Citrus Sinensis ID: 026599

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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------
Protein Sequence
MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNGLKESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHcccccccccccccccccHHHcccccccccccccccccccc
Coil and Loop (DISEMBL)
mvspentnwlldyplidditvpdgnfsvsasgftwtvqppingpsngcveidsafgdsnglkesskkrvrsescgsssskaCREKLRRDRLNDKFVELASilepgrppktdkaAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAmstqpsfltpppaipaafaaqgqapgnklmpfisypgvamwqfmppaavdtsqdhvlrppva
Flexible Loop (DISEMBL)
MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGdsnglkesskkrvrsescgsssskacreklrrdrlndKFVElasilepgrppktdkAAILIDAVRMVTQLRSEaqklkdsnsslqEKIKElkaeknelrdeKQRLKAEKEKIEQQLKAMSTQPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Low Complexity Region (SEG)
MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNGLkesskkrvrsescgssssKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLTpppaipaafaaqgqapgNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Disordered region (IsUnstruct)
*******NWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEI*************************************************************AAILIDAVRMV*****************************************************************************NKLMPFISYPGVAMWQFMPP****************
Disordered Region (DISOPRED)
******TNWLLDYPLIDDITVPDG*******************************************************************NDKFVELASILE*****KTDKAAILIDAVRMVTQLRS***********************************************************************************VA******************RPP**
Disordered Region (DISEMBL)
MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGD**************************EKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Disordered Region (DISPRO)
******TNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNG**E*****************************KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPP**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNGLKESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
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	236	2.2.26 [Sep-21-2011]
Q9FH37	234	Transcription factor ILR3	yes	no	0.978	0.987	0.715	2e-89
Q9C682	226	Transcription factor bHLH	no	no	0.936	0.977	0.647	1e-79
Q8L467	283	Transcription factor bHLH	no	no	0.775	0.646	0.505	3e-44
Q9LTC7	320	Transcription factor bHLH	no	no	0.779	0.575	0.527	1e-43
Q9LT23	337	Transcription factor bHLH	no	no	0.415	0.290	0.485	2e-18
Q8W2F2	286	Transcription factor bHLH	no	no	0.402	0.332	0.427	8e-14
Q9SN74	240	Transcription factor bHLH	no	no	0.419	0.412	0.34	5e-09
P36956	1147	Sterol regulatory element	yes	no	0.550	0.113	0.285	0.0006

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

 Score =  328 bits (841), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 171/239 (71%), Positives = 191/239 (79%), Gaps = 8/239 (3%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNG 60
           MVSPEN NW+ D  LID      G+F++   GF+W VQ PI   SN    +D + G+S  
Sbjct: 1   MVSPENANWICD--LID---ADYGSFTIQGPGFSWPVQQPIGVSSNSSAGVDGSAGNSEA 55

Query: 61  LKE-SSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDA 119
            KE  SKKR R ES  ++SSKACREK RRDRLNDKF+EL +ILEPG PPKTDKAAIL+DA
Sbjct: 56  SKEPGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDA 115

Query: 120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST-Q 178
           VRMVTQLR EAQKLKDSNSSLQ+KIKELK EKNELRDEKQRLK EKEK+EQQLKAM+  Q
Sbjct: 116 VRMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKLEQQLKAMNAPQ 175

Query: 179 PSFLTPPPAIPAAFA-AQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           PSF   PP +P AFA AQGQAPGNK++P ISYPGVAMWQFMPPA+VDTSQDHVLRPPVA
Sbjct: 176 PSFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFMPPASVDTSQDHVLRPPVA 234

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

 Score =  296 bits (757), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 156/241 (64%), Positives = 181/241 (75%), Gaps = 20/241 (8%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNG 60
           MVSPENTNWL DYPLI+      G FS     F W     I+G +   VE+D    D++ 
Sbjct: 1   MVSPENTNWLSDYPLIE------GAFSDQNPTFPWQ----IDGSATVSVEVDGFLCDADV 50

Query: 61  LKE-SSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDA 119
           +KE SS+KR+++ESC  S+SKACREK RRDRLNDKF EL+S+LEPGR PKTDK AI+ DA
Sbjct: 51  IKEPSSRKRIKTESCTGSNSKACREKQRRDRLNDKFTELSSVLEPGRTPKTDKVAIINDA 110

Query: 120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST-- 177
           +RMV Q R EAQKLKD NSSLQEKIKELK EKNELRDEKQ+LK EKE+I+QQLKA+ T  
Sbjct: 111 IRMVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQP 170

Query: 178 --QPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPV 235
             QP FL  P  +     +Q QAPG+KL+PF +YPG AMWQFMPPAAVDTSQDHVLRPPV
Sbjct: 171 QPQPCFLPNPQTL-----SQAQAPGSKLVPFTTYPGFAMWQFMPPAAVDTSQDHVLRPPV 225

Query: 236 A 236
           A
Sbjct: 226 A 226

Arabidopsis thaliana (taxid: 3702)

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

 Score =  178 bits (452), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 99/196 (50%), Positives = 132/196 (67%), Gaps = 13/196 (6%)

Query: 42  NGPSNGCVEIDSAFGDSNGLKESSKKRVRSESCG-SSSSKACREKLRRDRLNDKFVELAS 100
           +G S G V+ +    D +     S+KR R+ SC     +KACRE+LRR++LN++F++L+S
Sbjct: 100 SGSSGGAVKEEQEHLDDD----CSRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSS 155

Query: 101 ILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQR 160
           +LEPGR PKTDK AIL DA+R++ QLR EA KL+++N  L E+IK LKAEKNELR+EK  
Sbjct: 156 VLEPGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLV 215

Query: 161 LKAEKEKIEQQLKAMSTQPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPP 220
           LKA+KEK EQQLK+M+   S     P IPAAF        NK+  + SY  + MW +MP 
Sbjct: 216 LKADKEKTEQQLKSMTAPSSGFI--PHIPAAFNH------NKMAVYPSYGYMPMWHYMPQ 267

Query: 221 AAVDTSQDHVLRPPVA 236
           +  DTS+D  LRPP A
Sbjct: 268 SVRDTSRDQELRPPAA 283

Arabidopsis thaliana (taxid: 3702)

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

 Score =  176 bits (446), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 105/199 (52%), Positives = 135/199 (67%), Gaps = 15/199 (7%)

Query: 46  NGCVEIDSAFGDSNGL------KESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELA 99
           +G VEI+S+   S G       +E S KR R+ SC    +KACREKLRR++LNDKF++L+
Sbjct: 129 SGVVEINSS--SSVGAVKEEFEEECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLS 186

Query: 100 SILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQ 159
           S+LEPGR PKTDK+AIL DA+R+V QLR EA +L+++N  L E+IK LKA+KNELR+EK 
Sbjct: 187 SVLEPGRTPKTDKSAILDDAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKL 246

Query: 160 RLKAEKEKIEQQLKAMST-QPSFLTPPPAIPAAFAAQGQAPGNKLMPFISY-PGVAMWQF 217
            LKAEKEK+EQQLK+M    P F+  P   PAAF +   A      P+  Y P + MW  
Sbjct: 247 VLKAEKEKMEQQLKSMVVPSPGFM--PSQHPAAFHSHKMAVA---YPYGYYPPNMPMWSP 301

Query: 218 MPPAAVDTSQDHVLRPPVA 236
           +PPA  DTS+D    PPVA
Sbjct: 302 LPPADRDTSRDLKNLPPVA 320

Arabidopsis thaliana (taxid: 3702)

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

 Score = 92.4 bits (228), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/103 (48%), Positives = 74/103 (71%), Gaps = 5/103 (4%)

Query: 78  SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSN 137
           S KA REKLRR++LN+ FVEL ++L+P RP K DKA IL D V+++ +L SE  KLK   
Sbjct: 61  SQKAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEY 119

Query: 138 SSLQEKIKELKAEKNELRDEKQRLKAEKEKI----EQQLKAMS 176
           ++L ++ +EL  EKN+LR+EK  LK++ E +    +Q+L++MS
Sbjct: 120 TALTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMS 162

Arabidopsis thaliana (taxid: 3702)

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

 Score = 77.4 bits (189), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 41/96 (42%), Positives = 67/96 (69%), Gaps = 1/96 (1%)

Query: 78  SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSN 137
           S KA REKLRRD+L ++F+EL + L+P RP K+DKA++L D ++M+  + ++  +LK   
Sbjct: 47  SQKAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQVDRLKAEY 105

Query: 138 SSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK 173
            +L ++ +EL  EK+ELR+EK  LK++ E +  Q +
Sbjct: 106 ETLSQESRELIQEKSELREEKATLKSDIEILNAQYQ 141

Arabidopsis thaliana (taxid: 3702)

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

 Score = 61.6 bits (148), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 34/100 (34%), Positives = 62/100 (62%), Gaps = 1/100 (1%)

Query: 79  SKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNS 138
           +KA RE+L+R+ LN+ F+ELA  LE  +   + KA+IL +A R +  +  + + L+  ++
Sbjct: 31  NKAVRERLKREHLNELFIELADTLELNQQ-NSGKASILCEATRFLKDVFGQIESLRKEHA 89

Query: 139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
           SL  +   +  EKNEL++E   L+ E  K++ +++A + Q
Sbjct: 90  SLLSESSYVTTEKNELKEETSVLETEISKLQNEIEARANQ 129

Arabidopsis thaliana (taxid: 3702)

>sp|P36956|SRBP1_HUMAN Sterol regulatory element-binding protein 1 OS=Homo sapiens GN=SREBF1 PE=1 SV=2

 Score = 44.7 bits (104), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 40/140 (28%), Positives = 63/140 (45%), Gaps = 10/140 (7%)

Query: 14  PLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNGLKESSKKRVRSES 73
           PL+   TV  G      SG T     P+         +D+     N L   SK    ++S
Sbjct: 269 PLVSGTTVQTGPLPTLVSGGTILATVPL--------VVDAEKLPINRLAAGSKAPASAQS 320

Query: 74  CGSS-SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQK 132
            G   ++    EK  R  +NDK +EL  ++  G   K +K+A+L  A+  +  L+   QK
Sbjct: 321 RGEKRTAHNAIEKRYRSSINDKIIELKDLVV-GTEAKLNKSAVLRKAIDYIRFLQHSNQK 379

Query: 133 LKDSNSSLQEKIKELKAEKN 152
           LK  N SL+  + + K+ K+
Sbjct: 380 LKQENLSLRTAVHKSKSLKD 399

Transcriptional activator required for lipid homeostasis. Regulates transcription of the LDL receptor gene as well as the fatty acid and to a lesser degree the cholesterol synthesis pathway (By similarity). Binds to the sterol regulatory element 1 (SRE-1) (5'-ATCACCCCAC-3'). Has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').

Homo sapiens (taxid: 9606)

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	236
357474831	237	Transcription factor ILR3 [Medicago trun	1.0	0.995	0.793	1e-103
388521527	238	unknown [Lotus japonicus]	1.0	0.991	0.773	1e-100
357452673	230	Transcription factor ILR3 [Medicago trun	0.961	0.986	0.803	3e-99
357474833	261	Transcription factor ILR3 [Medicago trun	1.0	0.904	0.724	4e-99
255563653	235	DNA binding protein, putative [Ricinus c	0.991	0.995	0.827	5e-99
225461144	237	PREDICTED: transcription factor ILR3 [Vi	1.0	0.995	0.810	8e-99
356543170	236	PREDICTED: transcription factor ILR3-lik	0.987	0.987	0.799	1e-97
356517276	236	PREDICTED: transcription factor ILR3-lik	0.987	0.987	0.803	3e-96
255646584	236	unknown [Glycine max]	0.987	0.987	0.794	4e-95
359485584	240	PREDICTED: transcription factor ILR3-lik	0.987	0.970	0.734	3e-94

>gi|357474831|ref|XP_003607701.1| Transcription factor ILR3 [Medicago truncatula] gi|217071746|gb|ACJ84233.1| unknown [Medicago truncatula] gi|355508756|gb|AES89898.1| Transcription factor ILR3 [Medicago truncatula] gi|388493018|gb|AFK34575.1| unknown [Medicago truncatula]

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 188/237 (79%), Positives = 204/237 (86%), Gaps = 1/237 (0%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNG 60
           MVS ENTNW+ DY   DDI VPD  F++ +S FTW  QPP N  SN   E+D + GDS+G
Sbjct: 1   MVSRENTNWINDYGFYDDIPVPDSTFALPSSAFTWPTQPPFNLSSNVSAEVDGSLGDSDG 60

Query: 61  LKES-SKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDA 119
           LKES SKKRVRSESC ++SSKACREKLRRDRLNDKF+EL SILEPGRP KTDKAAILIDA
Sbjct: 61  LKESGSKKRVRSESCAATSSKACREKLRRDRLNDKFIELGSILEPGRPAKTDKAAILIDA 120

Query: 120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQP 179
           VRMVTQLR EAQKLKD+NS LQEKIKELK EKNELRDEKQRLKAEKEK+EQQLK+M+  P
Sbjct: 121 VRMVTQLRGEAQKLKDANSGLQEKIKELKVEKNELRDEKQRLKAEKEKLEQQLKSMNAPP 180

Query: 180 SFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           SFL  P A+PAAFAAQGQA GNKL+PFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 181 SFLPTPTALPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 237

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388521527|gb|AFK48825.1| unknown [Lotus japonicus]

 Score =  369 bits (946), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 184/238 (77%), Positives = 202/238 (84%), Gaps = 2/238 (0%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGC-VEIDSAFGDSN 59
           MVS ENTNWL DY LIDDI  P+  F+V  SGFTW    P+N  SN   VEID + GDS+
Sbjct: 1   MVSRENTNWLFDYGLIDDIPAPEVTFTVPPSGFTWPSSQPLNSSSNVVGVEIDGSLGDSD 60

Query: 60  GLKE-SSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILID 118
            LKE  SKKRVRSESC ++SSKACREKLRRD+LNDKFVEL SILEPGRPPKTDKAAILID
Sbjct: 61  SLKEPGSKKRVRSESCSATSSKACREKLRRDKLNDKFVELGSILEPGRPPKTDKAAILID 120

Query: 119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
           AVRMVTQLR EAQK+KD+N  LQEKIKELK EKNELRDEKQRLK EKE++EQQLK+M+ Q
Sbjct: 121 AVRMVTQLRGEAQKMKDTNMGLQEKIKELKTEKNELRDEKQRLKTEKERLEQQLKSMNAQ 180

Query: 179 PSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           PSF+ PP A+PAAFAAQGQA GNKL+PFISYPGVAMWQF+PPAA DTSQDH LRPPVA
Sbjct: 181 PSFMPPPQALPAAFAAQGQAHGNKLVPFISYPGVAMWQFLPPAARDTSQDHELRPPVA 238

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357452673|ref|XP_003596613.1| Transcription factor ILR3 [Medicago truncatula] gi|217071990|gb|ACJ84355.1| unknown [Medicago truncatula] gi|355485661|gb|AES66864.1| Transcription factor ILR3 [Medicago truncatula] gi|388518489|gb|AFK47306.1| unknown [Medicago truncatula]

 Score =  366 bits (940), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 192/239 (80%), Positives = 207/239 (86%), Gaps = 12/239 (5%)

Query: 1   MVSPENTNWLLDYPLIDDITVP-DGNFSVSASGFTWTVQPPINGPSNGCVEID-SAFGDS 58
           MVSPENTNWL DYPLID+I V  DG+F+     FTW   PP +  SNG +E+D S+  DS
Sbjct: 1   MVSPENTNWLFDYPLIDEIPVSVDGSFA-----FTW---PPPHL-SNGGIEMDDSSLVDS 51

Query: 59  NGLKE-SSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILI 117
           +G+KE  SKKR RS+SC  SSSKACREKLRRDRLNDKFVEL SILEPGRPPKTDKAAILI
Sbjct: 52  DGIKEPGSKKRGRSDSCAPSSSKACREKLRRDRLNDKFVELGSILEPGRPPKTDKAAILI 111

Query: 118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST 177
           DAVRMVTQLR EAQKLKDSNS LQEKIKELK EKNELRDEKQRLKAEKEK+EQQ+K+M+T
Sbjct: 112 DAVRMVTQLRGEAQKLKDSNSGLQEKIKELKVEKNELRDEKQRLKAEKEKLEQQVKSMNT 171

Query: 178 QPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           QP FLT PPAIPAAFA QGQAP NKLMPF+SYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 172 QPGFLTHPPAIPAAFAHQGQAPSNKLMPFMSYPGVAMWQFMPPAAVDTSQDHVLRPPVA 230

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357474833|ref|XP_003607702.1| Transcription factor ILR3 [Medicago truncatula] gi|355508757|gb|AES89899.1| Transcription factor ILR3 [Medicago truncatula]

 Score =  366 bits (940), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 189/261 (72%), Positives = 205/261 (78%), Gaps = 25/261 (9%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSN-----------GC- 48
           MVS ENTNW+ DY   DDI VPD  F++ +S FTW  QPP N  SN            C 
Sbjct: 1   MVSRENTNWINDYGFYDDIPVPDSTFALPSSAFTWPTQPPFNLSSNVRSGVRCSNFKQCN 60

Query: 49  ------------VEIDSAFGDSNGLKES-SKKRVRSESCGSSSSKACREKLRRDRLNDKF 95
                        E+D + GDS+GLKES SKKRVRSESC ++SSKACREKLRRDRLNDKF
Sbjct: 61  FPWTDAVDMRMGAEVDGSLGDSDGLKESGSKKRVRSESCAATSSKACREKLRRDRLNDKF 120

Query: 96  VELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR 155
           +EL SILEPGRP KTDKAAILIDAVRMVTQLR EAQKLKD+NS LQEKIKELK EKNELR
Sbjct: 121 IELGSILEPGRPAKTDKAAILIDAVRMVTQLRGEAQKLKDANSGLQEKIKELKVEKNELR 180

Query: 156 DEKQRLKAEKEKIEQQLKAMSTQPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMW 215
           DEKQRLKAEKEK+EQQLK+M+  PSFL  P A+PAAFAAQGQA GNKL+PFISYPGVAMW
Sbjct: 181 DEKQRLKAEKEKLEQQLKSMNAPPSFLPTPTALPAAFAAQGQAHGNKLVPFISYPGVAMW 240

Query: 216 QFMPPAAVDTSQDHVLRPPVA 236
           QFMPPAAVDTSQDHVLRPPVA
Sbjct: 241 QFMPPAAVDTSQDHVLRPPVA 261

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563653|ref|XP_002522828.1| DNA binding protein, putative [Ricinus communis] gi|223537912|gb|EEF39526.1| DNA binding protein, putative [Ricinus communis]

 Score =  366 bits (939), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 196/237 (82%), Positives = 213/237 (89%), Gaps = 3/237 (1%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNG 60
           MVSPENTNWL++Y LIDDI VPD NFSV  +GF+W VQ  +NG SN  VEID +FG+++ 
Sbjct: 1   MVSPENTNWLIEYGLIDDIPVPDANFSVPVTGFSWPVQT-LNGSSNVSVEIDGSFGNADT 59

Query: 61  LKES-SKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDA 119
            K+S SKKR RS+SC +SSSKACREKLRRDRLNDKF+EL SILEPGRPPKTDKAAILIDA
Sbjct: 60  QKDSTSKKRGRSDSC-ASSSKACREKLRRDRLNDKFLELGSILEPGRPPKTDKAAILIDA 118

Query: 120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQP 179
           VRMVTQLR EAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLK EKEK+EQQLKA++ QP
Sbjct: 119 VRMVTQLRGEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKVEKEKLEQQLKAVNAQP 178

Query: 180 SFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           SFL PPPAIPA FAAQGQAPGNKL+PFI YPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 179 SFLPPPPAIPAPFAAQGQAPGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 235

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461144|ref|XP_002282727.1| PREDICTED: transcription factor ILR3 [Vitis vinifera] gi|302143204|emb|CBI20499.3| unnamed protein product [Vitis vinifera]

 Score =  365 bits (937), Expect = 8e-99,   Method: Compositional matrix adjust.
 Identities = 192/237 (81%), Positives = 211/237 (89%), Gaps = 1/237 (0%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNG 60
           MVSPE TNWL +Y LI+DI VPD NF+ + SGF WT    +N  +N   EID +FGDS+G
Sbjct: 1   MVSPEATNWLYEYGLIEDIPVPDSNFANTNSGFAWTPVQALNTSANVSGEIDGSFGDSDG 60

Query: 61  LKES-SKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDA 119
           +KE+ SKKRVRSESCG+SSSKACREKLRRDRLNDKF+EL SILEPGRPPKTDK++ILIDA
Sbjct: 61  IKETGSKKRVRSESCGASSSKACREKLRRDRLNDKFMELGSILEPGRPPKTDKSSILIDA 120

Query: 120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQP 179
           VRMVTQLR E+QKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEK+EQQLKAM+ QP
Sbjct: 121 VRMVTQLRGESQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQLKAMNAQP 180

Query: 180 SFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           SFL P P+IPAAFAAQGQA GNKL+PFI YPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 181 SFLPPVPSIPAAFAAQGQAGGNKLVPFIGYPGVAMWQFMPPAAVDTSQDHVLRPPVA 237

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543170|ref|XP_003540036.1| PREDICTED: transcription factor ILR3-like [Glycine max]

 Score =  362 bits (928), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 191/239 (79%), Positives = 208/239 (87%), Gaps = 6/239 (2%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPP--INGPSNGCVEIDSAFGDS 58
           MVS ENTNWL DY LIDDI VPD  F V++S FTW   PP  ++ PSN  V+ID + GDS
Sbjct: 1   MVSRENTNWLFDYGLIDDIPVPDATFGVNSSAFTW---PPNALDAPSNVGVDIDGSLGDS 57

Query: 59  NGLKES-SKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILI 117
           +GLKES SKKRVRSESC +SSSKACREKLRRDRLNDKFVEL SILEPGRP KTDK AILI
Sbjct: 58  DGLKESGSKKRVRSESCAASSSKACREKLRRDRLNDKFVELGSILEPGRPAKTDKTAILI 117

Query: 118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST 177
           DAVRMVTQLR EAQKLKD+N  LQEKIK+LKAEKNELRD+KQRLKAEKEK+EQQLK+++ 
Sbjct: 118 DAVRMVTQLRGEAQKLKDTNQGLQEKIKDLKAEKNELRDQKQRLKAEKEKLEQQLKSLNG 177

Query: 178 QPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           QPSF+ PP AIPAAFA QGQA GNKL+PFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 178 QPSFMPPPAAIPAAFAVQGQAHGNKLVPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517276|ref|XP_003527314.1| PREDICTED: transcription factor ILR3-like isoform 1 [Glycine max]

 Score =  357 bits (915), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 192/239 (80%), Positives = 207/239 (86%), Gaps = 6/239 (2%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPP--INGPSNGCVEIDSAFGDS 58
           MVS ENTNWL DY LIDDI VPD  F V++S FTW   PP  +N  SN  VEID + GDS
Sbjct: 1   MVSRENTNWLFDYGLIDDIPVPDATFGVNSSAFTW---PPNALNASSNVGVEIDGSLGDS 57

Query: 59  NGLKES-SKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILI 117
           + LKES SKKRVRSESC +S SKACREKLRRDRLNDKFVEL +ILEPGRP KTDKAAILI
Sbjct: 58  DSLKESGSKKRVRSESCAASGSKACREKLRRDRLNDKFVELGAILEPGRPAKTDKAAILI 117

Query: 118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST 177
           DAVRMVTQLR EAQKLKD+N  LQEKIKELKAEKNELRDEKQRLKAEKEK+EQQLK+++ 
Sbjct: 118 DAVRMVTQLRGEAQKLKDTNQGLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQLKSLNA 177

Query: 178 QPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           QPSF+ PP A+PAAFAAQGQA GNKL+PFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 178 QPSFMPPPAAMPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255646584|gb|ACU23766.1| unknown [Glycine max]

 Score =  353 bits (905), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 190/239 (79%), Positives = 206/239 (86%), Gaps = 6/239 (2%)

Query: 1   MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPP--INGPSNGCVEIDSAFGDS 58
           MVS ENTNWL DY LIDDI VPD  F V++S FTW   PP  +N  SN  VEID + GDS
Sbjct: 1   MVSRENTNWLFDYGLIDDIPVPDATFGVNSSAFTW---PPNALNASSNVGVEIDGSLGDS 57

Query: 59  NGLKES-SKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILI 117
           + LKES SKKRVRSESC +S SKACREKLRRDRLNDKFVEL +ILEPGRP KTDKAAILI
Sbjct: 58  DSLKESGSKKRVRSESCAASGSKACREKLRRDRLNDKFVELGAILEPGRPAKTDKAAILI 117

Query: 118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST 177
           DAVRMVTQLR EAQKLKD++  LQEKIKELKAEKNELRDEKQRLKAEKEK+EQQLK+++ 
Sbjct: 118 DAVRMVTQLRGEAQKLKDTSQGLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQLKSLNA 177

Query: 178 QPSFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
           QPSF+ PP A+PAAFAAQGQA GNKL+PFISYPGVAMWQFMPPAAVDTSQDHV RPPVA
Sbjct: 178 QPSFMPPPAAMPAAFAAQGQAHGNKLVPFISYPGVAMWQFMPPAAVDTSQDHVFRPPVA 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485584|ref|XP_002274829.2| PREDICTED: transcription factor ILR3-like [Vitis vinifera]

 Score =  350 bits (898), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 174/237 (73%), Positives = 199/237 (83%), Gaps = 4/237 (1%)

Query: 3   SPENTNWLLDYPLIDDITVPDGNFS--VSASGFTWTVQPPINGPSNGCVEIDSAFGDSNG 60
           S EN+NWL DY L++DITVP G F      +GF+W  Q  +   S+  +E D +FGDS+G
Sbjct: 5   SSENSNWLFDYGLMEDITVPGGEFPEPTPGTGFSWPSQA-LKSSSSVSLEADCSFGDSDG 63

Query: 61  LKE-SSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDA 119
           LKE   +KR++ ESCG++ +KACREKLRRDRLN++F+EL SILEPGRPPKTDKAAIL DA
Sbjct: 64  LKELGPRKRLKHESCGATGTKACREKLRRDRLNERFLELGSILEPGRPPKTDKAAILSDA 123

Query: 120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQP 179
           VRMVTQLRSEAQKLK+SN  LQEKIKELKAEKNELRDEKQRLKAEKEK+EQQ+KA+S QP
Sbjct: 124 VRMVTQLRSEAQKLKESNGDLQEKIKELKAEKNELRDEKQRLKAEKEKLEQQVKAISAQP 183

Query: 180 SFLTPPPAIPAAFAAQGQAPGNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
            FL  P A+PAAFAAQG+APGNKLMPFI YP VAMWQFMPPAAVDTSQDHVLRPPVA
Sbjct: 184 GFLPHPSAMPAAFAAQGRAPGNKLMPFIGYPSVAMWQFMPPAAVDTSQDHVLRPPVA 240

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	236
TAIR|locus:2157538	234	ILR3 "AT5G54680" [Arabidopsis	0.978	0.987	0.615	6.3e-69
UNIPROTKB|Q6ZKI8	253	OJ1119_D01.9 "BHLH transcripti	0.932	0.869	0.431	5e-44
UNIPROTKB|Q6ZGM4	236	OJ1442_E05.19 "cDNA clone:006-	0.817	0.817	0.450	3e-37
TAIR|locus:2129710	283	bHLH104 "AT4G14410" [Arabidops	0.631	0.526	0.535	1e-36
TAIR|locus:2086198	320	bHLH34 "AT3G23210" [Arabidopsi	0.644	0.475	0.534	2.7e-36
UNIPROTKB|Q67U21	343	OSJNBa0065F08.2 "Basic helix-l	0.385	0.265	0.543	1.5e-19
TAIR|locus:2092216	337	bHLH121 "AT3G19860" [Arabidops	0.406	0.284	0.485	3.1e-19
TAIR|locus:2135169	286	bHLH11 "AT4G36060" [Arabidopsi	0.385	0.318	0.434	6e-16
UNIPROTKB|Q2R1K8	278	Os11g0601700 "Helix-loop-helix	0.398	0.338	0.4	3e-12
UNIPROTKB|Q69V10	265	P0506F02.119 "cDNA clone:J0230	0.419	0.373	0.366	3e-12

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

 Score = 699 (251.1 bits), Expect = 6.3e-69, P = 6.3e-69
 Identities = 147/239 (61%), Positives = 164/239 (68%)

Query:     1 MVSPENTNWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNG 60
             MVSPEN NW+ D  LID      G+F++   GF+W VQ PI   SN    +D + G+S  
Sbjct:     1 MVSPENANWICD--LID---ADYGSFTIQGPGFSWPVQQPIGVSSNSSAGVDGSAGNSEA 55

Query:    61 LXXXXXXXXXX-XXXXXXXXKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDA 119
                                 KACREK RRDRLNDKF+EL +ILEPG PPKTDKAAIL+DA
Sbjct:    56 SKEPGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGAILEPGNPPKTDKAAILVDA 115

Query:   120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST-Q 178
             VRMVTQLR EAQKLKDSNSSLQ+KIKELK EKNELRDEKQRLK EKEK+EQQLKAM+  Q
Sbjct:   116 VRMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQRLKTEKEKLEQQLKAMNAPQ 175

Query:   179 PSFLTXXXXXXXXXXXXXXXX-XNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
             PSF                    NK++P ISYPGVAMWQFMPPA+VDTSQDHVLRPPVA
Sbjct:   176 PSFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFMPPASVDTSQDHVLRPPVA 234

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

 Score = 464 (168.4 bits), Expect = 5.0e-44, P = 5.0e-44
 Identities = 104/241 (43%), Positives = 142/241 (58%)

