKETL--EQQVKILTATP-AYMPH 191

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2079102 PYE "AT3G47640" [Arabidopsis thaliana (taxid:3702)]

 Score = 206 (77.6 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 42/105 (40%), Positives = 66/105 (62%)

Query:    18 RKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTE 77
             +++ KA RE+L+R+ LNE F EL + L+ ++  + KA+IL +  + LKD+  Q+E L+ E
Sbjct:    28 KRINKAVRERLKREHLNELFIELADTLELNQQNSGKASILCEATRFLKDVFGQIESLRKE 87

Query:    78 HAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVP 122
             HA+L  ES  +T EKN+L+EE   L +EI  L  + + R     P
Sbjct:    88 HASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEARANQSKP 132

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;IDA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0010106 "cellular response to iron ion starvation" evidence=IMP

GO:0055072 "iron ion homeostasis" evidence=IMP

TAIR|locus:2086198 bHLH34 "AT3G23210" [Arabidopsis thaliana (taxid:3702)]

 Score = 199 (75.1 bits), Expect = 9.0e-16, P = 9.0e-16
 Identities = 46/120 (38%), Positives = 74/120 (61%)

Query:     3 CSQKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTV 61
             CS K       C+  +   KA REKLRR++LN+ F +L + L+P R PK DK+ IL D +
Sbjct:   151 CSGKRR-RTGSCS--KPGTKACREKLRREKLNDKFMDLSSVLEPGRTPKTDKSAILDDAI 207

Query:    62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMV 121
             +++  L  +  +L+  +  L EE + L  +KN+LREEKL L++E E +    +Q++++MV
Sbjct:   208 RVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEKM----EQQLKSMV 263

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0009718 "anthocyanin-containing compound biosynthetic process" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0010224 "response to UV-B" evidence=RCA

---

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)
Q9LT23	BH121_ARATH	No assigned EC number	0.6440	0.9397	0.8338	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.IV.993.1 hypothetical protein (291 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	299
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	6e-08
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	1e-07
smart00353	53	smart00353, HLH, helix loop helix domain	7e-07
pfam01496	707	pfam01496, V_ATPase_I, V-type ATPase 116kDa subuni	2e-04
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	5e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.001
PRK02224	880	PRK02224, PRK02224, chromosome segregation protein	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002

>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain

 Score = 47.8 bits (115), Expect = 6e-08
 Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 18 RKMQKADREKLRRDRLNEHFTELGNAL-DPDRPKNDKATILADTVQLLKDLT 68
          R+    +RE+ RRDR+N+ F EL   L  P   K  KA IL   ++ +K L 
Sbjct: 1  RRKAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

 Score = 47.6 bits (114), Expect = 1e-07
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 18 RKMQKADREKLRRDRLNEHFTELGNAL--DPDRPKNDKATILADTVQLLKDLTSQVE 72
          R+     RE+ RR+R+N+ F EL + L   P   K  KA IL   V  +K L   ++
Sbjct: 4  RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins. Length = 60

>gnl|CDD|197674 smart00353, HLH, helix loop helix domain

 Score = 44.9 bits (107), Expect = 7e-07
 Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 25 REKLRRDRLNEHFTELGNAL--DPDRPKNDKATILADTVQLLKDLTSQVEK 73
          RE+ RR ++NE F EL + L   P   K  KA IL   ++ +K L  +++K
Sbjct: 3  RERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 24/106 (22%), Positives = 45/106 (42%), Gaps = 1/106 (0%)

Query: 10  EVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTS 69
           EV+ C    +  +    K+++  +    T     + P +   D    + D    +K++  
Sbjct: 29  EVRRCDEVERKLRKLESKIKKLGIPLKDTGGKPDVPPSKEFLDLEEEILDLEAEIKEVEE 88

Query: 70  QVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ 115
            +E L+ E   L E    L +EK+ L E    L  E+ NL+I ++ 
Sbjct: 89  NLESLEKEINELEEWLNVLDEEKSFLDENLEELS-ELSNLDIDFKY 133

This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1. Length = 707

>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 41.6 bits (98), Expect = 5e-04
 Identities = 26/98 (26%), Positives = 41/98 (41%), Gaps = 15/98 (15%)

Query: 8   EGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDL 67
           E E K  AA    ++A+  +     LN    EL   ++         T+LA     + D 
Sbjct: 552 EAEEKREAAAEAEEEAEEAREEVAELNSKLAELKERIES---LERIRTLLAA----IADA 604

Query: 68  TSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSE 105
             ++E+L+        E RE   E ND R E+L+ + E
Sbjct: 605 EDEIERLR--------EKREALAELNDERRERLAEKRE 634

Length = 880

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

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 8/93 (8%)

Query: 22  KADREKLR--RDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHA 79
           K + E+L   R  L E   EL   L       +    L    + L+ L  + E+L+ E  
Sbjct: 778 KEEIEELEEKRQALQEELEELEEEL------EEAERRLDALERELESLEQRRERLEQEIE 831

Query: 80  ALTEESRELTQEKNDLREEKLSLRSEIENLNIQ 112
            L EE  EL ++ ++L EE   L  E+E L  +
Sbjct: 832 ELEEEIEELEEKLDELEEELEELEKELEELKEE 864

Length = 1163

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

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 26/104 (25%), Positives = 41/104 (39%), Gaps = 3/104 (2%)

Query: 13  DCAATRKMQKADREKLRRDRLNEHFTELGNAL-DPDRPKNDKATILADTVQLLKDLTSQV 71
           +  A R+     R +L    LNE    L   L   +R        L D  + +++L+  +
Sbjct: 797 ELKALREALDELRAELTL--LNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDI 854

Query: 72  EKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ 115
           E L  E   L E   EL  E   L  E+ SL   +  L  + ++
Sbjct: 855 ESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEE 898

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|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 18/96 (18%)

Query: 18  RKMQKADREKLRRDRL---NEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKL 74
           ++   A+    RR+RL    E   EL    D  R               +++     E+ 
Sbjct: 614 KREALAELNDERRERLAEKRERKRELEAEFDEAR---------------IEEAREDKERA 658

Query: 75  KTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN 110
           +     + E+  EL +E++DL+ E  ++ +E+E L 
Sbjct: 659 EEYLEQVEEKLDELREERDDLQAEIGAVENELEELE 694

Length = 880

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

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 26/107 (24%), Positives = 47/107 (43%), Gaps = 7/107 (6%)

Query: 19  KMQKADREKLRRD----RLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKL 74
           +  KA+  +L       +L E   EL      +   +     L +  + L++   ++E+L
Sbjct: 216 QELKAELRELELALLLAKLKELRKELEEL---EEELSRLEEELEELQEELEEAEKEIEEL 272

Query: 75  KTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMV 121
           K+E   L EE  EL +E  +L+EE   L  EI  L  + ++    + 
Sbjct: 273 KSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELE 319

Length = 1163

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	299
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.33
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.3
smart00353	53	HLH helix loop helix domain.	99.29
KOG1318	411	consensus Helix loop helix transcription factor EB	99.17
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.55
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.35
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.22
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	97.93
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.44
KOG0561	373	consensus bHLH transcription factor [Transcription	97.2
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.11
PRK15422	79	septal ring assembly protein ZapB; Provisional	97.06
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	96.99
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	96.79
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.63
KOG4029	228	consensus Transcription factor HAND2/Transcription	96.47
PRK11637	428	AmiB activator; Provisional	96.39
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	96.22
PLN03217	93	transcription factor ATBS1; Provisional	96.2
PRK00846	77	hypothetical protein; Provisional	96.18
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	96.17
PRK04406	75	hypothetical protein; Provisional	95.95
PRK02119	73	hypothetical protein; Provisional	95.89
PRK02793	72	phi X174 lysis protein; Provisional	95.39
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	95.35
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	95.34
PRK15422	79	septal ring assembly protein ZapB; Provisional	95.11
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	95.09
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	95.06
smart00338	65	BRLZ basic region leucin zipper.	95.03
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	94.97
PRK00736	68	hypothetical protein; Provisional	94.96
PRK00295	68	hypothetical protein; Provisional	94.86
PRK04325	74	hypothetical protein; Provisional	94.58
PRK10884	206	SH3 domain-containing protein; Provisional	94.58
KOG3910	632	consensus Helix loop helix transcription factor [T	94.54
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	94.49
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	94.47
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	94.21
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	94.1
PRK10884	206	SH3 domain-containing protein; Provisional	94.05
PRK13169	110	DNA replication intiation control protein YabA; Re	93.98
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	93.87
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	93.5
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	93.43
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	93.35
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	93.1
PRK11637	428	AmiB activator; Provisional	93.03
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	92.77
COG4026	290	Uncharacterized protein containing TOPRIM domain,	92.68
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	92.65
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	92.62
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	92.57
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	92.41
PRK13169	110	DNA replication intiation control protein YabA; Re	92.37
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	91.93
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	91.85
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	91.84
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	91.8
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	91.7
PRK05771	646	V-type ATP synthase subunit I; Validated	91.67
COG3937	108	Uncharacterized conserved protein [Function unknow	91.61
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	91.61
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	91.22
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	91.2
COG5570	57	Uncharacterized small protein [Function unknown]	91.13
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	91.08
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	91.08
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	91.03
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	90.87
PHA02562	562	46 endonuclease subunit; Provisional	90.75
PF10186	302	Atg14: UV radiation resistance protein and autopha	90.74
PRK10869	553	recombination and repair protein; Provisional	90.54
COG2900	72	SlyX Uncharacterized protein conserved in bacteria	90.51
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	90.45
KOG1962	216	consensus B-cell receptor-associated protein and r	90.26
PF09738	302	DUF2051: Double stranded RNA binding protein (DUF2	90.15
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	89.93
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	89.83
PF14662	193	CCDC155: Coiled-coil region of CCDC155	89.77
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	89.7
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	89.61
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	89.58
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	89.52
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	89.38
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	89.27
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	88.87
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	88.84
PRK13922	276	rod shape-determining protein MreC; Provisional	88.81
PF06637	442	PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 Th	88.66
COG4942	420	Membrane-bound metallopeptidase [Cell division and	88.63
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	88.44
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	88.41
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	88.24
PRK09039	343	hypothetical protein; Validated	88.22
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	88.09
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	87.93
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	87.92
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	87.89
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	87.89
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	87.87
PF01920	106	Prefoldin_2: Prefoldin subunit; InterPro: IPR00277	87.87
PF14662	193	CCDC155: Coiled-coil region of CCDC155	87.77
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	87.71
COG4467	114	Regulator of replication initiation timing [Replic	87.68
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	87.64
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	87.63
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	87.38
PRK00888	105	ftsB cell division protein FtsB; Reviewed	87.21
smart00338	65	BRLZ basic region leucin zipper.	87.18
PF14282	106	FlxA: FlxA-like protein	87.15
PF00038	312	Filament: Intermediate filament protein; InterPro:	87.06
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	86.91
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	86.83
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	86.72
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	86.66
PF05565	162	Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840	86.66
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	86.59
COG2919	117	Septum formation initiator [Cell division and chro	86.47
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	86.4
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	86.14
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	86.04
KOG4571	294	consensus Activating transcription factor 4 [Trans	85.92
PHA03011	120	hypothetical protein; Provisional	85.79
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	85.79
PF10186	302	Atg14: UV radiation resistance protein and autopha	85.69
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	85.65
PRK00888	105	ftsB cell division protein FtsB; Reviewed	85.58
PRK02195	201	V-type ATP synthase subunit D; Provisional	85.53
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	85.52
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	85.42
PHA02047	101	phage lambda Rz1-like protein	85.35
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	85.32
COG2433	652	Uncharacterized conserved protein [Function unknow	85.18
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	85.14
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	85.05
PF14282	106	FlxA: FlxA-like protein	85.0
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	84.95
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	84.91
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	84.89
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	84.82
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	84.71
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	84.68
PRK09039	343	hypothetical protein; Validated	84.6
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	84.34
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	84.28
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	84.2
KOG3898	254	consensus Transcription factor NeuroD and related	83.9
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	83.87
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	83.75
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	83.57
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	83.57
TIGR02231	525	conserved hypothetical protein. This family consis	83.54
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	83.47
PF12808	52	Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2	83.44
PF00038	312	Filament: Intermediate filament protein; InterPro:	83.36
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	83.35
PRK10803	263	tol-pal system protein YbgF; Provisional	83.2
PF12709	87	Kinetocho_Slk19: Central kinetochore-associated; I	83.03
KOG1853	333	consensus LIS1-interacting protein NUDE [Cytoskele	82.92
PRK11415	74	hypothetical protein; Provisional	82.48
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	82.38
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	82.19
KOG3650	120	consensus Predicted coiled-coil protein [General f	82.06
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	81.93
PF07334	76	IFP_35_N: Interferon-induced 35 kDa protein (IFP 3	81.88
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	81.82
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	81.73
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	81.71
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	81.66
PF15458	254	NTR2: Nineteen complex-related protein 2	81.62
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	81.38
PF14257	262	DUF4349: Domain of unknown function (DUF4349)	81.38
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	81.17
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	81.11
PRK03918	880	chromosome segregation protein; Provisional	81.05
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	81.02
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	80.98
PRK14011	144	prefoldin subunit alpha; Provisional	80.89
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	80.88
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	80.85
COG2433	652	Uncharacterized conserved protein [Function unknow	80.82
COG4942	420	Membrane-bound metallopeptidase [Cell division and	80.79
KOG3650	120	consensus Predicted coiled-coil protein [General f	80.76
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	80.74
PLN02678	448	seryl-tRNA synthetase	80.49
KOG3119	269	consensus Basic region leucine zipper transcriptio	80.49
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	80.47
PRK05431	425	seryl-tRNA synthetase; Provisional	80.26
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	80.21
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	80.19
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	80.14
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	80.03

>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

Probab=99.33  E-value=2.4e-12  Score=91.45  Aligned_cols=55  Identities=35%  Similarity=0.479  Sum_probs=48.9

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCC--CCCCChhhhHHHHHHHHHHHHHHH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPD--RPKNDKATILADTVQLLKDLTSQV   71 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~--~~K~DKASIL~DAI~ylKdLr~qV   71 (299)
                      .++..|..+||+||++||+.|.+|+.+|++.  ..|.||++||..||+||+.|+.++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4667788999999999999999999986555  279999999999999999999876

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and

>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt)

Probab=99.30  E-value=3.2e-12  Score=91.22  Aligned_cols=51  Identities=37%  Similarity=0.594  Sum_probs=45.8

Q ss_pred             hhccchHHHHHHHHHHHHHHHHhhhccCCC----CCCCChhhhHHHHHHHHHHHH
Q 022288           18 RKMQKADREKLRRDRLNEHFTELGNALDPD----RPKNDKATILADTVQLLKDLT   68 (299)
Q Consensus        18 Rk~~KAerERrRRdKLNErF~eLrslLvP~----~~K~DKASIL~DAI~ylKdLr   68 (299)
                      |+..|+.+||+||++||+.|.+|+.+|++.    ..|.+|++||..||+||++|+
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            467788999999999999999999997654    259999999999999999986

; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....

>smart00353 HLH helix loop helix domain

Probab=99.29  E-value=6.6e-12  Score=88.04  Aligned_cols=49  Identities=35%  Similarity=0.539  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhccCC--CCCCCChhhhHHHHHHHHHHHHHHHH
Q 022288           24 DREKLRRDRLNEHFTELGNALDP--DRPKNDKATILADTVQLLKDLTSQVE   72 (299)
Q Consensus        24 erERrRRdKLNErF~eLrslLvP--~~~K~DKASIL~DAI~ylKdLr~qVq   72 (299)
                      .+||+||++||+.|..|+.+|++  ...|.||++||.+||+||+.|+.+++
T Consensus         2 ~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        2 ARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999998544  45699999999999999999998875

>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]

Probab=99.17  E-value=6.5e-11  Score=116.38  Aligned_cols=82  Identities=23%  Similarity=0.466  Sum_probs=60.5

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCCCC----CCChhhhHHHHHHHHHHHHHHHHHHHH---HHhhhHHHHHHHH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPDRP----KNDKATILADTVQLLKDLTSQVEKLKT---EHAALTEESRELT   89 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~~~----K~DKASIL~DAI~ylKdLr~qVq~Lk~---en~~L~eE~~eLk   89 (299)
                      -||-.|++.|||||++||+|+.+|+.| +|...    +..|++||..+++||++|+...++..+   ....|+..++.|.
T Consensus       232 ~Krd~HNeVERRRR~nIN~~IkeLg~l-iP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~  310 (411)
T KOG1318|consen  232 RKRDNHNEVERRRRENINDRIKELGQL-IPKCNSEDMKSNKGTILKASCDYIRELQQTLQRARELENRQKKLESTNQELA  310 (411)
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHh-CCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHH
Confidence            567778899999999999999999998 56552    667999999999999999988774433   3334455555555


Q ss_pred             HHHHHHHHHH
Q 022288           90 QEKNDLREEK   99 (299)
Q Consensus        90 ~EkNELRdEn   99 (299)
                      ..+.||+.+.
T Consensus       311 ~rieeLk~~~  320 (411)
T KOG1318|consen  311 LRIEELKSEA  320 (411)
T ss_pred             HHHHHHHHHH
Confidence            5544444433

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.55  E-value=2.4e-07  Score=84.56  Aligned_cols=78  Identities=24%  Similarity=0.341  Sum_probs=69.2

Q ss_pred             hhccchHHHHHHHHHHHHHHHHhhhccCCCCC-------CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           18 RKMQKADREKLRRDRLNEHFTELGNALDPDRP-------KNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQ   90 (299)
Q Consensus        18 Rk~~KAerERrRRdKLNErF~eLrslLvP~~~-------K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~   90 (299)
                      ||..|-.+|++|||-||.-+..|..| +|..+       |..||.||-.+|+||..|..++.+-+++..+|+.++-.|+.
T Consensus        62 rr~aHtqaEqkRRdAIk~GYddLq~L-vP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL~i  140 (229)
T KOG1319|consen   62 RRRAHTQAEQKRRDAIKRGYDDLQTL-VPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTALKI  140 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhchHHHHHh-ccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45666688999999999999999996 78442       78899999999999999999999999999999999999998


Q ss_pred             HHHHHH
Q 022288           91 EKNDLR   96 (299)
Q Consensus        91 EkNELR   96 (299)
                      =+++..
T Consensus       141 Ik~~YE  146 (229)
T KOG1319|consen  141 IKVNYE  146 (229)
T ss_pred             HHHHHH
Confidence            877754

>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]

Probab=98.35  E-value=2.4e-06  Score=79.09  Aligned_cols=87  Identities=20%  Similarity=0.309  Sum_probs=63.9

Q ss_pred             cccchhhhhhccchHHHHHHHHHHHHHHHHhhhccCCCCCCCC--hhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 022288           10 EVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKND--KATILADTVQLLKDLTSQVEKLKTEHAALTEESRE   87 (299)
Q Consensus        10 e~~~~~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~~K~D--KASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~e   87 (299)
                      ......+.++.+|++-||+||++|.+.|..|+.+++......+  -++||..|++||+.|+.........++.|..+...
T Consensus        51 ~a~~~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~  130 (232)
T KOG2483|consen   51 PATSSAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSRENRK  130 (232)
T ss_pred             CCCCCCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            3333456778888999999999999999999998443334333  58999999999999998887776666555555555


Q ss_pred             HHHHHHHHH
Q 022288           88 LTQEKNDLR   96 (299)
Q Consensus        88 Lk~EkNELR   96 (299)
                      |+.+.++|.
T Consensus       131 l~~rl~ql~  139 (232)
T KOG2483|consen  131 LKARLEQLS  139 (232)
T ss_pred             HHHHHHHhc
Confidence            555554443

>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]

Probab=98.22  E-value=9.6e-07  Score=82.14  Aligned_cols=58  Identities=36%  Similarity=0.472  Sum_probs=50.3

Q ss_pred             hhhhhhccchHHHHHHHHHHHHHHHHhhhccCCC--------CCCCChhhhHHHHHHHHHHHHHHHH
Q 022288           14 CAATRKMQKADREKLRRDRLNEHFTELGNALDPD--------RPKNDKATILADTVQLLKDLTSQVE   72 (299)
Q Consensus        14 ~~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~--------~~K~DKASIL~DAI~ylKdLr~qVq   72 (299)
                      ....||+.|-.-|||||+|||+-+.+|+.|| +.        .+|++||-||.-|++||+.|+....
T Consensus        28 ~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li-~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   28 TRQYRKVRKPLLEKKRRARINRCLDELKDLI-PEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             hHHHhhhcchhHHHHHHHHHHHHHHHHHHHH-HHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            3458999999999999999999999999974 52        1589999999999999999997644

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]

Probab=97.93  E-value=1.1e-05  Score=85.37  Aligned_cols=54  Identities=31%  Similarity=0.453  Sum_probs=47.0

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCCCC----CCCChhhhHHHHHHHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDR----PKNDKATILADTVQLLKDLTSQ   70 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~----~K~DKASIL~DAI~ylKdLr~q   70 (299)
                      ..++..+++.||||||++|-.+.||.+| +|..    -|+||-+||-.||..||.+++.
T Consensus        18 r~~Re~~~~~EKrRRdq~N~yI~ELs~M-vp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   18 RKKRENRSEIEKRRRDQMNKYIEELSEM-VPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             hhccccchhHHHHHHHHHHHHHHHHHHh-hhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            3446677789999999999999999998 5644    3999999999999999999985

>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]

Probab=97.44  E-value=0.00034  Score=66.41  Aligned_cols=64  Identities=20%  Similarity=0.335  Sum_probs=49.9

Q ss_pred             ccchhhhhhccchHHHHHHHHHHHHHHHHhhhccCCCC-CCCChhhhHHHHHHHHHHHHHHHHHH
Q 022288           11 VKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTSQVEKL   74 (299)
Q Consensus        11 ~~~~~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~-~K~DKASIL~DAI~ylKdLr~qVq~L   74 (299)
                      .+.....|++----|||||=.|+||.|.+|..--.++- +..-|+.||-.||+||..|++-++++
T Consensus       111 rks~svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~  175 (284)
T KOG3960|consen  111 RKSTSVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQ  175 (284)
T ss_pred             ccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHh
Confidence            44555566655556999999999999999976544544 58899999999999999988755544

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.20  E-value=0.0003  Score=68.40  Aligned_cols=62  Identities=24%  Similarity=0.316  Sum_probs=49.7

Q ss_pred             ccchHHHHHHHHHHHHHHHHhhhccCCCC-CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022288           20 MQKADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTSQVEKLKTEHAAL   81 (299)
Q Consensus        20 ~~KAerERrRRdKLNErF~eLrslLvP~~-~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L   81 (299)
                      ---++-||||=.-||.-|..||+||+-.. -|..||+||..+.+||.+|..+--+|-..|..|
T Consensus        62 eIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~el  124 (373)
T KOG0561|consen   62 EIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNGEL  124 (373)
T ss_pred             HhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccchH
Confidence            33456799999999999999999853333 399999999999999999998877666555444

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.11  E-value=0.00029  Score=75.83  Aligned_cols=66  Identities=26%  Similarity=0.382  Sum_probs=60.1

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALT   82 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~   82 (299)
                      .||..|+-=|||=|--|||++.+|+.++++...|..|.+.|..||+|+++|+...+.|+.++..+.
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            678888899999999999999999998655557999999999999999999999999998888776

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=97.06  E-value=0.006  Score=48.96  Aligned_cols=60  Identities=18%  Similarity=0.425  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      +..||+-|.=|+-+|++|++.|..|.++++.++..+.+|+.||..|+.|-..-+    .||+++
T Consensus        13 IqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~Wq----erLr~L   72 (79)
T PRK15422         13 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQ----ERLQAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH----HHHHHH
Confidence            567888899999999999999999999999999999999999999999987766    666665

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.99  E-value=0.0074  Score=48.07  Aligned_cols=60  Identities=22%  Similarity=0.440  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      +..||+-|.-|+-+|++|++.|..|..|..++......|+.||.+||.|-..-+    .|++++
T Consensus        13 iqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQ----erlrsL   72 (79)
T COG3074          13 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQ----ERLRAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHH
Confidence            457899999999999999999999999999999999999999999999987776    666654

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

Probab=96.79  E-value=0.013  Score=45.84  Aligned_cols=51  Identities=31%  Similarity=0.479  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      ++.+.+|..+|+.+=+.+..|+.++.+|+.+.++|.+++..|+.+..+|+.
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~   53 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQ   53 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666655555555555555555543

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

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=96.63  E-value=0.014  Score=52.05  Aligned_cols=64  Identities=23%  Similarity=0.457  Sum_probs=57.5

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           57 LADTVQLLKDLTSQ---VEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        57 L~DAI~ylKdLr~q---Vq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      |.|.|.+|..|...   .+.|+.+|..|..++..|..+...|..|+..|+.++.-++..|+.-+..|
T Consensus        82 l~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im  148 (161)
T TIGR02894        82 LQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIM  148 (161)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999974   77888999999999999999999999999999999999999998877665

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.