Query:     8 NWLLDYPLIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCVEIDSAFGDSNGLXXXXXX 67
             +W LD  +++D+  P    + +   F W   P  + PS   VE+ S    ++ +      
Sbjct:    22 DWFLDCGILEDL--P----AAACGAFPWDASPSCSNPS---VEVSSYVNTTSYVLKEPGS 72

Query:    68 XXXXXXXXXX--XXKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQ 125
                           KA REK+RRD++ND+F+EL + LEPG+P K+DKAAIL DA RMV Q
Sbjct:    73 NKRVRSGSCGRPTSKASREKIRRDKMNDRFLELGTTLEPGKPVKSDKAAILSDATRMVIQ 132

Query:   126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLTXX 185
             LR+EA++LKD+N SL++KIKELKAEK+ELRDEKQ+LK EKE +EQQ+K ++  P+++   
Sbjct:   133 LRAEAKQLKDTNESLEDKIKELKAEKDELRDEKQKLKVEKETLEQQVKILTATPAYMPHP 192

Query:   186 XXXXX---------XXXXXXXXXXNKLM-PFISYPGVAMWQFMPPAAVDTSQDHVLRPPV 235
                                      KLM PF+ YPG  MWQFMPP+ VDTS+D    PPV
Sbjct:   193 TLMPAPYPQAPLAPFHHAQGQAAGQKLMMPFVGYPGYPMWQFMPPSEVDTSKDSEACPPV 252

Query:   236 A 236
             A
Sbjct:   253 A 253

GO:0005634 "nucleus" evidence=IC

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

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 92/204 (45%), Positives = 121/204 (59%)

Query:    44 PSNGCVEIDSAFGDSNGLXXXXXXXXXXXXXXXXX--XKACREKLRRDRLNDKFVELASI 101
             P +G + ID   GD+  L                    KACREK+RRDRLND+F+EL+S+
Sbjct:    33 PCDGGLGIDDVSGDTCCLDQSVLGKRGRDESSSSGPKSKACREKIRRDRLNDRFLELSSV 92

Query:   102 LEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRL 161
             + P +  K DKA IL DA R++ +LR EA+KLK+SN  L+E IK+LK EKNELRDEK  L
Sbjct:    93 INPDKQAKLDKANILSDAARLLAELRGEAEKLKESNEKLRETIKDLKVEKNELRDEKVTL 152

Query:   162 KAEKEKIEQQLKAMSTQPS-FLTXXXXXXXXXXXXX-------XXXXNKLMPF-ISYPGV 212
             KAEKE++EQQ+KA+S  P+ F+                         NK  P   ++ G+
Sbjct:   153 KAEKERLEQQVKALSVAPTGFVPHLPHPAAFHPAAFPPFIPPYQALGNKNAPTPAAFQGM 212

Query:   213 AMWQFMPPAAVDTSQDHVLRPPVA 236
             AMWQ++PP AVDT+QD  L PP A
Sbjct:   213 AMWQWLPPTAVDTTQDPKLWPPNA 236

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2129710 bHLH104 "AT4G14410" [Arabidopsis thaliana (taxid:3702)]

 Score = 395 (144.1 bits), Expect = 1.0e-36, P = 1.0e-36
 Identities = 84/157 (53%), Positives = 109/157 (69%)

Query:    80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
             KACRE+LRR++LN++F++L+S+LEPGR PKTDK AIL DA+R++ QLR EA KL+++N  
Sbjct:   135 KACRERLRREKLNERFMDLSSVLEPGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQK 194

Query:   140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLTXXXXXXXXXXXXXXXX 199
             L E+IK LKAEKNELR+EK  LKA+KEK EQQLK+M T PS                   
Sbjct:   195 LLEEIKSLKAEKNELREEKLVLKADKEKTEQQLKSM-TAPS-------SGFIPHIPAAFN 246

Query:   200 XNKLMPFISYPGVAMWQFMPPAAVDTSQDHVLRPPVA 236
              NK+  + SY  + MW +MP +  DTS+D  LRPP A
Sbjct:   247 HNKMAVYPSYGYMPMWHYMPQSVRDTSRDQELRPPAA 283

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

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

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 85/159 (53%), Positives = 108/159 (67%)

Query:    80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
             KACREKLRR++LNDKF++L+S+LEPGR PKTDK+AIL DA+R+V QLR EA +L+++N  
Sbjct:   167 KACREKLRREKLNDKFMDLSSVLEPGRTPKTDKSAILDDAIRVVNQLRGEAHELQETNQK 226

Query:   140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST-QPSFLTXXXXXXXXXXXXXXX 198
             L E+IK LKA+KNELR+EK  LKAEKEK+EQQLK+M    P F+                
Sbjct:   227 LLEEIKSLKADKNELREEKLVLKAEKEKMEQQLKSMVVPSPGFMPSQHPAAFHSHKMAVA 286

Query:   199 XXNKLMPFISYP-GVAMWQFMPPAAVDTSQDHVLRPPVA 236
                   P+  YP  + MW  +PPA  DTS+D    PPVA
Sbjct:   287 Y-----PYGYYPPNMPMWSPLPPADRDTSRDLKNLPPVA 320

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

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

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 50/92 (54%), Positives = 64/92 (69%)

Query:    80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
             KA REK+RRDRLN++F EL S L+P RP + DKA IL DA++M+  L S+  KLK   +S
Sbjct:    44 KADREKMRRDRLNEQFQELGSTLDPDRP-RNDKATILSDAIQMLKDLTSQVNKLKAEYTS 102

Query:   140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ 171
             L E+ +EL  EKNELRDEK  LK E + +  Q
Sbjct:   103 LSEEARELTQEKNELRDEKVSLKFEVDNLNTQ 134

GO:0005634 "nucleus" evidence=IC

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

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 49/101 (48%), Positives = 73/101 (72%)

Query:    80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
             KA REKLRR++LN+ FVEL ++L+P RP K DKA IL D V+++ +L SE  KLK   ++
Sbjct:    63 KAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVNKLKSEYTA 121

Query:   140 LQEKIKELKAEKNELRDEKQRLKAEKEKI----EQQLKAMS 176
             L ++ +EL  EKN+LR+EK  LK++ E +    +Q+L++MS
Sbjct:   122 LTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMS 162

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

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

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 40/92 (43%), Positives = 65/92 (70%)

Query:    80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
             KA REKLRRD+L ++F+EL + L+P RP K+DKA++L D ++M+  + ++  +LK    +
Sbjct:    49 KAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQVDRLKAEYET 107

Query:   140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ 171
             L ++ +EL  EK+ELR+EK  LK++ E +  Q
Sbjct:   108 LSQESRELIQEKSELREEKATLKSDIEILNAQ 139

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

 Score = 166 (63.5 bits), Expect = 3.0e-12, P = 3.0e-12
 Identities = 38/95 (40%), Positives = 63/95 (66%)

Query:    80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
             KA REKL+RD+LND FVEL+S+L+P R   + KA +L DA R++  L S+ + L+   S+
Sbjct:    51 KAEREKLKRDQLNDLFVELSSMLDPERQ-NSGKATVLGDAARVLRDLVSQVESLRKEQSA 109

Query:   140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
             L  + + + +E NEL++E   L+A+  ++  ++ A
Sbjct:   110 LLTERQYVGSENNELQEENIMLRAQILELHNEICA 144

GO:0005634 "nucleus" evidence=IC

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

 Score = 165 (63.1 bits), Expect = 3.0e-12, P = 3.0e-12
 Identities = 37/101 (36%), Positives = 60/101 (59%)

Query:    80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
             K+ REKL+RD+ ND F EL ++LEP R     KA +L +  R++  L S+ + L+  NSS
Sbjct:    40 KSEREKLKRDKQNDLFNELGNLLEPDRQ-NNGKACVLGETTRILKDLLSQVESLRKENSS 98

Query:   140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA-MSTQP 179
             L+ +   +  E+NEL D+   L+ E  +++ +L+  M   P
Sbjct:    99 LKNESHYVALERNELHDDNSMLRTEILELQNELRTRMEGNP 139

GO:0005634 "nucleus" evidence=IC

---

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)
Q9FH37	ILR3_ARATH	No assigned EC number	0.7154	0.9788	0.9871	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	236
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	7e-08
smart00353	53	smart00353, HLH, helix loop helix domain	8e-08
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	4e-07
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	1e-05
pfam07926	132	pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein	5e-05
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	9e-05
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	1e-04
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	2e-04
pfam06005	72	pfam06005, DUF904, Protein of unknown function (DU	3e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	4e-04
pfam06005	72	pfam06005, DUF904, Protein of unknown function (DU	4e-04
pfam13870	177	pfam13870, DUF4201, Domain of unknown function (DU	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	4e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	5e-04
COG2433	652	COG2433, COG2433, Uncharacterized conserved protei	5e-04
cd07596	218	cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) do	6e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	7e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	7e-04
pfam04111	356	pfam04111, APG6, Autophagy protein Apg6	7e-04
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
pfam07106	169	pfam07106, TBPIP, Tat binding protein 1(TBP-1)-int	0.001
COG4372	499	COG4372, COG4372, Uncharacterized protein conserve	0.001
pfam09744	158	pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated prot	0.001
PRK05771	646	PRK05771, PRK05771, V-type ATP synthase subunit I;	0.001
pfam12325	121	pfam12325, TMF_TATA_bd, TATA element modulatory fa	0.001
COG3074	79	COG3074, COG3074, Uncharacterized protein conserve	0.002
COG4026	290	COG4026, COG4026, Uncharacterized protein containi	0.002
TIGR02894	161	TIGR02894, DNA_bind_RsfA, transcription factor, Rs	0.002
smart00338	65	smart00338, BRLZ, basic region leucin zipper	0.002
cd12193	54	cd12193, B_zip1, basic leucine zipper DNA-binding	0.002
pfam01025	165	pfam01025, GrpE, GrpE	0.002
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	0.002
pfam10211	189	pfam10211, Ax_dynein_light, Axonemal dynein light	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.003
smart00787	312	smart00787, Spc7, Spc7 kinetochore protein	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	0.003
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.004
COG4026	290	COG4026, COG4026, Uncharacterized protein containi	0.004
pfam04977	80	pfam04977, DivIC, Septum formation initiator	0.004
pfam04977	80	pfam04977, DivIC, Septum formation initiator	0.004
pfam01496	707	pfam01496, V_ATPase_I, V-type ATPase 116kDa subuni	0.004

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

 Score = 47.5 bits (114), Expect = 7e-08
 Identities = 19/50 (38%), Positives = 26/50 (52%)

Query: 78  SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLR 127
            +   RE+ RRDR+ND F EL  +L      K  KA IL  A+  +  L+
Sbjct: 3   KAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

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

 Score = 47.2 bits (113), Expect = 8e-08
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 83  REKLRRDRLNDKFVELASILEPGRPP-KTDKAAILIDAVRMVTQLRSEAQK 132
           RE+ RR ++N+ F EL S+L       K  KA IL  A+  +  L+ E QK
Sbjct: 3   RERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

>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 = 45.7 bits (109), Expect = 4e-07
 Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 78  SSKACREKLRRDRLNDKFVELASIL-EPGRPPKTDKAAILIDAVRMVTQLRSEAQ 131
            +   RE+ RR+R+ND F EL S+L       K  KA IL  AV  +  L+   Q
Sbjct: 6   EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 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|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA binding

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 18/51 (35%), Positives = 27/51 (52%)

Query: 122 MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL 172
            + QL  E +KL          IK+L+A+  EL  E   LK + EK+E++L
Sbjct: 13  QIAQLMEEGEKLSKKELKHNNTIKKLRAKNKELEKEIAELKKKLEKLEKEL 63

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. 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. Length = 74

>gnl|CDD|149160 pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 14/69 (20%), Positives = 37/69 (53%), Gaps = 4/69 (5%)

Query: 118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRD----EKQRLKAEKEKIEQQLK 173
           + +  +  LR +  +LK   + L+ + +  +AE +E  +    +K+ L+ E  ++E++++
Sbjct: 56  EDIEELQALRKQLNELKKEIAQLKAEAESAQAELSEAEESWEEQKKMLEDELSELEKRIE 115

Query: 174 AMSTQPSFL 182
            ++ Q   L
Sbjct: 116 ELNEQNKLL 124

The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). 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 intra-nuclear 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. Length = 132

>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score = 42.5 bits (101), Expect = 9e-05
 Identities = 14/55 (25%), Positives = 35/55 (63%)

Query: 128 SEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFL 182
              + L++ NS L+E+I++L+ +  +L  E ++L+ E E+++ +L+ + + P  +
Sbjct: 1   ERLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIV 55

Length = 389

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

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 14/90 (15%)

Query: 83  REKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE 142
            E+ RRD+L +++ EL   LE              D    + ++  E  + +D     +E
Sbjct: 347 EERKRRDKLTEEYAELKEELE--------------DLRAELEEVDKEFAETRDELKDYRE 392

Query: 143 KIKELKAEKNELRDEKQRLKAEKEKIEQQL 172
           K+++LK E NEL+ E  RL+ E +++ ++L
Sbjct: 393 KLEKLKREINELKRELDRLQEELQRLSEEL 422

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

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

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 26/111 (23%), Positives = 61/111 (54%), Gaps = 5/111 (4%)

Query: 70  RSESCGSSSSKACREKLRR--DRLNDKFVELASILEPGRPPKT--DKAAILI-DAVRMVT 124
           R+   G   S++   +L+R  +RL     EL+S+    R  +   D+ +  + DA R + 
Sbjct: 660 RAPRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIG 719

Query: 125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
           ++  E ++L+     L+E+++EL+ + + L  E + +K+E +++E +++ +
Sbjct: 720 EIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEEL 770

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

>gnl|CDD|203371 pfam06005, DUF904, Protein of unknown function (DUF904)

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 16/50 (32%), Positives = 33/50 (66%)

Query: 125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
           +L S+ Q+  ++ + LQ +I+ELK E  +L +E + L+ E +K++++  A
Sbjct: 8   ELESKIQQAVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEERNA 57

This family consists of several bacterial and archaeal hypothetical proteins of unknown function. Length = 72

>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score = 40.6 bits (96), Expect = 4e-04
 Identities = 15/48 (31%), Positives = 29/48 (60%)

Query: 123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ 170
           +  L     +L++    L+ K+++L+AE  +L  E +RLK+E EK++ 
Sbjct: 3   LEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS 50

Length = 389

>gnl|CDD|203371 pfam06005, DUF904, Protein of unknown function (DUF904)

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 18/56 (32%), Positives = 34/56 (60%), Gaps = 4/56 (7%)

Query: 119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDE----KQRLKAEKEKIEQ 170
           AV  +  L+ E ++LK+ N  L E+ +EL+ E  +L++E    + RL+A   K+++
Sbjct: 16  AVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEERNAWQSRLRALLGKLDE 71

This family consists of several bacterial and archaeal hypothetical proteins of unknown function. Length = 72

>gnl|CDD|222426 pfam13870, DUF4201, Domain of unknown function (DUF4201)

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 16/59 (27%), Positives = 35/59 (59%)

Query: 120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
           V ++T L+ +   L++    L++++KE +    +LR E  ++K E++K+ +Q K +  Q
Sbjct: 76  VHILTHLKEKLHMLEEELERLKKELKEKEERLAKLRKELYKVKLERDKLRKQNKKLRQQ 134

This is a family of coiled-coil proteins from eukaryotes. The function is not known. Length = 177

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

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 80   KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSS 139
            +    + + +RL  +  EL   LE       +      +  R + +L  E + L   N  
Sbjct: 913  RLEELEAKLERLEVELPELEEELEEEYEDTLET-----ELEREIERLEEEIEALGPVNLR 967

Query: 140  LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
              E+ +E++    EL+ +++ L+  KEK+ + ++ +
Sbjct: 968  AIEEYEEVEERYEELKSQREDLEEAKEKLLEVIEEL 1003

Length = 1163

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

 Score = 40.5 bits (95), Expect = 5e-04
 Identities = 30/126 (23%), Positives = 60/126 (47%), Gaps = 23/126 (18%)

Query: 50  EIDSAFGDSNGLKESSKKRVRSESCGSSSSKACREKLRRD--RLNDKFVELASILEPGRP 107
            +     +     E +++R+ +      S +  RE+L ++   L ++  EL   L+    
Sbjct: 790 ALQEELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEELEEKLD---- 845

Query: 108 PKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEK 167
                            +L  E ++L+     L+E+++EL+AEK EL DE + L+ EKE+
Sbjct: 846 -----------------ELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEE 888

Query: 168 IEQQLK 173
           +E++L+
Sbjct: 889 LEEELR 894

Length = 1163

>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function unknown]

 Score = 40.5 bits (95), Expect = 5e-04
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 96  VELASILEPGRPPKTDKAAI-LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNEL 154
                     +    ++    +    + + +L    ++L++ NS L+ +++ELK E  +L
Sbjct: 396 KVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKL 455

Query: 155 RDEKQRLKAE---KEKIEQQLKAM 175
             E +R + E   K + +++++A 
Sbjct: 456 ESELERFRREVRDKVRKDREIRAR 479

Length = 652

>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins

 Score = 39.6 bits (93), Expect = 6e-04
 Identities = 13/59 (22%), Positives = 28/59 (47%)

Query: 116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
           L    + +   +++ +KLK +      K++EL+ E  E     +  +   E+I ++LK 
Sbjct: 119 LQSLKKDLASKKAQLEKLKAAPGIKPAKVEELEEELEEAESALEEARKRYEEISERLKE 177

BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. Length = 218

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

 Score = 40.1 bits (94), Expect = 7e-04
 Identities = 14/50 (28%), Positives = 32/50 (64%)

Query: 125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
            L    ++L+     L+E+I+EL+ + +EL +E + L+ E E+++++L+ 
Sbjct: 818 SLEQRRERLEQEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEE 867

Length = 1163

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

 Score = 39.2 bits (92), Expect = 7e-04
 Identities = 17/48 (35%), Positives = 33/48 (68%)

Query: 125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL 172
           +L+ E  +L++  + LQE++ EL+ E  EL+ E   L+AE E+++++L
Sbjct: 70  ELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKEL 117

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

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

 Score = 39.9 bits (93), Expect = 7e-04
 Identities = 16/49 (32%), Positives = 28/49 (57%)

Query: 123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ 171
              L SE  +LK     L ++++EL+ E ++L  E   L+ EKE++E +
Sbjct: 65  YEALDSELDELKKEEERLLDELEELEKEDDDLDGELVELQEEKEQLENE 113

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

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

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 21/89 (23%), Positives = 47/89 (52%)

Query: 85  KLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKI 144
           + + + L  +   L   LE  +    +    L +    + +L+   ++L++   SL+E +
Sbjct: 715 ERQLEELKRELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEAL 774

Query: 145 KELKAEKNELRDEKQRLKAEKEKIEQQLK 173
            +LK E  EL +++Q L+ E E++E++L+
Sbjct: 775 AKLKEEIEELEEKRQALQEELEELEEELE 803

Length = 1163

>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein (TBPIP)

 Score = 38.4 bits (90), Expect = 0.001
 Identities = 20/54 (37%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 123 VTQLRSEAQKLKDSNSSLQEKIKELKAE--KNELRDEKQRLKAEKEKIEQQLKA 174
           + +LR E Q LK   S+L+ ++K L ++    EL++E Q LK E  +IE++L++
Sbjct: 81  IEELREEVQLLKQDCSTLEIELKSLTSDLTTEELQEEIQELKKEVREIEEKLES 134

This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. 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. Length = 169

>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 15/56 (26%), Positives = 31/56 (55%)

Query: 123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
           +  L  + ++L+    SLQ   K+L+A   +L+ +   LK    +IEQ+ + ++T+
Sbjct: 153 LKTLAEQRRQLEAQAQSLQASQKQLQASATQLKSQVLDLKLRSAQIEQEAQNLATR 208

Length = 499

>gnl|CDD|150420 pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated protein-1

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 31/95 (32%), Positives = 45/95 (47%), Gaps = 4/95 (4%)

Query: 78  SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSN 137
           S++  REK  R +   K +E    LE     K +    + D    V QL  +A+ L D  
Sbjct: 63  STQYEREKELRKQAEQKLLEFEDELEQ---EKKELQKKIEDLEENVRQLELKAKNLSDQV 119

Query: 138 SSLQEKIKELKAEKNELRD-EKQRLKAEKEKIEQQ 171
           S L+E+  ELK E N L +   + LK   E +E+Q
Sbjct: 120 SRLEERETELKKEYNSLHERYTKLLKNYVEYVERQ 154

This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end. Length = 158

>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated

 Score = 39.1 bits (92), Expect = 0.001
 Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 12/90 (13%)

Query: 84  EKLRRDR--LNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSE--AQKLKDSNSS 139
            KLR     L++   +L S L         K   L +  + V+    E   + +++    
Sbjct: 46  RKLRSLLTKLSEALDKLRSYLP--------KLNPLREEKKKVSVKSLEELIKDVEEELEK 97

Query: 140 LQEKIKELKAEKNELRDEKQRLKAEKEKIE 169
           ++++IKEL+ E +EL +E + L+ E E++E
Sbjct: 98  IEKEIKELEEEISELENEIKELEQEIERLE 127

Length = 646

>gnl|CDD|192987 pfam12325, TMF_TATA_bd, TATA element modulatory factor 1 TATA binding

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 20/71 (28%)

Query: 121 RMVTQLR---SEAQKLKDSNSSLQEKIKELKAEKNELRDE----------KQRLKAEKEK 167
           R+ + LR    E   LKD  + L+       AE++E R E           + LK E E+
Sbjct: 21  RLSSTLRRLEGELASLKDELARLE-------AERDEARQEIVKLTEENEELRELKKEIEE 73

Query: 168 IEQQLKAMSTQ 178
           +E++L+ +  +
Sbjct: 74  LEKELEDLEQR 84

This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. 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. Length = 121

>gnl|CDD|225616 COG3074, COG3074, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 16/57 (28%), Positives = 38/57 (66%)

Query: 119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
           A+  +T L+ E ++LK+ N+SL ++++  + ++  L  E ++LK E+   +++L+A+
Sbjct: 16  AIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQERLRAL 72

Length = 79

>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

 Score = 38.4 bits (89), Expect = 0.002
 Identities = 22/71 (30%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 112 KAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ 171
           K A++   ++ + ++      LK+    L+EK++EL+ EK EL  E + L+AE E+++++
Sbjct: 113 KNALVRAGLKTLQRVPEYMD-LKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQER 171

Query: 172 LKAMSTQPSFL 182
           LK +  + S L
Sbjct: 172 LKRLEVENSRL 182

Length = 290

>gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 7/53 (13%)

Query: 123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
              L+ E ++LK+ N SLQ++ +       EL  E ++L+     IE+  + +
Sbjct: 99  DQALQKENERLKNQNESLQKRNE-------ELEKELEKLRQRLSTIEEDYQTL 144

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 [Regulatory functions, DNA interactions, Cellular processes, Sporulation and germination]. Length = 161

>gnl|CDD|197664 smart00338, BRLZ, basic region leucin zipper

 Score = 35.2 bits (82), Expect = 0.002
 Identities = 13/35 (37%), Positives = 25/35 (71%)

Query: 140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
           L+ K+++L+AE   L+ E +RL+ E EK++ +L+ 
Sbjct: 31  LERKVEQLEAENERLKKEIERLRRELEKLKSELEE 65

Length = 65

>gnl|CDD|213400 cd12193, B_zip1, basic leucine zipper DNA-binding and multimerization region of GCN4 and related proteins

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAE 164
            R    +  +    L++K++EL +E ++L DE  RLK  
Sbjct: 14  ARRSRARKMERMKQLEDKVEELTSENSDLEDEVDRLKKA 52

Basic leucine zipper (bZIP) transcription factors act in networks of homo- and hetero-dimers in the regulation in a diverse set of cellular pathways. Classical leucine zippers have alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization creates a pair of basic regions that bind DNA and undergo conformational change. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region. Length = 54

>gnl|CDD|216249 pfam01025, GrpE, GrpE

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 16/45 (35%), Positives = 29/45 (64%)

Query: 129 EAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK 173
           E ++L+D   +L+E+++EL+ E  EL+D   RL AE E   ++ +
Sbjct: 5   EEEELEDEEEALEEELEELEEEIEELKDRLLRLLAEFENYRKRTE 49

Length = 165

>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 14/36 (38%), Positives = 24/36 (66%)

Query: 138 SSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK 173
           S L+++IK+L+ EK EL      L+A+ E IE++ +
Sbjct: 123 SELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREE 158

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. 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. Length = 189

>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain

 Score = 37.6 bits (88), Expect = 0.002
 Identities = 15/67 (22%), Positives = 37/67 (55%), Gaps = 15/67 (22%)

Query: 124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNEL--RDEKQR-------------LKAEKEKI 168
           ++L  E +KL++    L++++ EL+A+   +  R+E++R             LK + +++
Sbjct: 123 SELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADEIAFLKKQNQQL 182

Query: 169 EQQLKAM 175
           + QL+ +
Sbjct: 183 KSQLEQI 189

Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. 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. Length = 189

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

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 16/67 (23%), Positives = 35/67 (52%)

Query: 110 TDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIE 169
              +A+L +   +   LR E  +L+   + ++ +++ELK E   L +  +RL    E ++
Sbjct: 365 EKLSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLK 424

Query: 170 QQLKAMS 176
           ++LK + 
Sbjct: 425 EELKELE 431

Length = 1163

>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein

 Score = 38.1 bits (89), Expect = 0.003
 Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQR-LKAEKEKIEQQLK 173
           +  L S   KL+D   +L+E++++LK  ++EL D     L   KEK+++ L+
Sbjct: 167 LELLNSIKPKLRDRKDALEEELRQLKQLEDELEDCDPTELDRAKEKLKKLLQ 218

This domain is found in cell division proteins which are required for kinetochore-spindle association. Length = 312

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

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 21/121 (17%), Positives = 48/121 (39%), Gaps = 6/121 (4%)

Query: 62  KESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVR 121
            E   K ++         +    +   + L ++  EL    E     K     I    + 
Sbjct: 208 LEEELKELKKLEEIQEEQEEEELEQEIEALEERLAELEEEKERLEELKARLLEIESLELE 267

Query: 122 MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLK------AEKEKIEQQLKAM 175
            +     E ++L+     L+EKI+ L+  + E+ + ++ L+       E E++ ++LK++
Sbjct: 268 ALKIREEELRELERLLEELEEKIERLEELEREIEELEEELEGLRALLEELEELLEKLKSL 327

Query: 176 S 176
            
Sbjct: 328 E 328

Length = 908

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

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 4/93 (4%)

Query: 83  REKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE 142
            +  R + L  +  EL   LE G     ++   L++ ++    L    +KL++    L+ 
Sbjct: 288 EKIERLEELEREIEELEEELE-GLRALLEELEELLEKLK---SLEERLEKLEEKLEKLES 343

Query: 143 KIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
           +++EL  EKNEL    +    E E+  ++L+  
Sbjct: 344 ELEELAEEKNELAKLLEERLKELEERLEELEKE 376

Length = 908

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

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 16/60 (26%), Positives = 33/60 (55%)

Query: 114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK 173
           A L +  + + +L  E + L+     LQE+  +LK +   +  E + L  +KE++E++L+
Sbjct: 812 ARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELE 871

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

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

 Score = 37.8 bits (88), Expect = 0.004
 Identities = 21/89 (23%), Positives = 44/89 (49%)

Query: 85  KLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKI 144
           +   + L  +  EL   LE     K +    L +      +L  E ++L+   + L+E+I
Sbjct: 848 EEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEI 907

Query: 145 KELKAEKNELRDEKQRLKAEKEKIEQQLK 173
           ++L+    EL  + +RL+ E  ++E++L+
Sbjct: 908 EKLRERLEELEAKLERLEVELPELEEELE 936

Length = 1163

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

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 125 QLRSEAQKLKDSNSSLQ---EKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
           +L+ E   L+     LQ    +IK+L A   EL +E + L+ E  +++Q+ +A+  +
Sbjct: 98  ELKQELSTLEAELERLQKELARIKQLSANAIELDEENRELREELAELKQENEALEAE 154

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

>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

 Score = 37.6 bits (87), Expect = 0.004
 Identities = 15/58 (25%), Positives = 35/58 (60%)

Query: 116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK 173
            +D      +L+ + ++L+     L ++++EL+AE  E+++  +RL+ E  ++E+ LK
Sbjct: 130 YMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLK 187

Length = 290

>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 10/37 (27%), Positives = 20/37 (54%)

Query: 125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRL 161
           QL  E   L+   + L+ + +EL+AE  +L+ +   +
Sbjct: 21  QLNQEIAALQAELAKLKAENEELEAEVKDLKSDPDYI 57

DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil. Length = 80

>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 113 AAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ 171
                  +  V  L S   +L    ++LQ ++ +LKAE  EL  E + LK++ + IE++
Sbjct: 3   LLFQYLLIFGVNGL-SAYYQLNQEIAALQAELAKLKAENEELEAEVKDLKSDPDYIEER 60

DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil. Length = 80

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

 Score = 37.7 bits (88), Expect = 0.004
 Identities = 21/114 (18%), Positives = 36/114 (31%), Gaps = 19/114 (16%)

Query: 84  EKLRR--DRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLK------- 134
           E   R   R    ++  A I EP   PK     I       + +++              
Sbjct: 155 EAFERELWRACRGYIRQAEIEEPLEDPKKTVFIIFFVGKEDLDKVKKILDSFGFELYDVP 214

Query: 135 -------DSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSF 181
                  +  S + ++I+EL+    +       L+    KI  +L A   Q S 
Sbjct: 215 ETEGERSELISKVNKRIEELQRVLEQTESH---LEKVLVKIADELLAWDEQVSK 265

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	236
KOG1318	411	consensus Helix loop helix transcription factor EB	99.35
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.34
smart00353	53	HLH helix loop helix domain.	99.33
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.31
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.84
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.35
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.35
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.32
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.02
KOG0561	373	consensus bHLH transcription factor [Transcription	97.97
PRK15422	79	septal ring assembly protein ZapB; Provisional	97.67
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	97.46
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.28
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.15
KOG3910	632	consensus Helix loop helix transcription factor [T	97.14
PLN03217	93	transcription factor ATBS1; Provisional	97.1
KOG4029	228	consensus Transcription factor HAND2/Transcription	96.91
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	96.68
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.59
smart00338	65	BRLZ basic region leucin zipper.	95.45
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	95.39
PRK15422	79	septal ring assembly protein ZapB; Provisional	95.36
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	95.33
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	95.31
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	95.2
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	95.18
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	94.66
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	94.55
PRK13169	110	DNA replication intiation control protein YabA; Re	94.44
PRK10884	206	SH3 domain-containing protein; Provisional	94.19
COG4026	290	Uncharacterized protein containing TOPRIM domain,	94.15
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.92
PRK10884	206	SH3 domain-containing protein; Provisional	93.88
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	93.85
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	93.84
PRK11637	428	AmiB activator; Provisional	93.7
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	93.62
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	93.62
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	93.6
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.48
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	93.27
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	93.22
PRK13169	110	DNA replication intiation control protein YabA; Re	93.14
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	93.02
PRK04406	75	hypothetical protein; Provisional	93.01
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	92.94
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	92.9
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	92.9
PRK02119	73	hypothetical protein; Provisional	92.81
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	92.8
PHA02562	562	46 endonuclease subunit; Provisional	92.73
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	92.62
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	92.58
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	92.58
PRK04325	74	hypothetical protein; Provisional	92.54
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	92.29
PRK00846	77	hypothetical protein; Provisional	92.0
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	91.98
PRK00295	68	hypothetical protein; Provisional	91.88
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	91.86
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	91.71
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	91.61
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	91.49
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	91.47
PRK11637	428	AmiB activator; Provisional	91.34
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	91.26
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	91.13
PRK02793	72	phi X174 lysis protein; Provisional	91.12
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	90.89
PF14662	193	CCDC155: Coiled-coil region of CCDC155	90.73
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	90.72
TIGR02231	525	conserved hypothetical protein. This family consis	90.71
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	90.69
PHA03011	120	hypothetical protein; Provisional	90.44
KOG0996	1293	consensus Structural maintenance of chromosome pro	90.26
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	90.24
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	90.24
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	90.18
COG4467	114	Regulator of replication initiation timing [Replic	90.13
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	89.94
KOG1962	216	consensus B-cell receptor-associated protein and r	89.81
PRK00736	68	hypothetical protein; Provisional	89.71
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	89.64
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	89.59
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	89.52
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	89.51
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	89.47
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	89.39
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	89.34
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	89.23
PHA02562	562	46 endonuclease subunit; Provisional	89.04
PF04420	161	CHD5: CHD5-like protein; InterPro: IPR007514 Membe	88.96
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	88.95
PRK13922	276	rod shape-determining protein MreC; Provisional	88.87
COG5570	57	Uncharacterized small protein [Function unknown]	88.78
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	88.38
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	88.38
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	88.34
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	88.21
PF10186	302	Atg14: UV radiation resistance protein and autopha	87.96
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	87.91
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	87.66
PF10498	359	IFT57: Intra-flagellar transport protein 57 ; Inte	87.65
PRK00888	105	ftsB cell division protein FtsB; Reviewed	87.59
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	87.33
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	87.31
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	87.29
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	87.22
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	87.19
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	87.02
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	87.0
smart00338	65	BRLZ basic region leucin zipper.	86.98
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	86.93
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	86.89
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	86.81
KOG4797	123	consensus Transcriptional regulator [Transcription	86.76
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	86.74
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	86.72
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	86.5
PRK09039	343	hypothetical protein; Validated	86.45
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	86.36
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	86.24
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	86.14
PF14662	193	CCDC155: Coiled-coil region of CCDC155	86.01
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	85.7
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	85.67
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	85.65
KOG3650	120	consensus Predicted coiled-coil protein [General f	85.61
PRK09039	343	hypothetical protein; Validated	85.39
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	85.1
PF10186	302	Atg14: UV radiation resistance protein and autopha	85.07
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	85.02
KOG4603	201	consensus TBP-1 interacting protein [Signal transd	84.99
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	84.88
KOG3584	348	consensus cAMP response element binding protein an	84.87
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	84.67
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	84.67
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	84.54
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	84.26
PF00038	312	Filament: Intermediate filament protein; InterPro:	84.08
COG0216	363	PrfA Protein chain release factor A [Translation,	84.05
COG4026	290	Uncharacterized protein containing TOPRIM domain,	83.92
KOG3119	269	consensus Basic region leucine zipper transcriptio	83.77
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	83.65
PF04325	49	DUF465: Protein of unknown function (DUF465); Inte	83.61
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	83.57
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	83.57
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	83.55
COG2433	652	Uncharacterized conserved protein [Function unknow	83.42
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	83.39
COG3937	108	Uncharacterized conserved protein [Function unknow	83.37
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	83.27
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	83.23
COG4942	420	Membrane-bound metallopeptidase [Cell division and	82.9
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	82.81
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	82.8
COG1256	552	FlgK Flagellar hook-associated protein [Cell motil	82.7
PF10482	120	CtIP_N: Tumour-suppressor protein CtIP N-terminal	82.56
KOG3433	203	consensus Protein involved in meiotic recombinatio	82.52
PF14282	106	FlxA: FlxA-like protein	82.25
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	81.84
KOG4571	294	consensus Activating transcription factor 4 [Trans	81.7
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	81.7
TIGR01554	378	major_cap_HK97 phage major capsid protein, HK97 fa	81.63
KOG3647	338	consensus Predicted coiled-coil protein [General f	81.39
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	81.36
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	81.36
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	81.33
PF14282	106	FlxA: FlxA-like protein	81.26
COG2433	652	Uncharacterized conserved protein [Function unknow	81.14
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	81.09
PF05377	55	FlaC_arch: Flagella accessory protein C (FlaC); In	81.06
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	80.73
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	80.69
PRK13922	276	rod shape-determining protein MreC; Provisional	80.68
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	80.65
PRK02224	880	chromosome segregation protein; Provisional	80.48
PRK00888	105	ftsB cell division protein FtsB; Reviewed	80.42
PRK05771	646	V-type ATP synthase subunit I; Validated	80.39
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	80.33
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	80.27
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	80.22
PF15294	278	Leu_zip: Leucine zipper	80.19
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	80.17
PRK14127	109	cell division protein GpsB; Provisional	80.03
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	80.03

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

Probab=99.35  E-value=5.7e-12  Score=120.39  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=63.9

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC---CCCCchhhhHHHHHHHHHHHHHHHHHHH---HhhhhHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR---PPKTDKAAILIDAVRMVTQLRSEAQKLK---DSNSSLQEKIKELKAEK  151 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~---~~K~DKAsIL~dAI~ylkqLr~qv~~Lk---~~n~~L~eeik~Lk~Ek  151 (236)
                      -.|++.|||||++||+|+.+|+.|| |.+   ..|..|.+||..+++||+.|++.-++..   ..-..|+..++.|...+
T Consensus       235 d~HNeVERRRR~nIN~~IkeLg~li-P~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~ri  313 (411)
T KOG1318|consen  235 DNHNEVERRRRENINDRIKELGQLI-PKCNSEDMKSNKGTILKASCDYIRELQQTLQRARELENRQKKLESTNQELALRI  313 (411)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHhC-CCCCcchhhcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHHH
Confidence            5799999999999999999999999 876   2378899999999999999999766433   33445666666666666


Q ss_pred             HHHHHHHH
Q 026599          152 NELRDEKQ  159 (236)
Q Consensus       152 nELrdEk~  159 (236)
                      .||..+..
T Consensus       314 eeLk~~~~  321 (411)
T KOG1318|consen  314 EELKSEAG  321 (411)
T ss_pred             HHHHHHHH
Confidence            66655444

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

Probab=99.34  E-value=2.1e-12  Score=89.70  Aligned_cols=52  Identities=40%  Similarity=0.547  Sum_probs=47.6

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      ..|+.+||.||++||+.|.+|+.+| |..  ..|+||++||..||+||+.|+.++
T Consensus         6 ~~~~~~Er~RR~~~n~~~~~L~~ll-p~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           6 EAHNLRERRRRERINDAFDELRSLL-PTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4699999999999999999999999 654  379999999999999999999875

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

>smart00353 HLH helix loop helix domain

Probab=99.33  E-value=3e-12  Score=87.60  Aligned_cols=50  Identities=40%  Similarity=0.548  Sum_probs=44.7

Q ss_pred             hhHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHH
Q 026599           81 ACREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEAQ  131 (236)
Q Consensus        81 a~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv~  131 (236)
                      +.+||+||++||+.|..|+++| |..  ..|+||++||..||+||+.|+.+++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~li-p~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLL-PTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            3689999999999999999999 531  3699999999999999999998875

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

Probab=99.31  E-value=2.9e-12  Score=89.14  Aligned_cols=49  Identities=41%  Similarity=0.551  Sum_probs=44.2

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCCC---CCCCCchhhhHHHHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEPG---RPPKTDKAAILIDAVRMVTQLR  127 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P~---~~~K~DKAsIL~dAI~ylkqLr  127 (236)
                      .|+.+||+||++||+.|.+|+.+|++.   ...|++|++||..||+||++||
T Consensus         4 ~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    4 KHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            589999999999999999999999443   2469999999999999999986

; 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 ....

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.84  E-value=7.8e-09  Score=91.18  Aligned_cols=76  Identities=25%  Similarity=0.384  Sum_probs=69.0

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCCCCCC------CCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEPGRPP------KTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKN  152 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P~~~~------K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn  152 (236)
                      .|...|++|||-||..+..|..|| |.|++      |+.||.||..+|+||.+|..+..+-+++...|+.+...|+.-++
T Consensus        65 aHtqaEqkRRdAIk~GYddLq~Lv-P~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL~iIk~  143 (229)
T KOG1319|consen   65 AHTQAEQKRRDAIKRGYDDLQTLV-PTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTALKIIKV  143 (229)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHhc-cccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            588999999999999999999999 86532      88999999999999999999999999999999999888888887


Q ss_pred             HHH
Q 026599          153 ELR  155 (236)
Q Consensus       153 ELr  155 (236)
                      +..
T Consensus       144 ~YE  146 (229)
T KOG1319|consen  144 NYE  146 (229)
T ss_pred             HHH
Confidence            754

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

Probab=98.35  E-value=2.5e-06  Score=76.73  Aligned_cols=78  Identities=24%  Similarity=0.294  Sum_probs=57.9

Q ss_pred             CCCCcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCc--hhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 026599           75 GSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTD--KAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKN  152 (236)
Q Consensus        75 ~~~~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~D--KAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn  152 (236)
                      +...+|+.-||+||++|.+.|..|+..| |..+..++  -++||..|++||+.|+.+........+.|..+-..|+.+.+
T Consensus        58 ~~R~~HN~LEk~RRahlk~~~~~Lk~~v-P~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~rl~  136 (232)
T KOG2483|consen   58 SSRAHHNALEKRRRAHLKDCFESLKDSV-PLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSRENRKLKARLE  136 (232)
T ss_pred             cchhhhhhhhHHHHHHHHHHHHHHHHhC-CCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567899999999999999999999999 54334443  58999999999999888777666655555444444444444


Q ss_pred             H
Q 026599          153 E  153 (236)
Q Consensus       153 E  153 (236)
                      +
T Consensus       137 q  137 (232)
T KOG2483|consen  137 Q  137 (232)
T ss_pred             H
Confidence            3

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

Probab=98.35  E-value=2.4e-07  Score=83.75  Aligned_cols=55  Identities=35%  Similarity=0.393  Sum_probs=47.4

Q ss_pred             CCcchhHHHHHHHHHHHhHHHHhhhcCCCC-------CCCCchhhhHHHHHHHHHHHHHHHHH
Q 026599           77 SSSKACREKLRRDRLNDKFVELASILEPGR-------PPKTDKAAILIDAVRMVTQLRSEAQK  132 (236)
Q Consensus        77 ~~~ka~rER~RRdkLNerF~eL~slL~P~~-------~~K~DKAsIL~dAI~ylkqLr~qv~~  132 (236)
                      +..|-.-||+||+|||+-+.+|+.|| +..       .+|++||-||.-|++||++|+...+.
T Consensus        33 k~~Kpl~EKkRRaRIN~~L~eLK~Li-~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   33 KVRKPLLEKKRRARINRCLDELKDLI-PEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             hhcchhHHHHHHHHHHHHHHHHHHHH-HHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            34577899999999999999999999 742       26999999999999999999986443

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

Probab=98.32  E-value=7.6e-07  Score=91.45  Aligned_cols=51  Identities=29%  Similarity=0.440  Sum_probs=47.1

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCC---CCCchhhhHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRP---PKTDKAAILIDAVRMVTQLRSE  129 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~---~K~DKAsIL~dAI~ylkqLr~q  129 (236)
                      ..|+..||||||++|.-+.||++|| |.+.   -|+||-+||..||..|+.+++.
T Consensus        22 e~~~~~EKrRRdq~N~yI~ELs~Mv-p~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   22 ENRSEIEKRRRDQMNKYIEELSEMV-PTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHhh-hcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            4688999999999999999999999 9864   5999999999999999999985

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.02  E-value=5.7e-06  Score=86.01  Aligned_cols=77  Identities=32%  Similarity=0.452  Sum_probs=68.8

Q ss_pred             ccccccCCCCCCCCCcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHH
Q 026599           64 SSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE  142 (236)
Q Consensus        64 ~~rKR~R~~s~~~~~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~e  142 (236)
                      .+.+|...+ ......|+.-|||=|--|||++.+|+.+| |+.+.|+.|.+.|..||+|+++|+...+.|+.++..++.
T Consensus       265 ~Pi~rl~~G-~~kRtAHN~IEKRYRsSINDKI~eLk~lV-~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~t  341 (953)
T KOG2588|consen  265 KPIKRLLPG-GEKRTAHNIIEKRYRSSINDKIIELKDLV-PGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLRT  341 (953)
T ss_pred             CchhhcCCC-CcccchhhHHHHHhhcchhHHHHHHHHhc-CccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhhh
Confidence            477776655 45677899999999999999999999999 877789999999999999999999999999999988874

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.97  E-value=7.8e-06  Score=76.70  Aligned_cols=63  Identities=29%  Similarity=0.407  Sum_probs=53.8

Q ss_pred             chhHHHHHHHHHHHhHHHHhhhcCCCCC-CCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Q 026599           80 KACREKLRRDRLNDKFVELASILEPGRP-PKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEK  143 (236)
Q Consensus        80 ka~rER~RRdkLNerF~eL~slL~P~~~-~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~ee  143 (236)
                      -++-||||=.-||..|..|++|| |-.. -|+.||+||..+.+||.+|..+.-+|-.+|.+|..-
T Consensus        64 ANsNERRRMQSINAGFqsLr~Ll-Pr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~elKr~  127 (373)
T KOG0561|consen   64 ANSNERRRMQSINAGFQSLRALL-PRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNGELKRL  127 (373)
T ss_pred             hcchHHHHHHhhhHHHHHHHHhc-CcccchhhHHHHHHHHHHHHHHHHHhcccccccccchHHHH
Confidence            34679999999999999999999 8542 399999999999999999999988888777765443

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=97.67  E-value=0.00039  Score=53.76  Aligned_cols=60  Identities=27%  Similarity=0.506  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +..||+-|.=|+-++++||+.|..|.+++..++..+.+|++||..||.|-..++..|.++
T Consensus        13 IqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~WqerLr~L   72 (79)
T PRK15422         13 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999999999999999999999999884

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.46  E-value=0.0012  Score=50.63  Aligned_cols=60  Identities=27%  Similarity=0.514  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +..||+-|.-|+-++++|++.|.+|..+..++......|+.||..||.|-..++..|+++
T Consensus        13 iqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQerlrsL   72 (79)
T COG3074          13 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQERLRAL   72 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999999999999999999999999984

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

Probab=97.28  E-value=0.0006  Score=62.76  Aligned_cols=56  Identities=23%  Similarity=0.337  Sum_probs=43.4

Q ss_pred             chhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHH
Q 026599           80 KACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKD  135 (236)
Q Consensus        80 ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~  135 (236)
                      -..|||||=.|+||-|..|+.---++-.+.+-|+-||-.||+||..|+.=.+++.+
T Consensus       122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~  177 (284)
T KOG3960|consen  122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQ  177 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34689999999999999997543233224899999999999999988775554443

>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=97.15  E-value=0.0043  Score=46.86  Aligned_cols=55  Identities=29%  Similarity=0.500  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKN-------ELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn-------ELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ++.+.+|..+|+.+-+.+..|+.++.+|+.+.+       +|++||..|+.+...++..|++
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~~   64 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLRS   64 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666665555555555555555544       4444444555554444444444

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.14  E-value=0.0011  Score=65.81  Aligned_cols=56  Identities=30%  Similarity=0.404  Sum_probs=42.8

Q ss_pred             CCcchhHHHHHH-----------HHHHHhHHHHhhhcCCC--CCCCCchhhhHHHHHHHHHHHHHHHHH
Q 026599           77 SSSKACREKLRR-----------DRLNDKFVELASILEPG--RPPKTDKAAILIDAVRMVTQLRSEAQK  132 (236)
Q Consensus        77 ~~~ka~rER~RR-----------dkLNerF~eL~slL~P~--~~~K~DKAsIL~dAI~ylkqLr~qv~~  132 (236)
                      +..|++|||.||           ..||+-|.||+.|.---  .....-|-.||..|+.+|..|++||.+
T Consensus       516 peqkaeREkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  516 PEQKAEREKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             hhhhhhHHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            556677666655           56999999999997221  123567899999999999999998864

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.10  E-value=0.0014  Score=51.79  Aligned_cols=58  Identities=26%  Similarity=0.458  Sum_probs=47.3

Q ss_pred             HHHHHHHHHhHHHHhhhcCCCC-----CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Q 026599           85 KLRRDRLNDKFVELASILEPGR-----PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEK  143 (236)
Q Consensus        85 R~RRdkLNerF~eL~slL~P~~-----~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~ee  143 (236)
                      |.--|.|||....|+.+| |..     ..|..-+-+|.+|+.||+.|+.+|..|.+...+|.+.
T Consensus        16 risddqi~dLvsKLq~ll-Pe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         16 RISEDQINDLIIKLQQLL-PELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             CCCHHHHHHHHHHHHHHC-hHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            334588999999999999 752     1355566799999999999999999999988877653

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

Probab=96.91  E-value=0.00096  Score=58.73  Aligned_cols=59  Identities=22%  Similarity=0.268  Sum_probs=48.7

Q ss_pred             CCcchhHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHH
Q 026599           77 SSSKACREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEAQKLKD  135 (236)
Q Consensus        77 ~~~ka~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~  135 (236)
                      ....+.|||.|=..+|..|.+||..|++.-  +.|..|+.+|--||+||+.|..-.+.-+.
T Consensus       110 ~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~  170 (228)
T KOG4029|consen  110 RQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA  170 (228)
T ss_pred             hhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence            355677899999999999999999994432  45999999999999999998876555443

>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=96.68  E-value=0.015  Score=43.97  Aligned_cols=58  Identities=28%  Similarity=0.464  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +..||+-|.-|+.++++|+++|..|.++...|+.+-..|++|-...+..+..|=..|+
T Consensus        13 i~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~~LL~kl~   70 (72)
T PF06005_consen   13 IQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLRSLLGKLE   70 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3578999999999999999999999999999999999999888877766665544443

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=96.59  E-value=0.014  Score=50.44  Aligned_cols=60  Identities=23%  Similarity=0.458  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          116 LIDAVRMVTQLRSE---AQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       116 L~dAI~ylkqLr~q---v~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      |.+.|.||..|+..   .+.++.+|..|+.++..|+.+..+|..|+..|+.+..-++..+++|
T Consensus        82 l~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L  144 (161)
T TIGR02894        82 LQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTL  144 (161)
T ss_pred             HHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999974   7788899999999999999998899999999999999999888874

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.

>smart00338 BRLZ basic region leucin zipper

Probab=95.45  E-value=0.047  Score=39.23  Aligned_cols=39  Identities=23%  Similarity=0.428  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEK  158 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk  158 (236)
                      -.|+.+|+.+++.|+.+|..|..++..|..|...|++++
T Consensus        25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       25 KAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            348888888888888888888887777777777666544

>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=95.39  E-value=0.064  Score=44.97  Aligned_cols=55  Identities=33%  Similarity=0.561  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEK--NELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~Ek--nELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      |.+|++++..|+.++..|..+++.|....  .||+++...|+.+++.++..|+.+..
T Consensus        81 i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~  137 (169)
T PF07106_consen   81 IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS  137 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            89999999999999999999999998887  48999999999999999999998754

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 [].

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=95.36  E-value=0.12  Score=40.16  Aligned_cols=52  Identities=29%  Similarity=0.460  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      .+++.+|.++|+..-+.+.-|+.||.+||...+.|.+|...++...+.|+++
T Consensus         3 ~EvleqLE~KIqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~e   54 (79)
T PRK15422          3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERE   54 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            4688999999999999999999999999998889988877754444444443

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=95.33  E-value=0.14  Score=52.47  Aligned_cols=95  Identities=28%  Similarity=0.369  Sum_probs=71.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-h-CCC-CCCCC---CCCC
Q 026599          115 ILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM-S-TQP-SFLTP---PPAI  188 (236)
Q Consensus       115 IL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~-~-~~p-~~~p~---~~~~  188 (236)
                      |+...-.-|.+|+.+-|+|..+++++..+|.+||.+.-.-+.|...||.+++.-|.+++.+ . .+| -|+|-   |-.+
T Consensus        87 I~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El~~~n~pkl~LP~sllP~~~  166 (907)
T KOG2264|consen   87 ILASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEELRETNNPKLFLPFSLLPLQI  166 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHHHhhcCCceeeccccCcccC
Confidence            4444556688999999999999999999999999999988999999999999999999984 2 233 35554   3445


Q ss_pred             chhhhccccCCCCccccccCC
Q 026599          189 PAAFAAQGQAPGNKLMPFISY  209 (236)
Q Consensus       189 p~a~~~~~qa~~~k~~p~~~~  209 (236)
                      |+.-.+..|+.+..|--...|
T Consensus       167 pr~l~pp~~~~~c~lhncfdy  187 (907)
T KOG2264|consen  167 PRELEPPSQISPCQLHNCFDY  187 (907)
T ss_pred             cccCCCccccCcccchhcccc
Confidence            555555667777666444444

>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=95.31  E-value=0.063  Score=38.55  Aligned_cols=35  Identities=23%  Similarity=0.519  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      .|+.+|+.++..|+.+|..|..++..|+.+...|.
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~   60 (64)
T PF00170_consen   26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLK   60 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35555555555555555555555444444444443

; 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 ....

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

Probab=95.20  E-value=0.11  Score=41.91  Aligned_cols=53  Identities=28%  Similarity=0.482  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      +|-.++..|++....|.+++.+||....+|-+||+.|+-|.+.|...|.....
T Consensus         5 ~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen    5 ELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44455566666666666677777777777777777777777777777766543

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

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=95.18  E-value=0.27  Score=45.57  Aligned_cols=96  Identities=25%  Similarity=0.354  Sum_probs=71.0

Q ss_pred             cccccCCCCCCCCCcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Q 026599           65 SKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKI  144 (236)
Q Consensus        65 ~rKR~R~~s~~~~~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eei  144 (236)
                      .|||.|..      +-+.-||.-|.||..|..+=-        ..-.|-+-..+-=..|++|.++.+.|..+|+.|++..
T Consensus        55 ~rKr~RL~------HLS~EEK~~RrKLKNRVAAQt--------aRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n  120 (292)
T KOG4005|consen   55 KRKRRRLD------HLSWEEKVQRRKLKNRVAAQT--------ARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAIN  120 (292)
T ss_pred             HHHHHhhc------ccCHHHHHHHHHHHHHHHHhh--------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66766653      344568888888887765421        1223334444445568899999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          145 KELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       145 k~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +.|-.+-+||+.+...|+.+...+.++-..
T Consensus       121 ~~L~~~n~el~~~le~~~~~l~~~~~~~~~  150 (292)
T KOG4005|consen  121 ESLLAKNHELDSELELLRQELAELKQQQQH  150 (292)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHhhHHHHHH
Confidence            999999999999999888888888776554

>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=94.66  E-value=0.25  Score=40.64  Aligned_cols=51  Identities=37%  Similarity=0.614  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKI  168 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekL  168 (236)
                      -.+..|..|..++..++.+...|++++..|..+++++++|...|-.+.+.+
T Consensus        13 ~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~   63 (120)
T PF12325_consen   13 PSVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEEL   63 (120)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346677777777777777777777777777777777777666554444443

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 [].

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=94.55  E-value=0.22  Score=49.45  Aligned_cols=34  Identities=29%  Similarity=0.351  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKA  149 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~  149 (236)
                      |..-|--+++||.+++.|..+|+.|.+|.+.|++
T Consensus        61 lrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~   94 (472)
T TIGR03752        61 LRTLVAEVKELRKRLAKLISENEALKAENERLQK   94 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455667888888888888888887777666544

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.

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=94.44  E-value=0.22  Score=40.56  Aligned_cols=51  Identities=22%  Similarity=0.394  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +|-.++..|++....+..++..||....+|-+||..|+.|.+.|...|..+
T Consensus         5 elfd~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~   55 (110)
T PRK13169          5 EIFDALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL   55 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            445556666666666667777777777777777777777777777777765

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.19  E-value=0.27  Score=43.59  Aligned_cols=85  Identities=11%  Similarity=0.141  Sum_probs=50.6

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDE  157 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdE  157 (236)
                      .+...++|.  .++...+.+|++-| -+         |-.+.-....+|+++++.+++....|.++.+.|+.+..+++.|
T Consensus        87 ~~p~~~~rl--p~le~el~~l~~~l-~~---------~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~  154 (206)
T PRK10884         87 TTPSLRTRV--PDLENQVKTLTDKL-NN---------IDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKK  154 (206)
T ss_pred             CCccHHHHH--HHHHHHHHHHHHHH-HH---------HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445544  67888999998887 22         2233335555666666666655555666666666666666666


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 026599          158 KQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       158 k~~Lk~ekekLe~qlk~  174 (236)
                      +..|+++.+.++..+..
T Consensus       155 ~~~l~~~~~~~~~~~~~  171 (206)
T PRK10884        155 VDAANLQLDDKQRTIIM  171 (206)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            66666666666655443

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

Probab=94.15  E-value=0.32  Score=44.89  Aligned_cols=58  Identities=26%  Similarity=0.476  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      |--+...+|+++.+++.++++.|..+..+|..+.++++++..+|..|+.+|+..++.+
T Consensus       132 d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l  189 (290)
T COG4026         132 DLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKL  189 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3344455666667777778888888888888888888888888888888888777763

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.92  E-value=0.41  Score=44.40  Aligned_cols=64  Identities=19%  Similarity=0.353  Sum_probs=41.9

Q ss_pred             chhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          111 DKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       111 DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .+-+.|.++-.-++.++.+++.|....+.++.++++++.+.+++..|...|+.+|+.++..|..
T Consensus        35 ~~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~   98 (265)
T COG3883          35 NQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVE   98 (265)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566666666777777777777777777777777666666666666666666666555443

>PRK10884 SH3 domain-containing protein; Provisional

Probab=93.88  E-value=1  Score=39.96  Aligned_cols=24  Identities=25%  Similarity=0.378  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          149 AEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       149 ~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      ...++|+.||+.|+.|...++.++
T Consensus       132 ~~~~~L~~~n~~L~~~l~~~~~~~  155 (206)
T PRK10884        132 SVINGLKEENQKLKNQLIVAQKKV  155 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334444444444433333333

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=93.85  E-value=0.048  Score=55.23  Aligned_cols=45  Identities=38%  Similarity=0.459  Sum_probs=38.0

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCC---CCCCCCchhhhHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEP---GRPPKTDKAAILIDAVRMVT  124 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P---~~~~K~DKAsIL~dAI~ylk  124 (236)
                      .|+---||-|||||--+.-|.+|| |   ++..|+||-|||-=++.||+
T Consensus        28 tkSNPSKRHRdRLNaELD~lAsLL-PfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   28 TKSNPSKRHRDRLNAELDHLASLL-PFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             ccCCcchhHHHHhhhHHHHHHHhc-CCCHHHHhhhhhhhhhhhhHHHHH
Confidence            444456888999999999999999 6   33369999999999999986

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

Probab=93.84  E-value=0.86  Score=42.31  Aligned_cols=15  Identities=13%  Similarity=0.468  Sum_probs=6.2

Q ss_pred             HHHHHHhHHHHhhhc
Q 026599           88 RDRLNDKFVELASIL  102 (236)
Q Consensus        88 RdkLNerF~eL~slL  102 (236)
                      ...|...+..|+++.
T Consensus       186 ~~~L~~e~~~Lk~~~  200 (325)
T PF08317_consen  186 KAELEEELENLKQLV  200 (325)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333444444444443

>PRK11637 AmiB activator; Provisional

Probab=93.70  E-value=0.88  Score=43.39  Aligned_cols=61  Identities=13%  Similarity=0.171  Sum_probs=42.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .-+.++...|..|..+++.+......++.+++.+..+.++++.+...++.+++.++.+|+.
T Consensus        68 ~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~  128 (428)
T PRK11637         68 QQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAA  128 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566667777777777777777777777777777777777777777777766666655

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=93.62  E-value=1  Score=33.75  Aligned_cols=57  Identities=23%  Similarity=0.349  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      .-|.+|-...++|+.+|..|.++...+..|...|.+.+..-++.+|.+=..|++|-.
T Consensus         7 ~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEamI~RLk~leq   63 (65)
T TIGR02449         7 AQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAMITRLKALEQ   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcc
Confidence            345667777778888888888888888888888888888778888888778877643

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.