>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]

Probab=96.47  E-value=0.0033  Score=56.82  Aligned_cols=59  Identities=22%  Similarity=0.308  Sum_probs=47.6

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCC---CCCCChhhhHHHHHHHHHHHHHHHHHHH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPD---RPKNDKATILADTVQLLKDLTSQVEKLK   75 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~---~~K~DKASIL~DAI~ylKdLr~qVq~Lk   75 (299)
                      .++...+.|||.|=.-+|..|.+||..|+..   ..|..|..+|--||.||+-|..-++.-+
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~  169 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQE  169 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccc
Confidence            3444556789999999999999999986443   3499999999999999999987655443

>PRK11637 AmiB activator; Provisional

Probab=96.39  E-value=0.03  Score=54.66  Aligned_cols=73  Identities=10%  Similarity=0.077  Sum_probs=63.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCC
Q 022288           55 TILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMD  127 (299)
Q Consensus        55 SIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~d  127 (299)
                      .-+.++...|..|..++..+...+..++.++..+..+.++|+.+...++.+++.++.+|.+|++.|+-...++
T Consensus        68 ~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~rlra~Y~~g~~~  140 (428)
T PRK11637         68 QQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAAQLDAAFRQGEHT  140 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence            4466777888888888888888888999999999999999999999999999999999999999997665544

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

Probab=96.22  E-value=0.057  Score=42.19  Aligned_cols=50  Identities=26%  Similarity=0.452  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      +..||+-|.-|+.++++|+++|..|.++...|+.|-..|+.|......-+
T Consensus        13 i~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl   62 (72)
T PF06005_consen   13 IQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERL   62 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45677777777777777777777766555555544444444444333333

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

>PLN03217 transcription factor ATBS1; Provisional

Probab=96.20  E-value=0.011  Score=48.61  Aligned_cols=58  Identities=24%  Similarity=0.409  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCC-----CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 022288           27 KLRRDRLNEHFTELGNALDPDRP-----KNDKATILADTVQLLKDLTSQVEKLKTEHAALTEE   84 (299)
Q Consensus        27 RrRRdKLNErF~eLrslLvP~~~-----K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE   84 (299)
                      |-=-|.|||.+..|+.+|+..+.     |..-+-+|.+|+.||+.|..+|..|.+....|.+-
T Consensus        16 risddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         16 RISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             CCCHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34458899999999998644222     45556699999999999999999999888776653

>PRK00846 hypothetical protein; Provisional

Probab=96.18  E-value=0.054  Score=43.15  Aligned_cols=68  Identities=19%  Similarity=0.179  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCccccCCCCC
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSY  137 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~~~~pp~y  137 (299)
                      .|..++.+|+..+.-.+.-+++|....-+...+...|+.++..|.    .||+.+-+....+|+.-.-||||
T Consensus        10 ~le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~----~rL~~~~~s~~~~~~dE~PPPHY   77 (77)
T PRK00846         10 ALEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLL----EDLGKVRSTLFADPADEPPPPHY   77 (77)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHhccccCCCCCCCCCcCCC
Confidence            466777777777776666777777777777777777777777776    67777766655567766677777

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=96.17  E-value=0.065  Score=51.20  Aligned_cols=89  Identities=26%  Similarity=0.343  Sum_probs=71.3

Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhH
Q 022288           24 DREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLR  103 (299)
Q Consensus        24 erERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~Lk  103 (299)
                      -.||.-|.||..|..+=-+       .-.|-.-..+-=..|++|.++.++|..+|+.|++..+.|-.+-+||+.+...|+
T Consensus        66 ~EEK~~RrKLKNRVAAQta-------RDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~  138 (292)
T KOG4005|consen   66 WEEKVQRRKLKNRVAAQTA-------RDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELELLR  138 (292)
T ss_pred             HHHHHHHHHHHHHHHHhhh-------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            3588888899888765432       122333345555678999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 022288          104 SEIENLNIQYQQRVRA  119 (299)
Q Consensus       104 sE~e~L~~qlqqrl~~  119 (299)
                      .++.+|++|+|..-..
T Consensus       139 ~~l~~~~~~~~~~~~v  154 (292)
T KOG4005|consen  139 QELAELKQQQQHNTRV  154 (292)
T ss_pred             HHHHhhHHHHHHhhHH
Confidence            9999999887766443

>PRK04406 hypothetical protein; Provisional

Probab=95.95  E-value=0.097  Score=41.09  Aligned_cols=68  Identities=16%  Similarity=0.243  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCccccCCCCC
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSY  137 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~~~~pp~y  137 (299)
                      .|..++.+|+..+.-++.-+++|....-+...+...|+.++..|.    +|++.+-+-..-+|+.---||||
T Consensus         8 ~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~----~rl~~~~~~~~~~~~~e~pPPHY   75 (75)
T PRK04406          8 QLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVV----GKVKNMDSSNLADPAEETPPPHY   75 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHhhccccCCCCCCCCCccCC
Confidence            577788888887777777778887777777777788888877776    45555533222234444446777

>PRK02119 hypothetical protein; Provisional

Probab=95.89  E-value=0.078  Score=41.30  Aligned_cols=70  Identities=16%  Similarity=0.246  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCccccCCCCC
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSY  137 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~~~~pp~y  137 (299)
                      +..|.+++.+|+..+.-.+.-+++|....-+.+.+...|+.++..|.    +|++.+-+-...++..---||||
T Consensus         4 ~~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~----~rl~~~~~~~~~~~~~e~~PPHY   73 (73)
T PRK02119          4 QQNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYMA----NKLKDMQPSNIASQAEETPPPHY   73 (73)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHhhccccCCCCCCCCCcCCC
Confidence            45677778888877777777777887777777777788888888776    44444422211223333355667

>PRK02793 phi X174 lysis protein; Provisional

Probab=95.39  E-value=0.19  Score=38.99  Aligned_cols=68  Identities=21%  Similarity=0.267  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCccccCCCCC
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSY  137 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~~~~pp~y  137 (299)
                      .+.+++.+|+..+.-.+.-+++|....-+.+.+...|..++..|..    |++.+-+-..-++..---||||
T Consensus         5 ~~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~----rl~~~~~~~~~~~~~e~~PPHY   72 (72)
T PRK02793          5 SLEARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTE----KLKASQPSNIASQAEETPPPHY   72 (72)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHhhccccCCCCCCCCCcCCC
Confidence            3566777777777766777777777777777777777777777764    4444422221233333456677

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=95.35  E-value=0.1  Score=53.35  Aligned_cols=59  Identities=32%  Similarity=0.403  Sum_probs=46.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH---------------HHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQ---------------EKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~---------------EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      |..-|.-+|+|+.+++.|..+|+.|.+|++.|++               +..+|..|...|+.++.+|+.++++
T Consensus        61 lrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~  134 (472)
T TIGR03752        61 LRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQ  134 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6677888999999999999999999999988866               4566777777777777666555443

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

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.34  E-value=0.11  Score=49.67  Aligned_cols=72  Identities=18%  Similarity=0.250  Sum_probs=43.1

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHH-------HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCc
Q 022288           53 KATILADTVQLLKDLTSQVEKLKTEHAALTEES-------RELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA  124 (299)
Q Consensus        53 KASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~-------~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~  124 (299)
                      +-+.|.++-.-+++++.+|+.|...++.+..++       +.+..|..+|..+...|+..|...+.-|..|+|+|+--.
T Consensus        36 ~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~r~~~l~~raRAmq~nG  114 (265)
T COG3883          36 QDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAMQVNG  114 (265)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            344566666666666666666665555554444       444445555555555555555566666778899986443

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=95.11  E-value=0.14  Score=41.19  Aligned_cols=55  Identities=20%  Similarity=0.311  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      .+++.+|.++|+..-+.+.-|+.|+++|+.+.+.|..|+..+++..+.|+.+.++
T Consensus         3 ~EvleqLE~KIqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~q   57 (79)
T PRK15422          3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNH   57 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            4678899999999888898899999999998888998888877777777666554

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

Probab=95.09  E-value=0.12  Score=42.96  Aligned_cols=46  Identities=33%  Similarity=0.441  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      +|-.++..|++.+..|.+++.+|+....+|-+||+.|+-|.+.|..
T Consensus         5 ~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~   50 (107)
T PF06156_consen    5 ELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRE   50 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555555566666666666666666666666666666653

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

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

Probab=95.06  E-value=0.085  Score=39.06  Aligned_cols=37  Identities=32%  Similarity=0.563  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREE   98 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdE   98 (299)
                      .||.+|+.++..|+.+|..|..++..|..+...|+.+
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e   62 (64)
T PF00170_consen   26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLKSE   62 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4555555555555555555555554444444444433

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

>smart00338 BRLZ basic region leucin zipper

Probab=95.03  E-value=0.079  Score=39.23  Aligned_cols=39  Identities=28%  Similarity=0.430  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEK   99 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEn   99 (299)
                      -.|+.+|+.+++.|+.+|..|..++..|..|...|++++
T Consensus        25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       25 KAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            358888888888888888888887777777777776554

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

Probab=94.97  E-value=0.12  Score=39.40  Aligned_cols=50  Identities=20%  Similarity=0.325  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           67 LTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        67 Lr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      |.+++.+|+..+.-++.-+++|....-+...+...|+.++..|.    .||+.+
T Consensus         2 le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~----~rl~~~   51 (69)
T PF04102_consen    2 LEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLR----ERLREL   51 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HT----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHh
Confidence            55666777776666666677777666666777777777777776    444444

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

>PRK00736 hypothetical protein; Provisional

Probab=94.96  E-value=0.25  Score=37.93  Aligned_cols=65  Identities=15%  Similarity=0.276  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCccccCCCCC
Q 022288           68 TSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSY  137 (299)
Q Consensus        68 r~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~~~~pp~y  137 (299)
                      ..++.+|+..+.-.+.-+++|....-+...+...|+.++..|.    .|++.+-+.. .++..---||||
T Consensus         4 e~Ri~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~----~rl~~~~~~~-~~~~~~~~PPHY   68 (68)
T PRK00736          4 EERLTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALT----ERFLSLEEQA-APDVPVTKPPHW   68 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHhcccc-CCCCCCCCcCCC
Confidence            3455555555555555555665555555666666666666665    4455443332 223333456677

>PRK00295 hypothetical protein; Provisional

Probab=94.86  E-value=0.3  Score=37.55  Aligned_cols=65  Identities=20%  Similarity=0.272  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCC-CccccCCCCC
Q 022288           67 LTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMD-HSVMMAPPSY  137 (299)
Q Consensus        67 Lr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~d-ps~~~~pp~y  137 (299)
                      |.+++.+|+..+.-.+.-+++|....-+...+...|+.++..|..    |++.+-  .++. +..---||||
T Consensus         3 ~e~Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~----rl~~~~--~~~~~~~~e~~PPHY   68 (68)
T PRK00295          3 LEERVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIK----RQEEMV--GQFGSFEEEAPPPHY   68 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHhh--ccCCCCCCCCCcCCC
Confidence            345566666666666666666666666666666777777777763    444432  1222 3333456677

>PRK04325 hypothetical protein; Provisional

Probab=94.58  E-value=0.43  Score=37.22  Aligned_cols=70  Identities=20%  Similarity=0.229  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCc-cccCCCCC
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHS-VMMAPPSY  137 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps-~~~~pp~y  137 (299)
                      +..+.+++.+|+..+.-.+.-+++|....-+...+...|+.++..|.    .||+.+-+.++=+.+ .---||||
T Consensus         4 ~~~~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~----~rl~~~~~~~~~~~~~~~e~PPHY   74 (74)
T PRK04325          4 VQEMEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLY----QQMRDANPDAAEPYSLRDEIPPHY   74 (74)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHhcccccCCCCCCcCCCCCC
Confidence            34566777777777777777777777777777777777777777776    445554333211112 23346777

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.58  E-value=0.21  Score=45.71  Aligned_cols=78  Identities=14%  Similarity=0.126  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           28 LRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        28 rRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      .|=.++...+.+|++-|         +.|-.+.-....+|+.+++.++..+..|.++...|+.|..+++.|+..|+++++
T Consensus        93 ~rlp~le~el~~l~~~l---------~~~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~  163 (206)
T PRK10884         93 TRVPDLENQVKTLTDKL---------NNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLD  163 (206)
T ss_pred             HHHHHHHHHHHHHHHHH---------HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33355667777776543         112233345555566666666666666666666666666666666666666666


Q ss_pred             HHHHHHH
Q 022288          108 NLNIQYQ  114 (299)
Q Consensus       108 ~L~~qlq  114 (299)
                      .++...+
T Consensus       164 ~~~~~~~  170 (206)
T PRK10884        164 DKQRTII  170 (206)
T ss_pred             HHHHHHH
Confidence            6654433

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=94.54  E-value=0.042  Score=56.78  Aligned_cols=51  Identities=33%  Similarity=0.473  Sum_probs=39.1

Q ss_pred             hHHHHHHHHHHHHHHHHhhhccCC---CCCCCChhhhHHHHHHHHHHHHHHHHH
Q 022288           23 ADREKLRRDRLNEHFTELGNALDP---DRPKNDKATILADTVQLLKDLTSQVEK   73 (299)
Q Consensus        23 AerERrRRdKLNErF~eLrslLvP---~~~K~DKASIL~DAI~ylKdLr~qVq~   73 (299)
                      +.|||.|=.-|||.|.||+.|---   ......|-.||-.|+.+|-.|++||++
T Consensus       531 NARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  531 NARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             hhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            345555556799999999987311   223567899999999999999999874

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

Probab=94.49  E-value=0.52  Score=44.95  Aligned_cols=82  Identities=28%  Similarity=0.336  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           27 KLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        27 RrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      +.|...|.+.+..|+.+ .......|+ .=|..+-.-|.++..+++.++.+...|+.+...++.+.+++..++..+..+|
T Consensus       183 ~~~~~~L~~e~~~Lk~~-~~e~~~~D~-~eL~~lr~eL~~~~~~i~~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI  260 (325)
T PF08317_consen  183 RERKAELEEELENLKQL-VEEIESCDQ-EELEALRQELAEQKEEIEAKKKELAELQEELEELEEKIEELEEQKQELLAEI  260 (325)
T ss_pred             HHHHHHHHHHHHHHHHH-HhhhhhcCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667788888888886 333333443 3345555555555555555555555555555555555555555555555555


Q ss_pred             HHHH
Q 022288          107 ENLN  110 (299)
Q Consensus       107 e~L~  110 (299)
                      ..++
T Consensus       261 ~e~~  264 (325)
T PF08317_consen  261 AEAE  264 (325)
T ss_pred             HHHH
Confidence            5444

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

Probab=94.47  E-value=0.27  Score=41.76  Aligned_cols=52  Identities=42%  Similarity=0.567  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      -.+..|..|..++..++.++..|+.++..|..+++++++|...|-.+.+.++
T Consensus        13 ~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~~   64 (120)
T PF12325_consen   13 PSVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEELR   64 (120)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3466777888888888888888888888888877777777777766665553

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 [].

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

Probab=94.21  E-value=1.4  Score=37.26  Aligned_cols=79  Identities=25%  Similarity=0.384  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhH
Q 022288           24 DREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLR  103 (299)
Q Consensus        24 erERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~Lk  103 (299)
                      .++...|+.|++.+..|++=             +...-.-+..|+.+++.++.++..++++...|..+...+..-+..++
T Consensus        48 ~r~~~~~e~l~~~~~~l~~d-------------~~~l~~~~~rL~~~~~~~ere~~~~~~~~~~l~~~~~~~~~~~k~~k  114 (151)
T PF11559_consen   48 DRDMEQREDLSDKLRRLRSD-------------IERLQNDVERLKEQLEELERELASAEEKERQLQKQLKSLEAKLKQEK  114 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHhH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57788888899988888764             33334455666666666666666555555555555444444444444


Q ss_pred             HHHHHHHHHHHH
Q 022288          104 SEIENLNIQYQQ  115 (299)
Q Consensus       104 sE~e~L~~qlqq  115 (299)
                      .|+.+|...+++
T Consensus       115 ee~~klk~~~~~  126 (151)
T PF11559_consen  115 EELQKLKNQLQQ  126 (151)
T ss_pred             HHHHHHHHHHHH
Confidence            444444444433

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

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.10  E-value=0.35  Score=46.24  Aligned_cols=58  Identities=17%  Similarity=0.318  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      +...=.-|++|+.+...++.+++.|..++.++..+.+++++|+..++.++.+|+.++.
T Consensus        33 i~~~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~   90 (265)
T COG3883          33 IQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIA   90 (265)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5556678999999999999999999999999999999999999999999998887664

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.05  E-value=0.52  Score=43.10  Aligned_cols=27  Identities=19%  Similarity=0.223  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           87 ELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        87 eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      .+..+.++|+.||..|+.++..+++++
T Consensus       129 ~~~~~~~~L~~~n~~L~~~l~~~~~~~  155 (206)
T PRK10884        129 QSDSVINGLKEENQKLKNQLIVAQKKV  155 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444445555555555555554443

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=93.98  E-value=0.31  Score=40.99  Aligned_cols=46  Identities=26%  Similarity=0.388  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ++|-.++..|+..+..|..++.+|+....+|-+||..|+-|-+.|.
T Consensus         4 ~elfd~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr   49 (110)
T PRK13169          4 KEIFDALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLR   49 (110)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555556666666666666666666666666666666666665

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

Probab=93.87  E-value=0.2  Score=43.13  Aligned_cols=51  Identities=35%  Similarity=0.508  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHH--HHHHHHHhhhHHHHHHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEK--NDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~Ek--NELRdEns~LksE~e~L~~qlq  114 (299)
                      |.+|++++..|+.++..|..+...|....  .+|+.+...|+.++..|+..|+
T Consensus        81 i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~  133 (169)
T PF07106_consen   81 IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLE  133 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888888888888888887775  6688888888888888874444

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 [].

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=93.50  E-value=0.44  Score=50.60  Aligned_cols=75  Identities=23%  Similarity=0.228  Sum_probs=55.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCcc
Q 022288           56 ILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSV  130 (299)
Q Consensus        56 IL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~  130 (299)
                      |+.-.-..|.+|+.+-++|..+++++...+++|+++.-.-+-|..+||.+|+.-|.|++.-+...-|-..++-++
T Consensus        87 I~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~n~pkl~LP~sl  161 (907)
T KOG2264|consen   87 ILASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRETNNPKLFLPFSL  161 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhhcCCceeecccc
Confidence            344444456667777777777788888888888888887788889999999999988888877776665544443

>smart00787 Spc7 Spc7 kinetochore protein

Probab=93.43  E-value=0.97  Score=43.65  Aligned_cols=82  Identities=26%  Similarity=0.318  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           27 KLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        27 RrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      +.|.+.|+..+..|+.+ .-.... =..+.|..+-.-|+++..++...+.....++.+...++...++...++..+..+|
T Consensus       178 ~~~~~~L~~e~~~L~~~-~~e~~~-~d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I  255 (312)
T smart00787      178 RDRKDALEEELRQLKQL-EDELED-CDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEI  255 (312)
T ss_pred             HHHHHHHHHHHHHHHHh-HHHHHh-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56677888888888886 222222 2356666666666666666665555555555555555555555555555555555


Q ss_pred             HHHH
Q 022288          107 ENLN  110 (299)
Q Consensus       107 e~L~  110 (299)
                      ..++
T Consensus       256 ~~ae  259 (312)
T smart00787      256 AEAE  259 (312)
T ss_pred             HHHH
Confidence            5444

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

>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins

Probab=93.35  E-value=0.12  Score=46.23  Aligned_cols=46  Identities=33%  Similarity=0.499  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      |.|++.+...--+.|.-|++|+    .||..|+.|.++||.|+..|.+++
T Consensus         2 LeD~EsklN~AIERnalLE~EL----dEKE~L~~~~QRLkDE~RDLKqEl   47 (166)
T PF04880_consen    2 LEDFESKLNQAIERNALLESEL----DEKENLREEVQRLKDELRDLKQEL   47 (166)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCH--------------
T ss_pred             HHHHHHHHHHHHHHhHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567777777777788888887    678888989999999888887776

Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []

Probab=93.10  E-value=0.25  Score=35.51  Aligned_cols=41  Identities=29%  Similarity=0.432  Sum_probs=24.1

Q ss_pred             HHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           74 LKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        74 Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      |+.+.+.|...-+.|+.+...|..||..|++++..|...++
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~   43 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQ   43 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            44455555555556666666666666666666666654443

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PRK11637 AmiB activator; Provisional

Probab=93.03  E-value=0.73  Score=45.11  Aligned_cols=59  Identities=22%  Similarity=0.234  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      ..++++..+++.|..++..+..+++.+..+.+++..+...|..+|..++.++..+-..+
T Consensus        68 ~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l  126 (428)
T PRK11637         68 QQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLL  126 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444445555555555555555566666666666666666666666666665554444

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]

Probab=92.77  E-value=0.084  Score=56.23  Aligned_cols=50  Identities=34%  Similarity=0.424  Sum_probs=40.1

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCC--CC-CCCChhhhHHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDP--DR-PKNDKATILADTVQLLK   65 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP--~~-~K~DKASIL~DAI~ylK   65 (299)
                      +-||-.-..+-|-||.|=|+-|++|..+|+-  .+ +..|||+|+-=||.||+
T Consensus        44 ~~rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   44 ELRKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             HHHhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH
Confidence            3445545568899999999999999998632  11 48999999999999986

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

Probab=92.68  E-value=0.7  Score=44.19  Aligned_cols=56  Identities=23%  Similarity=0.298  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      +..-+|++..+++.++++.|..+..+|..|.++++++..+|+.++.+|+..+..+.
T Consensus       135 e~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l~  190 (290)
T COG4026         135 EDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLP  190 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhch
Confidence            33445556666777788888888888888888888888888888888876655443

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=92.65  E-value=0.91  Score=35.28  Aligned_cols=44  Identities=34%  Similarity=0.400  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      |+.|..+|+.|-.....|..|...|+.+...++.|...|....+
T Consensus         2 L~~Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne   45 (65)
T TIGR02449         2 LQALAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNE   45 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555444444445555555544444444444444433

Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.

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

Probab=92.62  E-value=0.72  Score=38.46  Aligned_cols=50  Identities=32%  Similarity=0.415  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      ..|.+|..++..|-+++..|...+.+|-.|-.+|+-||..|+..+..++.
T Consensus         8 ~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen    8 DRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45677778888888888888888888888888888888888888887763

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

>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=92.57  E-value=1.3  Score=41.36  Aligned_cols=34  Identities=32%  Similarity=0.469  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDL   95 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNEL   95 (299)
                      .+|.+++.+.+.|..|-..+.++++...+++|.|
T Consensus        32 ~~L~e~~kE~~~L~~Er~~h~eeLrqI~~DIn~l   65 (230)
T PF10146_consen   32 KCLEEYRKEMEELLQERMAHVEELRQINQDINTL   65 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555544444444443333333333

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.

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.41  E-value=0.99  Score=36.24  Aligned_cols=55  Identities=22%  Similarity=0.319  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      .+++..|.+.|+.--+.+.-|+.|+++|+.+.|.|..|-+.+....+.|+.+.+|
T Consensus         3 lEv~ekLE~KiqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneq   57 (79)
T COG3074           3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQ   57 (79)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHH
Confidence            4567778888887777777788888888888787877777777777777655544

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=92.37  E-value=0.92  Score=38.22  Aligned_cols=49  Identities=35%  Similarity=0.439  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .-|.+|..++..|-.++..|...+.+|-.|-.+|+-||..|+..+.+++
T Consensus         8 d~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~   56 (110)
T PRK13169          8 DALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELE   56 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3455666666666666666666666676666667777777777776653

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=91.93  E-value=1.2  Score=34.58  Aligned_cols=55  Identities=24%  Similarity=0.420  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      .-|-+|-...++|+.+|..|.++...+..|...|.+.|..-++.++.+=    .||++|
T Consensus         7 ~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEamI----~RLk~l   61 (65)
T TIGR02449         7 AQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAMI----TRLKAL   61 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----Hhhhhh
Confidence            3466777788888888988999999999999999888888888888775    666655

Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.

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

Probab=91.85  E-value=1.1  Score=42.73  Aligned_cols=34  Identities=26%  Similarity=0.290  Sum_probs=13.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      .+..++.+|+.++.+++.+...+..++..++.++
T Consensus       227 ~~k~~l~el~~el~~l~~~i~~~~~~k~~l~~eI  260 (325)
T PF08317_consen  227 AKKKELAELQEELEELEEKIEELEEQKQELLAEI  260 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444444444444444444444444333

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

Probab=91.84  E-value=1.7  Score=34.97  Aligned_cols=46  Identities=26%  Similarity=0.393  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L  109 (299)
                      -.+|..++..|+..+..|-..++.++.|...|+.||.-|..=|.+|
T Consensus        18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL   63 (80)
T PF10224_consen   18 KEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL   63 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567777888888888888888888888888888888888888877

The exact function is unknown.

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

Probab=91.80  E-value=1.3  Score=32.72  Aligned_cols=35  Identities=31%  Similarity=0.478  Sum_probs=18.2

Q ss_pred             HhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           78 HAALTEESRELTQEKNDLREEKLSLRSEIENLNIQ  112 (299)
Q Consensus        78 n~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~q  112 (299)
                      +..|+.++..|..+...|+.++..|+.++..|..+
T Consensus        28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e   62 (64)
T PF00170_consen   28 IEELEEKVEELESENEELKKELEQLKKEIQSLKSE   62 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34445555555555555555555555555555543

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

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

Probab=91.70  E-value=0.98  Score=43.38  Aligned_cols=7  Identities=14%  Similarity=0.268  Sum_probs=1.9

Q ss_pred             HHHcCCC
Q 022288          117 VRAMVPW  123 (299)
Q Consensus       117 l~~~~pw  123 (299)
                      |+..-.|
T Consensus       132 L~ktNv~  138 (314)
T PF04111_consen  132 LRKTNVY  138 (314)
T ss_dssp             HHT--TT
T ss_pred             HHhcCch
Confidence            3333333

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.