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

Probab=93.62  E-value=0.1  Score=45.18  Aligned_cols=46  Identities=33%  Similarity=0.523  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      |.+++.+..+-=+.|.-|++|+    .||..|+.+.|+||.|...|.++|
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            3455556566666777777776    566777777777777777777777

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.

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=93.60  E-value=0.6  Score=39.42  Aligned_cols=71  Identities=25%  Similarity=0.435  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCCCCC
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLTPPP  186 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~~p~~~p~~~  186 (236)
                      .+.++..|..+++....+..++..+..++.........+|++...++.+.+++..+...+...-|.+..|.
T Consensus        72 ~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~l~~~~~~~~~P~  142 (177)
T PF13870_consen   72 IGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKKLRQQGGLLGVPA  142 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcH
Confidence            46788888999999999999999999999999999999999999999999999999999887777766655

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.48  E-value=0.36  Score=44.77  Aligned_cols=58  Identities=22%  Similarity=0.440  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       119 AI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      .=.-+++|+.+.+.++.+.+.|+..+.++..+.+++++|+..+++++++|+.+|+.+.
T Consensus        36 ~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~   93 (265)
T COG3883          36 QDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELK   93 (265)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455677777777777777777777777777777777777777777777777777653

>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=93.27  E-value=0.78  Score=34.56  Aligned_cols=58  Identities=29%  Similarity=0.477  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +-=..|.+|+.+-++|....-.+...|+.|+....++..+...|+..+++++..+..+
T Consensus         9 EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l   66 (74)
T PF12329_consen    9 EKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESL   66 (74)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3346788999999999988888888888888888888888888888888888877664

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.

>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=93.22  E-value=0.98  Score=35.00  Aligned_cols=45  Identities=27%  Similarity=0.431  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKI  168 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekL  168 (236)
                      .+|..++..|+.....|-..+..++.|...|+.||..|..=|..|
T Consensus        19 ~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL   63 (80)
T PF10224_consen   19 EELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL   63 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666666666666655555

The exact function is unknown.

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=93.14  E-value=0.63  Score=37.93  Aligned_cols=51  Identities=24%  Similarity=0.356  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      .+-|.+|..++..|-.+...|...+.+|-.|-.+|+-||..|+....++++
T Consensus         7 fd~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~   57 (110)
T PRK13169          7 FDALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA   57 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            345667777777787788888888888887877888888888888877644

>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=93.02  E-value=0.33  Score=33.70  Aligned_cols=38  Identities=29%  Similarity=0.532  Sum_probs=17.3

Q ss_pred             HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          135 DSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       135 ~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      ...+.|......|+.+...|..||..|++|+..|...+
T Consensus         5 ~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl   42 (45)
T PF02183_consen    5 RDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKL   42 (45)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33333433444444444444445555555555544433

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

>PRK04406 hypothetical protein; Provisional

Probab=93.01  E-value=1.4  Score=33.47  Aligned_cols=52  Identities=15%  Similarity=0.192  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      .|..++..|+....-.+.-|.+|....-+...+...|+.+...|..+|+.+.
T Consensus         8 ~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   59 (75)
T PRK04406          8 QLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNMD   59 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            4666666677666666666677776677777777778888888888888764

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=92.94  E-value=2.2  Score=42.65  Aligned_cols=57  Identities=12%  Similarity=0.342  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      .-|.+-+.+..+|+++.+.|+.|...+.....++..+...|++|+..|+.|++++..
T Consensus        69 SALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~  125 (475)
T PRK13729         69 HATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGA  125 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            334444455555555555555555555566666666666777777777777776544

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.90  E-value=0.73  Score=35.56  Aligned_cols=52  Identities=29%  Similarity=0.450  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      .+++.+|..+++.--+.+.-|+-||.+||.+.|.|..|-+.+....+.|+.+
T Consensus         3 lEv~ekLE~KiqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~e   54 (79)
T COG3074           3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERE   54 (79)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHH
Confidence            4678889999988888888888889888888888877777666666665543

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

Probab=92.90  E-value=0.85  Score=39.26  Aligned_cols=82  Identities=26%  Similarity=0.380  Sum_probs=36.1

Q ss_pred             HHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           86 LRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEK  165 (236)
Q Consensus        86 ~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ek  165 (236)
                      ++|..+..++..+..-+    . +.  -..+..--.-|.+|+.++..|+..+..|.+++++...-...|+||...|..+.
T Consensus        88 r~~~el~~~L~~~~~~l----~-~l--~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~  160 (194)
T PF08614_consen   88 RSKGELAQQLVELNDEL----Q-EL--EKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQL  160 (194)
T ss_dssp             ---------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccc----c-hh--hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555    1 11  12333444456666666777776666666666666666666666666666666


Q ss_pred             HHHHHHHHH
Q 026599          166 EKIEQQLKA  174 (236)
Q Consensus       166 ekLe~qlk~  174 (236)
                      .-++.+++.
T Consensus       161 ~~~e~k~~~  169 (194)
T PF08614_consen  161 NMLEEKLRK  169 (194)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            666665554

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.

>PRK02119 hypothetical protein; Provisional

Probab=92.81  E-value=1.6  Score=32.91  Aligned_cols=53  Identities=15%  Similarity=0.176  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      ..|..++.+|+....-.+.-|.+|....-+.+.+...|+.+...|.++|+.+.
T Consensus         5 ~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~~rl~~~~   57 (73)
T PRK02119          5 QNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYMANKLKDMQ   57 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            44566666666666666666666766667777777788888888888888764

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

Probab=92.80  E-value=0.69  Score=37.32  Aligned_cols=57  Identities=28%  Similarity=0.429  Sum_probs=45.1

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          110 TDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       110 ~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      |||-.|    .+.|.+|.+++..|-++...|...+.+|..|-.+|+-||..|+..+.++++
T Consensus         1 Mdk~~l----~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen    1 MDKKEL----FDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             CchHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            455444    346777888888888888888888888888888888999999888888776

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

>PHA02562 46 endonuclease subunit; Provisional

Probab=92.73  E-value=0.83  Score=44.03  Aligned_cols=77  Identities=18%  Similarity=0.238  Sum_probs=59.0

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           87 RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKE  166 (236)
Q Consensus        87 RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~eke  166 (236)
                      ++..+..++.+|+..+ -.      +-+-|.+.++-.+.|+.++++|+..+..+.++++.|..+.++++.+...+..++.
T Consensus       331 ~~~~~~~~i~el~~~i-~~------~~~~i~~~~~~~~~l~~ei~~l~~~~~~~~~~l~~l~~~l~~~~~~~~~~~ke~~  403 (562)
T PHA02562        331 EFNEQSKKLLELKNKI-ST------NKQSLITLVDKAKKVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKY  403 (562)
T ss_pred             HHHHHHHHHHHHHHHH-HH------HHHHHHHHHHHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566677777777777 11      1122777888899999999999999888888899988888888888888877776


Q ss_pred             HHHH
Q 026599          167 KIEQ  170 (236)
Q Consensus       167 kLe~  170 (236)
                      ..+.
T Consensus       404 ~~~~  407 (562)
T PHA02562        404 HRGI  407 (562)
T ss_pred             HHHH
Confidence            6544

>smart00787 Spc7 Spc7 kinetochore protein

Probab=92.62  E-value=1.5  Score=41.24  Aligned_cols=15  Identities=20%  Similarity=0.470  Sum_probs=6.6

Q ss_pred             HHHHHHhHHHHhhhc
Q 026599           88 RDRLNDKFVELASIL  102 (236)
Q Consensus        88 RdkLNerF~eL~slL  102 (236)
                      .+.|+..+..|+.+.
T Consensus       181 ~~~L~~e~~~L~~~~  195 (312)
T smart00787      181 KDALEEELRQLKQLE  195 (312)
T ss_pred             HHHHHHHHHHHHHhH
Confidence            334444444444444

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

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=92.58  E-value=1.1  Score=33.56  Aligned_cols=54  Identities=22%  Similarity=0.382  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      |+.|..++..|=.....|..|...|+.+...++.|...|....+--..+|++|-
T Consensus         2 L~~Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEamI   55 (65)
T TIGR02449         2 LQALAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAMI   55 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678888888888888889888888998888888899988888888888888863

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.

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

Probab=92.58  E-value=0.082  Score=54.63  Aligned_cols=41  Identities=32%  Similarity=0.472  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHhHHHHhhhcCCC---CCCCCchhhhHHHHHHHHH
Q 026599           83 REKLRRDRLNDKFVELASILEPG---RPPKTDKAAILIDAVRMVT  124 (236)
Q Consensus        83 rER~RRdkLNerF~eL~slL~P~---~~~K~DKAsIL~dAI~ylk  124 (236)
                      +-|-||.|=|+-|.+|..+| |-   +..-+|||||+-=||.||+
T Consensus        53 AARsRRsKEn~~FyeLa~~l-Plp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   53 AARSRRSKENEEFYELAKLL-PLPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             hhhhhcccchHHHHHHHHhC-CCcchhhhhhhhHHHHHHHHHHHH
Confidence            46789999999999999999 62   3358999999999999997

>PRK04325 hypothetical protein; Provisional

Probab=92.54  E-value=1.6  Score=32.93  Aligned_cols=53  Identities=15%  Similarity=0.172  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      ..+..++.+|+....-.+.-|.+|....-+.+.+...|+.++..|-.+|+.+.
T Consensus         5 ~~~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~~   57 (74)
T PRK04325          5 QEMEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDAN   57 (74)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34555566666666655656666666666666677777777777777887764

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

Probab=92.29  E-value=0.55  Score=43.78  Aligned_cols=19  Identities=32%  Similarity=0.429  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 026599          156 DEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       156 dEk~~Lk~ekekLe~qlk~  174 (236)
                      +|...|+.+++....+|..
T Consensus       113 ~e~~sl~~q~~~~~~~L~~  131 (314)
T PF04111_consen  113 EERDSLKNQYEYASNQLDR  131 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3444455555555555554

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.

>PRK00846 hypothetical protein; Provisional

Probab=92.00  E-value=2  Score=33.13  Aligned_cols=52  Identities=15%  Similarity=0.130  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      .|..++..|+....-.+.-|.+|....-+...+...|+.++..|-.+|+.+.
T Consensus        10 ~le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~   61 (77)
T PRK00846         10 ALEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR   61 (77)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3455666666666555556666666667777777888888888888888864

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

Probab=91.98  E-value=0.87  Score=33.64  Aligned_cols=51  Identities=18%  Similarity=0.291  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      |..++.+|+....-++.-|.+|....-+...+...|+.++..|..+|+.+.
T Consensus         2 le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen    2 LEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            455666666666666666666666666667777777778888888888765

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.

>PRK00295 hypothetical protein; Provisional

Probab=91.88  E-value=2.1  Score=31.81  Aligned_cols=50  Identities=14%  Similarity=0.192  Sum_probs=30.6

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          127 RSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       127 r~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      .+++.+|+....-.+.-|.+|....-+...+...|+.++..|..+|+.+.
T Consensus         4 e~Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00295          4 EERVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEEMV   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34455555555545555555555555666666677777777777777764

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=91.86  E-value=1.3  Score=33.21  Aligned_cols=52  Identities=27%  Similarity=0.467  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKN-------ELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn-------ELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +..||.+...+...++..+.+++.|..|.+       ...+++..|+.|++.|..+|+.
T Consensus         7 ~~~Lr~rLd~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~   65 (69)
T PF14197_consen    7 IATLRNRLDSLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEE   65 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566666666666666666666666654       3455778888888888888764

>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin

Probab=91.71  E-value=0.7  Score=42.83  Aligned_cols=60  Identities=18%  Similarity=0.429  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hCCCCCCC
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM-STQPSFLT  183 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~-~~~p~~~p  183 (236)
                      +.|+..++.+.++.+.++..+..|..+...|.....+.++|.++.+..|+++ ++.|.||-
T Consensus       165 ~~l~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmd  225 (267)
T PF10234_consen  165 KALKEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMD  225 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHH
Confidence            3444555566666666666677777777777777778889999999999997 56787774

Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=91.61  E-value=1.1  Score=44.57  Aligned_cols=60  Identities=7%  Similarity=0.113  Sum_probs=45.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +-|.+.=.-..+|++++++|+.+.+.+.....++....++|.+|+..|+.+.+-+-.+..
T Consensus        69 SALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~~~  128 (475)
T PRK13729         69 HATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANPV  128 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCCC
Confidence            445566667788888888888888777777777888888999999999999865555543

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

Probab=91.49  E-value=0.91  Score=43.78  Aligned_cols=44  Identities=36%  Similarity=0.459  Sum_probs=26.2

Q ss_pred             HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 026599          135 DSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ  178 (236)
Q Consensus       135 ~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~~  178 (236)
                      ++.+.++.+...|+.-..||+.-++.|+.++++||+|+..++.+
T Consensus       225 eeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~n  268 (365)
T KOG2391|consen  225 EEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKN  268 (365)
T ss_pred             HHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhh
Confidence            33444444455555556666666666777777777776665443

>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=91.47  E-value=1.6  Score=31.29  Aligned_cols=36  Identities=33%  Similarity=0.539  Sum_probs=19.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          137 NSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       137 n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      ...|+.++..|..+...|+.++..|+.++..|..++
T Consensus        28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~   63 (64)
T PF00170_consen   28 IEELEEKVEELESENEELKKELEQLKKEIQSLKSEN   63 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            344445555555555555555555555555555543

; 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 ....

>PRK11637 AmiB activator; Provisional

Probab=91.34  E-value=1.3  Score=42.17  Aligned_cols=25  Identities=32%  Similarity=0.361  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          149 AEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       149 ~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      .+.+++..+...|+.++..++.+|.
T Consensus        96 ~~i~~~~~ei~~l~~eI~~~q~~l~  120 (428)
T PRK11637         96 NTLNQLNKQIDELNASIAKLEQQQA  120 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333

>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=91.26  E-value=2.3  Score=37.00  Aligned_cols=16  Identities=25%  Similarity=0.318  Sum_probs=9.5

Q ss_pred             HHHHHHHhHHHHhhhc
Q 026599           87 RRDRLNDKFVELASIL  102 (236)
Q Consensus        87 RRdkLNerF~eL~slL  102 (236)
                      |++=.|.-|.+|--=|
T Consensus        60 r~~ly~~~F~ELIRQV   75 (189)
T PF10211_consen   60 REELYSQCFDELIRQV   75 (189)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4556666666665544

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 [].

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

Probab=91.13  E-value=1.2  Score=40.70  Aligned_cols=55  Identities=18%  Similarity=0.435  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      |-=+..|=.++++.|.+|++|...+..++..|+.|...|+++..+|-..++-+.+
T Consensus        81 LpIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqS  135 (248)
T PF08172_consen   81 LPIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQS  135 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3344567778888888888888888889999999999999999999999998754

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

>PRK02793 phi X174 lysis protein; Provisional

Probab=91.12  E-value=2.9  Score=31.37  Aligned_cols=51  Identities=20%  Similarity=0.223  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      +..++.+|+....-.+.-|.+|.....+.+.+...|+.+...|..+|+.+.
T Consensus         6 ~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   56 (72)
T PRK02793          6 LEARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLKASQ   56 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            455566666666555556666666666667777777788888888888764

>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=90.89  E-value=0.83  Score=31.69  Aligned_cols=36  Identities=31%  Similarity=0.500  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          140 LQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       140 L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      |+..-..|+...+.|+.++..|+.|+++|..++..+
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L   38 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQEL   38 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445556666666666666666666666666666654

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

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=90.73  E-value=1.6  Score=38.89  Aligned_cols=53  Identities=26%  Similarity=0.423  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      .|.++-.+|-..+..++.+...|..+...|++||..|..+.+.++.+.+.++.
T Consensus        78 ~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL~~  130 (193)
T PF14662_consen   78 SLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKELAT  130 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHH
Confidence            33444444444444555556667777777777777777777777777666543

>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=90.72  E-value=2.9  Score=34.40  Aligned_cols=47  Identities=19%  Similarity=0.281  Sum_probs=29.5

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 026599          112 KAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEK  158 (236)
Q Consensus       112 KAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk  158 (236)
                      -.+++..=-.-|++|..++..|+.++..|+.+-+.+..|.-.|..++
T Consensus        14 ~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~   60 (120)
T PF12325_consen   14 SVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEEN   60 (120)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555566677777777777777766666566655555554444

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 [].

>TIGR02231 conserved hypothetical protein

Probab=90.71  E-value=1.9  Score=42.21  Aligned_cols=86  Identities=17%  Similarity=0.244  Sum_probs=55.4

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHH---------------HHHHHHhhhhHHHHHHHHHHHH
Q 026599           87 RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSE---------------AQKLKDSNSSLQEKIKELKAEK  151 (236)
Q Consensus        87 RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~q---------------v~~Lk~~n~~L~eeik~Lk~Ek  151 (236)
                      +...|.+++.+|..-+    ..-.++.+.+..-+.+|..+...               +.++.+-...+.+++.++..+.
T Consensus        72 ~~~~l~~~l~~l~~~~----~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (525)
T TIGR02231        72 RLAELRKQIRELEAEL----RDLEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTED  147 (525)
T ss_pred             HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444566666666666    12345667777777777777642               3445555555666667777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          152 NELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       152 nELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      .++..+...|+.++.+|+.+|..++
T Consensus       148 ~~~~~~~~~~~~~l~~l~~~l~~l~  172 (525)
T TIGR02231       148 REAERRIRELEKQLSELQNELNALL  172 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            7777777777777777777776654

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.

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=90.69  E-value=0.16  Score=44.23  Aligned_cols=49  Identities=33%  Similarity=0.422  Sum_probs=41.3

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCC-CCCchhhhHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRP-PKTDKAAILIDAVRMVTQLR  127 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~-~K~DKAsIL~dAI~ylkqLr  127 (236)
                      .-|+.+||+|=.-||+-|..|+.++ |..+ .|..|.--|.-|.+||--|-
T Consensus        80 v~anvrerqRtqsLn~AF~~lr~ii-ptlPsdklSkiqtLklA~ryidfl~  129 (173)
T KOG4447|consen   80 VMANVRERQRTQSLNEAFAALRKII-PTLPSDKLSKIQTLKLAARYIDFLY  129 (173)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHhhc-CCCCccccccccchhhcccCCchhh
Confidence            3478899999999999999999999 7652 38888888999999887653

>PHA03011 hypothetical protein; Provisional

Probab=90.44  E-value=2.1  Score=35.17  Aligned_cols=60  Identities=20%  Similarity=0.325  Sum_probs=51.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          115 ILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       115 IL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      =...-++.+.+|+.|-.+|-++..-+..+++.+..-..+-.||..-|++|++||..++--
T Consensus        58 D~Nai~e~ldeL~~qYN~L~dEYn~i~Ne~k~~~~iIQdn~d~I~~LraeIDkLK~niaN  117 (120)
T PHA03011         58 DINAIIEILDELIAQYNELLDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENIAN  117 (120)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHhc
Confidence            345667888999999999999999999999999888888888999999999999988753

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

Probab=90.26  E-value=4  Score=44.87  Aligned_cols=83  Identities=23%  Similarity=0.408  Sum_probs=48.4

Q ss_pred             HHHhHHHHhhhcCCCCCCCCchh-hhHHHHHHHHHHHHHHHHHHHHh----------hhhHHHHHHHHHHHHHHHHHHHH
Q 026599           91 LNDKFVELASILEPGRPPKTDKA-AILIDAVRMVTQLRSEAQKLKDS----------NSSLQEKIKELKAEKNELRDEKQ  159 (236)
Q Consensus        91 LNerF~eL~slL~P~~~~K~DKA-sIL~dAI~ylkqLr~qv~~Lk~~----------n~~L~eeik~Lk~EknELrdEk~  159 (236)
                      +++++.+|+..+ |.......|. +=+.+.+..+..|..++.+++..          ...+++.|.+++.|.+++.++..
T Consensus       804 ~ee~~~~lr~~~-~~l~~~l~~~~~~~k~~~~~~~~l~~~i~~~E~~~~k~~~d~~~l~~~~~~ie~l~kE~e~~qe~~~  882 (1293)
T KOG0996|consen  804 LEERVRKLRERI-PELENRLEKLTASVKRLAELIEYLESQIAELEAAVLKKVVDKKRLKELEEQIEELKKEVEELQEKAA  882 (1293)
T ss_pred             HHHHHHHHHHhh-HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            566777777777 5431111221 12344555666666666666653          12345557777777777775444


Q ss_pred             HHHHHHHHHHHHHHHh
Q 026599          160 RLKAEKEKIEQQLKAM  175 (236)
Q Consensus       160 ~Lk~ekekLe~qlk~~  175 (236)
                      . |++++.|+.+|..+
T Consensus       883 K-k~~i~~lq~~i~~i  897 (1293)
T KOG0996|consen  883 K-KARIKELQNKIDEI  897 (1293)
T ss_pred             H-HHHHHHHHHHHHHh
Confidence            4 67777777777654

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

Probab=90.24  E-value=1.6  Score=40.60  Aligned_cols=10  Identities=20%  Similarity=0.484  Sum_probs=3.9

Q ss_pred             HhHHHHhhhc
Q 026599           93 DKFVELASIL  102 (236)
Q Consensus        93 erF~eL~slL  102 (236)
                      .....|..++
T Consensus       170 ~~~~~l~~~~  179 (325)
T PF08317_consen  170 KQLEQLDELL  179 (325)
T ss_pred             HHHHHHHHHH
Confidence            3333334444

>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal

Probab=90.24  E-value=2  Score=34.54  Aligned_cols=56  Identities=18%  Similarity=0.318  Sum_probs=33.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      -++.=+|+||-..++.   |...+..|+++++.+..+..+|+.+...++.++..|..++
T Consensus        62 rLaQl~ieYLl~~q~~---L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~  117 (118)
T PF13815_consen   62 RLAQLSIEYLLHCQEY---LSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKES  117 (118)
T ss_pred             HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3556678887665543   3444555666666666666666666666666666665554

>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=90.18  E-value=3.5  Score=39.22  Aligned_cols=45  Identities=20%  Similarity=0.295  Sum_probs=34.5

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 026599          109 KTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNE  153 (236)
Q Consensus       109 K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknE  153 (236)
                      +..=+.+|.++-+..+.|+.++..|++....++.+++.|+.....
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            445567899999999999999999998887777777666654443

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

Probab=90.13  E-value=1.5  Score=36.19  Aligned_cols=50  Identities=22%  Similarity=0.366  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +|-.++..|++....|..++-.||+..-+|-+||..|+-|.++|...|--
T Consensus         5 eiFd~v~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~   54 (114)
T COG4467           5 EIFDQVDNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE   54 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence            44556677888888888888888888889999999999999998887753

>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=89.94  E-value=3.2  Score=33.79  Aligned_cols=59  Identities=25%  Similarity=0.451  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHh
Q 026599          117 IDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKN----ELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       117 ~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn----ELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +++|.-|..|+.+.+.++.....|..+....+....    ....++..|..++..++..+.-+
T Consensus        55 a~~~~~L~~lr~e~~~~~~~~~~l~~~~~~a~~~l~~~e~sw~~qk~~le~e~~~~~~r~~dL  117 (132)
T PF07926_consen   55 AEDIKELQQLREELQELQQEINELKAEAESAKAELEESEASWEEQKEQLEKELSELEQRIEDL  117 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            567888888888888888877777776544333322    23345555555555555555543

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

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

Probab=89.81  E-value=3.5  Score=37.30  Aligned_cols=59  Identities=25%  Similarity=0.325  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ......=++.|++++++.+.+.+.++++...|+....++.+|-.+|..|-.+|+.|+..
T Consensus       153 ~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~  211 (216)
T KOG1962|consen  153 NDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIES  211 (216)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhc
Confidence            34444455666667777777777777777777777777888888888888888887764

>PRK00736 hypothetical protein; Provisional

Probab=89.71  E-value=4.3  Score=30.14  Aligned_cols=47  Identities=11%  Similarity=0.231  Sum_probs=24.9

Q ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          130 AQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       130 v~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      +.+|+....-.+.-|.+|....-+-..+...|+.++..|..+|+.+.
T Consensus         7 i~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00736          7 LTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSLE   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            33444444333344444444444555555666666667767777653

>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=89.64  E-value=1.3  Score=37.17  Aligned_cols=30  Identities=30%  Similarity=0.526  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNEL  154 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknEL  154 (236)
                      .|..++.+|++++..|..+++.|+.|.+.|
T Consensus        76 ~ld~ei~~L~~el~~l~~~~k~l~~eL~~L  105 (169)
T PF07106_consen   76 ELDAEIKELREELAELKKEVKSLEAELASL  105 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334444443333333333333333333

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 [].

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

Probab=89.59  E-value=1.7  Score=34.55  Aligned_cols=47  Identities=28%  Similarity=0.387  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHhhhhH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          126 LRSEAQKLKDSNSSL--QEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L--~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      +..+++.++.+.+.|  ..+++.|+.+..+++-+...+.++++-++.++
T Consensus        47 ~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~~   95 (106)
T PF10805_consen   47 HDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSHQL   95 (106)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            344444444444444  33444444444444444444444444444443

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

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

Probab=89.52  E-value=2.8  Score=36.85  Aligned_cols=60  Identities=20%  Similarity=0.417  Sum_probs=37.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      .|..+=+.+|+.|++++..++..-........++..|-..|.+....+..+++.|+.+|+
T Consensus        20 dIT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~   79 (201)
T PF13851_consen   20 DITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLK   79 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            466677788888888888887655544444555555555555555555555555555444

>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=89.51  E-value=1.8  Score=31.19  Aligned_cols=37  Identities=41%  Similarity=0.614  Sum_probs=15.5

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          137 NSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       137 n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      ...|+.++..++.+..+|+.|...|+...+.++..-+
T Consensus        26 i~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR   62 (80)
T PF04977_consen   26 IAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAR   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            3333334444444444444444444334444444443

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

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

Probab=89.47  E-value=2.9  Score=32.35  Aligned_cols=51  Identities=33%  Similarity=0.550  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKA---EKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~---EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ++|+.+++.|+.+-..+..+|..++.   +..+|..|...++.++..++.+++.
T Consensus        39 r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~   92 (108)
T PF02403_consen   39 RELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKE   92 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555566666555566666655544   3445555555566666655555554

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 ....

>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=89.39  E-value=2.2  Score=36.35  Aligned_cols=13  Identities=8%  Similarity=0.192  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRS  128 (236)
Q Consensus       116 L~dAI~ylkqLr~  128 (236)
                      +.....+|++|..
T Consensus       117 I~r~~~li~~l~~  129 (192)
T PF05529_consen  117 IRRVHSLIKELIK  129 (192)
T ss_pred             HHHHHHHHHHHHH
Confidence            4444444444443

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

>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=89.34  E-value=9.5  Score=31.30  Aligned_cols=20  Identities=35%  Similarity=0.494  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHhHHHHhhhc
Q 026599           83 REKLRRDRLNDKFVELASIL  102 (236)
Q Consensus        83 rER~RRdkLNerF~eL~slL  102 (236)
                      ++...|+.|++.+..|.+=+
T Consensus        49 r~~~~~e~l~~~~~~l~~d~   68 (151)
T PF11559_consen   49 RDMEQREDLSDKLRRLRSDI   68 (151)
T ss_pred             HHHHHHHHHHHHHHHHHhHH
Confidence            57778888998888888766

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.

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=89.23  E-value=0.31  Score=48.31  Aligned_cols=42  Identities=31%  Similarity=0.415  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHhHHHHhhhcCCC---CCCCCchhhhHHHHHHHHHH
Q 026599           83 REKLRRDRLNDKFVELASILEPG---RPPKTDKAAILIDAVRMVTQ  125 (236)
Q Consensus        83 rER~RRdkLNerF~eL~slL~P~---~~~K~DKAsIL~dAI~ylkq  125 (236)
                      .-|.||++=|--|.+|.++| |-   +....||++|+-=|+.|||-
T Consensus         8 aA~tRRekEN~EF~eLAklL-PLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLL-PLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhc-cchhhhhhccchhhhhhHHHHHHHH
Confidence            46889999999999999999 63   23469999999999999983

>PHA02562 46 endonuclease subunit; Provisional

Probab=89.04  E-value=5.5  Score=38.43  Aligned_cols=16  Identities=13%  Similarity=0.316  Sum_probs=8.1

Q ss_pred             HHHHHHHhHHHHhhhc
Q 026599           87 RRDRLNDKFVELASIL  102 (236)
Q Consensus        87 RRdkLNerF~eL~slL  102 (236)
                      .+..|+..+..|...+
T Consensus       307 ~i~~l~~~l~~l~~~i  322 (562)
T PHA02562        307 KLKELQHSLEKLDTAI  322 (562)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4444555555555555

>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein

Probab=88.96  E-value=2.4  Score=35.90  Aligned_cols=24  Identities=25%  Similarity=0.292  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhH
Q 026599          117 IDAVRMVTQLRSEAQKLKDSNSSL  140 (236)
Q Consensus       117 ~dAI~ylkqLr~qv~~Lk~~n~~L  140 (236)
                      ....+-.++|+.|+.+|++++..+
T Consensus        36 ~~~~~~~~~l~~Ei~~l~~E~~~i   59 (161)
T PF04420_consen   36 SKSSKEQRQLRKEILQLKRELNAI   59 (161)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             ccccHHHHHHHHHHHHHHHHHHcC
Confidence            445566677777777777766544

The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.