>PRK05771 V-type ATP synthase subunit I; Validated

Probab=91.67  E-value=1.5  Score=45.25  Aligned_cols=41  Identities=32%  Similarity=0.593  Sum_probs=21.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCcc
Q 022288           79 AALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSV  130 (299)
Q Consensus        79 ~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~  130 (299)
                      ..+.+++.++..++++|++|...|+.+++.           .-||..+|...
T Consensus        96 ~~~~~~i~~l~~~~~~L~~~~~~l~~~~~~-----------l~~~~~ld~~l  136 (646)
T PRK05771         96 EKIEKEIKELEEEISELENEIKELEQEIER-----------LEPWGNFDLDL  136 (646)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------hhhhhcCCCCH
Confidence            344444444444444444444444444444           44999877765

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=91.61  E-value=2.1  Score=36.39  Aligned_cols=75  Identities=15%  Similarity=0.297  Sum_probs=49.1

Q ss_pred             HHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHh-hhHHHHHHHHHHH--------HHHHHHHhh
Q 022288           31 DRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHA-ALTEESRELTQEK--------NDLREEKLS  101 (299)
Q Consensus        31 dKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~-~L~eE~~eLk~Ek--------NELRdEns~  101 (299)
                      +++|+...+|-.     .+++.    ..+|-+|+.+|..+++.-..+.+ .++..++++..+.        .+|+++...
T Consensus        24 ek~~klvDelVk-----kGeln----~eEak~~vddl~~q~k~~~~e~e~K~~r~i~~ml~~~~~~r~~~~~~l~~rvd~   94 (108)
T COG3937          24 EKVQKLVDELVK-----KGELN----AEEAKRFVDDLLRQAKEAQGELEEKIPRKIEEMLSDLEVARQSEMDELTERVDA   94 (108)
T ss_pred             HHHHHHHHHHHH-----cCCCC----HHHHHHHHHHHHHHHHHHhhhHHHhhhHHHHHHHhhccccccchHHHHHHHHHH
Confidence            444555554433     24555    67899999999999886555443 2444555554433        578888888


Q ss_pred             hHHHHHHHHHHHH
Q 022288          102 LRSEIENLNIQYQ  114 (299)
Q Consensus       102 LksE~e~L~~qlq  114 (299)
                      |+.++..|+++++
T Consensus        95 Lerqv~~Lenk~k  107 (108)
T COG3937          95 LERQVADLENKLK  107 (108)
T ss_pred             HHHHHHHHHHHhc
Confidence            8888888887765

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=91.61  E-value=5.6  Score=41.10  Aligned_cols=55  Identities=11%  Similarity=0.129  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      +...-|.+-+.++.+|+++++.|+.|.+.|.+...++..+...|++|+..|+.|+
T Consensus        66 VnqSALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql  120 (475)
T PRK13729         66 VRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV  120 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            3345566666677778888887877777777777778777788888888887665

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

Probab=91.22  E-value=13  Score=39.15  Aligned_cols=44  Identities=30%  Similarity=0.408  Sum_probs=31.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCcc
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAA  125 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~  125 (299)
                      .|..-++-+..||.+|++|++.|+..|++|+..|..-...  =|..
T Consensus       421 Elks~lrv~qkEKEql~~EkQeL~~yi~~Le~r~~~~~~~--~~~~  464 (546)
T PF07888_consen  421 ELKSSLRVAQKEKEQLQEEKQELLEYIERLEQRLDKVADE--KWKE  464 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh--hhhc
Confidence            4455556677789999999999999999998555543322  4764

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

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

Probab=91.20  E-value=1.7  Score=38.58  Aligned_cols=54  Identities=22%  Similarity=0.364  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      +..--.-|.+|+.++..|+..+..|.+++++...-...|+||...|.-+..-|+
T Consensus       111 ~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e  164 (194)
T PF08614_consen  111 LSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLNMLE  164 (194)
T ss_dssp             ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444556666666666666666666666555555555555555555444443

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

>COG5570 Uncharacterized small protein [Function unknown]

Probab=91.13  E-value=0.66  Score=35.31  Aligned_cols=45  Identities=33%  Similarity=0.520  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHhhhHHHHHHHHH-------HHHHHHHHHhhhHHHHHHHHHH
Q 022288           68 TSQVEKLKTEHAALTEESRELTQ-------EKNDLREEKLSLRSEIENLNIQ  112 (299)
Q Consensus        68 r~qVq~Lk~en~~L~eE~~eLk~-------EkNELRdEns~LksE~e~L~~q  112 (299)
                      ...+.+|+.....|++|+++-..       ...+|+..+.+||.+|++|..|
T Consensus         4 eshl~eL~kkHg~le~ei~ea~n~Ps~dd~~i~eLKRrKL~lKeeIEkLka~   55 (57)
T COG5570           4 ESHLAELEKKHGNLEREIQEAMNSPSSDDLAIRELKRRKLRLKEEIEKLKAQ   55 (57)
T ss_pred             HHHHHHHHHhhchHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHHHHhcc
Confidence            45566677777777777766543       5678888999999999999754

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

Probab=91.08  E-value=2.5  Score=37.13  Aligned_cols=30  Identities=30%  Similarity=0.462  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           90 QEKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        90 ~EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      .+.++|+.++..|+.|+++|++++++.+..
T Consensus        73 ~~~~~lr~~~e~L~~eie~l~~~L~~ei~~  102 (177)
T PF07798_consen   73 SEFAELRSENEKLQREIEKLRQELREEINK  102 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344556666666666666666666555443

>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=91.08  E-value=2.5  Score=41.46  Aligned_cols=45  Identities=18%  Similarity=0.281  Sum_probs=34.5

Q ss_pred             CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           50 KNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKND   94 (299)
Q Consensus        50 K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNE   94 (299)
                      +..=+.+|.++-+..+.|..++..|+..+..++.+++.|+...+.
T Consensus        67 ~~~La~lL~~sre~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~la~  111 (319)
T PF09789_consen   67 NKNLAQLLSESREQNKKLKEEVEELRQKLNEAQGDIKLLREKLAR  111 (319)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHh
Confidence            445567889999999999999888888887777777777664433

>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division []

Probab=91.03  E-value=1.9  Score=33.86  Aligned_cols=52  Identities=29%  Similarity=0.427  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHH--------HHHHHHhhhHHHHHHHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKN--------DLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkN--------ELRdEns~LksE~e~L~~qlqq  115 (299)
                      |++...++.+|+.+|=.|.-++..|....+        ++..+|..|+.++..|+.+++.
T Consensus         2 lrEqe~~i~~L~KENF~LKLrI~fLee~l~~~~~~~~~~~~keNieLKve~~~L~~el~~   61 (75)
T PF07989_consen    2 LREQEEQIDKLKKENFNLKLRIYFLEERLQKLGPESIEELLKENIELKVEVESLKRELQE   61 (75)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567777777777777666555554444322        2334444444444444444443

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=90.87  E-value=2.2  Score=33.06  Aligned_cols=54  Identities=22%  Similarity=0.321  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHH-------HHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQE-------KNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~E-------kNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      +..|+.++..+...+...+.+++.|+.|       ..+...++..|+.+++.|+.+++.+.
T Consensus         7 ~~~Lr~rLd~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r   67 (69)
T PF14197_consen    7 IATLRNRLDSLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELR   67 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4455555555555555555555555555       45667788888888888888876653

>PHA02562 46 endonuclease subunit; Provisional

Probab=90.75  E-value=2.5  Score=41.76  Aligned_cols=76  Identities=21%  Similarity=0.226  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           28 LRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        28 rRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      .++..+.+++.+|+..+     . .+-+-|.+.++..+.|+.++++|+.....+.++...|..+.++++.+...+..++.
T Consensus       330 ~~~~~~~~~i~el~~~i-----~-~~~~~i~~~~~~~~~l~~ei~~l~~~~~~~~~~l~~l~~~l~~~~~~~~~~~ke~~  403 (562)
T PHA02562        330 DEFNEQSKKLLELKNKI-----S-TNKQSLITLVDKAKKVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKY  403 (562)
T ss_pred             HHHHHHHHHHHHHHHHH-----H-HHHHHHHHHHHHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555666677776653     1 11122777889999999999999998888888888888888888888887777766


Q ss_pred             HH
Q 022288          108 NL  109 (299)
Q Consensus       108 ~L  109 (299)
                      .+
T Consensus       404 ~~  405 (562)
T PHA02562        404 HR  405 (562)
T ss_pred             HH
Confidence            54

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

Probab=90.74  E-value=2.9  Score=37.59  Aligned_cols=31  Identities=19%  Similarity=0.391  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      .++.+++.|+..++.+..++...+.+..+++
T Consensus        67 ~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~   97 (302)
T PF10186_consen   67 ELRERLERLRERIERLRKRIEQKRERLEELR   97 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333333333

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

>PRK10869 recombination and repair protein; Provisional

Probab=90.54  E-value=2.7  Score=43.15  Aligned_cols=92  Identities=14%  Similarity=0.165  Sum_probs=71.3

Q ss_pred             HHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHH---HHhhhHHHHHHHHHHHHHHHHHHhhhHH
Q 022288           28 LRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKT---EHAALTEESRELTQEKNDLREEKLSLRS  104 (299)
Q Consensus        28 rRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~---en~~L~eE~~eLk~EkNELRdEns~Lks  104 (299)
                      .|=+.+++|+..|..+-   + |-+  .=+.+.+.|..+++.+++.|+.   ....|+.++..++.+..++..+.+..+.
T Consensus       296 ~~l~~ie~Rl~~l~~L~---r-Kyg--~~~~~~~~~~~~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~A~~LS~~R~  369 (553)
T PRK10869        296 NRLAELEQRLSKQISLA---R-KHH--VSPEELPQHHQQLLEEQQQLDDQEDDLETLALAVEKHHQQALETAQKLHQSRQ  369 (553)
T ss_pred             HHHHHHHHHHHHHHHHH---H-HhC--CCHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34578899999999871   1 111  1489999999999999998874   5677888888888888888877776666


Q ss_pred             H-HHHHHHHHHHHHHHcCCCccCCCc
Q 022288          105 E-IENLNIQYQQRVRAMVPWAAMDHS  129 (299)
Q Consensus       105 E-~e~L~~qlqqrl~~~~pw~~~dps  129 (299)
                      + ..+|+..++..|+.+    +|+..
T Consensus       370 ~aA~~l~~~v~~~L~~L----~m~~a  391 (553)
T PRK10869        370 RYAKELAQLITESMHEL----SMPHG  391 (553)
T ss_pred             HHHHHHHHHHHHHHHHc----CCCCc
Confidence            5 678999999999998    66555

>COG2900 SlyX Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.51  E-value=3.3  Score=33.06  Aligned_cols=69  Identities=17%  Similarity=0.276  Sum_probs=44.9

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCccccCCCCC
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSY  137 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~~~~pp~y  137 (299)
                      ..|.+++.+|+...+.=+.-+.+|..-.-|.+-....+..++..|-    .|+..+-+.+.=+|++---||||
T Consensus         4 ~~lE~Ri~eLE~r~AfQE~tieeLn~~laEq~~~i~k~q~qlr~L~----~kl~~~~~~~~~~~~~etpPPHY   72 (72)
T COG2900           4 MELEARIIELEIRLAFQEQTIEELNDALAEQQLVIDKLQAQLRLLT----EKLKDLQPSAIASPAEETPPPHY   72 (72)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcccccCCCcccCCCCCC
Confidence            4577778888777665555566776666666666666666666665    66677666655455555555666

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

Probab=90.45  E-value=2.5  Score=38.24  Aligned_cols=62  Identities=23%  Similarity=0.341  Sum_probs=44.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           55 TILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        55 SIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      .|..+=+.+|+.|+++|..++..-......+.++.+|...|.+....+..++..|+.++.+.
T Consensus        20 dIT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~y   81 (201)
T PF13851_consen   20 DITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKNY   81 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            36667788899999999888876666666666666666666666666666666666665543

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

Probab=90.26  E-value=2.3  Score=39.75  Aligned_cols=58  Identities=19%  Similarity=0.204  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      .++.-.-++.|++++++.+.+.+.++++...|+..-.++.+|-.+|..|-.+|++|++
T Consensus       153 ~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~  210 (216)
T KOG1962|consen  153 NDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIE  210 (216)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHh
Confidence            4455556677777777777777788888888888888888888888888888887765

>PF09738 DUF2051: Double stranded RNA binding protein (DUF2051); InterPro: IPR019139 This entry represents transcriptional repressors which preferentially bind to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA

Probab=90.15  E-value=2  Score=41.71  Aligned_cols=89  Identities=26%  Similarity=0.325  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHHHhhhccCCCCC-CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           28 LRRDRLNEHFTELGNALDPDRP-KNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        28 rRRdKLNErF~eLrslLvP~~~-K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      --|+.|.+-=...+.+|+-+.+ -++|.+++..    |.-|+..+++|++.+..|+.++++...+..-++.....|+.++
T Consensus        81 ~lk~~l~evEekyrkAMv~naQLDNek~~l~yq----vd~Lkd~lee~eE~~~~~~re~~eK~~elEr~K~~~d~L~~e~  156 (302)
T PF09738_consen   81 DLKDSLAEVEEKYRKAMVSNAQLDNEKSALMYQ----VDLLKDKLEELEETLAQLQREYREKIRELERQKRAHDSLREEL  156 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467777776777777788776 7889888764    4556778888888888888888888888877888889999999


Q ss_pred             HHHHHHHHHHHHHc
Q 022288          107 ENLNIQYQQRVRAM  120 (299)
Q Consensus       107 e~L~~qlqqrl~~~  120 (299)
                      ..|+.+|.+|=..+
T Consensus       157 ~~Lre~L~~rdeli  170 (302)
T PF09738_consen  157 DELREQLKQRDELI  170 (302)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999887666

They may control smooth muscle cell proliferation following artery injury through PDGFA repression and may also bind double-stranded RNA. They interact with the leucine-rich repeat domain of human flightless-I (FliI) protein.

>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []

Probab=89.93  E-value=1.3  Score=32.82  Aligned_cols=37  Identities=32%  Similarity=0.494  Sum_probs=17.2

Q ss_pred             HHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           74 LKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        74 Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ++.+...|+.++..++.+..+|+.+...|+.+.+.++
T Consensus        22 ~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie   58 (80)
T PF04977_consen   22 LNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIE   58 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHH
Confidence            3333334444444444444444444555544555554

These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle

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

Probab=89.83  E-value=3  Score=37.75  Aligned_cols=76  Identities=26%  Similarity=0.399  Sum_probs=52.5

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH----------------------HhhhHHHHHH
Q 022288           51 NDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREE----------------------KLSLRSEIEN  108 (299)
Q Consensus        51 ~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdE----------------------ns~LksE~e~  108 (299)
                      .||+ .|..+-..++.+..++..|+-+++.|......|..|+++|...                      ...|...++.
T Consensus        83 kdK~-~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~~~i~evqQk~~~kn~lLEkKl~~l~~~lE~  161 (201)
T PF13851_consen   83 KDKQ-SLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELYRKFESAIQEVQQKTGLKNLLLEKKLQALSEQLEK  161 (201)
T ss_pred             HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3565 4677777788888888888888888888888888887777632                      2334445566


Q ss_pred             HHHHHHHHHHHcCCCccCCCccc
Q 022288          109 LNIQYQQRVRAMVPWAAMDHSVM  131 (299)
Q Consensus       109 L~~qlqqrl~~~~pw~~~dps~~  131 (299)
                      -+.||..=++++    ++||..+
T Consensus       162 keaqL~evl~~~----nldp~~~  180 (201)
T PF13851_consen  162 KEAQLNEVLAAA----NLDPAAL  180 (201)
T ss_pred             HHHHHHHHHHHc----CCCHHHH
Confidence            666666666666    6787743

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=89.77  E-value=2.1  Score=39.46  Aligned_cols=41  Identities=24%  Similarity=0.304  Sum_probs=25.2

Q ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           76 TEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        76 ~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      +.+..++.|...|..+...|++||..|..+.+.|+.++++-
T Consensus        88 aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL  128 (193)
T PF14662_consen   88 AQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKEL  128 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHH
Confidence            33344455555566666777777777777777776655543

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

Probab=89.70  E-value=4.9  Score=34.77  Aligned_cols=48  Identities=40%  Similarity=0.563  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L  109 (299)
                      +.++++.++++.++.....+.++..++..+..+++++...++.+..++
T Consensus       123 ~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~  170 (191)
T PF04156_consen  123 ELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERL  170 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444455555555665555666666555544444444444444444444

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 [].

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

Probab=89.61  E-value=1.9  Score=37.81  Aligned_cols=30  Identities=27%  Similarity=0.330  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           82 TEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        82 ~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      .+|++.|+.|..+...|...||.|.++|+.
T Consensus       160 ~~ei~~lk~el~~~~~~~~~LkkQ~~~l~~  189 (192)
T PF05529_consen  160 SEEIEKLKKELEKKEKEIEALKKQSEGLQK  189 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344444444444444444444444444443

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

>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles

Probab=89.58  E-value=5.3  Score=30.14  Aligned_cols=73  Identities=15%  Similarity=0.332  Sum_probs=43.7

Q ss_pred             HHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           32 RLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        32 KLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      .|+..+..+...     ...+|-..|.++=..|.+..+-+..++-|...+..      .+++.+.......++++.+|+.
T Consensus         7 ~i~~~l~~~~~~-----~~~~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~------s~r~~~~~kl~~yr~~l~~lk~   75 (79)
T PF05008_consen    7 EIKSKLERIKNL-----SGEQRKSLIREIERDLDEAEELLKQMELEVRSLPP------SERNQYKSKLRSYRSELKKLKK   75 (79)
T ss_dssp             HHHHHHHHGGGS------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-H------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcc-----ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCH------HHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444432     12455555666656666555555555555544432      6677788888888888888887


Q ss_pred             HHHH
Q 022288          112 QYQQ  115 (299)
Q Consensus       112 qlqq  115 (299)
                      +|++
T Consensus        76 ~l~~   79 (79)
T PF05008_consen   76 ELKK   79 (79)
T ss_dssp             HHHH
T ss_pred             HhcC
Confidence            7763

The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.

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

Probab=89.52  E-value=6.7  Score=33.17  Aligned_cols=79  Identities=15%  Similarity=0.256  Sum_probs=35.9

Q ss_pred             HHHHHHHHHhhhccCCCCC-CCC--hhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           31 DRLNEHFTELGNALDPDRP-KND--KATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        31 dKLNErF~eLrslLvP~~~-K~D--KASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      .-||..+..++=+ ..... ..+  -..=....|..|.+|-.+.++-....+.|...+..+..+...|.....+|+.+++
T Consensus         5 ~yiN~~L~s~G~~-~~~~~~~~~~~~~~~~~~vin~i~~Ll~~~~r~~~~~e~l~~~~~~l~~d~~~l~~~~~rL~~~~~   83 (151)
T PF11559_consen    5 EYINQQLLSRGYP-SDGLLFDSAEESEDNDVRVINCIYDLLQQRDRDMEQREDLSDKLRRLRSDIERLQNDVERLKEQLE   83 (151)
T ss_pred             HHHHHHHHHCCCC-CCCccCcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            3588888888832 22211 111  1222344555555555554444444444444444444444444444444444443


Q ss_pred             HHH
Q 022288          108 NLN  110 (299)
Q Consensus       108 ~L~  110 (299)
                      .++
T Consensus        84 ~~e   86 (151)
T PF11559_consen   84 ELE   86 (151)
T ss_pred             HHH
Confidence            333

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

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

Probab=89.38  E-value=3.7  Score=40.03  Aligned_cols=70  Identities=23%  Similarity=0.438  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           28 LRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        28 rRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      .+|+.||....++++-             -.+...-+++|+++++.|...-..+.+++.+|+.+++++....+.|..++.
T Consensus        27 ekR~El~~~~~~~~ek-------------Rdeln~kvrE~~e~~~elr~~rdeineev~elK~kR~ein~kl~eL~~~~~   93 (294)
T COG1340          27 EKRDELRKEASELAEK-------------RDELNAKVRELREKAQELREERDEINEEVQELKEKRDEINAKLQELRKEYR   93 (294)
T ss_pred             HHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456666666666653             335556677777777777777777777777777777766666666665555


Q ss_pred             HHH
Q 022288          108 NLN  110 (299)
Q Consensus       108 ~L~  110 (299)
                      .|-
T Consensus        94 ~l~   96 (294)
T COG1340          94 ELK   96 (294)
T ss_pred             HHH
Confidence            443

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=89.27  E-value=0.34  Score=49.62  Aligned_cols=47  Identities=32%  Similarity=0.376  Sum_probs=38.4

Q ss_pred             hccchHHHHHHHHHHHHHHHHhhhccCCCC---CCCChhhhHHHHHHHHHH
Q 022288           19 KMQKADREKLRRDRLNEHFTELGNALDPDR---PKNDKATILADTVQLLKD   66 (299)
Q Consensus        19 k~~KAerERrRRdKLNErF~eLrslLvP~~---~K~DKASIL~DAI~ylKd   66 (299)
                      +++| -+-|.||++-|--|.+|.++|+--+   +..||++|+-=|..|||-
T Consensus         3 ekSK-naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    3 EKSK-NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             ccch-hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence            3455 3679999999999999999874432   479999999999999973

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []

Probab=88.87  E-value=1.3  Score=31.94  Aligned_cols=34  Identities=29%  Similarity=0.342  Sum_probs=19.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           81 LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        81 L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      |+.+-+.|+...+.|+.++..|+.|.++|..|++
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~   36 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQ   36 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555555555555555555555555443

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

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

Probab=88.84  E-value=1.9  Score=35.36  Aligned_cols=52  Identities=21%  Similarity=0.348  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAAL--TEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L--~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      +-+.++..++..++.+++.|  ..+++.|..+..+++.+...|..++.-+..+.
T Consensus        42 ~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~~   95 (106)
T PF10805_consen   42 ERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSHQL   95 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            33455577777777777776  66777777777777777777777777665443

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

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=88.81  E-value=1.9  Score=39.71  Aligned_cols=14  Identities=36%  Similarity=0.408  Sum_probs=5.1

Q ss_pred             HHhhhHHHHHHHHH
Q 022288           77 EHAALTEESRELTQ   90 (299)
Q Consensus        77 en~~L~eE~~eLk~   90 (299)
                      +|+.|++|+.+|+.
T Consensus        77 en~~L~~e~~~l~~   90 (276)
T PRK13922         77 ENEELKKELLELES   90 (276)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333333333

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

Probab=88.66  E-value=4.1  Score=41.44  Aligned_cols=29  Identities=34%  Similarity=0.365  Sum_probs=19.8

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           91 EKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        91 EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      ||..||.|+..|..|++..+.|++|.--.
T Consensus       350 EKaaLrkerd~L~keLeekkreleql~~q  378 (442)
T PF06637_consen  350 EKAALRKERDSLAKELEEKKRELEQLKMQ  378 (442)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67777777777777777776666654433

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

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

Probab=88.63  E-value=5.7  Score=40.45  Aligned_cols=57  Identities=23%  Similarity=0.328  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      |.+.-+-...|+.++.+|+.++..+..++.+...+..+++..+..+...+..|+.|-
T Consensus        54 i~~~~~~~~kL~~~lk~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~l~~l~~q~  110 (420)
T COG4942          54 IREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNARLNALEVQE  110 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHH
Confidence            334444455566666666666666666666666677777777777777777777766

>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=88.44  E-value=4  Score=35.71  Aligned_cols=44  Identities=45%  Similarity=0.482  Sum_probs=31.5

Q ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           73 KLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        73 ~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      .-+.++.+|.+++..|+.+.+.|..|...|+.+++.|..++|.-
T Consensus        49 n~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~   92 (140)
T PF10473_consen   49 NSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKK   92 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33455566777777777777778878888888887777766543

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

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=88.41  E-value=3.9  Score=36.87  Aligned_cols=61  Identities=21%  Similarity=0.290  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           56 ILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        56 IL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      =|.+++..|.+=+.+.+.|..-|.-|.+..+..+..-..|.++...|..+.++|..++..+
T Consensus        61 dLe~~l~rLeEEqqR~~~L~qvN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~~k  121 (182)
T PF15035_consen   61 DLEEALIRLEEEQQRSEELAQVNALLREQLEQARKANEALQEDLQKLTQDWERLRDELEQK  121 (182)
T ss_pred             cHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3777888888888888888888888888887777777778888888777777776666544

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

Probab=88.24  E-value=6.2  Score=34.98  Aligned_cols=66  Identities=20%  Similarity=0.240  Sum_probs=45.1

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           52 DKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        52 DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      .+..-|.+.-..+..|+.++..|+.++.....-+..|+-|.-.|+-+.+.+...+.+|+.+.++-|
T Consensus       113 ~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv  178 (194)
T PF08614_consen  113 EKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLEEENRELV  178 (194)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566777777777777777777777766666666777766677777777777776666655544

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

>PRK09039 hypothetical protein; Validated

Probab=88.22  E-value=3.9  Score=39.79  Aligned_cols=55  Identities=15%  Similarity=0.183  Sum_probs=37.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           55 TILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        55 SIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L  109 (299)
                      ++.+++-..|..|+.||+.|+..+..|+.+++.++.+..+.+.....|+.+++.+
T Consensus       130 ~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a  184 (343)
T PRK09039        130 QVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVA  184 (343)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455666777778888888888887777777777766666665555555555443

>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP

Probab=88.09  E-value=3.5  Score=31.41  Aligned_cols=40  Identities=20%  Similarity=0.394  Sum_probs=19.0

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           71 VEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        71 Vq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      +.+|..++.+|..+++.|..+.+.||.+....+.|..+-+
T Consensus         5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN   44 (56)
T PF04728_consen    5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARAN   44 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444455555555444

The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.

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

Probab=87.93  E-value=1.9  Score=37.15  Aligned_cols=60  Identities=28%  Similarity=0.456  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH--hhhHHHHHHHHHHH---HHHHHHc
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEK--LSLRSEIENLNIQY---QQRVRAM  120 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEn--s~LksE~e~L~~ql---qqrl~~~  120 (299)
                      .+-+.+|..++..|++++..|..++..|+.|.+.|..+-  ..|..+|..|+.++   +.||..+
T Consensus        71 ~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l  135 (169)
T PF07106_consen   71 PEELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKL  135 (169)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345777777788888888888888888888888776654  46777777777654   4455543

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 [].

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

Probab=87.92  E-value=5.3  Score=35.08  Aligned_cols=27  Identities=30%  Similarity=0.396  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           90 QEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        90 ~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      .||.++|+|...+...+..+++.+...
T Consensus       113 ~eK~~~r~e~~~~~~ki~e~~~ki~~e  139 (177)
T PF07798_consen  113 LEKGRIREEQAKQELKIQELNNKIDTE  139 (177)
T ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345556666555555555554444433

>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6

Probab=87.89  E-value=3.3  Score=33.00  Aligned_cols=56  Identities=25%  Similarity=0.490  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHhhhHHH----------HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           65 KDLTSQVEKLKTEHAALTEE----------SRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE----------~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      +.|+.+++.|+.+...+..+          ..+|..+..+++++...|..+...++.+++..+...
T Consensus        39 r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e~~l~~~l~~i  104 (108)
T PF02403_consen   39 RELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKELEEELNELLLSI  104 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            34444445555444444433          345555666666666666666666666665554433

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....

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

Probab=87.89  E-value=6.3  Score=33.55  Aligned_cols=46  Identities=28%  Similarity=0.361  Sum_probs=26.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 022288           54 ATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEK   99 (299)
Q Consensus        54 ASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEn   99 (299)
                      ..++..--.-|++|..++..|+.++..|..+-+.++.|.-.|..++
T Consensus        15 ~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~   60 (120)
T PF12325_consen   15 VQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEEN   60 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555556666667766666666666555555555544444444

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 [].

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

Probab=87.87  E-value=2.8  Score=39.41  Aligned_cols=55  Identities=33%  Similarity=0.447  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      .+|-=+..|=++.+..|..|++|.+.+.+++..||.|...|++|-.+|=    .+++-+
T Consensus        79 siLpIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLY----EKiRyl  133 (248)
T PF08172_consen   79 SILPIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLY----EKIRYL  133 (248)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHH
Confidence            4444556666677777777777777777777777777777777777665    556555

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

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

Probab=87.87  E-value=1.8  Score=33.65  Aligned_cols=67  Identities=24%  Similarity=0.368  Sum_probs=51.4

Q ss_pred             HHHHHHHHhhhccCCCCC---CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 022288           32 RLNEHFTELGNALDPDRP---KNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEK   99 (299)
Q Consensus        32 KLNErF~eLrslLvP~~~---K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEn   99 (299)
                      .+..-..+|..+ ++++.   ..+++=|+.+.-.++..|..+++.++.++..|....+++..+.++++...
T Consensus        30 ~~~~~~~eL~~l-~~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l   99 (106)
T PF01920_consen   30 ELELTLEELEKL-DDDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKL   99 (106)
T ss_dssp             HHHHHHHHHHTS-STT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566778888875 77642   66788888888888888888888888888888888888877777766544

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

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=87.77  E-value=2.2  Score=39.42  Aligned_cols=49  Identities=31%  Similarity=0.404  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      +|-..|+.|+..|..|..++..|+....-+.+.++.|..+++.|..|++
T Consensus         5 dL~~~v~dL~~~n~~L~~en~kL~~~ve~~ee~na~L~~e~~~L~~q~~   53 (193)
T PF14662_consen    5 DLLSCVEDLQLNNQKLADENAKLQRSVETAEEGNAQLAEEITDLRKQLK   53 (193)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555556666666666665566666666666666665554

>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP

Probab=87.71  E-value=4.1  Score=31.04  Aligned_cols=48  Identities=19%  Similarity=0.363  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      -|.+|-.+|+.|...+..|..++..|+.+....++|-.+--..|+++-
T Consensus         4 kid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN~a   51 (56)
T PF04728_consen    4 KIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDNIA   51 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            467899999999999999999999999999999999888777777664

The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.