>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=88.95  E-value=3.3  Score=37.43  Aligned_cols=24  Identities=17%  Similarity=0.256  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEK  143 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~ee  143 (236)
                      -.+|.+++.+.+.|.++-..+.++
T Consensus        31 e~~L~e~~kE~~~L~~Er~~h~ee   54 (230)
T PF10146_consen   31 EKCLEEYRKEMEELLQERMAHVEE   54 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555555555555444333333

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.

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=88.87  E-value=1.6  Score=39.00  Aligned_cols=37  Identities=30%  Similarity=0.585  Sum_probs=15.5

Q ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          133 LKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       133 Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      |.++|+.|++|+.+|+.+..++    ..|+.|.++|...|.
T Consensus        74 l~~en~~L~~e~~~l~~~~~~~----~~l~~en~~L~~lL~  110 (276)
T PRK13922         74 LREENEELKKELLELESRLQEL----EQLEAENARLRELLN  110 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhc
Confidence            3334444444444444333322    134444455554444

>COG5570 Uncharacterized small protein [Function unknown]

Probab=88.78  E-value=1.6  Score=32.00  Aligned_cols=44  Identities=34%  Similarity=0.464  Sum_probs=28.1

Q ss_pred             HHHHHHHHhhhhHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHH
Q 026599          128 SEAQKLKDSNSSLQEKIKELKA-------EKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       128 ~qv~~Lk~~n~~L~eeik~Lk~-------EknELrdEk~~Lk~ekekLe~q  171 (236)
                      ..+..|+.....|++||++-..       ...||+..|.+||.|||+|..|
T Consensus         5 shl~eL~kkHg~le~ei~ea~n~Ps~dd~~i~eLKRrKL~lKeeIEkLka~   55 (57)
T COG5570           5 SHLAELEKKHGNLEREIQEAMNSPSSDDLAIRELKRRKLRLKEEIEKLKAQ   55 (57)
T ss_pred             HHHHHHHHhhchHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4455566666666666654332       3456777777888888887654

>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=88.38  E-value=1.2  Score=31.12  Aligned_cols=26  Identities=35%  Similarity=0.617  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          145 KELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       145 k~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      .+|..+..+|..+|..|+.++..|+.
T Consensus        28 ~~le~~~~~L~~en~~L~~~i~~L~~   53 (54)
T PF07716_consen   28 EELEQEVQELEEENEQLRQEIAQLER   53 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34444444444455555555544443

; 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 ....

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

Probab=88.38  E-value=4.1  Score=34.30  Aligned_cols=88  Identities=18%  Similarity=0.339  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhH----HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 026599           83 REKLRRDRLNDKFVELASILEPGRPPKTDKAAIL----IDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEK  158 (236)
Q Consensus        83 rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL----~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk  158 (236)
                      ..+.+-..+.+.+.++...+ -.   ......-+    ...-+..+.++++++.++.....+.+++.++..+..+.+++.
T Consensus        85 ~~~~~l~~l~~el~~l~~~~-~~---~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~  160 (191)
T PF04156_consen   85 ELQQQLQQLQEELDQLQERI-QE---LESELEKLKEDLQELRELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEV  160 (191)
T ss_pred             hHHHHHHHHHHHHHHHHHHH-HH---HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455556666666666666 21   11111111    122233445555566666666666666666665555555666


Q ss_pred             HHHHHHHHHHHHHHHH
Q 026599          159 QRLKAEKEKIEQQLKA  174 (236)
Q Consensus       159 ~~Lk~ekekLe~qlk~  174 (236)
                      ..++.+.+++++....
T Consensus       161 ~~~~~~~~~~~~~~~~  176 (191)
T PF04156_consen  161 QELRSQLERLQENLQQ  176 (191)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            6666666666555443

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 [].

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

Probab=88.34  E-value=2.7  Score=38.36  Aligned_cols=62  Identities=18%  Similarity=0.251  Sum_probs=52.3

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          110 TDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       110 ~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      .+-.+||.-.+.-=-+.|.++.+|++++..+..++..|+.|.+.|+.+|..|=..+--|+.-
T Consensus        75 ~~~~siLpIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqSY  136 (248)
T PF08172_consen   75 GGDSSILPIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQSY  136 (248)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            45678888888888889999999999999999999999999999999999998777766543

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

>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=88.21  E-value=3.2  Score=30.30  Aligned_cols=44  Identities=11%  Similarity=0.327  Sum_probs=19.9

Q ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          131 QKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       131 ~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .+|+.+...+...+..++.|..+++++...++..+.+|=.-++.
T Consensus         3 ~elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll~lYE~   46 (55)
T PF05377_consen    3 DELENELPRIESSINTVKKENEEISESVEKIEENVKDLLSLYEV   46 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444444433333

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) [].

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

Probab=87.96  E-value=3.8  Score=35.89  Aligned_cols=13  Identities=31%  Similarity=0.371  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHHHH
Q 026599          162 KAEKEKIEQQLKA  174 (236)
Q Consensus       162 k~ekekLe~qlk~  174 (236)
                      +.++..++.++..
T Consensus       125 ~~~~~~~~~~l~~  137 (302)
T PF10186_consen  125 QNELEERKQRLSQ  137 (302)
T ss_pred             HHHHHHHHHHHHH
Confidence            3344444444443

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

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=87.91  E-value=3.1  Score=36.22  Aligned_cols=51  Identities=25%  Similarity=0.379  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      ....+.|+.+.++|+.++..|+.+++.|..|..+|..+...++.+-+-|=.
T Consensus        96 ~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~  146 (161)
T TIGR02894        96 NPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLID  146 (161)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334556666666666666666666666666666666666666555554433

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.

>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=87.66  E-value=9.1  Score=31.41  Aligned_cols=52  Identities=19%  Similarity=0.451  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       119 AI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      .|..|..|-.+.++-....+.|.++++.+..+...|.....+|+.+++.++.
T Consensus        36 vin~i~~Ll~~~~r~~~~~e~l~~~~~~l~~d~~~l~~~~~rL~~~~~~~er   87 (151)
T PF11559_consen   36 VINCIYDLLQQRDRDMEQREDLSDKLRRLRSDIERLQNDVERLKEQLEELER   87 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444444444444444444433333

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.

>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms

Probab=87.65  E-value=3.5  Score=39.55  Aligned_cols=25  Identities=24%  Similarity=0.411  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCCCC
Q 026599          160 RLKAEKEKIEQQLKAMSTQPSFLTP  184 (236)
Q Consensus       160 ~Lk~ekekLe~qlk~~~~~p~~~p~  184 (236)
                      ..|.-+.+|.++|+.|.+.-|++-|
T Consensus       332 ~IKqAl~kLk~EI~qMdvrIGVleh  356 (359)
T PF10498_consen  332 KIKQALTKLKQEIKQMDVRIGVLEH  356 (359)
T ss_pred             HHHHHHHHHHHHHHHhhhhhheehh
Confidence            3455556666667767666666554

Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=87.59  E-value=2  Score=34.30  Aligned_cols=45  Identities=22%  Similarity=0.362  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ..+|+++++.++++|+.|+.+...|+.|...|       +...+-+|...+.
T Consensus        29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L-------~~~~dyiEe~AR~   73 (105)
T PRK00888         29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDL-------KGGQEAIEERARN   73 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------hCcHHHHHHHHHH
Confidence            45666666666666666665555555444444       4434556655555

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

Probab=87.33  E-value=5.6  Score=33.86  Aligned_cols=14  Identities=36%  Similarity=0.458  Sum_probs=6.8

Q ss_pred             HHHHHhHHHHhhhc
Q 026599           89 DRLNDKFVELASIL  102 (236)
Q Consensus        89 dkLNerF~eL~slL  102 (236)
                      +-+|+.+..+..-+
T Consensus        30 ~~l~~~~~~~~~~~   43 (177)
T PF07798_consen   30 EVLNDSLEKVAQDL   43 (177)
T ss_pred             HHHHHHHHHHHHHH
Confidence            35555555544433

>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=87.31  E-value=2.6  Score=30.32  Aligned_cols=33  Identities=30%  Similarity=0.345  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 026599          122 MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNEL  154 (236)
Q Consensus       122 ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknEL  154 (236)
                      -+.+++.++++|+.+++.++.++..|+.+...|
T Consensus        18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l   50 (80)
T PF04977_consen   18 RYYQLNQEIAELQKEIEELKKENEELKEEIERL   50 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345566666666666666666666666666666

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

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

Probab=87.29  E-value=4.8  Score=35.78  Aligned_cols=19  Identities=21%  Similarity=0.281  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 026599          156 DEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       156 dEk~~Lk~ekekLe~qlk~  174 (236)
                      .....++.++++|+.++..
T Consensus        77 ~~v~~q~~el~~L~~qi~~   95 (251)
T PF11932_consen   77 RQVASQEQELASLEQQIEQ   95 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3333444445555554444

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.

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

Probab=87.22  E-value=2.3  Score=43.24  Aligned_cols=59  Identities=25%  Similarity=0.393  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          117 IDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       117 ~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ...-.=+.+|+.++++|+.+.+.+..+++.++.+..++.+|....+.+.++++.+++..
T Consensus       324 ~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l~  382 (594)
T PF05667_consen  324 EEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKLK  382 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35567788899999999999999999999999999999999999999999999998864

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

Probab=87.19  E-value=2.3  Score=40.82  Aligned_cols=57  Identities=16%  Similarity=0.251  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCC
Q 026599          117 IDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPS  180 (236)
Q Consensus       117 ~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~~p~  180 (236)
                      +-+.--.+.|..+.++|+.++..|+.+++       ++.++...++.|+++++.+++.+..+|-
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (398)
T PTZ00454         11 SSTTHTERDLYEKLKELEKELEFLDIQEE-------YIKEEQKNLKRELIRAKEEVKRIQSVPL   67 (398)
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            33334445555555555544444444444       4444445555666667777777776663

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

Probab=87.02  E-value=5  Score=29.38  Aligned_cols=44  Identities=30%  Similarity=0.443  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      |.+|-.+|+.|......|..++..       ||.+.+..|.|-.|-.+.|-
T Consensus         5 id~Ls~dVq~L~~kvdqLs~dv~~-------lr~~v~~ak~EAaRAN~RlD   48 (56)
T PF04728_consen    5 IDQLSSDVQTLNSKVDQLSSDVNA-------LRADVQAAKEEAARANQRLD   48 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH
Confidence            445555555555555555544444       44444455555555444443

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.

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

Probab=87.00  E-value=6.8  Score=37.01  Aligned_cols=73  Identities=27%  Similarity=0.458  Sum_probs=48.6

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           87 RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKE  166 (236)
Q Consensus        87 RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~eke  166 (236)
                      +|+.||....++++--              .+...-+++|+++++.|...-..+.+++.+++.+.+++....+.|..+..
T Consensus        28 kR~El~~~~~~~~ekR--------------deln~kvrE~~e~~~elr~~rdeineev~elK~kR~ein~kl~eL~~~~~   93 (294)
T COG1340          28 KRDELRKEASELAEKR--------------DELNAKVRELREKAQELREERDEINEEVQELKEKRDEINAKLQELRKEYR   93 (294)
T ss_pred             HHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666666655544              23445677777778888777777777787777777777776666666665


Q ss_pred             HHHHHHH
Q 026599          167 KIEQQLK  173 (236)
Q Consensus       167 kLe~qlk  173 (236)
                      .+-....
T Consensus        94 ~l~e~~~  100 (294)
T COG1340          94 ELKEKRN  100 (294)
T ss_pred             HHHHHhh
Confidence            5554444

>smart00338 BRLZ basic region leucin zipper

Probab=86.98  E-value=2.3  Score=30.43  Aligned_cols=33  Identities=36%  Similarity=0.649  Sum_probs=14.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       139 ~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      .|+.++..|..+..+|+.+...|..++..|.++
T Consensus        30 ~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~   62 (65)
T smart00338       30 ELERKVEQLEAENERLKKEIERLRRELEKLKSE   62 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444433

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=86.93  E-value=4.2  Score=34.50  Aligned_cols=51  Identities=24%  Similarity=0.433  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          122 MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       122 ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      .+|.++.+ .+|+.++..|+.+++.|+.|..+++.|...++..-+.|....-
T Consensus        69 R~KRv~Qk-~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~~  119 (135)
T KOG4196|consen   69 RVKRVQQK-HELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSAV  119 (135)
T ss_pred             HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            45555443 4577777788888888887777777777777777777766654

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

Probab=86.89  E-value=4.7  Score=30.62  Aligned_cols=52  Identities=29%  Similarity=0.380  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKN--------ELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn--------ELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      |++...++.+|+.+|=.|.=+|..|....+        ++..||..||.+++.|..+++.
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            456667777777777655555544443333        2344555566666666655554

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

Probab=86.81  E-value=6.3  Score=33.39  Aligned_cols=41  Identities=32%  Similarity=0.514  Sum_probs=23.3

Q ss_pred             HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          135 DSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       135 ~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      .++..|.+++..++.+.+.|.-|...|+.+++.|.++++-+
T Consensus        52 ~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~   92 (140)
T PF10473_consen   52 AEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKK   92 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555556666666666666666665555543

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

>KOG4797 consensus Transcriptional regulator [Transcription]

Probab=86.76  E-value=2.7  Score=34.93  Aligned_cols=32  Identities=28%  Similarity=0.412  Sum_probs=21.7

Q ss_pred             HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          135 DSNSSLQEKIKELKAEKNELRDEKQRLKAEKE  166 (236)
Q Consensus       135 ~~n~~L~eeik~Lk~EknELrdEk~~Lk~eke  166 (236)
                      ++.+.|.+.|++|....+.|+.||..||.-..
T Consensus        67 EEVe~Lk~qI~eL~er~~~Le~EN~lLk~~~s   98 (123)
T KOG4797|consen   67 EEVEVLKEQIRELEERNSALERENSLLKTLAS   98 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            34445555677777777788888888887543

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

Probab=86.74  E-value=5.1  Score=35.20  Aligned_cols=34  Identities=24%  Similarity=0.306  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRD  156 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrd  156 (236)
                      .+.|..++.+-+.++..+.+++.+|+...-+|++
T Consensus       112 ~k~le~~~~~~~~~~~~~e~~i~~Le~ki~el~~  145 (190)
T PF05266_consen  112 RKKLEKKIEEKEAELKELESEIKELEMKILELQR  145 (190)
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence            3334444433333344444444444444444444

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

Probab=86.72  E-value=3.3  Score=45.00  Aligned_cols=48  Identities=27%  Similarity=0.511  Sum_probs=19.0

Q ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          129 EAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       129 qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      +|++|+..+.+|.++..+++.+..+-++|+..++.++..|...++-.+
T Consensus       409 evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~~  456 (1074)
T KOG0250|consen  409 EVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENIS  456 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333344444444444444444433

>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=86.50  E-value=5.8  Score=37.92  Aligned_cols=43  Identities=14%  Similarity=0.264  Sum_probs=27.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Q 026599          115 ILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDE  157 (236)
Q Consensus       115 IL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdE  157 (236)
                      +|+-++.-+.+|+.+++.|..+|+.|+.++..+..+..++-.+
T Consensus       131 l~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE~~v~~  173 (342)
T PF06632_consen  131 LFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLEKFVNA  173 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5566666677777777777777777766665555555444333

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.

>PRK09039 hypothetical protein; Validated

Probab=86.45  E-value=4.3  Score=38.32  Aligned_cols=55  Identities=13%  Similarity=0.144  Sum_probs=39.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKI  168 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekL  168 (236)
                      ++.+++-.-|..|+.|++.|+.+...|+.++..++....+.+.....|+.+++..
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            4566777788888888888888888888887777666666665555555444443

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

Probab=86.36  E-value=4.9  Score=29.44  Aligned_cols=27  Identities=22%  Similarity=0.348  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 026599          122 MVTQLRSEAQKLKDSNSSLQEKIKELK  148 (236)
Q Consensus       122 ylkqLr~qv~~Lk~~n~~L~eeik~Lk  148 (236)
                      =|.+|..+|.+|..+...|..++...+
T Consensus        11 dVq~L~~kvdqLs~dv~~lr~~v~~ak   37 (56)
T PF04728_consen   11 DVQTLNSKVDQLSSDVNALRADVQAAK   37 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356677777777777777777665444

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.

>TIGR00606 rad50 rad50

Probab=86.24  E-value=5.6  Score=43.45  Aligned_cols=85  Identities=8%  Similarity=0.204  Sum_probs=55.3

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHH------HHHHHHHHHHHHhhh-----hHHHHHHHHHHHHHHHH
Q 026599           87 RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMV------TQLRSEAQKLKDSNS-----SLQEKIKELKAEKNELR  155 (236)
Q Consensus        87 RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~yl------kqLr~qv~~Lk~~n~-----~L~eeik~Lk~EknELr  155 (236)
                      ..+.++..+..|+.-|    ......---|.|-+.|+      .+++.++..|..++.     .++.+..+|..+.++|.
T Consensus       992 e~~~l~~~i~~l~kel----~~~~~~kr~l~dnL~~~~~~~~l~el~~eI~~l~~~~~~~~~~~~~~e~~~l~~~~~~l~ 1067 (1311)
T TIGR00606       992 HQEKINEDMRLMRQDI----DTQKIQERWLQDNLTLRKRENELKEVEEELKQHLKEMGQMQVLQMKQEHQKLEENIDLIK 1067 (1311)
T ss_pred             HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHH
Confidence            5677888888888888    23344445567888888      566666666665553     34555566666666666


Q ss_pred             HHHHHHHHHHHHHHHHHHHh
Q 026599          156 DEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       156 dEk~~Lk~ekekLe~qlk~~  175 (236)
                      .++..+..++.+|+.+|..+
T Consensus      1068 ~~~a~l~g~~k~le~qi~~l 1087 (1311)
T TIGR00606      1068 RNHVLALGRQKGYEKEIKHF 1087 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            66666666666666666654

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

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

Probab=86.14  E-value=11  Score=31.73  Aligned_cols=61  Identities=20%  Similarity=0.399  Sum_probs=41.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .-+.+.-.-+..+....+++.++...|+.++++++.+..+++.+...+..+...+++.++.
T Consensus       123 ~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  183 (191)
T PF04156_consen  123 ELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERLQENLQQLEEKIQE  183 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666777777777777777777777666666666666666666666666666666554

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 [].

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=86.01  E-value=5.3  Score=35.69  Aligned_cols=61  Identities=30%  Similarity=0.376  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          115 ILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       115 IL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ++.-|...=+-|.++++.|+.....|+++.+.|-+....+..|++.|-++++.|+.+-..+
T Consensus        54 s~Qqal~~aK~l~eEledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl  114 (193)
T PF14662_consen   54 SLQQALQKAKALEEELEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGKL  114 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence            3455555555566666666666666666666666666666666666666666666655443

>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=85.70  E-value=5.2  Score=31.00  Aligned_cols=48  Identities=23%  Similarity=0.439  Sum_probs=42.6

Q ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          128 SEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       128 ~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ++-++|..+...||..+..|.....+.++|+..|+.|.+-|+.=|..+
T Consensus        16 e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL   63 (80)
T PF10224_consen   16 EEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL   63 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            446678888889999999999999999999999999999999999884

The exact function is unknown.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=85.67  E-value=6.4  Score=29.49  Aligned_cols=41  Identities=24%  Similarity=0.494  Sum_probs=23.1

Q ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          129 EAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIE  169 (236)
Q Consensus       129 qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe  169 (236)
                      ....|..++......+...-.+.++|++|+..|+.|.+.+.
T Consensus        27 ~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r   67 (69)
T PF14197_consen   27 ENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELR   67 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33334444444444455566666677777777777755443

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)

Probab=85.65  E-value=5.4  Score=32.68  Aligned_cols=50  Identities=34%  Similarity=0.434  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      =.+|+..++.|+.++..+...+.+|..+++|++.....-|..+..|+.++
T Consensus        39 kd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~eK~ak~~l~~r~   88 (107)
T PF09304_consen   39 KDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLEDEKQAKLELESRL   88 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34577777777777777777777777777777655544444444444443

The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.

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

Probab=85.61  E-value=3.4  Score=33.97  Aligned_cols=41  Identities=24%  Similarity=0.404  Sum_probs=25.1

Q ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          128 SEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKI  168 (236)
Q Consensus       128 ~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekL  168 (236)
                      .||-+|+...+.|...+..+|.|--.||.||+.|-+=|+.|
T Consensus        63 tQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL  103 (120)
T KOG3650|consen   63 TQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL  103 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence            34444555555565566666666666777777777666554

>PRK09039 hypothetical protein; Validated

Probab=85.39  E-value=6  Score=37.37  Aligned_cols=49  Identities=12%  Similarity=0.239  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .+.+|..|+.+++.|...+..|..+.+.+..+....+.+++.|+..|..
T Consensus       135 ~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~  183 (343)
T PRK09039        135 ALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNV  183 (343)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344555555555555555555555555555555555555555555544

>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=85.10  E-value=8  Score=31.57  Aligned_cols=62  Identities=27%  Similarity=0.407  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      +.+....+..|..+...|.+.|-.++.++..++.+..++.++...|+.+-..++.+++.+..
T Consensus        29 ~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~l~~   90 (150)
T PF07200_consen   29 VQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEKEQQQDELSS   90 (150)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            34445555666667777777777777778888888888888888888888888888887644

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.

>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=85.07  E-value=15  Score=32.21  Aligned_cols=22  Identities=27%  Similarity=0.397  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 026599          153 ELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       153 ELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ++.++....+.....++.++..
T Consensus       123 ~~~~~~~~~~~~l~~l~~~l~~  144 (302)
T PF10186_consen  123 ELQNELEERKQRLSQLQSQLAR  144 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555556665556666555

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

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

Probab=85.02  E-value=2.4  Score=40.78  Aligned_cols=42  Identities=24%  Similarity=0.311  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRL  161 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~L  161 (236)
                      ..++++|+.+++.|+.++..|..+.+.++.|...+++|...|
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   62 (398)
T PTZ00454         21 YEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRI   62 (398)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355677888899999999999888777766665555554443

>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]

Probab=84.99  E-value=4.5  Score=36.08  Aligned_cols=55  Identities=29%  Similarity=0.439  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHhhC
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKN--ELRDEKQRLKAEKEKIEQQLKAMST  177 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn--ELrdEk~~Lk~ekekLe~qlk~~~~  177 (236)
                      |..|+++++.|+++....+.||++|..-..  |++++.+.|+.+.......|+.+.+
T Consensus        88 i~~l~ek~q~l~~t~s~veaEik~L~s~Lt~eemQe~i~~L~kev~~~~erl~~~k~  144 (201)
T KOG4603|consen   88 IVALTEKVQSLQQTCSYVEAEIKELSSALTTEEMQEEIQELKKEVAGYRERLKNIKA  144 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666677777766666667766655433  6777888888888888888877543

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

Probab=84.88  E-value=4.4  Score=39.37  Aligned_cols=72  Identities=19%  Similarity=0.313  Sum_probs=51.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--CCCCCCCC
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMST--QPSFLTPP  185 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~--~p~~~p~~  185 (236)
                      +++..+=.-...|++-+.+++++|..|+-.+++++.|++|..+|.+.|..|....-.-.+.++.  +..|.+..
T Consensus       120 ~vf~k~k~~~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~layqq~L~~eyQatf~eq~  193 (401)
T PF06785_consen  120 EVFMKTKGDIQHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAEALAYQQELNDEYQATFVEQH  193 (401)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccch
Confidence            3555555666788888888889999999999999999999999999886666554444444443  33455543

>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]

Probab=84.87  E-value=1  Score=42.83  Aligned_cols=29  Identities=31%  Similarity=0.436  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKA  149 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~  149 (236)
                      +|||.|+.+|.-|+.+|..|-||+|.||.
T Consensus       312 EYVKCLENRVAVLENQNKaLIEELKtLKe  340 (348)
T KOG3584|consen  312 EYVKCLENRVAVLENQNKALIEELKTLKE  340 (348)
T ss_pred             HHHHHHHhHHHHHhcccHHHHHHHHHHHH
Confidence            79999999999999999999999999984

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

Probab=84.67  E-value=8  Score=32.35  Aligned_cols=34  Identities=18%  Similarity=0.364  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEK  151 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ek  151 (236)
                      .|+.-+.+|..++..|++++..+..+|..|....
T Consensus        11 ~a~~r~e~~e~~~K~le~~~~~~E~EI~sL~~K~   44 (143)
T PF12718_consen   11 NAQDRAEELEAKVKQLEQENEQKEQEITSLQKKN   44 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555666666666666655555555444333

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 [].

>TIGR00606 rad50 rad50

Probab=84.67  E-value=6.3  Score=43.06  Aligned_cols=84  Identities=17%  Similarity=0.143  Sum_probs=56.3

Q ss_pred             HHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           85 KLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAE  164 (236)
Q Consensus        85 R~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~e  164 (236)
                      ...++++++.+..|..-+ ...  + ++-.=|...+.-..+|+.++.+|+.++..+.+++++++.+...|..+...+..+
T Consensus       849 ~~e~e~~~~eI~~Lq~ki-~el--~-~~klkl~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~  924 (1311)
T TIGR00606       849 RKLIQDQQEQIQHLKSKT-NEL--K-SEKLQIGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQE  924 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHH-HHH--H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            445666677777776666 332  2 222333447778888888888888888888888887777777777776666666


Q ss_pred             HHHHHHHH
Q 026599          165 KEKIEQQL  172 (236)
Q Consensus       165 kekLe~ql  172 (236)
                      ++++..+.
T Consensus       925 ~~~~~~~~  932 (1311)
T TIGR00606       925 KEELISSK  932 (1311)
T ss_pred             HHHHHHHH
Confidence            65554433

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

>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=84.54  E-value=6.5  Score=37.61  Aligned_cols=38  Identities=16%  Similarity=0.308  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 026599          122 MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQ  159 (236)
Q Consensus       122 ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~  159 (236)
                      -+..|..+.++|+.+...+..++..+..+|.++..+..
T Consensus       145 ~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~L~  182 (342)
T PF06632_consen  145 ENEHLQKENERLESEANKLLKQLEKFVNAKEEHEEDLY  182 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34467777888888888888888888888877765543

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.

>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure

Probab=84.26  E-value=14  Score=27.23  Aligned_cols=55  Identities=29%  Similarity=0.454  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          115 ILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIE  169 (236)
Q Consensus       115 IL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe  169 (236)
                      -|..=|+--..|++++.+.+..|-.++..+++-.....+|..+...|+.+++.+.
T Consensus         5 aL~~EirakQ~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r   59 (61)
T PF08826_consen    5 ALEAEIRAKQAIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEELR   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3555566666777777777877777777776666555566666666666665543

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

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

Probab=84.08  E-value=6.3  Score=35.46  Aligned_cols=13  Identities=31%  Similarity=0.496  Sum_probs=5.0

Q ss_pred             HHHHHHHHHHHHH
Q 026599          122 MVTQLRSEAQKLK  134 (236)
Q Consensus       122 ylkqLr~qv~~Lk  134 (236)
                      =+++++.+++.|.
T Consensus       217 E~~~~r~~~~~l~  229 (312)
T PF00038_consen  217 ELKELRRQIQSLQ  229 (312)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhHhh
Confidence            3333333333333

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 ....