>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]

Probab=87.68  E-value=2.7  Score=36.06  Aligned_cols=51  Identities=33%  Similarity=0.417  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      |++-.++..|++.+..|-.++..|++...+|-+||..|+-|.++|.    .||..
T Consensus         4 keiFd~v~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR----~RL~~   54 (114)
T COG4467           4 KEIFDQVDNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLR----ERLGE   54 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHH----HHhCC
Confidence            3455667777777778888888888888888888888888888886    66655

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

Probab=87.64  E-value=5  Score=44.98  Aligned_cols=87  Identities=26%  Similarity=0.355  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHH
Q 022288           26 EKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSE  105 (299)
Q Consensus        26 ERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE  105 (299)
                      -|.+.+.++.++..+.+-+     ..+=.+-+.+.-.-++.|..+|++|+..+..|.++.++++.+.-+.++|+...+.+
T Consensus       370 ~k~~~d~l~k~I~~~~~~~-----~~~~~~~~~e~e~k~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~  444 (1074)
T KOG0250|consen  370 LKKEVDRLEKQIADLEKQT-----NNELGSELEERENKLEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGE  444 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHH-----HhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            3566777788888777753     12223347778888999999999999999999999999998888888888888888


Q ss_pred             HHHHHHHHHHHH
Q 022288          106 IENLNIQYQQRV  117 (299)
Q Consensus       106 ~e~L~~qlqqrl  117 (299)
                      |..|...+++.-
T Consensus       445 i~~l~k~i~~~~  456 (1074)
T KOG0250|consen  445 ILQLRKKIENIS  456 (1074)
T ss_pred             HHHHHHHHHHHH
Confidence            887777666544

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=87.63  E-value=4.1  Score=42.03  Aligned_cols=51  Identities=12%  Similarity=0.239  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      |.+.=.-.++|+.+++.|+.+++.+.....++..+.++|.+|+..|+.+++
T Consensus        71 LteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~  121 (475)
T PRK13729         71 TTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVK  121 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            333333444444444444444443334444444444444444444444443

>smart00787 Spc7 Spc7 kinetochore protein

Probab=87.38  E-value=4.2  Score=39.40  Aligned_cols=50  Identities=20%  Similarity=0.240  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      +.|++++.++..++.....++.+++.+..++.........++..++.+++
T Consensus       207 ~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~  256 (312)
T smart00787      207 DRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIA  256 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333334444444444444444444444444444444443

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

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=87.21  E-value=1.8  Score=35.73  Aligned_cols=33  Identities=24%  Similarity=0.317  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      +.+|+.+++.++.+++.|+.+...|+.|...|+
T Consensus        29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~   61 (105)
T PRK00888         29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK   61 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            455566666655555555555444444444443

>smart00338 BRLZ basic region leucin zipper

Probab=87.18  E-value=4  Score=30.16  Aligned_cols=34  Identities=29%  Similarity=0.449  Sum_probs=15.8

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           79 AALTEESRELTQEKNDLREEKLSLRSEIENLNIQ  112 (299)
Q Consensus        79 ~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~q  112 (299)
                      ..|+.++..|..+..+|+.+...|..++..|..+
T Consensus        29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~   62 (65)
T smart00338       29 EELERKVEQLEAENERLKKEIERLRRELEKLKSE   62 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444444444433

>PF14282 FlxA: FlxA-like protein

Probab=87.15  E-value=4  Score=33.54  Aligned_cols=57  Identities=18%  Similarity=0.296  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHH----HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEE----SRELTQEKNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE----~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      -..|+.|+.++..|.+++..|...    .+.-......|..+...|.++|..|+.+..+..
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~~~   78 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAEQQ   78 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567788888888888877777662    123333444566666667777766665544433

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

Probab=87.06  E-value=6.5  Score=36.36  Aligned_cols=62  Identities=29%  Similarity=0.487  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH-------HHHhhhHHHHHHHHH----HHHHHHHHHhhhHHHHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLK-------TEHAALTEESRELTQ----EKNDLREEKLSLRSEIENLNIQYQQRVR  118 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk-------~en~~L~eE~~eLk~----EkNELRdEns~LksE~e~L~~qlqqrl~  118 (299)
                      +..+-.-+++++.+++.|.       ..+..|...+.+|..    +...+......|..++..|..++++++.
T Consensus       211 ~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~~~~~~~~~~~i~~le~el~~l~~~~~~~~~  283 (312)
T PF00038_consen  211 LESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELEQRLDEEREEYQAEIAELEEELAELREEMARQLR  283 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHHHHH
Confidence            4444444444444444444       444445555544432    2333444455555666666555555543

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

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=86.91  E-value=4.7  Score=31.31  Aligned_cols=51  Identities=24%  Similarity=0.316  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           60 TVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        60 AI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      +.+-+.-.......|..+.+.....+...-.+.++|++|+..|+.|++.+.
T Consensus        17 ~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r   67 (69)
T PF14197_consen   17 LTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELR   67 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            333333333444444455555555566677777778888888887776654

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

Probab=86.83  E-value=5.8  Score=30.91  Aligned_cols=55  Identities=18%  Similarity=0.317  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           60 TVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        60 AI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      -=+.|.+|+.+-+.|....-.+..-|+.|+....++..+...|+..++.++.++.
T Consensus        10 KDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~   64 (74)
T PF12329_consen   10 KDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELE   64 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3356778888888887777777777777777777777777777777766665543

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

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=86.72  E-value=2.8  Score=37.78  Aligned_cols=51  Identities=24%  Similarity=0.345  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           60 TVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        60 AI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .+...+.|+.+.++|+.++..|+.+++.|..|...|..+...++.+-..|=
T Consensus        95 ~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~  145 (161)
T TIGR02894        95 TNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLI  145 (161)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455566666666666666666666666666666666666666665553

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.

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

Probab=86.66  E-value=5.8  Score=41.73  Aligned_cols=63  Identities=22%  Similarity=0.298  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      ....-.-+.+|+.++++|..+.+.+..+++.++.+..++.+|....+.+..+|+.++.-+-+.
T Consensus       323 ~~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l~~k~  385 (594)
T PF05667_consen  323 QEEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKLKKKT  385 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346678899999999999999999999999999999999999999999999999887755444

>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage

Probab=86.66  E-value=14  Score=32.18  Aligned_cols=86  Identities=19%  Similarity=0.307  Sum_probs=66.5

Q ss_pred             HHHHHHHHhhhccCCCCCCCChhhhHHHHHHHH-HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           32 RLNEHFTELGNALDPDRPKNDKATILADTVQLL-KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        32 KLNErF~eLrslLvP~~~K~DKASIL~DAI~yl-KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .|++.|..|-.++.-+.   ...-.+.|+++-| .++...+...-.-+..++.+++.++.|...|++.+.++++.+++|.
T Consensus         5 el~~~~~~l~~~~e~~~---~d~e~~~dtLe~i~~~~~~K~~~~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk   81 (162)
T PF05565_consen    5 ELTDEYLELLELLEEGD---LDEEAIADTLESIEDEIEEKADNIAKVIKNLEADIEAIKAEIKRLQERKKSIENRIDRLK   81 (162)
T ss_pred             HHHHHHHHHHHHHhcCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47888888888754332   3345677777773 3466667777777788999999999999999999999999999999


Q ss_pred             HHHHHHHHHc
Q 022288          111 IQYQQRVRAM  120 (299)
Q Consensus       111 ~qlqqrl~~~  120 (299)
                      +-|...|...
T Consensus        82 ~yL~~~m~~~   91 (162)
T PF05565_consen   82 EYLLDAMEAA   91 (162)
T ss_pred             HHHHHHHHHc
Confidence            8888777664

It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].

>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6

Probab=86.59  E-value=4.9  Score=32.07  Aligned_cols=58  Identities=28%  Similarity=0.432  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH----------HHHHHHHhhhHHHHHHHHHHHHH
Q 022288           58 ADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEK----------NDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        58 ~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~Ek----------NELRdEns~LksE~e~L~~qlqq  115 (299)
                      ...++.|.+|-.+...|..+.+.|..+.+.+..+.          .+|..+-..++.++..|+.++..
T Consensus        25 ~~~vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~   92 (108)
T PF02403_consen   25 EEDVDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKE   92 (108)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566666677777777777777888877777653          34555667777777777766544

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....

>COG2919 Septum formation initiator [Cell division and chromosome partitioning]

Probab=86.47  E-value=9.7  Score=31.74  Aligned_cols=68  Identities=19%  Similarity=0.184  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCCCChhhh-HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           24 DREKLRRDRLNEHFTELGNALDPDRPKNDKATI-LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREE   98 (299)
Q Consensus        24 erERrRRdKLNErF~eLrslLvP~~~K~DKASI-L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdE   98 (299)
                      +..++||..|......|...+       -..++ +...+..+..|..+++.++++++.|..+...|+.|.+.|+++
T Consensus        18 ~~~~~~~~~l~~~l~~~l~~f-------~~~~~~g~~~~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          18 ERRVRRRRILTLVLLALLALF-------QYLAWFGKNGAADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             HHhHHHHHHHHHHHHHHHHHH-------HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            455666666665555555442       11111 222344455566666666666666666666666666666555

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

Probab=86.40  E-value=5.8  Score=32.59  Aligned_cols=51  Identities=24%  Similarity=0.389  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHH--HHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESREL--TQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eL--k~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      +..|.+++...+.....++.+++.|  +.+.++|+-+...++.++..|+.+++
T Consensus        37 ~~~l~~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~   89 (106)
T PF10805_consen   37 IEKLEERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQ   89 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            4455566666677777777777777  77777777777788888777775554

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

>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins

Probab=86.14  E-value=4.8  Score=33.84  Aligned_cols=57  Identities=26%  Similarity=0.293  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      +....+..|..+...|.+.|-.++.++..++.+..++.++...|+.+-..++.+++.
T Consensus        31 ~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~   87 (150)
T PF07200_consen   31 ELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEKEQQQDE   87 (150)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555666665566666666666666666666666666666654443

The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.

>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []

Probab=86.04  E-value=3.2  Score=30.73  Aligned_cols=32  Identities=28%  Similarity=0.441  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDL   95 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNEL   95 (299)
                      +.+++.+++.|+.+++.+..+++.|+.+...|
T Consensus        19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l   50 (80)
T PF04977_consen   19 YYQLNQEIAELQKEIEELKKENEELKEEIERL   50 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444555555555555555555555555555

These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=85.92  E-value=6.4  Score=38.48  Aligned_cols=66  Identities=21%  Similarity=0.288  Sum_probs=36.2

Q ss_pred             hHHHHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhh
Q 022288           23 ADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSL  102 (299)
Q Consensus        23 AerERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~L  102 (299)
                      ...++.||.+.+...                     -|.||=+.-|++-+.|..+.+.       |..+-.+||+.-..|
T Consensus       223 ~~~~~~~rkr~qnk~---------------------AAtRYRqKkRae~E~l~ge~~~-------Le~rN~~LK~qa~~l  274 (294)
T KOG4571|consen  223 TPEKKLRRKRQQNKA---------------------AATRYRQKKRAEKEALLGELEG-------LEKRNEELKDQASEL  274 (294)
T ss_pred             CchHHHHHHHHHhHH---------------------HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence            345667777676655                     5777766666555555444444       444444445555555


Q ss_pred             HHHHHHHHHHHHHH
Q 022288          103 RSEIENLNIQYQQR  116 (299)
Q Consensus       103 ksE~e~L~~qlqqr  116 (299)
                      ..||..|.+-+..+
T Consensus       275 erEI~ylKqli~e~  288 (294)
T KOG4571|consen  275 EREIRYLKQLILEV  288 (294)
T ss_pred             HHHHHHHHHHHHHH
Confidence            55555555433333

>PHA03011 hypothetical protein; Provisional

Probab=85.79  E-value=6  Score=33.89  Aligned_cols=78  Identities=23%  Similarity=0.288  Sum_probs=56.6

Q ss_pred             HHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           34 NEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        34 NErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      ||-+..|+-  +|..---=|-+=...-|+.+.+|+.+-.+|-+|..-+..+++.+.+-..+--+|.--|++|+++|..++
T Consensus        38 dEYLanL~f--~P~qi~dfk~GD~Nai~e~ldeL~~qYN~L~dEYn~i~Ne~k~~~~iIQdn~d~I~~LraeIDkLK~ni  115 (120)
T PHA03011         38 DEYLANLIF--EPEQIFDFKEGDINAIIEILDELIAQYNELLDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENI  115 (120)
T ss_pred             HHHHHhhhc--CHHHHhhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHH
Confidence            344455552  453321122223566788899999999999999999999999998888888888888999999987543

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

Probab=85.79  E-value=5.7  Score=37.58  Aligned_cols=38  Identities=26%  Similarity=0.337  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhh
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSL  102 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~L  102 (299)
                      ..|..+++.++....+|..++..|..+..+|+++...|
T Consensus        92 ~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l  129 (239)
T COG1579          92 RALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDL  129 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444433334333333333333333333333

>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=85.69  E-value=10  Score=34.13  Aligned_cols=22  Identities=18%  Similarity=0.240  Sum_probs=9.9

Q ss_pred             HHHHhhhHHHHHHHHHHHHHHH
Q 022288           96 REEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        96 RdEns~LksE~e~L~~qlqqrl  117 (299)
                      .++....+..+..|+.++..+-
T Consensus       125 ~~~~~~~~~~l~~l~~~l~~~r  146 (302)
T PF10186_consen  125 QNELEERKQRLSQLQSQLARRR  146 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444555555443

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

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

Probab=85.65  E-value=5.5  Score=36.11  Aligned_cols=37  Identities=24%  Similarity=0.314  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           60 TVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        60 AI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      ..+..+.|..++.+-+.++..+.+++.+|....-+|+
T Consensus       108 ~~e~~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~  144 (190)
T PF05266_consen  108 LLEERKKLEKKIEEKEAELKELESEIKELEMKILELQ  144 (190)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Confidence            3344444444444333333333333333333333333

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=85.58  E-value=3.2  Score=34.18  Aligned_cols=51  Identities=18%  Similarity=0.220  Sum_probs=29.4

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCc
Q 022288           70 QVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA  124 (299)
Q Consensus        70 qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~  124 (299)
                      +..+++.+.+.++.++..|+++...|+.|...|+.+.+-++    ++.+....+.
T Consensus        28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiE----e~AR~~Lg~v   78 (105)
T PRK00888         28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIE----ERARNELGMV   78 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHH----HHHHHHcCCC
Confidence            45556666666666666666666666666666665555555    4455544443

>PRK02195 V-type ATP synthase subunit D; Provisional

Probab=85.53  E-value=6  Score=35.93  Aligned_cols=57  Identities=19%  Similarity=0.234  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           64 LKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      |..|+.++.-.+.-...|+..-+.|-.|.-++.++...|+.+++.+-......+...
T Consensus        12 L~~lk~~L~~a~rg~~lLk~KR~~Li~e~~~~~~~~~~lr~~~~~~~~~a~~~l~~a   68 (201)
T PRK02195         12 LKKQKKQLKMLERYLPTLKLKKAQLQAEVRRAKAEAAELEQEYQKLRQAIEAWISLF   68 (201)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            556788888888888888888888999999999999999988888776666655443

>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants

Probab=85.52  E-value=7  Score=38.54  Aligned_cols=51  Identities=16%  Similarity=0.243  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           56 ILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        56 IL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      +|+-++..+.+|..++..|..+|+.|..+.+.+..+..++-.+|..+..++
T Consensus       131 l~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~L  181 (342)
T PF06632_consen  131 LFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLEKFVNAKEEHEEDL  181 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555666777778888888888887777777777776666655555554443

XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.

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

Probab=85.42  E-value=8.4  Score=33.32  Aligned_cols=35  Identities=29%  Similarity=0.429  Sum_probs=13.8

Q ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           76 TEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        76 ~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      +....+.+..+.+..|..+|+.+...++.+...+.
T Consensus       130 ~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~  164 (191)
T PF04156_consen  130 ERLDSLDESIKELEKEIRELQKELQDSREEVQELR  164 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333344444444444444433333334444443

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 [].

>PHA02047 phage lambda Rz1-like protein

Probab=85.35  E-value=5.5  Score=33.59  Aligned_cols=51  Identities=18%  Similarity=0.274  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCcc
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAA  125 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~  125 (299)
                      -+..++|..+++.++..+..++..++.|.+.              -+.-.+++..-|....+|+.
T Consensus        33 h~~a~~la~qLE~a~~r~~~~Q~~V~~l~~k--------------ae~~t~Ei~~aL~~n~~WaD   83 (101)
T PHA02047         33 HEEAKRQTARLEALEVRYATLQRHVQAVEAR--------------TNTQRQEVDRALDQNRPWAD   83 (101)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHhCCCccc
Confidence            3444445555555544444444444444333              34444556677778889985

>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization

Probab=85.32  E-value=2.2  Score=30.75  Aligned_cols=28  Identities=43%  Similarity=0.597  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           83 EESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        83 eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ....+|..+..+|..+|..|+.++..|+
T Consensus        25 ~~~~~le~~~~~L~~en~~L~~~i~~L~   52 (54)
T PF07716_consen   25 QREEELEQEVQELEEENEQLRQEIAQLE   52 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3344455555555555555555555554

; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=85.18  E-value=4.7  Score=42.97  Aligned_cols=46  Identities=28%  Similarity=0.370  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhh
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSL  102 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~L  102 (299)
                      +..-.+.++.|..++++|+.+|..|..++.+|+.+..+|+.+..++
T Consensus       417 i~~~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~  462 (652)
T COG2433         417 ITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELERF  462 (652)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445556666777777777777777777766666666665554443

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=85.14  E-value=2.3  Score=42.01  Aligned_cols=56  Identities=18%  Similarity=0.370  Sum_probs=39.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           55 TILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        55 SIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ++-+-+--..+.|..+..+|+.++..|..+.++++.+.+.++.|...|+.++++|+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (398)
T PTZ00454          8 AVASSTTHTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQ   63 (398)
T ss_pred             cccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33344445566677777777777777777777777777777777777777777664

>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT)

Probab=85.05  E-value=11  Score=31.78  Aligned_cols=53  Identities=25%  Similarity=0.403  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH----HHHHHHhhhHHHHHHHH
Q 022288           58 ADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKN----DLREEKLSLRSEIENLN  110 (299)
Q Consensus        58 ~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkN----ELRdEns~LksE~e~L~  110 (299)
                      +++|.-|..|+.++..++..+..|..+.+..+.+..    .+..++..|..++..++
T Consensus        55 a~~~~~L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~~~e~sw~~qk~~le~e~~~~~  111 (132)
T PF07926_consen   55 AEDIKELQQLREELQELQQEINELKAEAESAKAELEESEASWEEQKEQLEKELSELE  111 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            566888888888888888877777776655444322    23333444444444443

These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore

>PF14282 FlxA: FlxA-like protein

Probab=85.00  E-value=3.5  Score=33.86  Aligned_cols=50  Identities=28%  Similarity=0.416  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHH---H-HHHHHhhhHHHHHHHHHHHHHHH
Q 022288           68 TSQVEKLKTEHAALTEESRELTQEKN---D-LREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        68 r~qVq~Lk~en~~L~eE~~eLk~EkN---E-LRdEns~LksE~e~L~~qlqqrl  117 (299)
                      -.+|+.|+..+..|.+++..|....+   | -+.....|..+|.-|+.||.+..
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq   71 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQ   71 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556666666666666666655222   1 22233456666666666655443

>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]

Probab=84.95  E-value=5  Score=40.16  Aligned_cols=38  Identities=26%  Similarity=0.432  Sum_probs=15.4

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           70 QVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        70 qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      +++.+..+.+.|....++|+..+++|+.++..|+.+..
T Consensus       226 eme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~  263 (365)
T KOG2391|consen  226 EMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQ  263 (365)
T ss_pred             HHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHH
Confidence            33344444444433334444444444444444443333

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

Probab=84.91  E-value=5.5  Score=38.86  Aligned_cols=54  Identities=22%  Similarity=0.424  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      -+..++++-..|......+.+.+++|+.+++++-++...|+.....++..++..
T Consensus        35 ~~~~~~ekRdeln~kvrE~~e~~~elr~~rdeineev~elK~kR~ein~kl~eL   88 (294)
T COG1340          35 EASELAEKRDELNAKVRELREKAQELREERDEINEEVQELKEKRDEINAKLQEL   88 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444455555666666666777777777777777777766666553

>TIGR00219 mreC rod shape-determining protein MreC

Probab=84.89  E-value=3.1  Score=39.41  Aligned_cols=31  Identities=29%  Similarity=0.416  Sum_probs=13.7

Q ss_pred             HHHHHhhhHHHHHHHHHHHH----HHHHHHhhhHH
Q 022288           74 LKTEHAALTEESRELTQEKN----DLREEKLSLRS  104 (299)
Q Consensus        74 Lk~en~~L~eE~~eLk~EkN----ELRdEns~Lks  104 (299)
                      |++||+.|.+++.+|+.+.+    +|+.||.+|+.
T Consensus        71 l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~  105 (283)
T TIGR00219        71 LEYENYKLRQELLKKNQQLEILTQNLKQENVRLRE  105 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555444433322    24444444443

MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=84.82  E-value=13  Score=32.24  Aligned_cols=62  Identities=27%  Similarity=0.414  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      .+.++..|..+++....+..++..+..++.....+...+|++...++.+.+++..++.. |+.
T Consensus        72 ~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~-l~~  133 (177)
T PF13870_consen   72 IGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKK-LRQ  133 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH
Confidence            67888888899999999999999999999999999999999999999999999877765 443

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

Probab=84.71  E-value=10  Score=34.79  Aligned_cols=58  Identities=22%  Similarity=0.268  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCc
Q 022288           67 LTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA  124 (299)
Q Consensus        67 Lr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~  124 (299)
                      |+..++.|+..+..++.++..|..++.++..-...|.--+.++-..|+++++.-.||.
T Consensus        68 L~~~~~~l~~~v~~q~~el~~L~~qi~~~~~~~~~l~p~m~~m~~~L~~~v~~d~Pf~  125 (251)
T PF11932_consen   68 LEVYNEQLERQVASQEQELASLEQQIEQIEETRQELVPLMEQMIDELEQFVELDLPFL  125 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            3333334444444444444444444444444444444444555556666666555654

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.

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=84.68  E-value=3.8  Score=42.22  Aligned_cols=49  Identities=35%  Similarity=0.492  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHhhhH---------------HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALT---------------EESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~---------------eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      ..|..+.+.|++||+.|+               .+-.+|..|...|++|.+.|+..+..|+.||
T Consensus        76 ~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l  139 (472)
T TIGR03752        76 AKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRL  139 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444555666665553               3446777888888888888888777776444

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

>PRK09039 hypothetical protein; Validated

Probab=84.60  E-value=7.5  Score=37.82  Aligned_cols=58  Identities=19%  Similarity=0.192  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      ....+...+|..|+.+++.|...+..|..+.++++.+....+.+++.|+..|+.-++.
T Consensus       130 ~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~~  187 (343)
T PRK09039        130 QVSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALAQ  187 (343)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555567777788888888888888888888777788888888888777776644

>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins

Probab=84.34  E-value=13  Score=28.87  Aligned_cols=48  Identities=23%  Similarity=0.411  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIEN  108 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~  108 (299)
                      +-.++.|...+.++....+.++++++.+..|.+++-.+-+.+..++..
T Consensus        18 ~~~l~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~~   65 (90)
T PF06103_consen   18 IKVLKKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHNTNELLEDVNE   65 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555555555555444444443

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

Probab=84.28  E-value=5.3  Score=34.50  Aligned_cols=40  Identities=23%  Similarity=0.394  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREE   98 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdE   98 (299)
                      .|+.-+-.|..++..|+.++..+..+|..|......|..+
T Consensus        11 ~a~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~e   50 (143)
T PF12718_consen   11 NAQDRAEELEAKVKQLEQENEQKEQEITSLQKKNQQLEEE   50 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555555555555544444444444433333333

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 [].

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

Probab=84.20  E-value=10  Score=30.55  Aligned_cols=62  Identities=13%  Similarity=0.242  Sum_probs=36.3

Q ss_pred             HHHHHHhhhccCCCCC---CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           34 NEHFTELGNALDPDRP---KNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        34 NErF~eLrslLvP~~~---K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      +.-..+|..+ +++..   ..+.+-|..+.-+.+..|..+++.|+.+...|...++++..+.++|+
T Consensus        33 ~~v~~EL~~l-~~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk   97 (105)
T cd00632          33 KKALEELEKL-ADDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQ   97 (105)
T ss_pred             HHHHHHHHcC-CCcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445566643 55543   45666666666666666666666666666666665555555555544

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

>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]

Probab=83.90  E-value=0.92  Score=42.59  Aligned_cols=56  Identities=21%  Similarity=0.338  Sum_probs=43.4

Q ss_pred             hhhhhhccchHHHHHHHHHHHHHHHHhhhccCCC--CCCCChhhhHHHHHHHHHHHHH
Q 022288           14 CAATRKMQKADREKLRRDRLNEHFTELGNALDPD--RPKNDKATILADTVQLLKDLTS   69 (299)
Q Consensus        14 ~~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~--~~K~DKASIL~DAI~ylKdLr~   69 (299)
                      ....|+..=+.|||.|=-.||+-|..||.+|+..  .+|+.|.-.|.-|-.||..|.+
T Consensus        68 ~~~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~  125 (254)
T KOG3898|consen   68 ALTLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE  125 (254)
T ss_pred             hhhhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence            3456666667899999999999999999985423  3599999999777777766553

>TIGR00634 recN DNA repair protein RecN

Probab=83.87  E-value=12  Score=38.33  Aligned_cols=88  Identities=17%  Similarity=0.290  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHH---HHhhhHHHHHHHHHHHHHHHHHHhhhH
Q 022288           27 KLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKT---EHAALTEESRELTQEKNDLREEKLSLR  103 (299)
Q Consensus        27 RrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~---en~~L~eE~~eLk~EkNELRdEns~Lk  103 (299)
                      -.|-+.|++++..|..+.    -|-  ..-+.+-++|+.+++.+++.|+.   ..+.|++++..++.+..++-.+....+
T Consensus       300 p~~L~ele~RL~~l~~Lk----rKy--g~s~e~l~~~~~~l~~eL~~l~~~~~~le~L~~el~~l~~~l~~~a~~Ls~~R  373 (563)
T TIGR00634       300 PERLNEIEERLAQIKRLK----RKY--GASVEEVLEYAEKIKEELDQLDDSDESLEALEEEVDKLEEELDKAAVALSLIR  373 (563)
T ss_pred             HHHHHHHHHHHHHHHHHH----HHh--CCCHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677888888888761    111  12478889999999999988774   455667777777777766666666553


Q ss_pred             HH-HHHHHHHHHHHHHHc
Q 022288          104 SE-IENLNIQYQQRVRAM  120 (299)
Q Consensus       104 sE-~e~L~~qlqqrl~~~  120 (299)
                      .+ ...|+..+...|+.+
T Consensus       374 ~~~a~~l~~~v~~~l~~L  391 (563)
T TIGR00634       374 RKAAERLAKRVEQELKAL  391 (563)
T ss_pred             HHHHHHHHHHHHHHHHhC
Confidence            33 356777777777775

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

>TIGR00606 rad50 rad50

Probab=83.75  E-value=5  Score=45.01  Aligned_cols=88  Identities=16%  Similarity=0.140  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           27 KLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        27 RrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      ...++++++.+..|..-+ ... + ++-.=|..++.-..+|..++.+|..++..+.+++.++..+...|..+...+..++
T Consensus       849 ~~e~e~~~~eI~~Lq~ki-~el-~-~~klkl~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~~  925 (1311)
T TIGR00606       849 RKLIQDQQEQIQHLKSKT-NEL-K-SEKLQIGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQEK  925 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHH-HHH-H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            444555566666664432 111 1 2222244577888888888888888888888888888777777777777777777


Q ss_pred             HHHHHHHHHHH
Q 022288          107 ENLNIQYQQRV  117 (299)
Q Consensus       107 e~L~~qlqqrl  117 (299)
                      +++..+.+..+
T Consensus       926 ~~~~~~~~~~~  936 (1311)
T TIGR00606       926 EELISSKETSN  936 (1311)
T ss_pred             HHHHHHHHHHH
Confidence            66655544443

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

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

Probab=83.57  E-value=5.2  Score=41.94  Aligned_cols=55  Identities=25%  Similarity=0.367  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHH-------HHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQE-------KNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~E-------kNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      .++.|..++..|+.+|..|..++..++.+       +.++....+.|+.++.-+..+..+.+
T Consensus       163 r~~~le~e~~~Lk~en~rl~~~l~~~r~~ld~Etllr~d~~n~~q~Lleel~f~~~~h~~eI  224 (546)
T KOG0977|consen  163 RIKALEDELKRLKAENSRLREELARARKQLDDETLLRVDLQNRVQTLLEELAFLKRIHKQEI  224 (546)
T ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhccHHHH
Confidence            34445555555555555555555544432       23333334445555544443333333

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

Probab=83.57  E-value=11  Score=34.26  Aligned_cols=47  Identities=26%  Similarity=0.383  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQ  112 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~q  112 (299)
                      +|..++.+|+..+..|+.+...+..++.+.-.|+.+|+++.+.|+.+
T Consensus       128 ~~e~~i~~Le~ki~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~  174 (190)
T PF05266_consen  128 ELESEIKELEMKILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEE  174 (190)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444444444444445555555555555433

>TIGR02231 conserved hypothetical protein

Probab=83.54  E-value=11  Score=38.03  Aligned_cols=63  Identities=14%  Similarity=0.217  Sum_probs=41.0

Q ss_pred             ChhhhHHHHHHHHHHHHHH---------------HHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           52 DKATILADTVQLLKDLTSQ---------------VEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        52 DKASIL~DAI~ylKdLr~q---------------Vq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      ++...+..-+.+|..+...               +.++.+....+.+++.++..++.+|..+...|+.++.+|+.+|.
T Consensus        92 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~  169 (525)
T TIGR02231        92 DRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTEDREAERRIRELEKQLSELQNELN  169 (525)
T ss_pred             HHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4666667777777777632               34455555666666677777777777777777777777765553

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.

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

Probab=83.47  E-value=6  Score=39.79  Aligned_cols=54  Identities=22%  Similarity=0.321  Sum_probs=45.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 022288           55 TILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIEN  108 (299)
Q Consensus        55 SIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~  108 (299)
                      +|+..+-.....|++-+..++++|..|+...+++.+|.+|..+|.+.|-.|+..
T Consensus       120 ~vf~k~k~~~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE  173 (401)
T PF06785_consen  120 EVFMKTKGDIQHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAE  173 (401)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            356666667788888899999999999999999999999999999988776653

>PF12808 Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2-binding region; InterPro: IPR024545 This domain occurs at the C terminus of microtubule organising proteins in both budding and fission fungi

Probab=83.44  E-value=3.7  Score=30.76  Aligned_cols=45  Identities=29%  Similarity=0.335  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .|++=..+|+.+-+.-.-+....+.+..+|+.||..|+++++.++
T Consensus         5 Rl~ELe~klkaerE~R~~d~~~a~~rl~~l~~EN~~Lr~eL~~~r   49 (52)
T PF12808_consen    5 RLEELERKLKAEREARSLDRSAARKRLSKLEGENRLLRAELERLR   49 (52)
T ss_pred             HHHHHHHHHHHhHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344444555555544444567778889999999999999998875

In Schizosaccharomyces pombe it has been shown to interact with the Mto2p protein, an interaction which is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis [, ].

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

Probab=83.36  E-value=12  Score=34.54  Aligned_cols=32  Identities=31%  Similarity=0.371  Sum_probs=14.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      .+.+|+..++...+.|+.+...|++.+..|+.
T Consensus       213 ~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~  244 (312)
T PF00038_consen  213 SAKEELKELRRQIQSLQAELESLRAKNASLER  244 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhHHHHHHhhhhHhhhhhhccccchhhhhh
Confidence            34444444444444444444444444444433

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

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

Probab=83.35  E-value=14  Score=33.15  Aligned_cols=27  Identities=26%  Similarity=0.545  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQE   91 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~E   91 (299)
                      .+|..++..|+.++..|..++.+|+..
T Consensus       123 ~~l~~~i~~L~~e~~~L~~~~~~l~~~  149 (189)
T PF10211_consen  123 QELEEEIEELEEEKEELEKQVQELKNK  149 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555555555555555555444443

Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=83.20  E-value=5.2  Score=37.45  Aligned_cols=26  Identities=8%  Similarity=0.161  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           82 TEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        82 ~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      +..++.|++|..+||..+..+.-+++
T Consensus        60 ~~ql~~lq~ev~~LrG~~E~~~~~l~   85 (263)
T PRK10803         60 QQQLSDNQSDIDSLRGQIQENQYQLN   85 (263)
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            33333333333333333333333333

>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore

Probab=83.03  E-value=13  Score=30.60  Aligned_cols=50  Identities=20%  Similarity=0.330  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHh-hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Q 022288           69 SQVEKLKTEHA-ALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVR  118 (299)
Q Consensus        69 ~qVq~Lk~en~-~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~  118 (299)
                      ..|..|+...+ ..+..++.|..+++.|.+|+..|+.+++.-..+-+.-|+
T Consensus        34 ~KV~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~~Ek~~Ll~   84 (87)
T PF12709_consen   34 TKVKALKKSYEARWEKKVDELENENKALKRENEQLKKKLDTEREEKQELLK   84 (87)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556665443 356667777777777777777777777666655555443

Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].

>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]

Probab=82.92  E-value=15  Score=35.98  Aligned_cols=39  Identities=26%  Similarity=0.256  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHH-cCCCccCCCc
Q 022288           91 EKNDLREEKLSLRSEIENLNIQYQQRVRA-MVPWAAMDHS  129 (299)
Q Consensus        91 EkNELRdEns~LksE~e~L~~qlqqrl~~-~~pw~~~dps  129 (299)
                      ||..|-++..+||.|...|.++|+-|-+. -.|-..+|.+
T Consensus       158 Eke~llesvqRLkdEardlrqelavr~kq~E~pR~~~Pss  197 (333)
T KOG1853|consen  158 EKEVLLESVQRLKDEARDLRQELAVRTKQTERPRIVEPSS  197 (333)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcCCccc
Confidence            34446667778888888888888887766 3566555444

>PRK11415 hypothetical protein; Provisional

Probab=82.48  E-value=4.8  Score=31.35  Aligned_cols=63  Identities=14%  Similarity=0.160  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH-HHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           58 ADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKND-LREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        58 ~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNE-LRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      .|.|..|+.=-.+..+|.++...|..+|..+.....- --.+...||.++..|..++.+.|+..
T Consensus         6 ~d~I~~Lk~~D~~F~~L~~~h~~Ld~~I~~lE~~~~~~~d~~i~~LKk~KL~LKDeI~~~L~~~   69 (74)
T PRK11415          6 RDLISRLKNENPRFMSLFDKHNKLDHEIARKEGSDGRGYNAEVVRMKKQKLQLKDEMLKILQQE   69 (74)
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHHHHHHHHHh
Confidence            3556666665566677777777777777666554221 13455667777777777777777654

>KOG0946 consensus ER-Golgi vesicle-tethering protein p115 [Intracellular trafficking, secretion, and vesicular transport]

Probab=82.38  E-value=6.3  Score=43.45  Aligned_cols=59  Identities=29%  Similarity=0.388  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           56 ILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        56 IL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      |..+=-+.|++|..+++.|++.+.+|+-|.++|..+..+.-.+.++|+.+.+.|++||.
T Consensus       658 ~~~kyK~lI~~lD~~~e~lkQ~~~~l~~e~eeL~~~vq~~~s~hsql~~q~~~Lk~qLg  716 (970)
T KOG0946|consen  658 IQQKYKGLIRELDYQIENLKQMEKELQVENEELEEEVQDFISEHSQLKDQLDLLKNQLG  716 (970)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44444556666666777777777777777777777777777777788888888887765

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=82.19  E-value=5.8  Score=38.31  Aligned_cols=51  Identities=22%  Similarity=0.337  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      .+-++..+|.+|.++|..|+.|.+.|+..-..|-.+|..|..+++.|+.+|
T Consensus        91 Rm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l  141 (292)
T KOG4005|consen   91 RMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQEL  141 (292)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            445566666666677777777766666555556667777777777665333

>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]

Probab=82.06  E-value=4.8  Score=34.37  Aligned_cols=51  Identities=29%  Similarity=0.330  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L  109 (299)
                      |.-+.-.+|-.+|-+|+...+.|...++.++.|--.||.||+.|-.=|++|
T Consensus        53 d~~EEKaRlItQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL  103 (120)
T KOG3650|consen   53 DVEEEKARLITQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL  103 (120)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence            333445556666777777777777777888777777888888888777777

>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=81.93  E-value=18  Score=27.76  Aligned_cols=54  Identities=20%  Similarity=0.382  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      |..=|+--..|.+++.+.+..|-.+....++-.....+|..+...|+.+++.++
T Consensus         6 L~~EirakQ~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r   59 (61)
T PF08826_consen    6 LEAEIRAKQAIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEELR   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            455567777778888888887777777777777766677777777777776654

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

>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []

Probab=81.88  E-value=2.4  Score=34.02  Aligned_cols=28  Identities=32%  Similarity=0.527  Sum_probs=23.1

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           92 KNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        92 kNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      .++|++||.+|+.+|.+|+.+||+.-+.
T Consensus         2 i~ei~eEn~~Lk~eiqkle~ELq~~~~~   29 (76)
T PF07334_consen    2 IHEIQEENARLKEEIQKLEAELQQNKRE   29 (76)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3678889999999999999888886665

This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.

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

Probab=81.82  E-value=5.7  Score=37.43  Aligned_cols=60  Identities=18%  Similarity=0.253  Sum_probs=55.3

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           51 NDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        51 ~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .+-.+||.-.+.-=-+.+.++.+|++++..+..++..|+.|.+.|+.+|..|=..+--|+
T Consensus        75 ~~~~siLpIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylq  134 (248)
T PF08172_consen   75 GGDSSILPIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQ  134 (248)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            366789999999889999999999999999999999999999999999999998888775

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

>TIGR00219 mreC rod shape-determining protein MreC

Probab=81.73  E-value=8.9  Score=36.39  Aligned_cols=24  Identities=21%  Similarity=0.043  Sum_probs=16.3

Q ss_pred             HhhhHHHHHHHHHHHHHHHHHHhh
Q 022288           78 HAALTEESRELTQEKNDLREEKLS  101 (299)
Q Consensus        78 n~~L~eE~~eLk~EkNELRdEns~  101 (299)
                      ...|.+|++.|+.|..+|+.+...
T Consensus        68 ~~~l~~EN~~Lr~e~~~l~~~~~~   91 (283)
T TIGR00219        68 VNNLEYENYKLRQELLKKNQQLEI   91 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345778888888887777555544

MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.

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

Probab=81.71  E-value=22  Score=31.66  Aligned_cols=61  Identities=20%  Similarity=0.308  Sum_probs=43.3

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           51 NDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        51 ~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      .+.-.+--.|+....++..++..|+.....+...+..|+....+|+.....++.+...|..
T Consensus        80 ~g~edLAr~al~~k~~~e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l~a  140 (221)
T PF04012_consen   80 AGREDLAREALQRKADLEEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREELKA  140 (221)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444556688888888888888888888777777777777666666666666666665543

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 [].

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

Probab=81.66  E-value=3  Score=37.47  Aligned_cols=54  Identities=26%  Similarity=0.419  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHH------HHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQ------EKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~------EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      -.-+..|+.+++.++.....|..++...+.      |+.++-.+...|+.++..|+.+|+
T Consensus        68 ~~~~~~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~  127 (188)
T PF03962_consen   68 QNKLEKLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEELKKELKELKKELE  127 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555666666666666666555555443      333444455555555555555555

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

>PF15458 NTR2: Nineteen complex-related protein 2

Probab=81.62  E-value=13  Score=34.83  Aligned_cols=16  Identities=19%  Similarity=0.607  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q 022288           24 DREKLRRDRLNEHFTE   39 (299)
Q Consensus        24 erERrRRdKLNErF~e   39 (299)
                      ...++||..|-+.+.+
T Consensus       145 ~~~~~rR~~i~e~I~~  160 (254)
T PF15458_consen  145 EQKRRRREEIEEAIND  160 (254)
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            5667788888777776

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=81.38  E-value=9  Score=41.19  Aligned_cols=64  Identities=19%  Similarity=0.302  Sum_probs=50.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           56 ILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        56 IL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      ||-|-.+.+.....++.+|+..-..|+.||.++.....||+.+..+-+.|++.|+..+.|--.+
T Consensus        80 ~~~e~~RI~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~  143 (907)
T KOG2264|consen   80 ILREQKRILASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQ  143 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHH
Confidence            4555566666666677788888888999999999999999999999999999998877664433

>PF14257 DUF4349: Domain of unknown function (DUF4349)

Probab=81.38  E-value=14  Score=33.90  Aligned_cols=80  Identities=21%  Similarity=0.295  Sum_probs=40.1

Q ss_pred             HHHHHHHHHhhhc---cCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhh--hHHHHHHHHHHHHHHHHHHhhhHHH
Q 022288           31 DRLNEHFTELGNA---LDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAA--LTEESRELTQEKNDLREEKLSLRSE  105 (299)
Q Consensus        31 dKLNErF~eLrsl---LvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~--L~eE~~eLk~EkNELRdEns~LksE  105 (299)
                      +++.+-+..|..+   +.-+..-.|...=..|+-..|+.|+.+.++|.+..+.  -.+++-++..|.+++|.|...++.+
T Consensus       105 ~~~~~~l~~l~~~g~v~~~~~~~~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~~  184 (262)
T PF14257_consen  105 DKFDSFLDELSELGKVTSRNISSEDVTEQYVDLEARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEGQ  184 (262)
T ss_pred             HHHHHHHHHHhccCceeeeeccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555543   2222234555555555555666666666666554432  2333444555555555555555555


Q ss_pred             HHHHH
Q 022288          106 IENLN  110 (299)
Q Consensus       106 ~e~L~  110 (299)
                      +..|+
T Consensus       185 ~~~l~  189 (262)
T PF14257_consen  185 LKYLD  189 (262)
T ss_pred             HHHHH
Confidence            55444

>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]

Probab=81.17  E-value=8.1  Score=38.75  Aligned_cols=61  Identities=23%  Similarity=0.275  Sum_probs=38.5

Q ss_pred             ChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           52 DKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        52 DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      +|..|-+..|..+.+.-.+  +++++++++..+...|++-..||+.-++.|+.++++||+|.+
T Consensus       203 ~~~~irasvisa~~eklR~--r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~  263 (365)
T KOG2391|consen  203 GKLVIRASVISAVREKLRR--RREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQ  263 (365)
T ss_pred             cccchhHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHH
Confidence            3444555555544443332  345566667777777777777777777778888877776543

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

Probab=81.11  E-value=7.1  Score=41.23  Aligned_cols=19  Identities=37%  Similarity=0.636  Sum_probs=8.8

Q ss_pred             HHHHHHHHHhhhHHHHHHH
Q 022288           91 EKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        91 EkNELRdEns~LksE~e~L  109 (299)
                      |+|+|..+...+..++++|
T Consensus       340 Er~~l~r~l~~i~~~~d~l  358 (581)
T KOG0995|consen  340 ERNKLKRELNKIQSELDRL  358 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444443

>PRK03918 chromosome segregation protein; Provisional

Probab=81.05  E-value=20  Score=37.72  Aligned_cols=14  Identities=21%  Similarity=0.579  Sum_probs=5.1

Q ss_pred             HHHHHHHHHHHHHH
Q 022288           84 ESRELTQEKNDLRE   97 (299)
Q Consensus        84 E~~eLk~EkNELRd   97 (299)
                      ++..+..+.++|+.
T Consensus       681 ~~~~l~~~i~~l~~  694 (880)
T PRK03918        681 ELEELEKRREEIKK  694 (880)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333333333333

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

Probab=81.02  E-value=9.3  Score=29.02  Aligned_cols=22  Identities=14%  Similarity=0.309  Sum_probs=10.0

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHH
Q 022288           92 KNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        92 kNELRdEns~LksE~e~L~~ql  113 (299)
                      .+.+|.|+..|+.++++|+.-+
T Consensus        16 i~tvk~en~~i~~~ve~i~env   37 (55)
T PF05377_consen   16 INTVKKENEEISESVEKIEENV   37 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444555554333

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

>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins

Probab=80.98  E-value=21  Score=27.76  Aligned_cols=51  Identities=16%  Similarity=0.304  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 022288           58 ADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIEN  108 (299)
Q Consensus        58 ~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~  108 (299)
                      -..-+.++++...++.++++.+.+..|++.+-.+-|++-++-..-...++.
T Consensus        22 ~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~~k~~~v~~   72 (90)
T PF06103_consen   22 KKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHNTNELLEDVNEKLEKVDP   72 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence            344455666666666666666666666666666666666554444444433

>PRK14011 prefoldin subunit alpha; Provisional

Probab=80.89  E-value=10  Score=33.14  Aligned_cols=39  Identities=26%  Similarity=0.407  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREE   98 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdE   98 (299)
                      +.+||+|++   .+++.|++..+.|.+.+.++..+.++|+.+
T Consensus        86 ~~eA~~~~~---~ri~~l~~~~~~l~~~i~~~~~~~~~l~~~  124 (144)
T PRK14011         86 VSEVIEDFK---KSVEELDKTKKEGNKKIEELNKEITKLRKE  124 (144)
T ss_pred             HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567777655   577777777778888888888887777754

>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins

Probab=80.88  E-value=15  Score=30.89  Aligned_cols=57  Identities=26%  Similarity=0.440  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRA  119 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~  119 (299)
                      .++++...++.|..+|..|.+.+-.+..+..++|.+...+..++..|+.+|+.....
T Consensus        28 ~~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~   84 (150)
T PF07200_consen   28 QVQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEKEQQ   84 (150)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            477778888888888888888887777777888888888888888888777665543

The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.

>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []

Probab=80.85  E-value=1.2  Score=36.13  Aligned_cols=50  Identities=34%  Similarity=0.528  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           58 ADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        58 ~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      .+.-.||.+|..++..|..++..|..++..|..+..+++.....|+..+.
T Consensus        21 ~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~~l~   70 (131)
T PF05103_consen   21 DEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQRALI   70 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT----------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHhhh
Confidence            45567788888888888877777777777777777666666666665543

Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=80.82  E-value=6.8  Score=41.81  Aligned_cols=29  Identities=28%  Similarity=0.354  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQE   91 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~E   91 (299)
                      .|..|+.+++.|+.+++.+..++..|+.+
T Consensus       430 ~ve~l~~e~~~L~~~~ee~k~eie~L~~~  458 (652)
T COG2433         430 TVERLEEENSELKRELEELKREIEKLESE  458 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444433

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

Probab=80.79  E-value=24  Score=36.04  Aligned_cols=17  Identities=35%  Similarity=0.559  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHhhh
Q 022288           26 EKLRRDRLNEHFTELGN   42 (299)
Q Consensus        26 ERrRRdKLNErF~eLrs   42 (299)
                      ||.||++|-+.+.+|--
T Consensus       110 ~r~qr~~La~~L~A~~r  126 (420)
T COG4942         110 EREQRRRLAEQLAALQR  126 (420)
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            46888888888888765

>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]

Probab=80.76  E-value=5  Score=34.28  Aligned_cols=72  Identities=26%  Similarity=0.327  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCc
Q 022288           58 ADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHS  129 (299)
Q Consensus        58 ~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps  129 (299)
                      -+|.+.-.+.+++-.+|-...-.|+.-.+.|.+..+-.++||..|++|-.-|-+=++--+.+..-|-+-+|+
T Consensus        45 l~a~e~~~d~~EEKaRlItQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNLMSaSSVFQst~ps  116 (120)
T KOG3650|consen   45 LDAVEAENDVEEEKARLITQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENLMSASSVFQSTDPS  116 (120)
T ss_pred             ccccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHhhhhhhhcCCCc
Confidence            367888888888888998888899999999999999999999999999888865555555555445444443

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=80.74  E-value=7.6  Score=34.22  Aligned_cols=36  Identities=33%  Similarity=0.530  Sum_probs=21.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           81 LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        81 L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      |+.+..+|.+|...|+.|++++.-|.+.+...|++-
T Consensus        79 LE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l  114 (135)
T KOG4196|consen   79 LEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEAL  114 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455555566666666666666666666666555443

>PLN02678 seryl-tRNA synthetase

Probab=80.49  E-value=17  Score=37.05  Aligned_cols=37  Identities=16%  Similarity=0.399  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           84 ESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        84 E~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      +..+|..+..+|++|...|..++..|+.++.+.+..+
T Consensus        72 ~~~~l~~~~~~Lk~ei~~le~~~~~~~~~l~~~~~~i  108 (448)
T PLN02678         72 DATELIAETKELKKEITEKEAEVQEAKAALDAKLKTI  108 (448)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            4456667778888888888888888888888877776

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

Probab=80.49  E-value=6.7  Score=37.03  Aligned_cols=31  Identities=26%  Similarity=0.456  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDL   95 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNEL   95 (299)
                      .+.+.+|..|+.+|+.|..++..|++|...|
T Consensus       218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~  248 (269)
T KOG3119|consen  218 DEMAHRVAELEKENEALRTQVEQLKKELATL  248 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444443333

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

Probab=80.47  E-value=14  Score=31.83  Aligned_cols=18  Identities=22%  Similarity=0.458  Sum_probs=6.4

Q ss_pred             HHHHHHHHhhhHHHHHHH
Q 022288           92 KNDLREEKLSLRSEIENL  109 (299)
Q Consensus        92 kNELRdEns~LksE~e~L  109 (299)
                      +..|...+..|..+++++
T Consensus        37 I~sL~~K~~~lE~eld~~   54 (143)
T PF12718_consen   37 ITSLQKKNQQLEEELDKL   54 (143)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            333333333333333333

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 [].