>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]

Probab=84.05  E-value=11  Score=36.51  Aligned_cols=91  Identities=21%  Similarity=0.323  Sum_probs=58.0

Q ss_pred             HHHHHhHHHHhhhcC-CCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH----HHH-HHHHHHHHH
Q 026599           89 DRLNDKFVELASILE-PGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAE----KNE-LRDEKQRLK  162 (236)
Q Consensus        89 dkLNerF~eL~slL~-P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~E----knE-LrdEk~~Lk  162 (236)
                      +.|-++|.+|..+|- |..-+..++..=|+.-...|..+-....++++..+.|.+--.-|..+    ..| .++|...|+
T Consensus        10 ~~~~~r~~el~~~L~~p~v~~d~~~~~~lske~a~l~~iv~~~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~~~~   89 (363)
T COG0216          10 ESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKELE   89 (363)
T ss_pred             HHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHH
Confidence            456779999998882 33223456666666666666666666666665555554322222222    123 477899999


Q ss_pred             HHHHHHHHHHHHhhCCC
Q 026599          163 AEKEKIEQQLKAMSTQP  179 (236)
Q Consensus       163 ~ekekLe~qlk~~~~~p  179 (236)
                      .+++.|+.+|+.+=.|+
T Consensus        90 ~~~~~le~~L~~lLlPk  106 (363)
T COG0216          90 AKIEELEEELKILLLPK  106 (363)
T ss_pred             HHHHHHHHHHHHhcCCC
Confidence            99999999999875543

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

Probab=83.92  E-value=15  Score=34.28  Aligned_cols=89  Identities=18%  Similarity=0.171  Sum_probs=43.3

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEK  158 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk  158 (236)
                      .|..-|=.|.+-=|....+--.-| -+.+.-||----+.+--+-+.+++.+..+|.++++.|+.+..++..+..+|+-||
T Consensus       101 EhiD~elvrkEl~nAlvRAGLktL-~~v~~~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~  179 (290)
T COG4026         101 EHIDVELVRKELKNALVRAGLKTL-QRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVEN  179 (290)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHH-hccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555555554443333 2222334444444444444555555555555555555555555544444455455


Q ss_pred             HHHHHHHHHH
Q 026599          159 QRLKAEKEKI  168 (236)
Q Consensus       159 ~~Lk~ekekL  168 (236)
                      ++|.....+|
T Consensus       180 s~LeE~~~~l  189 (290)
T COG4026         180 SRLEEMLKKL  189 (290)
T ss_pred             HHHHHHHHhc
Confidence            4444433333

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

Probab=83.77  E-value=5.2  Score=36.63  Aligned_cols=28  Identities=21%  Similarity=0.446  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEK  151 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~Ek  151 (236)
                      .+.+.++..|+.+|+.|..++..|+.|.
T Consensus       218 ~e~~~r~~~leken~~lr~~v~~l~~el  245 (269)
T KOG3119|consen  218 DEMAHRVAELEKENEALRTQVEQLKKEL  245 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444445555555554444444444333

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

Probab=83.65  E-value=11  Score=41.03  Aligned_cols=88  Identities=25%  Similarity=0.369  Sum_probs=63.4

Q ss_pred             HHHHHHHHHhHHHHhhhcCCC----CCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 026599           85 KLRRDRLNDKFVELASILEPG----RPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQR  160 (236)
Q Consensus        85 R~RRdkLNerF~eL~slL~P~----~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~  160 (236)
                      |.+.+.++.++..+.+-+.=.    .+.--+|-.-|...|   ..|+.++.+|+++...+.++++....|+...+.+...
T Consensus       371 k~~~d~l~k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~ev---ek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~  447 (1074)
T KOG0250|consen  371 KKEVDRLEKQIADLEKQTNNELGSELEERENKLEQLKKEV---EKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQ  447 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            446667777777776665111    111235555555544   4567788999999999999999888888888888889


Q ss_pred             HHHHHHHHHHHHHHh
Q 026599          161 LKAEKEKIEQQLKAM  175 (236)
Q Consensus       161 Lk~ekekLe~qlk~~  175 (236)
                      |+..++....+|+.+
T Consensus       448 l~k~i~~~~~~l~~l  462 (1074)
T KOG0250|consen  448 LRKKIENISEELKDL  462 (1074)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999988888875

>PF04325 DUF465: Protein of unknown function (DUF465); InterPro: IPR007420 Family members are found in small bacterial proteins, and also in the heavy chains of eukaryotic myosin and kinesin, C-terminal of the motor domain

Probab=83.61  E-value=3.6  Score=28.38  Aligned_cols=14  Identities=43%  Similarity=0.579  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHHHH
Q 026599          155 RDEKQRLKAEKEKI  168 (236)
Q Consensus       155 rdEk~~Lk~ekekL  168 (236)
                      +.++..||.++.++
T Consensus        33 Kk~kL~LKDei~~l   46 (49)
T PF04325_consen   33 KKEKLRLKDEIYRL   46 (49)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333444444333

Members of this family may form coiled coil structures.; PDB: 1ZHC_A.

>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=83.57  E-value=17  Score=27.40  Aligned_cols=34  Identities=18%  Similarity=0.357  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          122 MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       122 ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      .++++...++.++++...+..|+..+..+.|++-
T Consensus        27 ~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~   60 (90)
T PF06103_consen   27 TLDEVNKTIDTLQEQVDPITKEINDLLHNTNELL   60 (90)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444443

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

Probab=83.57  E-value=5  Score=41.11  Aligned_cols=46  Identities=24%  Similarity=0.480  Sum_probs=23.7

Q ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          130 AQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       130 v~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ++.|+.++..+++++..+..+.+.|+.|+...-..+..|+.+|..+
T Consensus        17 a~~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eL   62 (617)
T PF15070_consen   17 AQQLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSEL   62 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444445555555555555555555555555555555555443

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

Probab=83.55  E-value=5.4  Score=42.55  Aligned_cols=60  Identities=23%  Similarity=0.322  Sum_probs=39.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          115 ILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       115 IL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      |..+=-+.|++|..+++.|++.+..|+-+.++|..+..++..+.+.|+.+.+.|+.||+-
T Consensus       658 ~~~kyK~lI~~lD~~~e~lkQ~~~~l~~e~eeL~~~vq~~~s~hsql~~q~~~Lk~qLg~  717 (970)
T KOG0946|consen  658 IQQKYKGLIRELDYQIENLKQMEKELQVENEELEEEVQDFISEHSQLKDQLDLLKNQLGI  717 (970)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            334444455555555666666666666666666666666666777788888888888874

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=83.42  E-value=4.1  Score=42.02  Aligned_cols=44  Identities=25%  Similarity=0.434  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQ  159 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~  159 (236)
                      +..-.+-++.|..++++|+.+|..|+.++.+++.+..+|+.+..
T Consensus       417 i~~~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~  460 (652)
T COG2433         417 ITVYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELE  460 (652)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445566677777777777777777777776666666655433

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

Probab=83.39  E-value=8.6  Score=33.78  Aligned_cols=50  Identities=30%  Similarity=0.420  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +|..++.+|+.....|+++...++.++.+...|..+|+++.+.+++++..
T Consensus       128 ~~e~~i~~Le~ki~el~~~~~~~~~~ke~~~~ei~~lks~~~~l~~~~~~  177 (190)
T PF05266_consen  128 ELESEIKELEMKILELQRQAAKLKEKKEAKDKEISRLKSEAEALKEEIEN  177 (190)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555555544444444444444555555555554444443

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=83.37  E-value=7.7  Score=31.88  Aligned_cols=58  Identities=24%  Similarity=0.381  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhh-hHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNS-SLQEKIKELKAEK--------NELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~-~L~eeik~Lk~Ek--------nELrdEk~~Lk~ekekLe~qlk  173 (236)
                      ..+|-+|+.+|..+++.-..+.+ .++..|+.+....        .+|+.+...|+.++.+||++++
T Consensus        41 ~eEak~~vddl~~q~k~~~~e~e~K~~r~i~~ml~~~~~~r~~~~~~l~~rvd~Lerqv~~Lenk~k  107 (108)
T COG3937          41 AEEAKRFVDDLLRQAKEAQGELEEKIPRKIEEMLSDLEVARQSEMDELTERVDALERQVADLENKLK  107 (108)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhHHHhhhHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence            36788899998888875444332 2333344433333        4677777777777777777765

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

Probab=83.27  E-value=6.7  Score=33.78  Aligned_cols=49  Identities=20%  Similarity=0.427  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      +++|..+++.+...++.|+.|+-.|..+.|-+.+....|+.|-..|=+.
T Consensus       132 ~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~R  180 (194)
T PF08614_consen  132 IKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLEEENRELVER  180 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3355555555555666677777777777777777777777666665443

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.

>smart00787 Spc7 Spc7 kinetochore protein

Probab=83.23  E-value=6.6  Score=36.89  Aligned_cols=12  Identities=33%  Similarity=0.241  Sum_probs=5.0

Q ss_pred             HHHhHHHHhhhc
Q 026599           91 LNDKFVELASIL  102 (236)
Q Consensus        91 LNerF~eL~slL  102 (236)
                      |+.....|..++
T Consensus       163 L~~~~~~l~~~~  174 (312)
T smart00787      163 LMKELELLNSIK  174 (312)
T ss_pred             HHHHHHHHHHHH
Confidence            334444444444

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

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

Probab=82.90  E-value=12  Score=37.11  Aligned_cols=47  Identities=23%  Similarity=0.342  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      +|+.++.+++.++.++..++.+...+.++++..+..+...+..|+.|
T Consensus        63 kL~~~lk~~e~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~l~~l~~q  109 (420)
T COG4942          63 KLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNARLNALEVQ  109 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444444444444444444433

>TIGR00219 mreC rod shape-determining protein MreC

Probab=82.81  E-value=4.3  Score=37.34  Aligned_cols=15  Identities=20%  Similarity=0.286  Sum_probs=7.2

Q ss_pred             HHHhhhhHHHHHHHH
Q 026599          133 LKDSNSSLQEKIKEL  147 (236)
Q Consensus       133 Lk~~n~~L~eeik~L  147 (236)
                      |+++|+.|.+++.+|
T Consensus        71 l~~EN~~Lr~e~~~l   85 (283)
T TIGR00219        71 LEYENYKLRQELLKK   85 (283)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            444555555444444

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.

>TIGR00219 mreC rod shape-determining protein MreC

Probab=82.80  E-value=7.4  Score=35.83  Aligned_cols=45  Identities=20%  Similarity=0.324  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKA  163 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~  163 (236)
                      +.+-+.-+.+|++|.++|++++..|..+...   ...+|+.||.+|+.
T Consensus        61 ~~~~~~~~~~l~~EN~~Lr~e~~~l~~~~~~---~~~~l~~EN~rLr~  105 (283)
T TIGR00219        61 ISENLKDVNNLEYENYKLRQELLKKNQQLEI---LTQNLKQENVRLRE  105 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH
Confidence            3444445556677888888877766444322   22335555555554

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.

>COG1256 FlgK Flagellar hook-associated protein [Cell motility and secretion]

Probab=82.70  E-value=10  Score=38.43  Aligned_cols=79  Identities=23%  Similarity=0.300  Sum_probs=55.8

Q ss_pred             HHHHHHHHHhHHHHhhhcC-CCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           85 KLRRDRLNDKFVELASILE-PGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKA  163 (236)
Q Consensus        85 R~RRdkLNerF~eL~slL~-P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~  163 (236)
                      --=+..||+-|..|..+.. |.  ...-|.+||+.|=.++.++...-+.|+.....+..+|.....+.|.|-++...|-.
T Consensus       107 ~sl~~~L~~ff~s~q~la~~P~--~~a~r~~vl~~a~~l~~~in~~~~~L~~l~~~i~~~I~~~V~~vNsLl~qIa~lN~  184 (552)
T COG1256         107 SSLSTLLNDFFNSLQELASNPS--DTAARQAVLSKAQTLVNQINNTYEQLTDLRKDINAEIAATVDEVNSLLKQIADLNK  184 (552)
T ss_pred             ccHHHHHHHHHHHHHHHHhCcc--cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            3345678888888888872 33  24678889999988888888888888777777777777777777766555444444


Q ss_pred             HH
Q 026599          164 EK  165 (236)
Q Consensus       164 ek  165 (236)
                      +|
T Consensus       185 qI  186 (552)
T COG1256         185 QI  186 (552)
T ss_pred             HH
Confidence            43

>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1)

Probab=82.56  E-value=4.7  Score=33.61  Aligned_cols=65  Identities=31%  Similarity=0.419  Sum_probs=41.8

Q ss_pred             HHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHH-HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           91 LNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQL-RSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEK  165 (236)
Q Consensus        91 LNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqL-r~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ek  165 (236)
                      |++.+..|-.=|   +       +.|.|-+-+..++ +..-++++.....-..-|-.|+.|+|-|++||..|+.|.
T Consensus        54 L~e~i~~LE~RL---R-------aGlCDRC~VtqE~akK~qqefe~s~~qsLq~i~~L~nE~n~L~eEN~~L~eEl  119 (120)
T PF10482_consen   54 LHENIKVLENRL---R-------AGLCDRCTVTQELAKKKQQEFESSHLQSLQHIFELTNEMNTLKEENKKLKEEL  119 (120)
T ss_pred             HHHHHHHHHHHH---h-------cccchHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence            555555555555   1       3345555555554 334556666555444468889999999999999998875

At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].

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

Probab=82.52  E-value=7.6  Score=34.87  Aligned_cols=48  Identities=21%  Similarity=0.275  Sum_probs=29.4

Q ss_pred             HHhhhcCCCCCCCCchhhhH-----------HHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Q 026599           97 ELASILEPGRPPKTDKAAIL-----------IDAVRMVTQLRSEAQKLKDSNSSLQEKIK  145 (236)
Q Consensus        97 eL~slL~P~~~~K~DKAsIL-----------~dAI~ylkqLr~qv~~Lk~~n~~L~eeik  145 (236)
                      .|.+|+|-+. -..+|..+-           .+--.|+.+|.++.+...+...+|.+.+.
T Consensus        47 vLQsLvDD~l-V~~eKIgtSnyywsfps~a~~~~ks~~qeLe~~L~~~~qk~~tl~e~~e  105 (203)
T KOG3433|consen   47 VLQSLVDDGL-VIKEKIGTSNYYWSFPSEAICDRKSVLQELESQLATGSQKKATLGESIE  105 (203)
T ss_pred             HHHHHhccch-HHHHHhcccccccccchHHHHHHHHHHHHHHHHHHHhhhhHhHHHHHHH
Confidence            4666665553 345555544           33345677788888877777766666543

>PF14282 FlxA: FlxA-like protein

Probab=82.25  E-value=6  Score=31.46  Aligned_cols=54  Identities=17%  Similarity=0.282  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEK----IKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~ee----ik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      -..|+.|+.+++.|.+.+..|...    .+.-......|..+...|.+++-.++.+..
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~   75 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQA   75 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566777777777777766666551    112222222344445555555555444443

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

Probab=81.84  E-value=34  Score=38.15  Aligned_cols=9  Identities=44%  Similarity=0.630  Sum_probs=4.5

Q ss_pred             CCCCCcccc
Q 026599           29 SASGFTWTV   37 (236)
Q Consensus        29 ~~~~f~w~~   37 (236)
                      |.=||++..
T Consensus       396 PFIGfTy~~  404 (1317)
T KOG0612|consen  396 PFIGFTYTH  404 (1317)
T ss_pred             Ceeeeeecc
Confidence            334566653

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=81.70  E-value=16  Score=34.69  Aligned_cols=50  Identities=24%  Similarity=0.322  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      -|+||=+.=|.+-+.|..+.+.       |..+-.+||+.-+.|..||..|.+.|..
T Consensus       238 AAtRYRqKkRae~E~l~ge~~~-------Le~rN~~LK~qa~~lerEI~ylKqli~e  287 (294)
T KOG4571|consen  238 AATRYRQKKRAEKEALLGELEG-------LEKRNEELKDQASELEREIRYLKQLILE  287 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6788876655555555444444       4444444555555555555555554443

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

Probab=81.70  E-value=13  Score=29.49  Aligned_cols=53  Identities=19%  Similarity=0.357  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKEL--KAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~L--k~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      ..|++++.+.+.....++.+++.|  ..+.++|+-+...++.++..++.+|+.++
T Consensus        38 ~~l~~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~   92 (106)
T PF10805_consen   38 EKLEERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVS   92 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            344455555566666666666666  66666666666666666666666666654

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

>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family

Probab=81.63  E-value=5.5  Score=37.21  Aligned_cols=62  Identities=19%  Similarity=0.307  Sum_probs=34.4

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 026599           87 RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKN  152 (236)
Q Consensus        87 RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn  152 (236)
                      =|+++|+.=.+.+++++ ....+.+.   +.+.-.-+++|++++++++.+.+.+.++++++....+
T Consensus         4 l~~~~~~~~~~~r~l~~-~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (378)
T TIGR01554         4 LKEQREEIVAEIRSLLD-KAEKLEKE---LTAAALEKEELETDVEKLKEEIKLLEDAIADLEKVTE   65 (378)
T ss_pred             HHHHHHHHHHHHHHHHh-hhhhhhHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            37788888888888884 11112222   2222223446666666666666666666555544333

This family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease.

>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]

Probab=81.39  E-value=5.5  Score=37.79  Aligned_cols=60  Identities=23%  Similarity=0.381  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hCCCCCCCC
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM-STQPSFLTP  184 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~-~~~p~~~p~  184 (236)
                      -|+..|+....+.+++...+..+..+.++|.....+-|.|.|++.+.|.++ ++.|+||..
T Consensus       109 vlk~aIq~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdE  169 (338)
T KOG3647|consen  109 VLKSAIQAIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRLEALQSIRPAHMDE  169 (338)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHH
Confidence            345555555556666666667777777788888888889999999999986 567888765

>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=81.36  E-value=12  Score=38.22  Aligned_cols=37  Identities=32%  Similarity=0.512  Sum_probs=30.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       139 ~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      .|...++-+..||.+|++|++.|+..+++|+..|..+
T Consensus       421 Elks~lrv~qkEKEql~~EkQeL~~yi~~Le~r~~~~  457 (546)
T PF07888_consen  421 ELKSSLRVAQKEKEQLQEEKQELLEYIERLEQRLDKV  457 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444456667788999999999999999999999885

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 [].

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

Probab=81.36  E-value=12  Score=34.92  Aligned_cols=14  Identities=14%  Similarity=0.389  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHHHHh
Q 026599          162 KAEKEKIEQQLKAM  175 (236)
Q Consensus       162 k~ekekLe~qlk~~  175 (236)
                      ..+.+.++.|+...
T Consensus       112 ~~e~~sl~~q~~~~  125 (314)
T PF04111_consen  112 QEERDSLKNQYEYA  125 (314)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            33444444444443

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.

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

Probab=81.33  E-value=14  Score=31.48  Aligned_cols=13  Identities=31%  Similarity=0.296  Sum_probs=8.6

Q ss_pred             HHHHhHHHHhhhc
Q 026599           90 RLNDKFVELASIL  102 (236)
Q Consensus        90 kLNerF~eL~slL  102 (236)
                      .+...|.+|++=+
T Consensus        55 ~~~a~~~eLr~el   67 (177)
T PF07798_consen   55 LFKAAIAELRSEL   67 (177)
T ss_pred             HHHHHHHHHHHHH
Confidence            4556677777766

>PF14282 FlxA: FlxA-like protein

Probab=81.26  E-value=8.1  Score=30.70  Aligned_cols=54  Identities=19%  Similarity=0.340  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHH----hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKD----SNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIE  169 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~----~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe  169 (236)
                      +..--+-|+.|+.++++|..    ..+.-++.++.|..++..|......|..++..-+
T Consensus        21 I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~~~   78 (106)
T PF14282_consen   21 IEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAEQQ   78 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444445555555544    1123334444444455555444444444443333

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=81.14  E-value=5.7  Score=41.05  Aligned_cols=40  Identities=25%  Similarity=0.383  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      +..--+.|+.|+.+++.|+..++.++.+|..|+.+..+++
T Consensus       424 i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~  463 (652)
T COG2433         424 IKKLEETVERLEEENSELKRELEELKREIEKLESELERFR  463 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455666666666666666666666555555555443

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=81.09  E-value=7.2  Score=39.06  Aligned_cols=55  Identities=29%  Similarity=0.506  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEK---------------IKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~ee---------------ik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      .-+..|..+.+.|+++|+.|+..               -.++..+..+|.+|.+.|+..+..|+.+|+.+
T Consensus        73 ~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l~~~  142 (472)
T TIGR03752        73 KRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRLAGV  142 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34555666666777777776542               23444455555555555566666666666543

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.

>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=81.06  E-value=5.9  Score=28.92  Aligned_cols=37  Identities=22%  Similarity=0.473  Sum_probs=24.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          138 SSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       138 ~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ..|+.++..+....+-+|.|++.++.+++++++-++-
T Consensus         3 ~elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~   39 (55)
T PF05377_consen    3 DELENELPRIESSINTVKKENEEISESVEKIEENVKD   39 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566666666666666677777777777776666655

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) [].

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=80.73  E-value=13  Score=32.45  Aligned_cols=60  Identities=18%  Similarity=0.375  Sum_probs=39.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      .=|.+++..|.+=+.+...|.+-|.-|.+........-..|.+|...|..+-+++..+|.
T Consensus        60 ~dLe~~l~rLeEEqqR~~~L~qvN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~  119 (182)
T PF15035_consen   60 PDLEEALIRLEEEQQRSEELAQVNALLREQLEQARKANEALQEDLQKLTQDWERLRDELE  119 (182)
T ss_pred             ccHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            446667777766666677777777777666666666555666666666666666555554

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

Probab=80.69  E-value=9.5  Score=28.11  Aligned_cols=50  Identities=14%  Similarity=0.254  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      ..|.+|+.++.-++..++.|.+.+-....+...|+.+...|...+..++.
T Consensus         4 ~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~~   53 (69)
T PF04102_consen    4 ERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELED   53 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            45666777777777777777766666666666777666666666666553

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.

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=80.68  E-value=11  Score=33.63  Aligned_cols=47  Identities=26%  Similarity=0.458  Sum_probs=26.4

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          113 AAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKA  163 (236)
Q Consensus       113 AsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~  163 (236)
                      ..=.-+.+..+.+|+++.++|++++..|+.+..++    +++++||.+|+.
T Consensus        61 ~~~~~~~~~~~~~l~~en~~L~~e~~~l~~~~~~~----~~l~~en~~L~~  107 (276)
T PRK13922         61 VSGVFESLASLFDLREENEELKKELLELESRLQEL----EQLEAENARLRE  107 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHH
Confidence            33344445556666666667776666666654433    245555555554

>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function

Probab=80.65  E-value=10  Score=31.69  Aligned_cols=50  Identities=18%  Similarity=0.378  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +|..+++.|....++..+-++..+.+..+++++....+.+++.+++-+..
T Consensus        65 hLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~  114 (126)
T PF07889_consen   65 HLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVEG  114 (126)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            34456666665555555555556666666666666666666666555544

The region featured in this family is approximately 100 amino acids long.

>PRK02224 chromosome segregation protein; Provisional

Probab=80.48  E-value=14  Score=38.13  Aligned_cols=41  Identities=27%  Similarity=0.426  Sum_probs=17.4

Q ss_pred             HHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          134 KDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       134 k~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +.....+++++..+..+..++.++...++.++.+++.+++.
T Consensus       257 ~~~~~~l~~~i~~~e~~~~~l~~~i~~~~~~~~~le~e~~~  297 (880)
T PRK02224        257 EAEIEDLRETIAETEREREELAEEVRDLRERLEELEEERDD  297 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444444444444444444444444444444443333

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=80.42  E-value=6  Score=31.53  Aligned_cols=32  Identities=13%  Similarity=0.328  Sum_probs=18.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       139 ~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      .++.++.+++.+..+|+++|..|+.|+++|+.
T Consensus        31 ~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~   62 (105)
T PRK00888         31 RVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG   62 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            34445555555555666666666666666654

>PRK05771 V-type ATP synthase subunit I; Validated

Probab=80.39  E-value=7.2  Score=39.31  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=12.6

Q ss_pred             HHHHHHHHHhHHHHhhhc
Q 026599           85 KLRRDRLNDKFVELASIL  102 (236)
Q Consensus        85 R~RRdkLNerF~eL~slL  102 (236)
                      .++.+++++.+..|+...
T Consensus        49 ~~~~~~~~~~l~~L~~~~   66 (646)
T PRK05771         49 RSLLTKLSEALDKLRSYL   66 (646)
T ss_pred             HHHHHHHHHHHHHHHHhc
Confidence            345666777777777776

>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=80.33  E-value=7.8  Score=36.94  Aligned_cols=49  Identities=22%  Similarity=0.439  Sum_probs=38.7

Q ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hC
Q 026599          129 EAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM-ST  177 (236)
Q Consensus       129 qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~-~~  177 (236)
                      +.+++...+..|+.+++.+..|+.|+..|....+....||+++|-.+ +.
T Consensus       134 qLEk~~~q~~qLe~d~qs~lDEkeEl~~ERD~yk~K~~RLN~ELn~~L~g  183 (319)
T PF09789_consen  134 QLEKLREQIEQLERDLQSLLDEKEELVTERDAYKCKAHRLNHELNYILNG  183 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            34677777888888888888888888888888888888888888773 44

>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold)

Probab=80.27  E-value=12  Score=30.65  Aligned_cols=38  Identities=18%  Similarity=0.250  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKA  163 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~  163 (236)
                      |..+-..|+..+..|+.+...+...+++|+.+...+..
T Consensus        35 L~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~   72 (107)
T PF09304_consen   35 LAKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARR   72 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33334444444444444444444444444444443333

The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=80.22  E-value=12  Score=27.56  Aligned_cols=33  Identities=27%  Similarity=0.353  Sum_probs=14.4

Q ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          130 AQKLKDSNSSLQEKIKELKAEKNELRDEKQRLK  162 (236)
Q Consensus       130 v~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk  162 (236)
                      ...+..+...++.++..++.|.++|+.|...|.
T Consensus        26 ~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~   58 (85)
T TIGR02209        26 TRQLNNELQKLQLEIDKLQKEWRDLQLEVAELS   58 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            334444444444444444444444444444443

This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.

>PF15294 Leu_zip: Leucine zipper

Probab=80.19  E-value=5.5  Score=37.31  Aligned_cols=58  Identities=26%  Similarity=0.411  Sum_probs=41.8

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          112 KAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       112 KAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      |-.-|.+. .-.--|..++.+|+++|++|.+.++.+.......-+|+..|+.++..|+.
T Consensus       117 KL~pl~e~-g~~~ll~kEi~rLq~EN~kLk~rl~~le~~at~~l~Ek~kl~~~L~~lq~  174 (278)
T PF15294_consen  117 KLEPLNES-GGSELLNKEIDRLQEENEKLKERLKSLEKQATSALDEKSKLEAQLKELQD  174 (278)
T ss_pred             cccccccc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444443 22344667788888888888888888888888888888888888777776

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

Probab=80.17  E-value=8  Score=28.26  Aligned_cols=58  Identities=16%  Similarity=0.317  Sum_probs=34.0

Q ss_pred             CchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          110 TDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       110 ~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      -+|-..|.++-..|.+...-+.+++-+...+..      .+++.+.......+++..+|+.+|+
T Consensus        21 ~~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~------s~r~~~~~kl~~yr~~l~~lk~~l~   78 (79)
T PF05008_consen   21 EQRKSLIREIERDLDEAEELLKQMELEVRSLPP------SERNQYKSKLRSYRSELKKLKKELK   78 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-H------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCH------HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            456666666666666666666666655544432      4445555555566666666666664

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.

>PRK14127 cell division protein GpsB; Provisional

Probab=80.03  E-value=11  Score=30.78  Aligned_cols=26  Identities=35%  Similarity=0.556  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          149 AEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       149 ~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .|..+|++|+..|+.++..++.++..
T Consensus        44 ~e~~~Lk~e~~~l~~~l~e~~~~~~~   69 (109)
T PRK14127         44 KEIEELQQENARLKAQVDELTKQVSV   69 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            33444445555555555555555543

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

Probab=80.03  E-value=7.9  Score=39.40  Aligned_cols=37  Identities=35%  Similarity=0.542  Sum_probs=26.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       139 ~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      .|+.++..++..+.-|.+|+..||.|..+|..+|+.+
T Consensus       152 ~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~  188 (546)
T KOG0977|consen  152 ELEAEINTLKRRIKALEDELKRLKAENSRLREELARA  188 (546)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Confidence            3444556667777777778888888888888877764

---

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	236
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	6e-13
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	7e-13
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	1e-12
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	6e-09
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	5e-08
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	2e-07
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	4e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	9e-07
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	5e-04
4f3l_A	361	Mclock, circadian locomoter output cycles protein	3e-06
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	2e-05
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	4e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	6e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	9e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	2e-04
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	2e-04
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	3e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	5e-04

>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 = 61.6 bits (150), Expect = 6e-13
 Identities = 16/72 (22%), Positives = 29/72 (40%)

Query: 84  EKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEK 143
           E+ RRD + D F  L   +   +  K  +A IL  A   +  +R +    +     L+ +
Sbjct: 10  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 69

Query: 144 IKELKAEKNELR 155
              L+ +   L 
Sbjct: 70  NALLEQQVRALG 81

>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 = 61.6 bits (150), Expect = 7e-13
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 84  EKLRRDRLNDKFVELASIL-EPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE 142
           E+ RR+ L   F  L   + E     K  K  IL  A   +  +++E QKL      L++
Sbjct: 14  ERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK 73

Query: 143 KIKELKAEKNELR 155
           + ++LK +  +L 
Sbjct: 74  RREQLKHKLEQLG 86

>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 = 60.5 bits (147), Expect = 1e-12
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 84  EKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEK 143
           EK  R  +NDK +EL  ++  G   K +K+A+L  A+  +  L+   QKLK  N SL+  
Sbjct: 14  EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72

Query: 144 IKELKAEK 151
           + + K+ K
Sbjct: 73  VHKSKSLK 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 = 50.8 bits (122), Expect = 6e-09
 Identities = 14/60 (23%), Positives = 25/60 (41%)

Query: 84  EKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEK 143
           E+ RRD + D F  L   +   +  K  +A IL  A   +  +R +    +     L+ +
Sbjct: 20  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 79

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387

 Score = 51.5 bits (123), Expect = 5e-08
 Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 7/85 (8%)

Query: 63  ESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASIL--EPGRPPKTDKAAIL---I 117
           E ++ + R ++   + S+   EK RRD++N    ELAS++        K DK  +L   +
Sbjct: 2   EYAEHQGRIKNAREAHSQI--EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAV 59

Query: 118 DAVRMVTQLRSEAQKLKDSNSSLQE 142
             ++ +    +   +     + L +
Sbjct: 60  QHMKTLRGATNPYTEANYKPTFLSD 84

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 1/72 (1%)

Query: 84  EKLRRDRLNDKFVELASIL-EPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE 142
           EK RR  L     +L  ++       +    ++L  A   + +L    +K       LQ 
Sbjct: 9   EKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR 68

Query: 143 KIKELKAEKNEL 154
           + + LK +  +L
Sbjct: 69  EQRHLKRQLEKL 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 = 46.2 bits (110), Expect = 2e-07
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 84  EKLRRDRLNDKFVELASIL----EPGRPPKTDKAAILIDAVRMVTQLRSEAQK 132
           E+ RRD++N+  V+L+ I+             K  IL  A   + +LR    +
Sbjct: 13  ERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 49.4 bits (118), Expect = 4e-07
 Identities = 28/122 (22%), Positives = 55/122 (45%), Gaps = 7/122 (5%)

Query: 62   KESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVR 121
            +   +K +  E   + +      +  R RL  K  EL  IL        +  A + +   
Sbjct: 889  QLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILH-------EMEARIEEEEE 941

Query: 122  MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSF 181
               QL++E +K++     L+E+++E +A + +L+ EK     + +K+E  +  M  Q + 
Sbjct: 942  RSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNK 1001

Query: 182  LT 183
            LT
Sbjct: 1002 LT 1003

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 48.3 bits (115), Expect = 9e-07
 Identities = 19/120 (15%), Positives = 51/120 (42%), Gaps = 2/120 (1%)

Query: 61   LKESSKKRVRSESCGSSSSKACREKLRR--DRLNDKFVELASILEPGRPPKTDKAAILID 118
            LK   +  +          +  R++L +   +L  +  +L   +   +    +  A L  
Sbjct: 1033 LKNKHESMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAK 1092

Query: 119  AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
                +    +  +      ++  +KI+EL++  ++L+++ +  KA + K E+Q + +S +
Sbjct: 1093 KEEELQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEE 1152

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 42.9 bits (101), Expect = 5e-05
 Identities = 17/117 (14%), Positives = 47/117 (40%)

Query: 62   KESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVR 121
             E+       E     ++K    +     +  +  E     +  +  K      ++D   
Sbjct: 903  AETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEE 962

Query: 122  MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
             + +  +  QKL+    +   KIK+++ +   + D+  +L  E++ +E+++  ++T 
Sbjct: 963  QLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTN 1019

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.0 bits (96), Expect = 3e-04
 Identities = 13/89 (14%), Positives = 32/89 (35%)

Query: 87   RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKE 146
            +   L ++  E  +  +  +  K      +      +  +  +  KL      L+E++ +
Sbjct: 956  QMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSD 1015

Query: 147  LKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
            L     E  ++ + L   K K E  +  +
Sbjct: 1016 LTTNLAEEEEKAKNLTKLKNKHESMISEL 1044

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 15/60 (25%), Positives = 33/60 (55%)

Query: 121  RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPS 180
            +   +L    +KL+  +S L E+I EL+A+  EL+ +  + + E +    +L+  ++Q +
Sbjct: 1053 KSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKN 1112

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score = 46.5 bits (110), Expect = 3e-06
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 8/77 (10%)

Query: 64  SSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRM- 122
           + ++  + ++   S +K+  EK RRD+ N    EL S+L PG   K DK+ +L    +  
Sbjct: 2   AVEEDDKDKAKRVSRNKS--EKKRRDQFNVLIKELGSML-PGNARKMDKSTVL----QKS 54

Query: 123 VTQLRSEAQKLKDSNSS 139
           +  LR   +    S++S
Sbjct: 55  IDFLRKHKETTAQSDAS 71

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli} Length = 81

 Score = 41.1 bits (96), Expect = 2e-05
 Identities = 16/57 (28%), Positives = 37/57 (64%)

Query: 119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM 175
           A+  +T L+ E ++LK+ N+SL ++++  + ++ EL  E   LK ++   +++L+A+
Sbjct: 18  AIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL 74

>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 Length = 62

 Score = 39.3 bits (92), Expect = 4e-05
 Identities = 11/44 (25%), Positives = 26/44 (59%)

Query: 131 QKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
           ++  +  + L+EK+K LKA+ +EL      L+ +  +++Q++  
Sbjct: 18  KRKLERIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMN 61

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

 Score = 42.8 bits (101), Expect = 6e-05
 Identities = 13/60 (21%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 123  VTQLRSEAQKLKDSNSSLQEKIKELKAE----KNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
            + +LR E  + +    +++E   + K E     +EL+++   LK EKE++ +++   + +
Sbjct: 993  IAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSELKEQNTLLKTEKEELNRRIHDQAKE 1052

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

 Score = 42.0 bits (99), Expect = 9e-05
 Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 125 QLRSEA---QKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
           +L+ EA   ++ K  +  L+ KI +L+ + +E   E + L  +   +E      + +
Sbjct: 908 KLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEK 964

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

 Score = 40.9 bits (96), Expect = 2e-04
 Identities = 14/117 (11%), Positives = 40/117 (34%), Gaps = 21/117 (17%)

Query: 62  KESSKKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVR 121
           +E  K ++ + S         R K     L +K ++L   ++              +  +
Sbjct: 904 RELKKLKIEARSVE-------RYKKLHIGLENKIMQLQRKID--------------EQNK 942

Query: 122 MVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
               L  +   L+ + S+  EK++          +E +        +++++  +  +
Sbjct: 943 EYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKE 999

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1 Length = 61

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 14/44 (31%), Positives = 25/44 (56%)

Query: 131 QKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
           QK K    SL++K ++L +   +L+ E   L+ E  +++Q L A
Sbjct: 18  QKRKVWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLLLA 61

>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 Length = 63

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 15/44 (34%), Positives = 25/44 (56%)

Query: 131 QKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA 174
            + ++   +LQ +  +L+ EK+ L+ E   L  EKEK+E  L A
Sbjct: 19  NRRRELTDTLQAETDQLEDEKSALQTEIANLLKEKEKLEFILAA 62

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 4e-04
 Identities = 26/192 (13%), Positives = 58/192 (30%), Gaps = 51/192 (26%)

Query: 9   W-LLDYP------LIDDITVPDGNFSVSASGFTWTVQPPINGPSNGCV----EIDSAFGD 57
           W LL          ++++   +  F +S        +     PS        + D  + D
Sbjct: 69  WTLLSKQEEMVQKFVEEVLRINYKFLMSP----IKTEQ--RQPSMMTRMYIEQRDRLYND 122

Query: 58  SNGLKESSKKR-------------VRSES---------CGSSS--SKACREKLRRDRLND 93
           +    + +  R             +R             G +      C     + +++ 
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182

Query: 94  K-F-VELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEK 151
           K F + L +   P          +L    +++ Q+        D +S+++ +I  ++AE 
Sbjct: 183 KIFWLNLKNCNSPE--------TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234

Query: 152 NELRDEKQRLKA 163
             L   K     
Sbjct: 235 RRLLKSKPYENC 246

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens} Length = 168

 Score = 38.6 bits (89), Expect = 5e-04
 Identities = 12/58 (20%), Positives = 30/58 (51%), Gaps = 3/58 (5%)

Query: 124 TQLRSE---AQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQ 178
             LR+E   A +L+ S++ + + I +L++   EL++  + L+  K + ++    +   
Sbjct: 20  DLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQLQAI 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	236
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.73
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.65
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.64
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.62
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.58
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.57
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.56
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.46
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.42
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.4
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.25
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.09
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.0
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	98.92
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	98.91
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.84
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.64
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	97.81
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.55
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	96.51
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.24
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	95.92
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	95.43
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	94.95
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	94.78
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	94.62
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	94.55
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	93.79
2oqq_A	42	Transcription factor HY5; homodimer leucine zipper	93.78
3he5_B	52	Synzip2; heterodimeric coiled-coil, de novo protei	93.55
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	93.28
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	93.11
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.95
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	92.08
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	91.99
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	91.52
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	91.39
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	91.17
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	91.09
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	90.97
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	90.89
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	90.81
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	90.79
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	90.47
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	90.42
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	90.42
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	90.32
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	90.22
3htk_A	60	Structural maintenance of chromosomes protein 5; S	90.16
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	90.09
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	89.99
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	89.93
3swf_A	74	CGMP-gated cation channel alpha-1; coiled-coil, as	89.76
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	89.37
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	89.3
3swy_A	46	Cyclic nucleotide-gated cation channel alpha-3; co	89.15
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	89.08
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	88.94
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	88.79
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	88.71
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	88.62
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	88.36
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	88.32
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	88.26
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	88.15
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	87.83
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	87.5
3vmx_A	48	Voltage-gated hydrogen channel 1; coiled-coil, ION	87.41
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	87.19
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	87.16
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	87.12
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	87.11
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	87.05
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	87.0
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	86.71
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	86.68
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	86.63
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	86.59
3u06_A	412	Protein claret segregational; motor domain, stalk	86.2
2w6a_A	63	ARF GTPase-activating protein GIT1; PIX, zinc, sig	86.16
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	85.92
3htk_A	60	Structural maintenance of chromosomes protein 5; S	85.89
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	85.26
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	84.7
3v86_A	27	De novo design helix; computational design of A pr	84.56
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	84.41
2wt7_B	90	Transcription factor MAFB; transcription, transcri	84.34
1c1g_A	284	Tropomyosin; contractIle protein; 7.00A {Sus scrof	84.3
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	83.76
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	83.53
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	83.47
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	83.47
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	83.46
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	82.98
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	82.86
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	82.86
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	82.71
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	82.62
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	82.26
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	82.21
2zvf_A	171	Alanyl-tRNA synthetase; C-terminal, oligomerizatio	81.79
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	81.77
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	81.6
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	81.46
3m48_A	33	General control protein GCN4; leucine zipper, synt	81.42
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	81.2
3a2a_A	58	Voltage-gated hydrogen channel 1; voltage-gated pr	81.13
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	80.55
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	80.47
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	80.22
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	80.03

>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=99.73  E-value=8.4e-18  Score=126.58  Aligned_cols=70  Identities=33%  Similarity=0.476  Sum_probs=64.4

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELK  148 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk  148 (236)
                      .+|+..||+||++||++|.+|+++| |+...|+||++||.+||+||++|+.+++.|++++..|..+++..+
T Consensus         8 ~~H~~~ErrRR~~in~~f~~L~~lv-P~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~~~~   77 (82)
T 1am9_A            8 TAHNAIEKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-TCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHHHHhc-cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3699999999999999999999999 776679999999999999999999999999999999988876554

>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=99.65  E-value=4e-16  Score=119.15  Aligned_cols=75  Identities=25%  Similarity=0.386  Sum_probs=61.0

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCC--CCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRP--PKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNE  153 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~--~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknE  153 (236)
                      .+|+.+||+||++||+.|..|+++| |..+  .|++|++||..||+||+.|+.+.+.|..+.+.|+.+...|+.+..+
T Consensus         8 ~~Hn~~ER~RR~~ln~~f~~Lr~~v-P~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~n~~L~~rl~~   84 (88)
T 1nkp_A            8 RTHNVLERQRRNELKRSFFALRDQI-PELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQ   84 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTC-GGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999999999999999 8642  5999999999999999999998888877665555544444444333

>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=99.64  E-value=4.4e-16  Score=116.51  Aligned_cols=69  Identities=23%  Similarity=0.347  Sum_probs=56.6

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC-CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR-PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKEL  147 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~-~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~L  147 (236)
                      ..|+.+||+||++||+.|.+|+++| |.. ..|++|++||..||+||+.|+.++++|+.+.+.|..+...|
T Consensus         4 ~~hn~~Er~RR~~in~~f~~Lr~lv-P~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~~L   73 (83)
T 1nkp_B            4 AHHNALERKRRDHIKDSFHSLRDSV-PSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALL   73 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTS-GGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHhhhHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999999999999999 653 36999999999999999999998888866544444433333

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=99.62  E-value=5.8e-16  Score=123.84  Aligned_cols=84  Identities=25%  Similarity=0.393  Sum_probs=52.4

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC---CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR---PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNEL  154 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~---~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknEL  154 (236)
                      ..|+..||+||++||++|.+|+++| |++   ..|++|++||.+||+||+.|+.++++|+++...+           ..|
T Consensus        29 ~~Hn~~ERrRR~~In~~~~~L~~lv-P~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~~~-----------~~l   96 (118)
T 4ati_A           29 DNHNLIERRRRFNINDRIKELGTLI-PKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQ-----------KKL   96 (118)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHS-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC----------------
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHH-hhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHH
Confidence            4799999999999999999999999 765   2489999999999999999999999998754322           234


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 026599          155 RDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       155 rdEk~~Lk~ekekLe~qlk  173 (236)
                      +.++..|...+..||.|.+
T Consensus        97 ~~~n~~L~~riqeLE~~a~  115 (118)
T 4ati_A           97 EHANRHLLLRVQELEMQAR  115 (118)
T ss_dssp             -------------------
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            4555566666666665544

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

Probab=99.58  E-value=7.5e-15  Score=110.55  Aligned_cols=74  Identities=22%  Similarity=0.266  Sum_probs=62.5

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKN  152 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn  152 (236)
                      .+|+..||+||++||+.|..|+++| |..  ..|.+|++||..|++||++|+.+.++|..+++.|..+...|+.+.+
T Consensus         3 ~~HN~~ER~RR~~lk~~f~~Lr~~v-P~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e~~~L~~~L~   78 (80)
T 1nlw_A            3 STHNEMEKNRRAHLRLSLEKLKGLV-PLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLE   78 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSS-CCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHc-CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3689999999999999999999999 753  2589999999999999999999999888877777766666655443

>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=99.57  E-value=4.7e-15  Score=110.50  Aligned_cols=65  Identities=23%  Similarity=0.379  Sum_probs=58.5

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC-CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR-PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEK  143 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~-~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~ee  143 (236)
                      ..|+.+||+||++||+.|.+|+++| |.. ..|++|++||..||+||+.|+.++++|+.+++.|..+
T Consensus        14 ~~hn~~Er~RR~~in~~f~~Lr~lv-P~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~~   79 (80)
T 1hlo_A           14 AHHNALERKRRDHIKDSFHSLRDSV-PSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   79 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS-GGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHC-cCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4699999999999999999999999 764 2599999999999999999999999999888877653

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.56  E-value=3.4e-15  Score=110.96  Aligned_cols=56  Identities=32%  Similarity=0.469  Sum_probs=50.7

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLK  134 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk  134 (236)
                      .+|+..||+||++||++|.+|+++| |+...|+||++||..||+||++|+.++.=|+
T Consensus        10 ~~Hn~iErrRRd~IN~~i~eL~~Lv-P~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B           10 VSRNKSEKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTS-SSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhhhHHHhhHHHHHHHHHHHHHHhC-CCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            3699999999999999999999999 7655799999999999999999999876553

>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=99.46  E-value=1.6e-14  Score=103.49  Aligned_cols=53  Identities=28%  Similarity=0.474  Sum_probs=47.4

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCC-----CCCchhhhHHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRP-----PKTDKAAILIDAVRMVTQLRSEAQ  131 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~-----~K~DKAsIL~dAI~ylkqLr~qv~  131 (236)
                      .+|+..||+||++||+.|.+|+++| |++.     .|+||++||.+||+||++|+.+.+
T Consensus         7 ~~H~~~Er~RR~~in~~~~~L~~lv-P~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            7 AQHNEVERRRRDKINNWIVQLSKII-PDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHS-CCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HhhchHHHHHHHHHHHHHHHHHHHC-cCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            5799999999999999999999999 7653     278999999999999999987653

>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=99.42  E-value=4.9e-14  Score=101.85  Aligned_cols=52  Identities=31%  Similarity=0.456  Sum_probs=46.5

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC------CCCCchhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR------PPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~------~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      .+|...||+||++||..|.+|+++| |++      ..|.+||+||..||+||++|+.++
T Consensus         4 ~~H~~aEr~RR~rIn~~~~~L~~Ll-P~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            4 ESHKHAEQARRNRLAVALHELASLI-PAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TGGGGGTHHHHHHHHHHHHHHHHTS-CHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHC-CCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            4799999999999999999999999 742      258889999999999999998765

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.40  E-value=6.2e-14  Score=104.29  Aligned_cols=50  Identities=38%  Similarity=0.466  Sum_probs=45.5

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC---CCCCchhhhHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR---PPKTDKAAILIDAVRMVTQLRS  128 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~---~~K~DKAsIL~dAI~ylkqLr~  128 (236)
                      ..|+..||+||++||+.|.+|++|| |.+   ..|+|||+||..||+||+.|+.
T Consensus        11 ~~H~~~ERrRR~rIN~~l~eL~~Lv-P~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A           11 EAHSQIEKRRRDKMNSFIDELASLV-PTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS-HHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HhcchHHHHHHHHHHHHHHHHHHHc-cccccccccccHHHHHHHHHHHHHHHhc
Confidence            4699999999999999999999999 754   2699999999999999999874

>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=3.6e-12  Score=95.34  Aligned_cols=57  Identities=25%  Similarity=0.318  Sum_probs=48.4

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCC-C-CCCC-chhhhHHHHHHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPG-R-PPKT-DKAAILIDAVRMVTQLRSEAQKLKD  135 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~-~-~~K~-DKAsIL~dAI~ylkqLr~qv~~Lk~  135 (236)
                      ..|+.+||+||+.||+.|.+|+.+| |. . ..|. .|++||..||+||+.|+.++++++.
T Consensus         7 ~~hN~~ER~Rr~~IN~~f~~Lr~~v-P~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            7 AHHNALERKRRRDINEAFRELGRMC-QMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHHHH-HHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             hhchHHHhhhHHHHHHHHHHHHHHc-CCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4689999999999999999999999 63 1 2355 7999999999999999999988753

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.09  E-value=7.2e-11  Score=106.01  Aligned_cols=52  Identities=33%  Similarity=0.512  Sum_probs=42.9

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      .+|+..||+|||+||+.|.+|++|| |+...|+||++||..||.||+.|+...
T Consensus        14 ~~~~~~e~~rr~~~n~~~~~l~~~~-p~~~~~~dk~~il~~~~~~~~~~~~~~   65 (361)
T 4f3l_A           14 VSRNKSEKKRRDQFNVLIKELGSML-PGNARKMDKSTVLQKSIDFLRKHKETT   65 (361)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHTC-CSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHhC-CCCCCCcCHHHHHHHHHHHHHHHHhhc
Confidence            4688899999999999999999999 754479999999999999999987643

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=99.00  E-value=2.8e-09  Score=81.43  Aligned_cols=74  Identities=26%  Similarity=0.413  Sum_probs=54.6

Q ss_pred             HHHHHHhHHHHhhhcCCC---CCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           88 RDRLNDKFVELASILEPG---RPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAE  164 (236)
Q Consensus        88 RdkLNerF~eL~slL~P~---~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~e  164 (236)
                      |+.||++|.+|+.+| |.   ...|.+|++||..||+||+.|+.+.++++++...+           ..|...|..|...
T Consensus         4 R~nIN~~I~EL~~Li-P~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r~-----------k~le~~n~~l~~r   71 (83)
T 4ath_A            4 RFNINDRIKELGTLI-PKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQ-----------KKLEHANRHLLLR   71 (83)
T ss_dssp             HHHHHHHHHHHHHHS-CCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHHH-----------HHHHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccC-CCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHhhhhhHHHHHH
Confidence            889999999999999 53   23589999999999999999999988887654322           1233445555555


Q ss_pred             HHHHHHHHH
Q 026599          165 KEKIEQQLK  173 (236)
Q Consensus       165 kekLe~qlk  173 (236)
                      +-.||-|-+
T Consensus        72 iqELE~qa~   80 (83)
T 4ath_A           72 VQELEMQAR   80 (83)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555544

>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=98.92  E-value=1.1e-09  Score=80.44  Aligned_cols=52  Identities=23%  Similarity=0.351  Sum_probs=46.3

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC-CCCCchhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR-PPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~-~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      ..|+.+||+|+..||+.|..|+.+| |.. ..|++|+.||..||+||..|+..+
T Consensus        14 ~~aN~rER~R~~~iN~af~~LR~~i-P~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           14 KAATMRERRRLSKVNEAFETLKRST-SSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTS-CSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hHhhHHHHHHHHHHHHHHHHHHHhc-CCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3589999999999999999999999 653 359999999999999999998754

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=98.91  E-value=1.7e-09  Score=77.43  Aligned_cols=51  Identities=24%  Similarity=0.208  Sum_probs=45.9

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      .++.+||.|+..||+.|..|+.+| |..  ..|++|+.||..||+||..|++.+
T Consensus         5 ~~N~rER~R~~~iN~af~~LR~~l-P~~~~~~klSKi~tLr~Ai~YI~~L~~~L   57 (60)
T 2ql2_B            5 KANARERNRMHGLNAALDNLRKVV-PCYSKTQKLSKIETLRLAKNYIWALSEIL   57 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTS-SSCCSSSCCCHHHHHHHHHHHHHHHHHHT
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHc-cCCCCcCcCCHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999 754  249999999999999999998765

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.84  E-value=1.9e-09  Score=98.19  Aligned_cols=52  Identities=37%  Similarity=0.455  Sum_probs=45.5

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCC---CCCCCchhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPG---RPPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~---~~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      .+|+..||+||+++|+.|.+|++|| |.   ...|+||++||..||.||+.|+...
T Consensus        15 ~~~~~~ek~rR~~~n~~~~~L~~l~-p~~~~~~~k~dk~~il~~~~~~l~~~~~~~   69 (387)
T 4f3l_B           15 EAHSQIEKRRRDKMNSFIDELASLV-PTCNAMSRKLDKLTVLRMAVQHMKTLRGAT   69 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHC-HHHHHCSSCCCHHHHHHHHHHHHHHHHCC-
T ss_pred             ccccchhhcchHHHHHHHHHHHHhc-CCCCccccccCHHHHHHHHHHHHHHhhccc
Confidence            3699999999999999999999999 72   2369999999999999999998543

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.64  E-value=1.1e-08  Score=75.63  Aligned_cols=50  Identities=20%  Similarity=0.337  Sum_probs=44.0

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCC--CCCchhhhHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRP--PKTDKAAILIDAVRMVTQLRS  128 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~--~K~DKAsIL~dAI~ylkqLr~  128 (236)
                      ..-+++||+|+..||+-|..|+.+| |..+  .|++|..||.-||+||..|+.
T Consensus        16 ~~a~erER~Rm~~lN~aF~~LR~~V-P~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           16 GPAAEEPLSLLDDMNHCYSRLRELV-PGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCCBCCCSCSSSHHHHHHHHHHHHC-CCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            3456899999999999999999999 7642  499999999999999999974

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=97.81  E-value=0.00014  Score=55.33  Aligned_cols=60  Identities=27%  Similarity=0.506  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +..||+-|.-|+-++++|++.|..|.++..+++.....|++||..|+.|...++..|.++
T Consensus        15 Iq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~wq~Rl~~L   74 (81)
T 2jee_A           15 VQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQAL   74 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999999999999999999999999874

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=97.55  E-value=0.00014  Score=56.87  Aligned_cols=55  Identities=16%  Similarity=0.192  Sum_probs=45.3

Q ss_pred             hHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHHhh
Q 026599           82 CREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEAQKLKDSN  137 (236)
Q Consensus        82 ~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n  137 (236)
                      .+||.|=..+|+-|..|+..| |..  ..|+.|..||.-||+||..|+.-++.-...+
T Consensus        31 ~~~r~Rm~~lN~AF~~LR~~v-P~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~~~~   87 (97)
T 4aya_A           31 DDPMSLLYNMNDCYSKLKELV-PSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKPS   87 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHC-TTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTTSTT
T ss_pred             ccHHHHHHHHHHHHHHHHHHC-CCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence            346778888999999999999 754  2499999999999999999998776544433

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=96.51  E-value=0.015  Score=44.07  Aligned_cols=56  Identities=29%  Similarity=0.423  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHh
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQR-------LKAEKEKIEQQLKAM  175 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~-------Lk~ekekLe~qlk~~  175 (236)
                      .+++.+|..+|+.+-+.+.-|+.|+.+||.+.+.|.+++..       |..+..+|.++...+
T Consensus         5 ~ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~w   67 (81)
T 2jee_A            5 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGW   67 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence            47889999999999999999999999998888888888877       556777777766654

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

Probab=96.24  E-value=0.04  Score=44.87  Aligned_cols=83  Identities=18%  Similarity=0.208  Sum_probs=45.3

Q ss_pred             HHHHHHhHHHHhhh--cCCCCCCCCchhhhHHH--HH-HH------HHHHHHHHHH-------HHHhhhhHHHHHHHHHH
Q 026599           88 RDRLNDKFVELASI--LEPGRPPKTDKAAILID--AV-RM------VTQLRSEAQK-------LKDSNSSLQEKIKELKA  149 (236)
Q Consensus        88 RdkLNerF~eL~sl--L~P~~~~K~DKAsIL~d--AI-~y------lkqLr~qv~~-------Lk~~n~~L~eeik~Lk~  149 (236)
                      -..+|+++.++++.  - |..  -.++.+||.-  .+ +|      +.+|+.++++       |+.++..++.++.+++.
T Consensus        34 A~~vd~km~ei~~~~~~-~~l--~~~r~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~  110 (138)
T 3hnw_A           34 ASYINNKITEFNKEESY-RRM--SAELRTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAK  110 (138)
T ss_dssp             HHHHHHHHHHHTTCHHH-HTS--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCC-CCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35789999999976  6 554  6788888752  11 22      2233333333       33333334444445555


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          150 EKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       150 EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +..+|++++..|..++-+||..++
T Consensus       111 e~~~l~~~~~~l~~~~~~le~~~~  134 (138)
T 3hnw_A          111 EIKELKSEINKYQKNIVKLETELN  134 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555555555555555555544

>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=95.92  E-value=0.011  Score=43.57  Aligned_cols=41  Identities=20%  Similarity=0.246  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQR  160 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~  160 (236)
                      -.||++|..+|..|+..+..|..++..|+.+...|+.|+..
T Consensus        28 ~~~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~~   68 (70)
T 1gd2_E           28 EDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRI   68 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46888888888888877776655555555444444444443

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

Probab=95.43  E-value=0.057  Score=43.96  Aligned_cols=43  Identities=28%  Similarity=0.330  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEK  165 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ek  165 (236)
                      +..|+.++..++..++.+..++.+|+.+.++|+.++..|.++.
T Consensus        91 ~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~  133 (138)
T 3hnw_A           91 IYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETEL  133 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555555555555555555555555443

>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=94.95  E-value=0.051  Score=38.51  Aligned_cols=36  Identities=33%  Similarity=0.517  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      ..++.+|+.++..|+.+|..|..+|..|+.|+..|+
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            457777788888888777777777766665555554

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

Probab=94.78  E-value=0.2  Score=41.87  Aligned_cols=91  Identities=15%  Similarity=0.114  Sum_probs=42.7

Q ss_pred             HHHH-HHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 026599           83 REKL-RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRL  161 (236)
Q Consensus        83 rER~-RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~L  161 (236)
                      .+|. =|++|-.+|.+|-+-+ -+.++. .=+|=+.+-+..|..|+.+...|+..+..|.+++++-......|+||...|
T Consensus        31 ~~rL~~Rd~~E~~~~~l~~e~-~~~~~~-~~vs~~~~~~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aL  108 (152)
T 3a7p_A           31 IRRLTDRNDKEAHLNELFQDN-SGAIGG-NIVSHDDALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISG  108 (152)
T ss_dssp             ---------------------------C-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHHHHhh-ccCCCc-ccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444 4677666676666654 121111 123333444556777777777777777777777666555566678888877


Q ss_pred             HHHHHHHHHHHHHh
Q 026599          162 KAEKEKIEQQLKAM  175 (236)
Q Consensus       162 k~ekekLe~qlk~~  175 (236)
                      ..+..-+|..++.+
T Consensus       109 qlq~n~lE~kl~kL  122 (152)
T 3a7p_A          109 TIENNVLQQKLSDL  122 (152)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            77777777766653

>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=94.62  E-value=0.07  Score=37.36  Aligned_cols=34  Identities=29%  Similarity=0.393  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNEL  154 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknEL  154 (236)
                      .|+.+|+.++..|+.+|..|..++..|+.|...|
T Consensus        22 ~~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~L   55 (61)
T 1t2k_D           22 VWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQL   55 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555666666666665555555554444443333

>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=94.55  E-value=0.048  Score=38.01  Aligned_cols=38  Identities=18%  Similarity=0.307  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHH-------HHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          118 DAVRMVTQLRS-------EAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       118 dAI~ylkqLr~-------qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      +|++||++--.       .++.|+.+|..|+.++..|+.+..||+
T Consensus         2 ~AlefIk~~LG~~~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el~   46 (53)
T 2yy0_A            2 SALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKLK   46 (53)
T ss_dssp             --------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68888887644       455555555555555555554444443

>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=93.79  E-value=0.08  Score=37.23  Aligned_cols=34  Identities=24%  Similarity=0.383  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNEL  154 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknEL  154 (236)
                      .|+.+|+.++..|+.+|..|..++..|..|...|
T Consensus        22 ~~~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~~L   55 (62)
T 1jnm_A           22 ERIARLEEKVKTLKAQNSELASTANMLREQVAQL   55 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666666666666666655555444444433

>2oqq_A Transcription factor HY5; homodimer leucine zipper; 2.00A {Arabidopsis thaliana}

Probab=93.78  E-value=0.14  Score=34.48  Aligned_cols=35  Identities=29%  Similarity=0.548  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      .||.+|..++..|+..|..|++.+..|..|-.=||
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            49999999999999999999998877776544444

>3he5_B Synzip2; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=93.55  E-value=0.17  Score=34.84  Aligned_cols=43  Identities=33%  Similarity=0.414  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEK  167 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekek  167 (236)
                      -|+.++.+|++.|-+|+..-+.|..-...||||..+|..|...
T Consensus         7 ylrkkiarlkkdnlqlerdeqnlekiianlrdeiarlenevas   49 (52)
T 3he5_B            7 YLRKKIARLKKDNLQLERDEQNLEKIIANLRDEIARLENEVAS   49 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHHHHHHHHHhh
Confidence            4788999999999888877777777777888888888776543

>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=93.28  E-value=0.19  Score=37.37  Aligned_cols=49  Identities=20%  Similarity=0.171  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIE  169 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe  169 (236)
                      .-|.+|+..+++-.++....++.|++|..+..|..++...|+.+.++++
T Consensus        19 gti~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfr   67 (72)
T 3nmd_A           19 GSLRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYR   67 (72)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3388899888888888888888899999999998888888888887764