>PRK05431 seryl-tRNA synthetase; Provisional

Probab=80.26  E-value=21  Score=35.75  Aligned_cols=36  Identities=22%  Similarity=0.417  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           85 SRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        85 ~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      ..+|..+..+|+++...|+.++..++.++...+..+
T Consensus        68 ~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i  103 (425)
T PRK05431         68 AEALIAEVKELKEEIKALEAELDELEAELEELLLRI  103 (425)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            345777777888888888888888888888877765

>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=80.21  E-value=6.9  Score=38.47  Aligned_cols=56  Identities=25%  Similarity=0.362  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      .+|-.++++++..+..|+.+++.+.-|+.||..|....+.-..||+.||..-|.+-
T Consensus       129 e~lV~qLEk~~~q~~qLe~d~qs~lDEkeEl~~ERD~yk~K~~RLN~ELn~~L~g~  184 (319)
T PF09789_consen  129 EDLVEQLEKLREQIEQLERDLQSLLDEKEELVTERDAYKCKAHRLNHELNYILNGD  184 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            34445557778888888888888888888888888888888999998887777553

>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants

Probab=80.19  E-value=8.1  Score=38.12  Aligned_cols=52  Identities=19%  Similarity=0.219  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      +++-.+-..+.+|+..+..|..+.+.|+.+.+++..+...+-.+++.+|.+|
T Consensus       130 el~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~L  181 (342)
T PF06632_consen  130 ELFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLEKFVNAKEEHEEDL  181 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555556666677777777777777777777777777777777777776554

XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=80.14  E-value=1.3  Score=46.89  Aligned_cols=45  Identities=36%  Similarity=0.502  Sum_probs=37.5

Q ss_pred             ccchHHHHHHHHHHHHHHHHhhhccCC----CCCCCChhhhHHHHHHHHH
Q 022288           20 MQKADREKLRRDRLNEHFTELGNALDP----DRPKNDKATILADTVQLLK   65 (299)
Q Consensus        20 ~~KAerERrRRdKLNErF~eLrslLvP----~~~K~DKASIL~DAI~ylK   65 (299)
                      ..|.---||-|||||.-+..|.+|| |    .++|.||-|||-=++.||+
T Consensus        27 ~tkSNPSKRHRdRLNaELD~lAsLL-PfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   27 LTKSNPSKRHRDRLNAELDHLASLL-PFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             cccCCcchhHHHHhhhHHHHHHHhc-CCCHHHHhhhhhhhhhhhhHHHHH
Confidence            4555556888999999999999986 5    2369999999999999986

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

Probab=80.03  E-value=42  Score=36.16  Aligned_cols=16  Identities=31%  Similarity=0.447  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEH   78 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en   78 (299)
                      ..++|..++.+|+.+.
T Consensus       546 r~~~lE~E~~~lr~el  561 (697)
T PF09726_consen  546 RRRQLESELKKLRREL  561 (697)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3344444444444333

; GO: 0016021 integral to membrane

---

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	299
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	2e-09
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	8e-09
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-08
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	3e-06
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	8e-06
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-05
4f3l_A	361	Mclock, circadian locomoter output cycles protein	5e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	3e-04

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Length = 82

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 16/67 (23%), Positives = 30/67 (44%)

Query: 26 EKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEES 85
          EK  R  +N+   EL + +     K +K+ +L   +  ++ L    +KLK E+ +L    
Sbjct: 14 EKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAV 73

Query: 86 RELTQEK 92
           +    K
Sbjct: 74 HKSKSLK 80

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 Length = 88

 Score = 50.8 bits (122), Expect = 8e-09
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 26 EKLRRDRLNEHFTELGNAL--DPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTE 83
          E+ RR+ L   F  L + +    +  K  K  IL      +  + ++ +KL +E   L +
Sbjct: 14 ERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK 73

Query: 84 ESRELTQEKNDLR 96
             +L  +   L 
Sbjct: 74 RREQLKHKLEQLG 86

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B Length = 83

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 15/85 (17%)

Query: 26  EKLRRDRLNEHFTELGNAL-DPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEE 84
           E+ RRD + + F  L +++      K  +A IL    + ++ +                +
Sbjct: 10  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR--------------RK 55

Query: 85  SRELTQEKNDLREEKLSLRSEIENL 109
           +    Q+ +DL+ +   L  ++  L
Sbjct: 56  NHTHQQDIDDLKRQNALLEQQVRAL 80

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 16/86 (18%)

Query: 26  EKLRRDRLNEHFTELGNAL--DPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTE 83
           EK RR  L     +L   +   PD  ++   ++L      +K L                
Sbjct: 9   EKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSD------------ 56

Query: 84  ESRELTQEKNDLREEKLSLRSEIENL 109
             R+   + + L+ E+  L+ ++E L
Sbjct: 57  --RKAVHQIDQLQREQRHLKRQLEKL 80

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 42.3 bits (100), Expect = 8e-06
 Identities = 11/61 (18%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 26 EKLRRDRLNEHFTELGNAL-DPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEE 84
          E+ RRD + + F  L +++      K  +A IL    + ++ +  +    + +   L  +
Sbjct: 20 ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 79

Query: 85 S 85
          +
Sbjct: 80 N 80

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 5/53 (9%)

Query: 26 EKLRRDRLNEHFTELGNAL-----DPDRPKNDKATILADTVQLLKDLTSQVEK 73
          E+ RRD++N    +L   +     +  +    K  IL+     +++L     +
Sbjct: 13 ERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score = 43.4 bits (102), Expect = 5e-05
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 26 EKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLK 65
          EK RRD+ N    ELG+ L  +  K DK+T+L  ++  L+
Sbjct: 20 EKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59

>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 = 3e-04
 Identities = 15/110 (13%), Positives = 41/110 (37%), Gaps = 7/110 (6%)

Query: 5    QKNEGEVKDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLL 64
            +      +  +   ++ K  +E  +     +   E  +       K++   ++++  +  
Sbjct: 978  EAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKY-----KHETEQLVSELKEQN 1032

Query: 65   KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ 114
              L ++ E+L        +E  E    +  L EE   L  ++ +  ++YQ
Sbjct: 1033 TLLKTEKEELNRRIHDQAKEITE--TMEKKLVEETKQLELDLNDERLRYQ 1080

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	299
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.69
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.64
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.63
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.57
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.56
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.5
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.49
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.39
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.34
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.33
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.25
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.97
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	98.89
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	98.82
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.81
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.81
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.36
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.65
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	97.54
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	96.07
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	95.69
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	95.17
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	95.06
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	94.32
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	94.01
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	93.99
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	93.88
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	93.63
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	93.47
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	93.42
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	92.76
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	92.74
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	92.49
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	92.45
3he5_B	52	Synzip2; heterodimeric coiled-coil, de novo protei	92.41
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.17
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	92.01
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	91.3
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	91.09
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	90.93
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	90.88
2oqq_A	42	Transcription factor HY5; homodimer leucine zipper	90.8
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	90.79
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	90.38
1m1j_A	491	Fibrinogen alpha subunit; coiled coils, disulfide	90.13
3htk_A	60	Structural maintenance of chromosomes protein 5; S	90.04
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	90.02
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	89.87
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	89.74
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	89.67
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	89.44
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	89.36
1s94_A	180	S-syntaxin; three helix bundle, structural plastic	89.23
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	89.15
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	89.1
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	88.98
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	88.21
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	88.21
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	88.17
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	88.0
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	87.56
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	87.48
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	87.3
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	87.29
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	87.12
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	86.97
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	86.93
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	86.4
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	86.21
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	86.15
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	86.11
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	86.08
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	85.61
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	85.46
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	85.37
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	85.23
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	84.96
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	84.79
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	84.75
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	84.69
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	84.51
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	84.38
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	84.3
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	84.26
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	84.22
1wle_A	501	Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bo	84.07
2wt7_B	90	Transcription factor MAFB; transcription, transcri	84.04
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	83.84
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	83.67
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	83.62
3htk_A	60	Structural maintenance of chromosomes protein 5; S	83.54
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	83.22
1m1j_C	409	Fibrinogen gamma chain; coiled coils, disulfide ri	82.69
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	82.44
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	82.27
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	82.24
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	82.21
3u06_A	412	Protein claret segregational; motor domain, stalk	81.87
3qne_A	485	Seryl-tRNA synthetase, cytoplasmic; amino acid bio	81.58
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	81.44
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	81.17
2dq0_A	455	Seryl-tRNA synthetase; coiled-coil, homodimer, str	81.15
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	80.99
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	80.66
1zhc_A	76	Hypothetical protein HP1242; A-helical protein, un	80.64
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	80.46
3v86_A	27	De novo design helix; computational design of A pr	80.38

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C

Probab=99.69  E-value=5.7e-17  Score=125.28  Aligned_cols=73  Identities=21%  Similarity=0.318  Sum_probs=64.5

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCCCC-CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELT   89 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~-~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk   89 (299)
                      ..|+..|..+||+||++||++|.+|+++| |+. .|+|||+||.+||+||+.|+.+++.|+.++..|..+++...
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lv-P~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~~~~   77 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            45778888999999999999999999985 655 79999999999999999999999999998888887766543

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1

Probab=99.64  E-value=4.8e-16  Score=121.93  Aligned_cols=79  Identities=22%  Similarity=0.339  Sum_probs=63.2

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCCCC---CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDR---PKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEK   92 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~---~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~Ek   92 (299)
                      +.++..|..+||+||++||++|.+|+.+ +|..   .|++|++||.+||+||+.|+.+.+.|..+.+.|..+...|+.+.
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~-vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~n~~L~~rl   82 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQ-IPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKL   82 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTT-CGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4577888899999999999999999997 6764   59999999999999999999998888766655444444444444


Q ss_pred             HHH
Q 022288           93 NDL   95 (299)
Q Consensus        93 NEL   95 (299)
                      .+|
T Consensus        83 ~~L   85 (88)
T 1nkp_A           83 EQL   85 (88)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            333

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B

Probab=99.63  E-value=7e-16  Score=118.36  Aligned_cols=71  Identities=18%  Similarity=0.355  Sum_probs=57.5

Q ss_pred             hhccchHHHHHHHHHHHHHHHHhhhccCCC--CCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           18 RKMQKADREKLRRDRLNEHFTELGNALDPD--RPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELT   89 (299)
Q Consensus        18 Rk~~KAerERrRRdKLNErF~eLrslLvP~--~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk   89 (299)
                      |+..|..+||+||+.||+.|.+|+++ +|.  ..|++|++||.+||+||+.|+.+++.|+.+++.|..++..|.
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~l-vP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~~L~   74 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDS-VPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLE   74 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTT-SGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHH-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56677899999999999999999998 565  369999999999999999999998888765544444433333

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=99.57  E-value=2.4e-15  Score=123.51  Aligned_cols=85  Identities=24%  Similarity=0.350  Sum_probs=50.9

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCCCC----CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDR----PKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQE   91 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~----~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~E   91 (299)
                      ..++..|...||+||++||++|.+|+.+ +|..    .|++||+||.+||+||+.|+.+++.|+++..           +
T Consensus        25 ~~kr~~Hn~~ERrRR~~In~~~~~L~~l-vP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~-----------~   92 (118)
T 4ati_A           25 RQKKDNHNLIERRRRFNINDRIKELGTL-IPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN-----------R   92 (118)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHH-SCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC------------
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHH-HhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------H
Confidence            3577788899999999999999999998 5643    3889999999999999999999999987542           2


Q ss_pred             HHHHHHHHhhhHHHHHHHHHH
Q 022288           92 KNDLREEKLSLRSEIENLNIQ  112 (299)
Q Consensus        92 kNELRdEns~LksE~e~L~~q  112 (299)
                      ...|+.+|..|...+..||.|
T Consensus        93 ~~~l~~~n~~L~~riqeLE~~  113 (118)
T 4ati_A           93 QKKLEHANRHLLLRVQELEMQ  113 (118)
T ss_dssp             ---------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            233566667777777666643

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1

Probab=99.56  E-value=1.2e-14  Score=112.57  Aligned_cols=74  Identities=20%  Similarity=0.260  Sum_probs=61.4

Q ss_pred             hccchHHHHHHHHHHHHHHHHhhhccCCCC---CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           19 KMQKADREKLRRDRLNEHFTELGNALDPDR---PKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKN   93 (299)
Q Consensus        19 k~~KAerERrRRdKLNErF~eLrslLvP~~---~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkN   93 (299)
                      +.+|+..||+||+.||++|.+|+++ +|..   .|++|++||.+||+||+.|+.+.++|..+++.|..+...|+.+.+
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~-vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e~~~L~~~L~   78 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGL-VPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLE   78 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS-SCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3456689999999999999999998 5743   599999999999999999999999888877766666666655543

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1

Probab=99.50  E-value=2.7e-14  Score=109.23  Aligned_cols=69  Identities=19%  Similarity=0.363  Sum_probs=60.3

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHhhhccCCCC--CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 022288           15 AATRKMQKADREKLRRDRLNEHFTELGNALDPDR--PKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEE   84 (299)
Q Consensus        15 ~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~--~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE   84 (299)
                      ...++..|..+||+||+.||+.|.+|+++ +|..  .|++|++||..||+||+.|+.++++|+.+++.|..+
T Consensus         9 ~~~~R~~hn~~Er~RR~~in~~f~~Lr~l-vP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~~   79 (80)
T 1hlo_A            9 DADKRAHHNALERKRRDHIKDSFHSLRDS-VPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   79 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             hHHHHHHhhHHHHHHHHHHHHHHHHHHHH-CcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34677788899999999999999999998 5654  599999999999999999999999998888776654

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.49  E-value=2.6e-14  Score=109.42  Aligned_cols=60  Identities=28%  Similarity=0.463  Sum_probs=51.8

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLK   75 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk   75 (299)
                      ..++..|...||+||++||++|.+|+++|+....|+||++||.+||+||+.|+.++.=|+
T Consensus         6 ~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            6 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            456777889999999999999999999853344699999999999999999999887553

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1

Probab=99.39  E-value=8.7e-14  Score=102.34  Aligned_cols=54  Identities=26%  Similarity=0.509  Sum_probs=47.3

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCCCC------CCChhhhHHHHHHHHHHHHHHH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPDRP------KNDKATILADTVQLLKDLTSQV   71 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~~~------K~DKASIL~DAI~ylKdLr~qV   71 (299)
                      .|+..|...||+||++||+.|.+|+.+| |...      |+|||+||.+||+||+.|+.+.
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lv-P~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKII-PDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHS-CCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHC-cCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4677788999999999999999999985 5432      7899999999999999998764

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1

Probab=99.34  E-value=3.1e-13  Score=100.43  Aligned_cols=53  Identities=23%  Similarity=0.352  Sum_probs=46.1

Q ss_pred             hhccchHHHHHHHHHHHHHHHHhhhccCCC-------CCCCChhhhHHHHHHHHHHHHHHH
Q 022288           18 RKMQKADREKLRRDRLNEHFTELGNALDPD-------RPKNDKATILADTVQLLKDLTSQV   71 (299)
Q Consensus        18 Rk~~KAerERrRRdKLNErF~eLrslLvP~-------~~K~DKASIL~DAI~ylKdLr~qV   71 (299)
                      |+..|..+||+||++||+.|.+|+++ +|.       ..+.+||+||..||+||++|+.++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~L-lP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASL-IPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHT-SCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHH-CCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            45667799999999999999999997 462       357889999999999999998765

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.33  E-value=3.9e-13  Score=102.92  Aligned_cols=55  Identities=33%  Similarity=0.399  Sum_probs=47.7

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHhhhccCCCC----CCCChhhhHHHHHHHHHHHHHH
Q 022288           15 AATRKMQKADREKLRRDRLNEHFTELGNALDPDR----PKNDKATILADTVQLLKDLTSQ   70 (299)
Q Consensus        15 ~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~----~K~DKASIL~DAI~ylKdLr~q   70 (299)
                      ...|+..|...||+||++||+.|.+|+.| +|..    .|+|||+||..||+||+.|+.-
T Consensus         6 ~~~rR~~H~~~ERrRR~rIN~~l~eL~~L-vP~~~~~~~KldKasIL~~tV~ylk~l~~~   64 (73)
T 4h10_A            6 IKNAREAHSQIEKRRRDKMNSFIDELASL-VPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   64 (73)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHH-SHHHHTCSSCCCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHHHH-ccccccccccccHHHHHHHHHHHHHHHhcC
Confidence            34567778899999999999999999998 5643    6999999999999999998743

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=99.25  E-value=2.7e-12  Score=98.82  Aligned_cols=60  Identities=32%  Similarity=0.414  Sum_probs=46.8

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHhhhccCCC---CCCC-ChhhhHHHHHHHHHHHHHHHHHHH
Q 022288           15 AATRKMQKADREKLRRDRLNEHFTELGNALDPD---RPKN-DKATILADTVQLLKDLTSQVEKLK   75 (299)
Q Consensus        15 ~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~---~~K~-DKASIL~DAI~ylKdLr~qVq~Lk   75 (299)
                      .+.|+..++.+||+||+.||+.|.+|+.+ +|.   ..|. .|++||..||+||+.|+.++++++
T Consensus         2 ~~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~-vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            2 GADKRAHHNALERKRRRDINEAFRELGRM-CQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             -------CCHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             chhHHhhchHHHhhhHHHHHHHHHHHHHH-cCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45677888899999999999999999998 562   2355 799999999999999999998765

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.97  E-value=4.1e-10  Score=103.23  Aligned_cols=55  Identities=29%  Similarity=0.506  Sum_probs=41.4

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQ   70 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~q   70 (299)
                      ..++..|+..||+||++||+.|.+|++||+....|+||++||..||.||+.|+..
T Consensus        10 ~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           10 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             chhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            3556667789999999999999999998543557999999999999999998753

>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex, transcription/DNA complex; HET: DNA; 2.80A {Mus musculus} SCOP: a.38.1.1 PDB: 1mdy_B*

Probab=98.89  E-value=1.8e-09  Score=81.58  Aligned_cols=56  Identities=23%  Similarity=0.389  Sum_probs=48.6

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHhhhccCCCC--CCCChhhhHHHHHHHHHHHHHHH
Q 022288           15 AATRKMQKADREKLRRDRLNEHFTELGNALDPDR--PKNDKATILADTVQLLKDLTSQV   71 (299)
Q Consensus        15 ~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~--~K~DKASIL~DAI~ylKdLr~qV   71 (299)
                      ...++..++.+||+|+..||+.|..||.+| |..  .|++|+.||-.||+||..|++.+
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~i-P~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRST-SSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-CSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            445677788999999999999999999984 643  49999999999999999998754

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=98.82  E-value=4.8e-09  Score=77.40  Aligned_cols=54  Identities=24%  Similarity=0.292  Sum_probs=46.5

Q ss_pred             hhccchHHHHHHHHHHHHHHHHhhhccCCCC---CCCChhhhHHHHHHHHHHHHHHHH
Q 022288           18 RKMQKADREKLRRDRLNEHFTELGNALDPDR---PKNDKATILADTVQLLKDLTSQVE   72 (299)
Q Consensus        18 Rk~~KAerERrRRdKLNErF~eLrslLvP~~---~K~DKASIL~DAI~ylKdLr~qVq   72 (299)
                      |+...+.+||+|+..||+.|..||.+| |..   .|..|+.||-.||+||..|++.++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~l-P~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVV-PCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTS-SSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHc-cCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            455567899999999999999999984 543   499999999999999999997653

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=98.81  E-value=3e-08  Score=78.25  Aligned_cols=72  Identities=22%  Similarity=0.374  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHhhhccCCCC---CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           30 RDRLNEHFTELGNALDPDR---PKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        30 RdKLNErF~eLrslLvP~~---~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      |..||++|.+|+.++++..   .|..|++||..|++||+.|+.++++++++...           ...|...|..|.--+
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r-----------~k~le~~n~~l~~ri   72 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENR-----------QKKLEHANRHLLLRV   72 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHH-----------HHHHHHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHhhhhhHHHHHHH
Confidence            8899999999999854322   48999999999999999999999888765432           222445555555555


Q ss_pred             HHHHHH
Q 022288          107 ENLNIQ  112 (299)
Q Consensus       107 e~L~~q  112 (299)
                      -.||.|
T Consensus        73 qELE~q   78 (83)
T 4ath_A           73 QELEMQ   78 (83)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555533

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.81  E-value=2.6e-09  Score=99.39  Aligned_cols=53  Identities=34%  Similarity=0.414  Sum_probs=47.1

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCC----CCCCCChhhhHHHHHHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDP----DRPKNDKATILADTVQLLKDLTS   69 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP----~~~K~DKASIL~DAI~ylKdLr~   69 (299)
                      ..++..|...||+||++||+.|.+|+.+ +|    ...|+||++||..||.|||.|+.
T Consensus        11 ~~~~~~~~~~ek~rR~~~n~~~~~L~~l-~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           11 KNAREAHSQIEKRRRDKMNSFIDELASL-VPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHH-CHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hhhcccccchhhcchHHHHHHHHHHHHh-cCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            4566777799999999999999999998 56    56799999999999999999874

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.36  E-value=9e-08  Score=73.13  Aligned_cols=46  Identities=20%  Similarity=0.288  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHHHHHHHHhhhccCCCC---CCCChhhhHHHHHHHHHHHHH
Q 022288           23 ADREKLRRDRLNEHFTELGNALDPDR---PKNDKATILADTVQLLKDLTS   69 (299)
Q Consensus        23 AerERrRRdKLNErF~eLrslLvP~~---~K~DKASIL~DAI~ylKdLr~   69 (299)
                      +++||+|+..||+-|..||.+ +|..   .|..|..||--||+||..|+.
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~-VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLREL-VPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHH-CCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            489999999999999999998 5644   499999999999999999974

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=97.65  E-value=6.2e-05  Score=60.81  Aligned_cols=57  Identities=19%  Similarity=0.290  Sum_probs=42.5

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCCC---CCCChhhhHHHHHHHHHHHHHHHHHH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPDR---PKNDKATILADTVQLLKDLTSQVEKL   74 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~~---~K~DKASIL~DAI~ylKdLr~qVq~L   74 (299)
                      .|.++..++||.|=..||+-|..||.+| |..   .|..|..||--||.||..|+.-++.-
T Consensus        24 ~R~k~~~~~~r~Rm~~lN~AF~~LR~~v-P~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~   83 (97)
T 4aya_A           24 SRSKTPVDDPMSLLYNMNDCYSKLKELV-PSIPQNKKVSKMEILQHVIDYILDLQIALDSH   83 (97)
T ss_dssp             -------CCHHHHHHHHHHHHHHHHHHC-TTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHhcccccHHHHHHHHHHHHHHHHHHC-CCCCCCCcccHHHHHHHHHHHHHHHHHHHhcC
Confidence            4555554566778888999999999984 543   49999999999999999999877643

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=97.54  E-value=0.0007  Score=53.21  Aligned_cols=61  Identities=16%  Similarity=0.342  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      +..||+-|.-|+-+|++|+.+|.+|.++..+++.....|+.||.+|+.|...-+..++.-|
T Consensus        15 Iq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~LL   75 (81)
T 2jee_A           15 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQALL   75 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999988874444443

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1

Probab=96.07  E-value=0.0087  Score=45.54  Aligned_cols=42  Identities=38%  Similarity=0.376  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhh
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSL  102 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~L  102 (299)
                      -.||++|..+|..|+..+..|..|+..|+.+...|+.|+..|
T Consensus        28 ~~~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~~l   69 (70)
T 1gd2_E           28 EDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL   69 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            468899999999888888777666666666666666665554

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=95.69  E-value=0.06  Score=42.27  Aligned_cols=59  Identities=27%  Similarity=0.388  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhh-------hHHHHHHHHHHH---HHHHHHc
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLS-------LRSEIENLNIQY---QQRVRAM  120 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~-------LksE~e~L~~ql---qqrl~~~  120 (299)
                      +++.+|.++|+.+=+.+.-|+.|+++|+.+.+.|..++..       |..+..+|+.+.   +.||+++
T Consensus         6 ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~L   74 (81)
T 2jee_A            6 EVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL   74 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5677788888877777777777777777766666666666       555666665443   3455543

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

Probab=95.17  E-value=0.15  Score=42.72  Aligned_cols=82  Identities=18%  Similarity=0.193  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHhhhc--cCCCCCCCChhhhHHH--HHHHHH-------HHHHHHH-------HHHHHHhhhHHHHHHHHHH
Q 022288           30 RDRLNEHFTELGNA--LDPDRPKNDKATILAD--TVQLLK-------DLTSQVE-------KLKTEHAALTEESRELTQE   91 (299)
Q Consensus        30 RdKLNErF~eLrsl--LvP~~~K~DKASIL~D--AI~ylK-------dLr~qVq-------~Lk~en~~L~eE~~eLk~E   91 (299)
                      -..+|+++.+++..  - |. -..++++||+-  .+.-+-       .|+.+++       .|+.++..++.+++.++.+
T Consensus        34 A~~vd~km~ei~~~~~~-~~-l~~~r~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e  111 (138)
T 3hnw_A           34 ASYINNKITEFNKEESY-RR-MSAELRTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKE  111 (138)
T ss_dssp             HHHHHHHHHHHTTCHHH-HT-SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCC-CC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36789999999953  1 22 25578888763  222222       3333333       3333344444555555555


Q ss_pred             HHHHHHHHhhhHHHHHHHHHHH
Q 022288           92 KNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        92 kNELRdEns~LksE~e~L~~ql  113 (299)
                      ..+|++++..|..++-+|+.++
T Consensus       112 ~~~l~~~~~~l~~~~~~le~~~  133 (138)
T 3hnw_A          112 IKELKSEINKYQKNIVKLETEL  133 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            5555556666666665555444

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

Probab=95.06  E-value=0.13  Score=43.10  Aligned_cols=46  Identities=20%  Similarity=0.321  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e  107 (299)
                      +-+.+|+.++..++..++.+..++.+|+.+.++|+.++..|.+++.
T Consensus        89 kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~  134 (138)
T 3hnw_A           89 KEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELN  134 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555656666666666666666666666666655554

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=94.32  E-value=0.1  Score=40.15  Aligned_cols=68  Identities=19%  Similarity=0.196  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCccCCCccccCCCCC
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWAAMDHSVMMAPPSY  137 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~~~dps~~~~pp~y  137 (299)
                      +|..++.+|+..++-++.-+++|....-+...+...|+.++..|.    +|++.+-+-..-++.----||||
T Consensus        11 ~le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~----~rl~~~~~~~~~~~~~e~~PPHY   78 (78)
T 3efg_A           11 ELEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLL----EDLGKVRSTLFADAADEPPPPHY   78 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HTC--------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHhhhccCCCCCCCCCccCC
Confidence            455666666666666666666666666666666666666666665    44444322111123323346676

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D

Probab=94.01  E-value=0.11  Score=37.88  Aligned_cols=36  Identities=31%  Similarity=0.460  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      ..++.+|..+++.|+.+|..|..++..|+.|+..|+
T Consensus        22 k~~~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk   57 (63)
T 2wt7_A           22 RELTDTLQAETDQLEDEKSALQTEIANLLKEKEKLE   57 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456677777777777777666666666555555554

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=93.99  E-value=0.25  Score=49.99  Aligned_cols=85  Identities=20%  Similarity=0.167  Sum_probs=63.7

Q ss_pred             HHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHH-HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH----
Q 022288           32 RLNEHFTELGNALDPDRPKNDKATILADTVQLLK-DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI----  106 (299)
Q Consensus        32 KLNErF~eLrslLvP~~~K~DKASIL~DAI~ylK-dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~----  106 (299)
                      .++..|..+-.+|   +.+...+.=+..++..|- +|+.+++.|+.++..--..++.|+.-+.+++.+.++|+.+|    
T Consensus        82 dseqy~k~~~E~L---r~rq~q~~dNdNtynE~S~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDIdiqi  158 (562)
T 3ghg_A           82 DSHSLTTNIMEIL---RGDFSSANNRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKI  158 (562)
T ss_dssp             HHHHHHHHHHHTT---SSHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH---HHHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555666666654   123333334555666666 99999999999887766899999999999999999999998    


Q ss_pred             --------------------HHHHHHHHHHHHH
Q 022288          107 --------------------ENLNIQYQQRVRA  119 (299)
Q Consensus       107 --------------------e~L~~qlqqrl~~  119 (299)
                                          +.+|.||+|-.+.
T Consensus       159 rsCKgsCsr~~~~~vd~~sY~~~QKQLeQv~a~  191 (562)
T 3ghg_A          159 RSCRGSCSRALAREVDLKDYEDQQKQLEQVIAK  191 (562)
T ss_dssp             HHGGGTBSCCCCCCCCHHHHHHHHHHHHHHHTT
T ss_pred             HhccccccchheeecchHHHHHHHHHHHHHhhc
Confidence                                6788888876655

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}

Probab=93.88  E-value=0.083  Score=38.10  Aligned_cols=11  Identities=18%  Similarity=0.323  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHH
Q 022288           59 DTVQLLKDLTS   69 (299)
Q Consensus        59 DAI~ylKdLr~   69 (299)
                      +|++|||+-..
T Consensus         2 ~AlefIk~~LG   12 (53)
T 2yy0_A            2 SALDFLKHHLG   12 (53)
T ss_dssp             -----------
T ss_pred             cHHHHHHHHcC
Confidence            68888887643

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

Probab=93.63  E-value=0.14  Score=54.63  Aligned_cols=20  Identities=35%  Similarity=0.516  Sum_probs=10.2

Q ss_pred             HHHHHHHHhhhHHHHHHHHH
Q 022288           92 KNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        92 kNELRdEns~LksE~e~L~~  111 (299)
                      .+.|++||..|+.+++.|+.
T Consensus      1025 v~~L~~e~~~L~qq~~~l~~ 1044 (1080)
T 2dfs_A         1025 VSELKEQNTLLKTEKEELNR 1044 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33445555555555555553

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=93.47  E-value=0.17  Score=36.58  Aligned_cols=27  Identities=22%  Similarity=0.307  Sum_probs=11.6

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELT   89 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk   89 (299)
                      |+.+|+.++..|+.+|..|..++..|+
T Consensus        23 ~~~~Le~~~~~L~~~n~~L~~~i~~L~   49 (61)
T 1t2k_D           23 WVQSLEKKAEDLSSLNGQLQSEVTLLR   49 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444443333333

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

Probab=93.42  E-value=0.48  Score=40.98  Aligned_cols=81  Identities=16%  Similarity=0.099  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHhhhccCCCCCCC-ChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 022288           30 RDRLNEHFTELGNALDPDRPKN-DKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIEN  108 (299)
Q Consensus        30 RdKLNErF~eLrslLvP~~~K~-DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~  108 (299)
                      |++|--+|.+|-.-  |+.... .=+|=+.+-+..|..|+.++..|+..+..|.+++++-......|+||...|..+..-
T Consensus        37 Rd~~E~~~~~l~~e--~~~~~~~~~vs~~~~~~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~  114 (152)
T 3a7p_A           37 RNDKEAHLNELFQD--NSGAIGGNIVSHDDALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNV  114 (152)
T ss_dssp             ----------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHh--hccCCCcccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666666666553  221111 012223344556667777777777766666666655555555666776666666655


Q ss_pred             HHHH
Q 022288          109 LNIQ  112 (299)
Q Consensus       109 L~~q  112 (299)
                      ++..
T Consensus       115 lE~k  118 (152)
T 3a7p_A          115 LQQK  118 (152)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5433

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=92.76  E-value=0.24  Score=38.18  Aligned_cols=50  Identities=20%  Similarity=0.154  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      +.-|.+|+..+++-.+++...++.+++|..+..+..++...|++++++++
T Consensus        18 mgti~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfr   67 (72)
T 3nmd_A           18 RGSLRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYR   67 (72)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            44588999999888888888899999999999999999999999998874

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

Probab=92.74  E-value=0.91  Score=35.65  Aligned_cols=54  Identities=26%  Similarity=0.312  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhh------------hHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAA------------LTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~------------L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      |+-|+.|..+...|+.++..            .+.++.+|+....++..|+..|..|+++|+.++.
T Consensus        22 IdKVR~LEqqN~~Le~~i~~l~~~~~~~~~~~ye~~i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~   87 (93)
T 3s4r_A           22 IDKVRFLEQQNKILLAELEQLKGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIM   87 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555544332            2567788888888888888888888888876654

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=92.49  E-value=0.6  Score=35.83  Aligned_cols=53  Identities=13%  Similarity=0.240  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      ..+..+++.++.+|..|+..+..|.....+-+.+-..++.|+.++..+|-.++
T Consensus         3 ~~~~~kLq~~E~~N~~Le~~v~~le~~Le~s~~~q~~~~~Elk~~~e~Ld~KI   55 (72)
T 3cve_A            3 HNSHMKLQEVEIRNKDLEGQLSEMEQRLEKSQSEQDAFRSNLKTLLEILDGKI   55 (72)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            35667777788888888888888888877777777777777777776655544

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A

Probab=92.45  E-value=0.16  Score=36.86  Aligned_cols=31  Identities=19%  Similarity=0.359  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEK   92 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~Ek   92 (299)
                      +++.+|+.+|..|+.+|..|..++..|+.|.
T Consensus        22 ~~~~~Le~~v~~L~~~n~~L~~~v~~L~~e~   52 (62)
T 1jnm_A           22 ERIARLEEKVKTLKAQNSELASTANMLREQV   52 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555555554444444444333

>3he5_B Synzip2; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=92.41  E-value=0.38  Score=34.48  Aligned_cols=43  Identities=23%  Similarity=0.425  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIEN  108 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~  108 (299)
                      -|+..+.+|+..|-.|+.+-..|..-...||||..+|.+|...
T Consensus         7 ylrkkiarlkkdnlqlerdeqnlekiianlrdeiarlenevas   49 (52)
T 3he5_B            7 YLRKKIARLKKDNLQLERDEQNLEKIIANLRDEIARLENEVAS   49 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHHHHHHHHHhh
Confidence            3778899999999888877777877788888888888877643

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

Probab=92.17  E-value=0.57  Score=34.33  Aligned_cols=43  Identities=19%  Similarity=0.268  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRS  104 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~Lks  104 (299)
                      +|=..=+.+++.|+.+...|..++.+|+.+.+.|+.|+..|+.
T Consensus        16 R~R~KKk~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~   58 (63)
T 1ci6_A           16 RYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYLKD   58 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444444444444444444444444444444444443

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=92.01  E-value=0.39  Score=34.62  Aligned_cols=33  Identities=24%  Similarity=0.409  Sum_probs=16.6

Q ss_pred             HhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           78 HAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        78 n~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      +..|+.+++.|..+..+|+.+...|+.|+..|.
T Consensus        24 ~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk   56 (61)
T 1t2k_D           24 VQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLK   56 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555555555555555555444

>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=91.30  E-value=0.52  Score=44.97  Aligned_cols=38  Identities=18%  Similarity=0.186  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           83 EESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        83 eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      .+..+++....+.++....|+.|+..+..++++.+...
T Consensus       544 ~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~  581 (597)
T 3oja_B          544 QENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKK  581 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44444444444444455555566666666666665544

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=91.09  E-value=0.75  Score=37.58  Aligned_cols=63  Identities=16%  Similarity=0.210  Sum_probs=48.1

Q ss_pred             CChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           51 NDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        51 ~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      ++|.+.+..    |.-|+..++++++.+..+.-+.++...+..-++.....|+.++..|+.||.+|=
T Consensus        23 NEKsal~Yq----VdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~~L~qRD   85 (103)
T 4h22_A           23 NEKTNFMYQ----VDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALKQRE   85 (103)
T ss_dssp             HHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             cHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345554432    445666777788888888888888888888888888999999999998887763

>1go4_E MAD1 (mitotic arrest deficient)-like 1; mitotic spindle checkpoint, cell cycle, mitosis, nuclear Pro; 2.05A {Homo sapiens} SCOP: h.1.22.1

Probab=90.93  E-value=0.84  Score=36.94  Aligned_cols=30  Identities=33%  Similarity=0.420  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQE   91 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~E   91 (299)
                      +-+..|+.+|+.|+.++..|.++++.|..+
T Consensus        12 e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~   41 (100)
T 1go4_E           12 EEADTLRLKVEELEGERSRLEEEKRMLEAQ   41 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456667777777777777777777666554

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=90.88  E-value=0.2  Score=36.07  Aligned_cols=30  Identities=27%  Similarity=0.417  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQE   91 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~E   91 (299)
                      .||.+|..+|..|+.+|..|..++..|+.+
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~   51 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALKDL   51 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566666666666666665555555555443

>2oqq_A Transcription factor HY5; homodimer leucine zipper; 2.00A {Arabidopsis thaliana}

Probab=90.80  E-value=0.54  Score=33.00  Aligned_cols=35  Identities=29%  Similarity=0.460  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      .||.+|..++.+|+..|..|++.+..|..|-.-||
T Consensus         3 aYl~eLE~r~k~le~~naeLEervstLq~EN~mLR   37 (42)
T 2oqq_A            3 AYLSELENRVKDLENKNSELEERLSTLQNENQMLR   37 (42)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence            48999999999999999888888887777765555

>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D

Probab=90.79  E-value=0.84  Score=33.59  Aligned_cols=33  Identities=15%  Similarity=0.303  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           83 EESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        83 eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      +.+.+|..+..+|..||..|+.+++.|..++.+
T Consensus        30 ~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l~~   62 (63)
T 2dgc_A           30 QRMKQLEDKVEELLSKNYHLENEVARLKKLVGE   62 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344555555555666666666677766665554

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A

Probab=90.38  E-value=0.38  Score=34.86  Aligned_cols=30  Identities=23%  Similarity=0.410  Sum_probs=12.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~e~L  109 (299)
                      .|+.++..|..+..+|+.+...|+.++..|
T Consensus        26 ~Le~~v~~L~~~n~~L~~~v~~L~~e~~~L   55 (62)
T 1jnm_A           26 RLEEKVKTLKAQNSELASTANMLREQVAQL   55 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444433

>1m1j_A Fibrinogen alpha subunit; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: h.1.8.1 PDB: 1ei3_A

Probab=90.13  E-value=5.6  Score=39.83  Aligned_cols=44  Identities=18%  Similarity=0.220  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      |..+|+.++.-|+..+..--..++.|+.-..+++.+.++|+.+|
T Consensus       112 ~S~eLe~ri~yIK~kVd~qi~~IrvLq~~l~~q~skIQRLE~dI  155 (491)
T 1m1j_A          112 VSTELRRRIVTLKQRVATQVNRIKALQNSIQEQVVEMKRLEVDI  155 (491)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33456666666665444322666777777777777788887777

>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=90.04  E-value=2.5  Score=29.73  Aligned_cols=52  Identities=25%  Similarity=0.258  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      .-+..|+..+..++.....+..+...++...+.+..+....+.+|.+++.|+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi   56 (60)
T 3htk_A            5 NTKKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQN   56 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566666666555555666666666666666666666666666665443

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

Probab=90.02  E-value=1  Score=35.04  Aligned_cols=52  Identities=19%  Similarity=0.312  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRV  117 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl  117 (299)
                      ++..+++.++.+|..|+..+..|.....+-+.+-..++.|+.++..+|-.+|
T Consensus        10 ~~~~klq~~E~rN~~Le~~v~~le~~Le~s~~~q~~~~~Elk~l~e~Ld~KI   61 (79)
T 3cvf_A           10 ETQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLDVSL   61 (79)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            3455667777777777777777777777777777777777777665555444

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

Probab=89.87  E-value=4.7  Score=35.23  Aligned_cols=85  Identities=21%  Similarity=0.381  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHH-------HHHHHHHHHHHHHHHHhh
Q 022288           29 RRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTE-------ESRELTQEKNDLREEKLS  101 (299)
Q Consensus        29 RRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~e-------E~~eLk~EkNELRdEns~  101 (299)
                      -|+.|-.-+..|.+.|.-.+  .+    ..-+-+.+++|+.++..|..+++.+..       +.+.|.-..+.|..|++.
T Consensus        63 ~k~~Leke~~~LQa~L~qEr--~~----r~q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~  136 (168)
T 3o0z_A           63 SKSQTDKDYYQLQAILEAER--RD----RGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNN  136 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH--HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH--HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34555556666666553322  11    233445556666666666655555544       444444444555555555


Q ss_pred             hH----HHHHHHHHHHHHHHHH
Q 022288          102 LR----SEIENLNIQYQQRVRA  119 (299)
Q Consensus       102 Lk----sE~e~L~~qlqqrl~~  119 (299)
                      +.    -++-.|++-|+|-+++
T Consensus       137 ~eid~~~eLKalQ~~~eqE~~~  158 (168)
T 3o0z_A          137 LEIDLNYKLKSLQQRLEQEVNE  158 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHH
Confidence            54    2344555555555543

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=89.74  E-value=2  Score=33.84  Aligned_cols=55  Identities=27%  Similarity=0.318  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      +-|.-|++|+-+|.+|+.+-..-+-..+.-+.|...|+.....=.+++.+|+.|+
T Consensus        23 ~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l   77 (81)
T 3qh9_A           23 ELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQL   77 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            5688899999999999877766666666666677777777777777888887665

>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=89.67  E-value=3.5  Score=39.31  Aligned_cols=35  Identities=23%  Similarity=0.364  Sum_probs=15.4

Q ss_pred             HHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           76 TEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        76 ~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ++...++..+++.+....||++|++.++.++..|+
T Consensus       544 ~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~  578 (597)
T 3oja_B          544 QENIALEKQLDNKRAKQAELRQETSLKRQKVKQLE  578 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444444444444444444

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

Probab=89.44  E-value=1.2  Score=36.71  Aligned_cols=26  Identities=15%  Similarity=0.328  Sum_probs=14.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022288           56 ILADTVQLLKDLTSQVEKLKTEHAAL   81 (299)
Q Consensus        56 IL~DAI~ylKdLr~qVq~Lk~en~~L   81 (299)
                      |..++=+||.+|+.+|..|+.+++.-
T Consensus        34 l~~E~q~~v~ql~~~i~~Le~eL~e~   59 (120)
T 3i00_A           34 MKTESQRVVLQLKGHVSELEADLAEQ   59 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35556666666666666655555433

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=89.36  E-value=1.2  Score=31.98  Aligned_cols=37  Identities=24%  Similarity=0.470  Sum_probs=21.6

Q ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           73 KLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        73 ~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L  109 (299)
                      +|+..+..|...+..|..-..+.|++...|+.++++|
T Consensus        13 ~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           13 QLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444444444444455555556666677777777776

>1s94_A S-syntaxin; three helix bundle, structural plasticity, endocytosis-exocy complex; 3.34A {Loligo pealei} SCOP: a.47.2.1

Probab=89.23  E-value=1.4  Score=36.96  Aligned_cols=27  Identities=15%  Similarity=0.343  Sum_probs=20.0

Q ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           94 DLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        94 ELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      .++.+...|-.++.++..+++.+|+.+
T Consensus        78 ~~k~~le~l~~~i~~~a~~ik~~Lk~l  104 (180)
T 1s94_A           78 QMKEELEELMTDIKRTANKVRGKLKTI  104 (180)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456777777788888888888888776

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D

Probab=89.15  E-value=1.1  Score=32.70  Aligned_cols=31  Identities=35%  Similarity=0.459  Sum_probs=13.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .|+.++..|..+..+|+.+...|+.++..|.
T Consensus        27 ~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk   57 (63)
T 2wt7_A           27 TLQAETDQLEDEKSALQTEIANLLKEKEKLE   57 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444443

>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D

Probab=89.10  E-value=0.47  Score=34.94  Aligned_cols=32  Identities=28%  Similarity=0.360  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           61 VQLLKDLTSQVEKLKTEHAALTEESRELTQEK   92 (299)
Q Consensus        61 I~ylKdLr~qVq~Lk~en~~L~eE~~eLk~Ek   92 (299)
                      ..++.+|..+|+.|+.+|..|..++..|+.+.
T Consensus        29 ~~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l   60 (63)
T 2dgc_A           29 LQRMKQLEDKVEELLSKNYHLENEVARLKKLV   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36778888888888888877777777666554

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

Probab=88.98  E-value=0.52  Score=43.50  Aligned_cols=41  Identities=22%  Similarity=0.464  Sum_probs=31.7

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           70 QVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        70 qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ++++|+.++..|.+.+++|+.+.++++.|...|+.|+++|+
T Consensus        55 ~l~eL~~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~   95 (251)
T 3m9b_A           55 DIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLG   95 (251)
T ss_dssp             HHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45566666677777777788888888888888888888885

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

Probab=88.21  E-value=2.3  Score=34.89  Aligned_cols=22  Identities=36%  Similarity=0.436  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHH
Q 022288           64 LKDLTSQVEKLKTEHAALTEES   85 (299)
Q Consensus        64 lKdLr~qVq~Lk~en~~L~eE~   85 (299)
                      .++|+..++.|..+++.+....
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~   26 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKL   26 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555555554444433

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1

Probab=88.21  E-value=0.86  Score=34.52  Aligned_cols=38  Identities=18%  Similarity=0.212  Sum_probs=24.4

Q ss_pred             HHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           77 EHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        77 en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      .+..|+.++.+|..+...|..||..|+.++..|+.++.
T Consensus        30 ~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~   67 (70)
T 1gd2_E           30 HLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELR   67 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555666666666667777777777777776654

>1go4_E MAD1 (mitotic arrest deficient)-like 1; mitotic spindle checkpoint, cell cycle, mitosis, nuclear Pro; 2.05A {Homo sapiens} SCOP: h.1.22.1

Probab=88.17  E-value=0.6  Score=37.79  Aligned_cols=35  Identities=29%  Similarity=0.378  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           82 TEESRELTQEKNDLREEKLSLRSEIENLNIQYQQR  116 (299)
Q Consensus        82 ~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqr  116 (299)
                      .+++..|+.++.+|+.|+..|+.+++.|+.+|.++
T Consensus        11 ~e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~   45 (100)
T 1go4_E           11 REEADTLRLKVEELEGERSRLEEEKRMLEAQLERR   45 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45777788888888888888888888888777654

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

Probab=88.00  E-value=3.3  Score=32.63  Aligned_cols=45  Identities=20%  Similarity=0.364  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .|..+++.|+.+-..|..++..|..++..|..+...++.+..+|.
T Consensus         8 ~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~   52 (96)
T 3q8t_A            8 QLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLD   52 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHh
Confidence            334444444444444444444444444444444444444444433

>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=3.3  Score=36.69  Aligned_cols=19  Identities=37%  Similarity=0.417  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHHHHhhh
Q 022288           63 LLKDLTSQVEKLKTEHAAL   81 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L   81 (299)
                      -+++|+.++..|+.+++.+
T Consensus        57 ~~~~L~~~~~~L~~E~e~~   75 (189)
T 2v71_A           57 RNRDLQADNQRLKYEVEAL   75 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444333

>1ik9_A DNA repair protein XRCC4; DNA END joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil; HET: DNA; 2.30A {Homo sapiens} SCOP: b.59.1.1 h.1.11.1 PDB: 3ii6_A* 1fu1_A* 3rwr_A*

Probab=87.48  E-value=3.7  Score=36.51  Aligned_cols=38  Identities=13%  Similarity=0.227  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKND   94 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNE   94 (299)
                      +.=++.-+..|+.++..|..+|..|+.+.+.|..+..+
T Consensus       127 fd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~  164 (213)
T 1ik9_A          127 IAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEK  164 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444444444444444433333

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

Probab=87.30  E-value=5.3  Score=32.34  Aligned_cols=36  Identities=11%  Similarity=0.208  Sum_probs=14.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      .+..++..+..+...++.+...++.++.+++.++..
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  276 (284)
T 1c1g_A          241 FAERSVTKLEKSIDDLEDELYAQKLKYKAISEELDH  276 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333334444444444444444444444444433

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=87.29  E-value=2.7  Score=32.68  Aligned_cols=30  Identities=10%  Similarity=0.187  Sum_probs=13.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           81 LTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        81 L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      |...++.|+.|..+||..+..+.-+++.|+
T Consensus        25 Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~   54 (83)
T 2xdj_A           25 LQQQLSDNQSDIDSLRGQIQENQYQLNQVV   54 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            344444444444444444444444444443

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=87.12  E-value=3.8  Score=32.14  Aligned_cols=30  Identities=20%  Similarity=0.282  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 022288           85 SRELTQEKNDLREEKLSLRSEIENLNIQYQ  114 (299)
Q Consensus        85 ~~eLk~EkNELRdEns~LksE~e~L~~qlq  114 (299)
                      ..++..+..+|..||..|+.+++.|+.+++
T Consensus        38 ~~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~   67 (87)
T 1hjb_A           38 NLETQHKVLELTAENERLQKKVEQLSRELS   67 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555555566666665555554

>2fxo_A Myosin heavy chain, cardiac muscle beta isoform; coiled coil (dimeric, parallel), familial hypertrophic cardiomyopathy, FHC-associated mutant E924K; 2.50A {Homo sapiens} SCOP: h.1.26.1 PDB: 2fxm_A

Probab=86.97  E-value=4.9  Score=32.67  Aligned_cols=59  Identities=17%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           55 TILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        55 SIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      ..|.||-+.+..|..+-..|+..+..|.+...+.....++|..++..|..++..|+.++
T Consensus        62 ~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~l  120 (129)
T 2fxo_A           62 DNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDI  120 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44666666666666665555555555555544444444444444444444444444443

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

Probab=86.93  E-value=4.7  Score=32.68  Aligned_cols=6  Identities=0%  Similarity=0.224  Sum_probs=2.1

Q ss_pred             HHHHHH
Q 022288           70 QVEKLK   75 (299)
Q Consensus        70 qVq~Lk   75 (299)
                      ++..++
T Consensus        49 ~~~~~~   54 (284)
T 1c1g_A           49 KLKATE   54 (284)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            333333

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

Probab=86.40  E-value=0.84  Score=42.16  Aligned_cols=38  Identities=16%  Similarity=0.157  Sum_probs=24.8

Q ss_pred             HhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           78 HAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        78 n~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      +..|+.++..|.....-|.++...++.|+.+|+.|+++
T Consensus        56 l~eL~~ql~~L~arNe~L~~~Lk~ar~El~~LkeEler   93 (251)
T 3m9b_A           56 IHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDR   93 (251)
T ss_dssp             HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566666666444444777888888888888766643

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=86.21  E-value=1.7  Score=41.47  Aligned_cols=51  Identities=22%  Similarity=0.261  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      ..|+++++.|+++...|+++++.++.+..+|.++.........+|-+++|.
T Consensus         6 ~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~e   56 (403)
T 4etp_A            6 AALKEKIAALKEKIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQE   56 (403)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666655544444444555555544

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=86.15  E-value=3.4  Score=30.18  Aligned_cols=46  Identities=26%  Similarity=0.391  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      -+|-.||+.|+.||..|..|...=....+.|..|..-+|.=+..|+
T Consensus         6 dQL~~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKevlk~lq   51 (54)
T 1deb_A            6 DQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQ   51 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHc
Confidence            4688899999999988888877777777777777776666555554

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

Probab=86.11  E-value=2.1  Score=38.05  Aligned_cols=35  Identities=17%  Similarity=0.159  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhH
Q 022288           69 SQVEKLKTEHAALTEESRELTQEKNDLREEKLSLR  103 (299)
Q Consensus        69 ~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~Lk  103 (299)
                      .+++.|+.+...+...+..++.+..+++.+...++
T Consensus        32 ~el~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e   66 (256)
T 3na7_A           32 KDLDKALNDKEAKNKAILNLEEEKLALKLQVSKNE   66 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333333333

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}

Probab=86.08  E-value=0.92  Score=32.60  Aligned_cols=29  Identities=21%  Similarity=0.224  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           83 EESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        83 eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      .+++.|++|..+||.+...|+.+++.|..
T Consensus        19 ~d~eaLk~E~~eLk~k~~~L~~~~~el~~   47 (53)
T 2yy0_A           19 PEIELLRLELAEMKEKYEAIVEENKKLKA   47 (53)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555555543

>1jcd_A Major outer membrane lipoprotein; protein folding, coiled coil, helix capping, alanine-zipper, membrane protein; 1.30A {Escherichia coli} SCOP: h.1.16.1 PDB: 1eq7_A 1t8z_A* 2guv_A 2gus_A 1jcc_A 1kfn_A 1kfm_A

Probab=85.61  E-value=3.5  Score=29.77  Aligned_cols=41  Identities=7%  Similarity=0.251  Sum_probs=26.1

Q ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           70 QVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        70 qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ++..|...+.+|..+++.|..+.+.||.+...-+.|-.|-+
T Consensus         5 ki~~Lss~V~~L~~kVdqLssdV~al~~~v~~ak~eA~RAN   45 (52)
T 1jcd_A            5 KADQASSDAQTANAKADQASNDANAARSDAQAAKDDAARAN   45 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555566666666666666666667777777766

>1lwu_C Fibrinogen gamma chain; heterotrimer, protein-peptide complex, blood clotting; HET: NDG MAN NAG BMA GAL; 2.80A {Petromyzon marinus} SCOP: d.171.1.1 h.1.8.1 PDB: 1n73_C*

Probab=85.37  E-value=1.6  Score=41.28  Aligned_cols=53  Identities=9%  Similarity=0.105  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      ++|.=++.|++++.+|+..+....+++..|+.....++.....|+.++..|+.
T Consensus         2 ~~~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l~~   54 (323)
T 1lwu_C            2 SGQKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQ   54 (323)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45556777888888888777777777777777766666666666665555553

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=85.23  E-value=1.5  Score=34.53  Aligned_cols=32  Identities=25%  Similarity=0.386  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      .++..++..|+.+|..|..++..|+.|...|+
T Consensus        39 ~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~Lr   70 (87)
T 1hjb_A           39 LETQHKVLELTAENERLQKKVEQLSRELSTLR   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455556666666555555555555544444

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

Probab=84.96  E-value=5.7  Score=34.69  Aligned_cols=17  Identities=29%  Similarity=0.483  Sum_probs=7.3

Q ss_pred             HHHHHhhhHHHHHHHHH
Q 022288           74 LKTEHAALTEESRELTQ   90 (299)
Q Consensus        74 Lk~en~~L~eE~~eLk~   90 (299)
                      |+..+..|.+|++.++.
T Consensus        95 lq~ri~~L~~El~~~k~  111 (168)
T 3o0z_A           95 LQARITSLQEEVKHLKH  111 (168)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33344444444444443

>3s9g_A Protein hexim1; cyclin T-binding domain (TBD), cyclin T1/P-TEFB/7SK snRNA, N transcription; 2.10A {Homo sapiens} PDB: 2gd7_A

Probab=84.79  E-value=5.4  Score=32.61  Aligned_cols=54  Identities=28%  Similarity=0.425  Sum_probs=31.8

Q ss_pred             CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHH-------HHHHHHHHHHHHHHHHhhhHHHHH
Q 022288           50 KNDKATILADTVQLLKDLTSQVEKLKTEHAALTE-------ESRELTQEKNDLREEKLSLRSEIE  107 (299)
Q Consensus        50 K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~e-------E~~eLk~EkNELRdEns~LksE~e  107 (299)
                      .|.|.-++.+-+    +|...+..|++++..|+.       .+.+|..|...|+.||+.|+.|-+
T Consensus        29 ~mSKqELIqEYl----~LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~   89 (104)
T 3s9g_A           29 NMSKQELIKEYL----ELEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENE   89 (104)
T ss_dssp             TSCHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457777766554    456666667666666665       455555555555555555554443

>3mq7_A Bone marrow stromal antigen 2; HIV, antiviral protein; 2.28A {Homo sapiens} PDB: 3mqc_A 3mqb_A 3mkx_A 3nwh_A 2xg7_A* 2x7a_A

Probab=84.75  E-value=2.4  Score=35.44  Aligned_cols=26  Identities=31%  Similarity=0.279  Sum_probs=9.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           81 LTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        81 L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      |+.||..|+++..+.-.|..+|+.+.
T Consensus        76 LqgEI~~Lnq~Lq~a~ae~erlr~~~  101 (121)
T 3mq7_A           76 LEGEITTLNHKLQDASAEVERLRREN  101 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            33333333333333333333333333

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

Probab=84.69  E-value=8.7  Score=31.02  Aligned_cols=59  Identities=17%  Similarity=0.369  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH-----------HHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQ-----------EKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~-----------EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      +.+.-+.|..|+.+++.|+..+..|+..+.++..           ...+|..+...++.++.+...+||.
T Consensus        38 i~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EYq~  107 (129)
T 3tnu_B           38 ISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQE  107 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            4444555556666666666666666655544433           2334444444455555544444443

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

Probab=84.51  E-value=5.3  Score=34.49  Aligned_cols=81  Identities=20%  Similarity=0.142  Sum_probs=31.4

Q ss_pred             HHHHHHHHHhhhccCCC----CCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           31 DRLNEHFTELGNALDPD----RPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        31 dKLNErF~eLrslLvP~----~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      .++++.|.++..+ ++.    .-++... .|...-..+..|+.++..|+.++..-...+..|..|.-.|+-+...+...+
T Consensus        42 ~~~~~l~~e~~~~-~~~~~vs~~~~~~~-~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl  119 (152)
T 3a7p_A           42 AHLNELFQDNSGA-IGGNIVSHDDALLN-TLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKL  119 (152)
T ss_dssp             ----------------CHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhccC-CCcccccchhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4578999999876 443    1122222 344445556677777777776554433334444444444444444444444


Q ss_pred             HHHHHHH
Q 022288          107 ENLNIQY  113 (299)
Q Consensus       107 e~L~~ql  113 (299)
                      .+|+.+.
T Consensus       120 ~kLq~EN  126 (152)
T 3a7p_A          120 SDLKKEH  126 (152)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444433

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A

Probab=84.38  E-value=6.7  Score=30.14  Aligned_cols=28  Identities=21%  Similarity=0.288  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           86 RELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        86 ~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      .++.....+|..||..|+.+++.|+.++
T Consensus        39 ~e~~~r~~~L~~eN~~L~~~v~~L~~E~   66 (78)
T 1gu4_A           39 LETQHKVLELTAENERLQKKVEQLSREL   66 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444555555555555555555444

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

Probab=84.30  E-value=6.4  Score=31.96  Aligned_cols=59  Identities=19%  Similarity=0.294  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH-----------HHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQ-----------EKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~-----------EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      +.+.-+.|..|+.+++.|+..+..|+..+.++..           ...+|..+...++.++.+...+||.
T Consensus        40 i~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~em~~ql~EYq~  109 (131)
T 3tnu_A           40 ISELRRTMQNLEIELQSQLSMKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEYKI  109 (131)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555566666666666666666655544433           2334444444455555444444443

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=84.26  E-value=3.3  Score=29.77  Aligned_cols=41  Identities=27%  Similarity=0.354  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhh
Q 022288           62 QLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSL  102 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~L  102 (299)
                      +-+.+|+.++..|...|..|.+..+.-+.+...|+++...|
T Consensus         9 ~r~~~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A            9 RDIHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34568899999999999999999999999988888887765

>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}

Probab=84.07  E-value=5.2  Score=39.55  Aligned_cols=37  Identities=16%  Similarity=0.232  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           84 ESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        84 E~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      +..+|..+..+|+++...|+.+...++.+++..+..+
T Consensus       117 ~~~~l~~~~~~l~~~i~~l~~~~~~~~~~l~~~l~~i  153 (501)
T 1wle_A          117 QYQSLRARGREIRKQLTLLYPKEAQLEEQFYLRALRL  153 (501)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            4446666667777777777777777888887777665

>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A

Probab=84.04  E-value=6  Score=31.36  Aligned_cols=37  Identities=22%  Similarity=0.334  Sum_probs=27.2

Q ss_pred             HHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           77 EHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        77 en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      +...|+.+...|..++..|+.|+..+..|++.+...|
T Consensus        49 q~~~LE~e~~~L~~e~~~L~~e~~~~~~e~d~~k~k~   85 (90)
T 2wt7_B           49 QKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKS   85 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3356777777788888888888888888887776444

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=83.84  E-value=8.8  Score=30.91  Aligned_cols=54  Identities=19%  Similarity=0.221  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 022288           59 DTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQ  112 (299)
Q Consensus        59 DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~q  112 (299)
                      ++-+-|.+|+.++...+.+...|..+..+-+..+-+...++..+..|++.|-..
T Consensus         9 ~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTas   62 (97)
T 2eqb_B            9 QLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTAS   62 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444333333334444444444444444333

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

Probab=83.67  E-value=4.1  Score=36.10  Aligned_cols=29  Identities=17%  Similarity=0.299  Sum_probs=11.4

Q ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 022288           71 VEKLKTEHAALTEESRELTQEKNDLREEK   99 (299)
Q Consensus        71 Vq~Lk~en~~L~eE~~eLk~EkNELRdEn   99 (299)
                      ++.++..+..|...+..|+.|..++|+..
T Consensus        51 L~~~Ek~~~~L~~~~~~L~~E~e~~k~K~   79 (189)
T 2v71_A           51 LVQAEQRNRDLQADNQRLKYEVEALKEKL   79 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333344444444444433333333

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

Probab=83.62  E-value=4.6  Score=43.26  Aligned_cols=56  Identities=18%  Similarity=0.191  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVR  118 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~  118 (299)
                      -++.+..+...++..+..|++|+.+|+.+..++..|+..|+..+.+++.+|++.+.
T Consensus       971 ~le~~~~e~~~~~~~v~~L~~e~~~l~~~~~~~~ke~~~lee~~~~~~~~L~~kv~ 1026 (1080)
T 2dfs_A          971 RLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETEQLVS 1026 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333334444444444455555555555555554555444444444444444443

>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=83.54  E-value=5.6  Score=27.87  Aligned_cols=50  Identities=18%  Similarity=0.244  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           60 TVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENL  109 (299)
Q Consensus        60 AI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L  109 (299)
                      .-+++.++.+++..++.+...+...++.+..+.+..+++...++.+++.+
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~y   59 (60)
T 3htk_A           10 LENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYY   59 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34566677777788888888888888888888888888888888887653

>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=83.22  E-value=2.7  Score=32.34  Aligned_cols=40  Identities=20%  Similarity=0.298  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      |...++-|+...+.|++|+.++....+++.+|+.+.+.+|
T Consensus        28 L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfr   67 (72)
T 3nmd_A           28 LQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYR   67 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3344455555666666666666666666666666665554

>1m1j_C Fibrinogen gamma chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_C

Probab=82.69  E-value=4.7  Score=39.15  Aligned_cols=75  Identities=11%  Similarity=0.113  Sum_probs=49.2

Q ss_pred             HHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           34 NEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        34 NErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      ++....|.....+. .+ -+......++++.+.+.+++.+|+..+...+++++.|+...+.++.....|+..+..|+
T Consensus        58 ~~Lvk~iq~~~~~~-Q~-~~~d~~e~~tq~skkml~~~~~~e~~~~~~~~~i~~l~~~~~~~~~~i~~l~~~i~~l~  132 (409)
T 1m1j_C           58 EYLIQHIKTIYPSE-KQ-TLPQSIEQLTQKSKKIIEEIIRYENTILAHENTIQQLTDMHIMNSNKITQLKQKIAQLE  132 (409)
T ss_dssp             HHHHHHHHHHSCSS-TT-CCSSCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccc-cC-CCCCchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence            34444444443342 23 34445566799999999999999888877788888887777666655555555555444

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A

Probab=82.44  E-value=2  Score=33.13  Aligned_cols=32  Identities=25%  Similarity=0.386  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      .++..++..|+.+|..|..++..|+.|...|+
T Consensus        39 ~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~Lr   70 (78)
T 1gu4_A           39 LETQHKVLELTAENERLQKKVEQLSRELSTLR   70 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555666666666666666666655555554

>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=82.27  E-value=13  Score=27.89  Aligned_cols=57  Identities=7%  Similarity=0.102  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           57 LADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        57 L~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      +..|.+-+.++..++...+.....+.+++..|+.....|.++...+...+...+..|
T Consensus        15 ~d~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kL   71 (81)
T 1ic2_A           15 KENALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKL   71 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345556666666666666666666666666666655555555555555554444433

>3s9g_A Protein hexim1; cyclin T-binding domain (TBD), cyclin T1/P-TEFB/7SK snRNA, N transcription; 2.10A {Homo sapiens} PDB: 2gd7_A

Probab=82.24  E-value=10  Score=30.91  Aligned_cols=59  Identities=17%  Similarity=0.199  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHcCCCc
Q 022288           66 DLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAMVPWA  124 (299)
Q Consensus        66 dLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~~pw~  124 (299)
                      +|-.+--.|+..++.+++|.+-|++...+.-.....|..++++|..+.|.-+...-.|.
T Consensus        34 ELIqEYl~LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~~~   92 (104)
T 3s9g_A           34 ELIKEYLELEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENELHR   92 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            45555556777777788888777776555555566777777777777766665555554

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=82.21  E-value=5  Score=28.44  Aligned_cols=42  Identities=26%  Similarity=0.370  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNI  111 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~  111 (299)
                      .+.+|..+|..|+.+|++|....-.       -+|-..-|..||.+|..
T Consensus         4 lvaqlenevaslenenetlkkknlh-------kkdliaylekeianlrk   45 (49)
T 3he5_A            4 LVAQLENEVASLENENETLKKKNLH-------KKDLIAYLEKEIANLRK   45 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccHHHHHhccc-------HHHHHHHHHHHHHHHHH
Confidence            5677888888888887776543211       12333455555555543

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=81.87  E-value=4.4  Score=38.97  Aligned_cols=51  Identities=16%  Similarity=0.192  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           65 KDLTSQVEKLKTEHAALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        65 KdLr~qVq~Lk~en~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      ..|++++.+|++....|+.+++.++.|..+++++......+..+|-++++.
T Consensus         6 ~~l~~el~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~rr~l~n~~~~   56 (412)
T 3u06_A            6 AALSTEVVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMD   56 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356666666666666666666666666666655544444444555555543

>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis, CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A* 3qo8_A* 3qo5_A

Probab=81.58  E-value=8.3  Score=38.18  Aligned_cols=36  Identities=17%  Similarity=0.338  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           85 SRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        85 ~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      ..+|..|..+|+++...|+.++..++.+++..+..+
T Consensus        73 ~~~l~~~~~~l~~~i~~le~~~~~~~~~~~~~l~~i  108 (485)
T 3qne_A           73 AKDLIAEKEKLSNEKKEIIEKEAEADKNLRSKINQV  108 (485)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            456777888888888888888889998888877775

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=81.44  E-value=5.3  Score=30.75  Aligned_cols=63  Identities=14%  Similarity=0.260  Sum_probs=39.3

Q ss_pred             HHHHHHHhhhccCCCCC---CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 022288           33 LNEHFTELGNALDPDRP---KNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDLR   96 (299)
Q Consensus        33 LNErF~eLrslLvP~~~---K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNELR   96 (299)
                      +..-..+|..+ +++..   ..+.+-|..+--+++..|..+++.++..+..|.....++..+.++|+
T Consensus        39 ~~~~~~eL~~l-~~d~~vy~~iG~vfv~~~~~ea~~~L~~~~e~ie~~i~~le~~~~~l~~~l~~lk  104 (117)
T 2zqm_A           39 AKKALDEIESL-PDDAVVYKTVGTLIVKTTKDKAVAELKEKIETLEVRLNALERQEKKLNEKLKELT  104 (117)
T ss_dssp             HHHHHHHHHTS-CTTCCEEEEETTEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC-CCCcHhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555667654 55542   55666666666677777777777777766666666666555554444

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

Probab=81.17  E-value=15  Score=30.25  Aligned_cols=67  Identities=19%  Similarity=0.296  Sum_probs=35.5

Q ss_pred             CCCChhhhHHHHHHHHHHHHHHHHHHHHHH----hhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           49 PKNDKATILADTVQLLKDLTSQVEKLKTEH----AALTEESRELTQEKNDLREEKLSLRSEIENLNIQYQQ  115 (299)
Q Consensus        49 ~K~DKASIL~DAI~ylKdLr~qVq~Lk~en----~~L~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqq  115 (299)
                      .+.+|-.++..=-+-|..|+.+++.++.+.    ..|...+..|..|..+-|..+.....|.+.|..++..
T Consensus         9 ~~d~rD~~Ie~Lkreie~lk~ele~l~~E~q~~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~   79 (120)
T 3i00_A            9 NKDEKDHLIERLYREISGLKAQLENMKTESQRVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDE   79 (120)
T ss_dssp             -CCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355555555544455556666666555333    3455555556666555555544555555555555543

>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: SSA; 2.60A {Pyrococcus horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A

Probab=81.15  E-value=9.2  Score=37.12  Aligned_cols=36  Identities=17%  Similarity=0.233  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           85 SRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        85 ~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      ..+|..+..+|+++...|+.++..++.+++..+..+
T Consensus        71 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  106 (455)
T 2dq0_A           71 VDELLAKSREIVKRIGELENEVEELKKKIDYYLWRL  106 (455)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            456777888888888888888889998888887776

>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=80.99  E-value=2.6  Score=32.86  Aligned_cols=31  Identities=29%  Similarity=0.290  Sum_probs=17.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~e~L~  110 (299)
                      .|-.++++|+.|+.-|+.|..+++.-+.+++
T Consensus        34 DLI~rvdELt~E~e~l~~El~s~~~~~~r~~   64 (77)
T 2w83_C           34 DLIAKVDELTCEKDVLQGELEAVKQAKLKLE   64 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555555555555555554

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B

Probab=80.66  E-value=1.9  Score=32.41  Aligned_cols=27  Identities=15%  Similarity=0.340  Sum_probs=11.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           80 ALTEESRELTQEKNDLREEKLSLRSEI  106 (299)
Q Consensus        80 ~L~eE~~eLk~EkNELRdEns~LksE~  106 (299)
                      .|+.++..|..|+++|+.++..|+.++
T Consensus        51 ~L~~~~~~l~~e~~~L~~~~~~L~~~l   77 (83)
T 1nkp_B           51 YMRRKNHTHQQDIDDLKRQNALLEQQV   77 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444433

>1zhc_A Hypothetical protein HP1242; A-helical protein, unknown function; NMR {Helicobacter pylori}

Probab=80.64  E-value=1.3  Score=33.52  Aligned_cols=19  Identities=26%  Similarity=0.552  Sum_probs=8.6

Q ss_pred             HHHHHHHHhhhHHHHHHHH
Q 022288           92 KNDLREEKLSLRSEIENLN  110 (299)
Q Consensus        92 kNELRdEns~LksE~e~L~  110 (299)
                      ..+|+.++..||.+|.++-
T Consensus        46 l~~LKk~KL~LKDeI~~lL   64 (76)
T 1zhc_A           46 VSHMKKQKLKLKDEIHSMI   64 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHH
Confidence            3344444444444444443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=80.46  E-value=6.2  Score=36.99  Aligned_cols=31  Identities=13%  Similarity=0.189  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           83 EESRELTQEKNDLREEKLSLRSEIENLNIQY  113 (299)
Q Consensus        83 eE~~eLk~EkNELRdEns~LksE~e~L~~ql  113 (299)
                      .+.+....+.+.|++|+.+|+.+++++..++
T Consensus       435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  465 (487)
T 3oja_A          435 RDWDMYQHKETQLAEENARLKKLNGEADLAL  465 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHhhhhhhhhhhhhhhh
Confidence            3334444444445555555555555544443

>3v86_A De novo design helix; computational design of A protein crystal, helical coil, DE designed helix, de novo protein; 2.91A {Synthetic}

Probab=80.38  E-value=1.4  Score=27.97  Aligned_cols=26  Identities=35%  Similarity=0.501  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHH
Q 022288           63 LLKDLTSQVEKLKTEHAALTEESREL   88 (299)
Q Consensus        63 ylKdLr~qVq~Lk~en~~L~eE~~eL   88 (299)
                      |+-+|+.++-+|+.+...|..|++.|
T Consensus         1 yvyqlkdevgelkgevralkdevkdl   26 (27)
T 3v86_A            1 YVYQLKDEVGELKGEVRALKDEVKDL   26 (27)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchhhHHHHHHHhHHHHHHHHHhcc
Confidence            34456666666655555555544443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	299
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	1e-14
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	3e-13
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-12
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	4e-12
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	5e-11
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	9e-08
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	4e-07
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	2e-05

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.0 bits (161), Expect = 1e-14
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 18 RKMQKADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTSQVEKLKT 76
          ++      E+ RRD + + F  L +++   +  K  +A IL    + ++ +  +    + 
Sbjct: 2  KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ 61

Query: 77 EHAALTEESRELTQEKNDLR 96
          +   L  ++  L Q+   L 
Sbjct: 62 DIDDLKRQNALLEQQVRALG 81

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.2 bits (151), Expect = 3e-13
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 18 RKMQKADREKLRRDRLNEHFTELGNAL--DPDRPKNDKATILADTVQLLKDLTSQVEKLK 75
          ++      E+ RR+ L   F  L + +    +  K  K  IL      +  + ++ +KL 
Sbjct: 6  KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLI 65

Query: 76 TEHAALTEESRELTQEKNDLR 96
          +E   L +   +L  +   L 
Sbjct: 66 SEEDLLRKRREQLKHKLEQLG 86

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.3 bits (146), Expect = 1e-12
 Identities = 16/77 (20%), Positives = 32/77 (41%)

Query: 16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLK 75
            ++      EK  R  +N+   EL + +     K +K+ +L   +  ++ L    +KLK
Sbjct: 4  GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLK 63

Query: 76 TEHAALTEESRELTQEK 92
           E+ +L     +    K
Sbjct: 64 QENLSLRTAVHKSKSLK 80

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (141), Expect = 4e-12
 Identities = 13/58 (22%), Positives = 26/58 (44%)

Query: 30 RDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRE 87
          R  +N+   EL + +     K  K+ +L   +  +K L     KL+ E+  L   +++
Sbjct: 1  RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQK 58

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.7 bits (134), Expect = 5e-11
 Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 2/69 (2%)

Query: 25 REKLRRDRLNEHFTELGNAL--DPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALT 82
           EK RR  L     +L   +   PD  ++   ++L      +K L     K   +   L 
Sbjct: 8  MEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ 67

Query: 83 EESRELTQE 91
           E R L ++
Sbjct: 68 REQRHLKRQ 76

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.4 bits (110), Expect = 9e-08
 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 1/62 (1%)

Query: 12 KDCAATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKN-DKATILADTVQLLKDLTSQ 70
          K   A R+     RE+ R  ++NE F  L  +   +  +   K  IL + ++ ++ L + 
Sbjct: 6  KTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQAL 65

Query: 71 VE 72
          + 
Sbjct: 66 LR 67

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (105), Expect = 4e-07
 Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 5/61 (8%)

Query: 18 RKMQKADREKLRRDRLNEHFTELGNAL-----DPDRPKNDKATILADTVQLLKDLTSQVE 72
          R+ Q  + E+ RRD++N    +L   +     +  +    K  IL+     +++L     
Sbjct: 5  RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

Query: 73 K 73
          +
Sbjct: 65 R 65

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.9 bits (93), Expect = 2e-05
 Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 6/61 (9%)

Query: 18 RKMQKADREKLRRDRLNEHFTELGNAL------DPDRPKNDKATILADTVQLLKDLTSQV 71
          ++      E+ RR+RL     EL + +              KAT +    + ++ L    
Sbjct: 2  KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

Query: 72 E 72
           
Sbjct: 62 S 62

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	299
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.63
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.48
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.38
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.37
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.21
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	91.4

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.5e-16  Score=120.11  Aligned_cols=78  Identities=18%  Similarity=0.330  Sum_probs=63.9

Q ss_pred             hhccchHHHHHHHHHHHHHHHHhhhccCCCC-CCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 022288           18 RKMQKADREKLRRDRLNEHFTELGNALDPDR-PKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKNDL   95 (299)
Q Consensus        18 Rk~~KAerERrRRdKLNErF~eLrslLvP~~-~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNEL   95 (299)
                      |+..|..+||+||++||+.|.+|+++|++.. .|++|++||..||.||+.|+.+++.|..++..|..+...|..+.+.|
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~L   80 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRAL   80 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5677889999999999999999999864332 59999999999999999999999988877766666665555555443

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.1e-16  Score=119.14  Aligned_cols=74  Identities=20%  Similarity=0.304  Sum_probs=63.5

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 022288           16 ATRKMQKADREKLRRDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELT   89 (299)
Q Consensus        16 a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk   89 (299)
                      +.++..|...||+||++||+.|.+|+++|++...|+||++||.+||+||++|+.+++.|+.++..|..+++.++
T Consensus         4 ~~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~~~~~~   77 (80)
T d1am9a_           4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            45677888999999999999999999986445579999999999999999999999998888877766655543

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=4.5e-16  Score=118.54  Aligned_cols=79  Identities=20%  Similarity=0.314  Sum_probs=64.3

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCC--CCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPD--RPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEKND   94 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~--~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~EkNE   94 (299)
                      .|+..|..+||+||++||+.|.+|+++|++.  ..|++|++||..||+||+.|+.+++.|..+.+.|..+.+.|..+.+.
T Consensus         5 ~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~   84 (88)
T d1nkpa_           5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQ   84 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566778999999999999999999986432  25899999999999999999999998887776666666666555555


Q ss_pred             H
Q 022288           95 L   95 (299)
Q Consensus        95 L   95 (299)
                      |
T Consensus        85 L   85 (88)
T d1nkpa_          85 L   85 (88)
T ss_dssp             H
T ss_pred             h
Confidence            4

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.5e-15  Score=113.59  Aligned_cols=72  Identities=19%  Similarity=0.252  Sum_probs=60.1

Q ss_pred             cchHHHHHHHHHHHHHHHHhhhccCCC--CCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Q 022288           21 QKADREKLRRDRLNEHFTELGNALDPD--RPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEESRELTQEK   92 (299)
Q Consensus        21 ~KAerERrRRdKLNErF~eLrslLvP~--~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~~eLk~Ek   92 (299)
                      .|...||+||++||+.|.+|+++|++.  ..|++|++||.+||+||++|+.+++.|..+...|..+...|+...
T Consensus         4 ~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~~~~L~~~l   77 (79)
T d1nlwa_           4 THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQL   77 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            455899999999999999999986543  358999999999999999999999988877777776666665543

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=1.4e-14  Score=104.74  Aligned_cols=56  Identities=23%  Similarity=0.338  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHhhhccCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 022288           30 RDRLNEHFTELGNALDPDRPKNDKATILADTVQLLKDLTSQVEKLKTEHAALTEES   85 (299)
Q Consensus        30 RdKLNErF~eLrslLvP~~~K~DKASIL~DAI~ylKdLr~qVq~Lk~en~~L~eE~   85 (299)
                      |++||++|.+|+++|+....|+|||+||.+||+||+.|+.+++.|+.++..|..+.
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   56 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLAN   56 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999998633457999999999999999999999999998888776654

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.38  E-value=9.5e-14  Score=100.49  Aligned_cols=54  Identities=20%  Similarity=0.321  Sum_probs=46.6

Q ss_pred             hhccchHHHHHHHHHHHHHHHHhhhccCC------CCCCCChhhhHHHHHHHHHHHHHHH
Q 022288           18 RKMQKADREKLRRDRLNEHFTELGNALDP------DRPKNDKATILADTVQLLKDLTSQV   71 (299)
Q Consensus        18 Rk~~KAerERrRRdKLNErF~eLrslLvP------~~~K~DKASIL~DAI~ylKdLr~qV   71 (299)
                      |+..|..+||+||++||+.|.+|+++|++      ...|+|||+||..||+||+.|++++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            46677799999999999999999998532      1359999999999999999998765

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.37  E-value=1.8e-13  Score=100.75  Aligned_cols=59  Identities=22%  Similarity=0.369  Sum_probs=50.6

Q ss_pred             chhhhhhccchHHHHHHHHHHHHHHHHhhhccCCCC--CCCChhhhHHHHHHHHHHHHHHHH
Q 022288           13 DCAATRKMQKADREKLRRDRLNEHFTELGNALDPDR--PKNDKATILADTVQLLKDLTSQVE   72 (299)
Q Consensus        13 ~~~a~Rk~~KAerERrRRdKLNErF~eLrslLvP~~--~K~DKASIL~DAI~ylKdLr~qVq   72 (299)
                      ...+.++..|+.+||+||++||+.|.+|+++| |..  .|+||++||..||+||+.|+..++
T Consensus         7 ~~~~~rR~~hn~~Er~Rr~~in~~~~~L~~ll-P~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_           7 TTNADRRKAATMRERRRLSKVNEAFETLKRST-SSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-CSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            34556777888999999999999999999985 543  489999999999999999997654

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=2e-12  Score=93.87  Aligned_cols=54  Identities=26%  Similarity=0.509  Sum_probs=46.8

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHhhhccCCCC------CCCChhhhHHHHHHHHHHHHHHH
Q 022288           17 TRKMQKADREKLRRDRLNEHFTELGNALDPDR------PKNDKATILADTVQLLKDLTSQV   71 (299)
Q Consensus        17 ~Rk~~KAerERrRRdKLNErF~eLrslLvP~~------~K~DKASIL~DAI~ylKdLr~qV   71 (299)
                      .|+..|..+||+||++||+.|.+|+++| |..      .|++|++||..||+||+.|+++.
T Consensus         4 ~rR~~H~~~Er~RR~~in~~f~~L~~lv-P~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           4 KRRAQHNEVERRRRDKINNWIVQLSKII-PDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHS-CCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHc-ccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            4667788999999999999999999985 532      49999999999999999998653

>d1seta1 a.2.7.1 (A:1-110) Seryl-tRNA synthetase (SerRS) {Thermus thermophilus, strain hb27 [TaxId: 274]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Seryl-tRNA synthetase (SerRS)
domain: Seryl-tRNA synthetase (SerRS)
species: Thermus thermophilus, strain hb27 [TaxId: 274]

Probab=91.40  E-value=0.98  Score=33.45  Aligned_cols=59  Identities=17%  Similarity=0.302  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhh--------HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHc
Q 022288           62 QLLKDLTSQVEKLKTEHAAL--------TEESRELTQEKNDLREEKLSLRSEIENLNIQYQQRVRAM  120 (299)
Q Consensus        62 ~ylKdLr~qVq~Lk~en~~L--------~eE~~eLk~EkNELRdEns~LksE~e~L~~qlqqrl~~~  120 (299)
                      .-.++|+.+++.|+.+...+        .++..+|..+..+|+++...|..+...++.+++..+-..
T Consensus        35 ~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~ll~i  101 (110)
T d1seta1          35 REVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQV  101 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            33445555555555443333        234466777777777777777777777777777766665