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=93.11  E-value=0.091  Score=36.58  Aligned_cols=31  Identities=29%  Similarity=0.385  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEK  151 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ek  151 (236)
                      .||.+|..+|..|+.+|..|..++..|+.+.
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~~   52 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALKDLY   52 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5777777777777777777777766666543

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

Probab=92.95  E-value=0.21  Score=35.44  Aligned_cols=16  Identities=31%  Similarity=0.572  Sum_probs=5.9

Q ss_pred             HHHHHHHHHHhhhhHH
Q 026599          126 LRSEAQKLKDSNSSLQ  141 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~  141 (236)
                      |..+++.|+.+|..|.
T Consensus        28 le~~~~~L~~~N~~L~   43 (63)
T 1ci6_A           28 LTGECKELEKKNEALK   43 (63)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333333333333333

>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=92.08  E-value=0.93  Score=35.69  Aligned_cols=58  Identities=26%  Similarity=0.430  Sum_probs=37.4

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          109 KTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE-------KIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       109 K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~e-------eik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      .|+|.-++.+-+.    |...+..|+++|..|+.       .+.+|..|...|+.||+.|+.|.+-+.+
T Consensus        29 ~mSKqELIqEYl~----LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~~~~   93 (104)
T 3s9g_A           29 NMSKQELIKEYLE----LEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENELHRQ   93 (104)
T ss_dssp             TSCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHH----HHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            5778877776554    55566666666666655       4566666666666666666666555444

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

Probab=91.99  E-value=1.4  Score=33.41  Aligned_cols=34  Identities=21%  Similarity=0.597  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          141 QEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       141 ~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +.+|..|+....++..|+..|..|+..|+..+..
T Consensus        55 e~~i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~~   88 (93)
T 3s4r_A           55 EEEMRELRRQVDQLTNDKARVEVERDNLAEDIMR   88 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3446667777777777777777777777766654

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=91.52  E-value=0.66  Score=34.32  Aligned_cols=50  Identities=12%  Similarity=0.251  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      ..+..+++.++.+|..|++.+..|+....+-+.+-..++.|..++-++|-
T Consensus         3 ~~~~~kLq~~E~~N~~Le~~v~~le~~Le~s~~~q~~~~~Elk~~~e~Ld   52 (72)
T 3cve_A            3 HNSHMKLQEVEIRNKDLEGQLSEMEQRLEKSQSEQDAFRSNLKTLLEILD   52 (72)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35667778888888888888888888888877777778787777776654

>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=91.39  E-value=0.51  Score=32.87  Aligned_cols=37  Identities=27%  Similarity=0.362  Sum_probs=21.2

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          136 SNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       136 ~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      ....|+.++..|+.+..+|+.+...|+.|+..|.++|
T Consensus        23 ~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk~~l   59 (61)
T 1t2k_D           23 WVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLL   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445555555666555566666666666665555544

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

Probab=91.17  E-value=1.1  Score=35.62  Aligned_cols=52  Identities=25%  Similarity=0.381  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAE----KNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~E----knELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .++|+..+..|..+++.+.++.+....+    .+.|++|...|+..++.+...|+-
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~El~~lr~~~~~l~~~iRe   60 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRE   60 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566677777766666665555444333    344555555555555555555443

>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=91.09  E-value=0.81  Score=35.78  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIK  145 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik  145 (236)
                      +..|+.+++.|+.++..|.+++.
T Consensus        14 ~~~lr~ei~~Le~E~~rLr~~~~   36 (100)
T 1go4_E           14 ADTLRLKVEELEGERSRLEEEKR   36 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444433

>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=90.97  E-value=0.28  Score=34.95  Aligned_cols=28  Identities=25%  Similarity=0.425  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELK  148 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk  148 (236)
                      .++.+|+.+++.|+.+|..|..++..|+
T Consensus        30 ~~~~~Le~~v~~L~~eN~~L~~ev~~Lr   57 (63)
T 2dgc_A           30 QRMKQLEDKVEELLSKNYHLENEVARLK   57 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555444444444443333

>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=90.89  E-value=0.74  Score=42.88  Aligned_cols=16  Identities=25%  Similarity=0.331  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHHHHH
Q 026599          159 QRLKAEKEKIEQQLKA  174 (236)
Q Consensus       159 ~~Lk~ekekLe~qlk~  174 (236)
                      ..++.|...+.++++.
T Consensus       561 ~~l~~e~~~~~~~~~~  576 (597)
T 3oja_B          561 AELRQETSLKRQKVKQ  576 (597)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444444444444444

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

Probab=90.81  E-value=1.3  Score=31.28  Aligned_cols=45  Identities=31%  Similarity=0.364  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKA  163 (236)
Q Consensus       119 AI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~  163 (236)
                      |.+|=..=+.+.+.|+.+...|..+..+|+.+.+.|+.|+..|+.
T Consensus        14 A~R~R~KKk~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk~   58 (63)
T 1ci6_A           14 ATRYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYLKD   58 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444445555555555555555555555554444444443

>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=90.79  E-value=2.1  Score=31.83  Aligned_cols=32  Identities=25%  Similarity=0.375  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          144 IKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       144 ik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ..++.....+|..||..|+.+++.|+.++..+
T Consensus        38 ~~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~L   69 (78)
T 1gu4_A           38 NLETQHKVLELTAENERLQKKVEQLSRELSTL   69 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555566666666666666666666654

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

Probab=90.47  E-value=0.31  Score=43.58  Aligned_cols=44  Identities=20%  Similarity=0.388  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCC
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPS  180 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~~p~  180 (236)
                      +++|+.+++.|...|+.|.+++              ..++.|+.+|+.||+.+..||.
T Consensus        56 l~eL~~ql~~L~arNe~L~~~L--------------k~ar~El~~LkeElerL~sPPL   99 (251)
T 3m9b_A           56 IHQLEARIDSLAARNSKLMETL--------------KEARQQLLALREEVDRLGQPPS   99 (251)
T ss_dssp             HHHHHHHHHHHTTTHHHHHHHH--------------HHHHHHHHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHhcCCCc
Confidence            4455555555555544444333              3344445555555666666663

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=90.42  E-value=0.72  Score=42.89  Aligned_cols=54  Identities=20%  Similarity=0.370  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      |.+|+++++.|+++...|+++++.++.+..++.++.........+|.++++.+.
T Consensus         5 ~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~elk   58 (403)
T 4etp_A            5 IAALKEKIAALKEKIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQELR   58 (403)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            457888888888888888888888888888888877777777888888888863

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

Probab=90.42  E-value=1.7  Score=37.26  Aligned_cols=59  Identities=25%  Similarity=0.383  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAE----KNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~E----knELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      |..+=.-+++|+.++..|+.+...+..+.+....+    .+.|++|.+.|+..+..|...|..
T Consensus        51 L~~~Ek~~~~L~~~~~~L~~E~e~~k~K~~~~~~e~~~~~~~Lq~el~~l~~~~~~l~~~ire  113 (189)
T 2v71_A           51 LVQAEQRNRDLQADNQRLKYEVEALKEKLEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRE  113 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555666666666666655555554444444    555666666666666666555543

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

Probab=90.32  E-value=1.7  Score=36.81  Aligned_cols=76  Identities=20%  Similarity=0.364  Sum_probs=42.2

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           87 RRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKE  166 (236)
Q Consensus        87 RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~eke  166 (236)
                      -|+.|-.-+..|.+.|+-.+       .-...+-+.+++|+.++..|..+++.+.+....+..+...|.+....|..++.
T Consensus        63 ~k~~Leke~~~LQa~L~qEr-------~~r~q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a  135 (168)
T 3o0z_A           63 SKSQTDKDYYQLQAILEAER-------RDRGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKN  135 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35556666666666662221       11233445566666666666666665555555555555555555555555555


Q ss_pred             HHH
Q 026599          167 KIE  169 (236)
Q Consensus       167 kLe  169 (236)
                      .++
T Consensus       136 ~~e  138 (168)
T 3o0z_A          136 NLE  138 (168)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            555

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

Probab=90.22  E-value=1.1  Score=35.87  Aligned_cols=25  Identities=20%  Similarity=0.340  Sum_probs=15.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhh
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNS  138 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~  138 (236)
                      .|..++=+||.+|+.+|..|+.+++
T Consensus        33 ~l~~E~q~~v~ql~~~i~~Le~eL~   57 (120)
T 3i00_A           33 NMKTESQRVVLQLKGHVSELEADLA   57 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666666665544

>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=90.16  E-value=2.3  Score=28.90  Aligned_cols=51  Identities=18%  Similarity=0.225  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +.+|+..+..++.....+..+...++...+++..+......+|.+++.+++
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~   57 (60)
T 3htk_A            7 KKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNE   57 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555555544455555555555555555555556666666655554

>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=90.09  E-value=0.89  Score=31.99  Aligned_cols=37  Identities=38%  Similarity=0.472  Sum_probs=20.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          137 NSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       137 n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +..|+.++..|+.+..+|+.+...|+.|+..|...|.
T Consensus        25 ~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~~l~   61 (63)
T 2wt7_A           25 TDTLQAETDQLEDEKSALQTEIANLLKEKEKLEFILA   61 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555555555555555555555555555543

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=89.99  E-value=2  Score=32.58  Aligned_cols=56  Identities=23%  Similarity=0.373  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +-|.=|++|+-+|.+|+.+--+-+.+++.-+.|...|++....-.+++++|+.+|-
T Consensus        23 ~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~   78 (81)
T 3qh9_A           23 ELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLS   78 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence            44567888999999888766666666777777777788777777888888888875

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

Probab=89.93  E-value=1.4  Score=33.66  Aligned_cols=47  Identities=19%  Similarity=0.434  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      ..|+.+++.|+.+-..|..++..|..++.++..+...++.+.++|..
T Consensus         7 ~~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L~~   53 (96)
T 3q8t_A            7 EQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERLDQ   53 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhh
Confidence            44555555555555555555555555555555555555555555443

>3swf_A CGMP-gated cation channel alpha-1; coiled-coil, assembly domain, transport protein; 2.14A {Bos taurus}

Probab=89.76  E-value=0.97  Score=33.72  Aligned_cols=49  Identities=27%  Similarity=0.409  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ++|.++|++|+...+.||....-|-.|....+   .+||+.+.+||.+++..
T Consensus         3 ~dlEEKv~~LE~sld~LQTrfARLLaEy~ssQ---~KLKqRit~LE~~~~~~   51 (74)
T 3swf_A            3 MGLEEKVTRMESSVDLLQTRFARILAEYESMQ---QKLKQRLTKVEKFLKPL   51 (74)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHhccc
Confidence            45788999999999999999888887766543   78999999999999973

>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=89.37  E-value=2.8  Score=33.04  Aligned_cols=61  Identities=18%  Similarity=0.301  Sum_probs=37.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          114 AILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       114 sIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ..|.++-+....|..+-..|+.....+.+.+.+.....++|..++..|..++..|+.+|..
T Consensus        62 ~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~led  122 (129)
T 2fxo_A           62 DNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDIDD  122 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566777777777666666666666665555555555555555555555555555555554

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

Probab=89.30  E-value=1.5  Score=33.28  Aligned_cols=55  Identities=20%  Similarity=0.318  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHH----HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEK----IKE-LKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~ee----ik~-Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +-|+.|..+...|+.+...++..    +.. -..+..+||.....+..++.+++.++..|
T Consensus        23 dKVR~LEqqN~~Le~~i~~l~~~~~~~~~~~ye~~i~~Lr~~i~~~~~ek~~l~~e~dnl   82 (93)
T 3s4r_A           23 DKVRFLEQQNKILLAELEQLKGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNL   82 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33455555555555444444332    111 24556667777777777777777777654

>3swy_A Cyclic nucleotide-gated cation channel alpha-3; coiled-coil, assembly domain, transport protein; 1.90A {Homo sapiens}

Probab=89.15  E-value=1.3  Score=30.13  Aligned_cols=45  Identities=27%  Similarity=0.388  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      +|.+.|++|+...+.|+....-|-.|....   -.+||..+.+||.++
T Consensus         2 dlEekv~~Le~~ld~LqTr~ArLlae~~ss---q~KlKqRit~lE~~v   46 (46)
T 3swy_A            2 ALEEKVEQLGSSLDTLQTRFARLLAEYNAT---QMKMKQRLSQLESQV   46 (46)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHhcC
Confidence            578889999999999999888877776654   367999999998763

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1

Probab=89.08  E-value=0.72  Score=33.75  Aligned_cols=39  Identities=18%  Similarity=0.321  Sum_probs=27.7

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          136 SNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       136 ~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .+..|+.++.+|..+...|..||..|+.++..|..+++.
T Consensus        30 ~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~~   68 (70)
T 1gd2_E           30 HLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRI   68 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344566666666666667778888888888888887764

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=88.94  E-value=1.2  Score=31.33  Aligned_cols=40  Identities=25%  Similarity=0.376  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKA  163 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~  163 (236)
                      .||-.||+.|+.+|..|..|++.=....+.|..|..-+|.
T Consensus         6 dQL~~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKe   45 (54)
T 1deb_A            6 DQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKE   45 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHH
Confidence            4788899999999998887765555555554444444443

>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=88.79  E-value=2.1  Score=36.94  Aligned_cols=39  Identities=10%  Similarity=0.237  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 026599          116 LIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNEL  154 (236)
Q Consensus       116 L~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknEL  154 (236)
                      ++=++.-+..|+.++..|.++|..|+.+++.|..+..++
T Consensus       127 fd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~  165 (213)
T 1ik9_A          127 IAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKA  165 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555555666666666655555555555444444443

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

Probab=88.71  E-value=1.2  Score=33.51  Aligned_cols=49  Identities=24%  Similarity=0.427  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +..+++.++..|..|++.+..|.....+-+.+-..++.|+.++-++|-.
T Consensus        11 ~~~klq~~E~rN~~Le~~v~~le~~Le~s~~~q~~~~~Elk~l~e~Ld~   59 (79)
T 3cvf_A           11 TQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLDV   59 (79)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4456777777777777777777777777777777777777777666543

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=88.62  E-value=3  Score=31.61  Aligned_cols=29  Identities=28%  Similarity=0.438  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          146 ELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       146 ~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ++..+..+|..||..|+.+++.|+.++..
T Consensus        40 e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~   68 (87)
T 1hjb_A           40 ETQHKVLELTAENERLQKKVEQLSRELST   68 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444455555555555555555555554

>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=88.36  E-value=0.45  Score=33.34  Aligned_cols=32  Identities=34%  Similarity=0.547  Sum_probs=12.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQ  170 (236)
Q Consensus       139 ~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~  170 (236)
                      .|+.++..|+.+..+|+.+...|..|+..|.+
T Consensus        26 ~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk~   57 (62)
T 1jnm_A           26 RLEEKVKTLKAQNSELASTANMLREQVAQLKQ   57 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444443333

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

Probab=88.32  E-value=1.2  Score=46.28  Aligned_cols=24  Identities=29%  Similarity=0.534  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          149 AEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       149 ~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      ...+.|++||+.|+++++.|+.++
T Consensus      1023 ~kv~~L~~e~~~L~qq~~~l~~~~ 1046 (1080)
T 2dfs_A         1023 QLVSELKEQNTLLKTEKEELNRRI 1046 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333445556666666666665433

>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=88.26  E-value=1.6  Score=30.22  Aligned_cols=41  Identities=32%  Similarity=0.468  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKI  168 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekL  168 (236)
                      +-+.+|+.++..|...|..|.+..+       +.|++...|+.++++|
T Consensus         9 ~r~~~l~~~l~~L~~rN~rL~~~L~-------~AR~el~~Lkeele~L   49 (51)
T 3m91_A            9 RDIHQLEARIDSLAARNSKLMETLK-------EARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Confidence            3455777777777777777766543       4455566666666665

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

Probab=88.15  E-value=0.45  Score=42.53  Aligned_cols=41  Identities=15%  Similarity=0.214  Sum_probs=29.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          115 ILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       115 IL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      =+.+....+.+|..+.++|++....+..|+..|+.|.+.|+
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            35566777788888888888888888877766666655543

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=87.83  E-value=1.9  Score=42.30  Aligned_cols=72  Identities=18%  Similarity=0.134  Sum_probs=49.7

Q ss_pred             HHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHH-HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599           90 RLNDKFVELASILEPGRPPKTDKAAILIDAVRMVT-QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEK  165 (236)
Q Consensus        90 kLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylk-qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ek  165 (236)
                      .++..+..+..+|    ..+...+.=+..++.-|. +|+.+++.|+.++..-...|+.|+.-..+++.+.++|...|
T Consensus        82 dseqy~k~~~E~L----r~rq~q~~dNdNtynE~S~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDI  154 (562)
T 3ghg_A           82 DSHSLTTNIMEIL----RGDFSSANNRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDI  154 (562)
T ss_dssp             HHHHHHHHHHHTT----SSHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH----HHHHHhhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445566666666    134444445555555555 89999999988776655778888888888888888886655

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=87.50  E-value=0.82  Score=34.72  Aligned_cols=29  Identities=24%  Similarity=0.384  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNE  153 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknE  153 (236)
                      +++.++..|+.+|..|..+|..|+.|...
T Consensus        40 e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~   68 (87)
T 1hjb_A           40 ETQHKVLELTAENERLQKKVEQLSRELST   68 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555444444333

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}

Probab=87.41  E-value=1.5  Score=30.33  Aligned_cols=41  Identities=29%  Similarity=0.372  Sum_probs=30.0

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          127 RSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       127 r~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      +.++.+|++.|..|-..+.+|...++++       ..||++|+.-|+.
T Consensus         3 eq~l~kLKe~n~~L~~kv~~Le~~c~~~-------eQEieRL~~LLkq   43 (48)
T 3vmx_A            3 ERQILRLKQINIQLATKIQHLEFSCSEK-------EQEIERLNKLLKQ   43 (48)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHccHH-------HHHHHHHHHHHHH
Confidence            3567889999999988887777666664       4566777766664

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=87.19  E-value=2.3  Score=28.86  Aligned_cols=23  Identities=35%  Similarity=0.605  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEK  143 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~ee  143 (236)
                      .++.||..++..|+.+|+.|..+
T Consensus         3 nlvaqlenevaslenenetlkkk   25 (49)
T 3he5_A            3 NLVAQLENEVASLENENETLKKK   25 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhhcccHHHHHh
Confidence            46789999999999999888755

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=87.16  E-value=9.9  Score=35.28  Aligned_cols=40  Identities=20%  Similarity=0.380  Sum_probs=24.6

Q ss_pred             HhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          135 DSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       135 ~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ++...++..+++-+....|+++|++.+++++..|++.+..
T Consensus       544 ~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~~  583 (597)
T 3oja_B          544 QENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKNR  583 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             hhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3344444445555556667777777777777777766654

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=87.12  E-value=3  Score=32.44  Aligned_cols=18  Identities=22%  Similarity=0.259  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHhhhhH
Q 026599          123 VTQLRSEAQKLKDSNSSL  140 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L  140 (236)
                      |.+|+.++...+.+...|
T Consensus        14 l~~le~~~~~~~~e~~~L   31 (97)
T 2eqb_B           14 YNTLKRELSDRDDEVKRL   31 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHH
Confidence            333333333333333333

>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=87.11  E-value=2.2  Score=29.50  Aligned_cols=23  Identities=4%  Similarity=0.215  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Q 026599          153 ELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       153 ELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      .|-+-...-+.++.+|..+|..+
T Consensus        27 rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           27 KLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHh
Confidence            44555555666666666666554

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

Probab=87.05  E-value=2.3  Score=44.29  Aligned_cols=22  Identities=9%  Similarity=0.205  Sum_probs=12.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Q 026599          155 RDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       155 rdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      ++....|+.|+.+|++|+..++
T Consensus      1022 ~~kv~~L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A         1022 EQLVSELKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3444456666666666665543

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=87.00  E-value=1.7  Score=32.19  Aligned_cols=50  Identities=16%  Similarity=0.137  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      |..++.+|+....-++.-|.+|....-+...+...|+.+...|..+++.+
T Consensus        12 le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~rl~~~   61 (78)
T 3efg_A           12 LEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKV   61 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444444444444444444444444444445555555555555555544

>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=86.71  E-value=1.5  Score=34.33  Aligned_cols=43  Identities=30%  Similarity=0.438  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCC
Q 026599          141 QEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSFLT  183 (236)
Q Consensus       141 ~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~~p~~~p  183 (236)
                      .+++..|+.++.+|+.|+..|+.+|+.||-+|......-.|-|
T Consensus        11 ~e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~Gd~~~   53 (100)
T 1go4_E           11 REEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQ   53 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSCCCT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCC
Confidence            3467778888888888999999999999999988655555544

>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=86.63  E-value=5.4  Score=31.36  Aligned_cols=55  Identities=18%  Similarity=0.303  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      ...+.+.......|......|...++++.....+..+.+..|.+++.+++.++..
T Consensus        61 ~~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~  115 (129)
T 2fxo_A           61 QDNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSE  115 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444445555555555666666666666666666677777777777666654

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.59  E-value=0.78  Score=43.02  Aligned_cols=43  Identities=21%  Similarity=0.448  Sum_probs=30.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCC
Q 026599          139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMSTQPSF  181 (236)
Q Consensus       139 ~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~~~p~~  181 (236)
                      .|+.+++.|..+.+.+++|...|+.|..+++.+++.+...|.+
T Consensus        53 ~le~~~~~L~~e~e~l~~~~~~~~~e~~~~~ee~~~l~~~~~~   95 (428)
T 4b4t_K           53 KLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPLV   95 (428)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSCEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCce
Confidence            4445555666666677777778888888888888888776643

>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=86.20  E-value=2.6  Score=39.40  Aligned_cols=53  Identities=13%  Similarity=0.224  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      ..|+.++.+|++..++|+++++.++.+..++.++......+..+|.++|+.+.
T Consensus         6 ~~l~~el~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~rr~l~n~~~~l~   58 (412)
T 3u06_A            6 AALSTEVVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMDLR   58 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            46888888888888888888888888888888877777778888888888864

>2w6a_A ARF GTPase-activating protein GIT1; PIX, zinc, signaling protein, CAT-1, cytoplasm, ANK repeat, coiled-coil, zinc-finger, metal-binding; 1.40A {Rattus norvegicus}

Probab=86.16  E-value=1.6  Score=31.58  Aligned_cols=36  Identities=31%  Similarity=0.529  Sum_probs=28.9

Q ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          127 RSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLK  162 (236)
Q Consensus       127 r~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk  162 (236)
                      .++|++|-+-|..|.+|++-+..+.+.|+.||..|+
T Consensus        26 eAkiQQLmkVN~~ls~Elr~mQ~~lq~LQsen~~Lr   61 (63)
T 2w6a_A           26 EAKVQQLMKVNSSLSDELRKLQREIHKLQAENLQLR   61 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHhhhHHHHHHHHHHHHHHhhhhhhc
Confidence            456788888888888888888888888888888776

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

Probab=85.92  E-value=4.6  Score=33.70  Aligned_cols=80  Identities=18%  Similarity=0.189  Sum_probs=40.4

Q ss_pred             HHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHH-------HhhhhHHHHHHHHHHHHHHHHHHHHH
Q 026599           90 RLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEAQKLK-------DSNSSLQEKIKELKAEKNELRDEKQR  160 (236)
Q Consensus        90 kLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv~~Lk-------~~n~~L~eeik~Lk~EknELrdEk~~  160 (236)
                      ++++.|.+++...+|..  .-++... .+..--.-+..|+.++..|+       ..++.|+.|+..|..+.|.+.+....
T Consensus        43 ~~~~l~~e~~~~~~~~~vs~~~~~~~-~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~k  121 (152)
T 3a7p_A           43 HLNELFQDNSGAIGGNIVSHDDALLN-TLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSD  121 (152)
T ss_dssp             --------------CHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhccCCCcccccchhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667777776663310  0122221 33444445556666666666       45677888888888888888888888


Q ss_pred             HHHHHHHHHH
Q 026599          161 LKAEKEKIEQ  170 (236)
Q Consensus       161 Lk~ekekLe~  170 (236)
                      |+.|-..|=+
T Consensus       122 Lq~EN~~LV~  131 (152)
T 3a7p_A          122 LKKEHSQLVA  131 (152)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            8887765544

>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=85.89  E-value=5.4  Score=27.02  Aligned_cols=50  Identities=26%  Similarity=0.270  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEK  167 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekek  167 (236)
                      ..-+++.++.+++..++.+...+...++.+....+..+++...++.+++.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~   58 (60)
T 3htk_A            9 TLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEY   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34456777777888888888888888888888999999999999888764

>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=85.26  E-value=1.2  Score=33.07  Aligned_cols=32  Identities=28%  Similarity=0.425  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      .+++.++..|+.+|..|..+|..|+.|...|+
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            44556667777777777766666665555544

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

Probab=84.70  E-value=3.7  Score=35.41  Aligned_cols=47  Identities=15%  Similarity=0.164  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          126 LRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       126 Lr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      |+.++..|+.....+..++..++.++..+..+...+++.+++.+.++
T Consensus        37 le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l   83 (256)
T 3na7_A           37 ALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKM   83 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333333333333333333333

>3v86_A De novo design helix; computational design of A protein crystal, helical coil, DE designed helix, de novo protein; 2.91A {Synthetic}

Probab=84.56  E-value=0.78  Score=27.84  Aligned_cols=26  Identities=35%  Similarity=0.561  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHH
Q 026599          122 MVTQLRSEAQKLKDSNSSLQEKIKEL  147 (236)
Q Consensus       122 ylkqLr~qv~~Lk~~n~~L~eeik~L  147 (236)
                      |+-||+.++-+|+-+...|..|++.|
T Consensus         1 yvyqlkdevgelkgevralkdevkdl   26 (27)
T 3v86_A            1 YVYQLKDEVGELKGEVRALKDEVKDL   26 (27)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchhhHHHHHHHhHHHHHHHHHhcc
Confidence            34556666665555555454444433

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

Probab=84.41  E-value=4.3  Score=32.28  Aligned_cols=19  Identities=21%  Similarity=0.508  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 026599          154 LRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       154 LrdEk~~Lk~ekekLe~ql  172 (236)
                      +..||..|+.++..|+.|+
T Consensus        88 l~~eKe~L~~ql~~Lq~q~  106 (110)
T 2v4h_A           88 LVEKKEYLQEQLEQLQREF  106 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHH
Confidence            3344444444444444443

>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=84.34  E-value=5.7  Score=30.39  Aligned_cols=39  Identities=18%  Similarity=0.345  Sum_probs=27.7

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          137 NSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       137 n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ...|+.+...|..+...|+.|+..+..|++.+.+.++++
T Consensus        50 ~~~LE~e~~~L~~e~~~L~~e~~~~~~e~d~~k~k~~~L   88 (90)
T 2wt7_B           50 KHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEKL   88 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345666677777777777777777777777777777654

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

Probab=84.30  E-value=7.1  Score=30.89  Aligned_cols=25  Identities=24%  Similarity=0.322  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          147 LKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       147 Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      +..+...++++...++.++.+++.+
T Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~~  273 (284)
T 1c1g_A          249 LEKSIDDLEDELYAQKLKYKAISEE  273 (284)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333333333

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=83.76  E-value=20  Score=32.68  Aligned_cols=36  Identities=17%  Similarity=0.175  Sum_probs=15.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          138 SSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       138 ~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +..+++++.++.|++.++.+...+..++++..+.++
T Consensus       438 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  473 (487)
T 3oja_A          438 DMYQHKETQLAEENARLKKLNGEADLALASANATLQ  473 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHhhhhhhhhhhhhhhhHhcccHHH
Confidence            333444444444444444444444444444443333

>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=83.53  E-value=1.6  Score=31.73  Aligned_cols=33  Identities=21%  Similarity=0.419  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          144 IKELKAEKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       144 ik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      |+.|..+..+|..|+..|+.+...|+++|.++.
T Consensus        49 I~~L~~~~~~l~~e~~~L~~~~~~L~~~l~~L~   81 (83)
T 1nkp_B           49 IQYMRRKNHTHQQDIDDLKRQNALLEQQVRALG   81 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            455666666667777777777777777776543

>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=83.47  E-value=5.3  Score=27.74  Aligned_cols=44  Identities=16%  Similarity=0.256  Sum_probs=24.0

Q ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          130 AQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       130 v~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +.+|......|..++..|+.+.+.|+.+...-|.|-.|-.++|.
T Consensus         6 i~~Lss~V~~L~~kVdqLssdV~al~~~v~~ak~eA~RAN~RlD   49 (52)
T 1jcd_A            6 ADQASSDAQTANAKADQASNDANAARSDAQAAKDDAARANQRAD   49 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            34444444444445555555555555566666666666666554

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=83.47  E-value=5.7  Score=31.23  Aligned_cols=52  Identities=15%  Similarity=0.213  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      |.-|+...+++++.+..++-+.++...+...++.....|+.+...++.+|+.
T Consensus        32 VdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~~L~q   83 (103)
T 4h22_A           32 VDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALKQ   83 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445556666666677777666666666667777777777787777777775

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=83.46  E-value=8.9  Score=29.76  Aligned_cols=49  Identities=18%  Similarity=0.389  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      .|+.++.+|+.++.....++..|..+..+-+........++.+++++|.
T Consensus         9 ~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElE   57 (97)
T 2eqb_B            9 QLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVE   57 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444443333333222233333344444443

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

Probab=82.98  E-value=13  Score=29.52  Aligned_cols=67  Identities=19%  Similarity=0.344  Sum_probs=40.5

Q ss_pred             CCchhhhHHHHHHHHHHHHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          109 KTDKAAILIDAVRMVTQLRSEAQKLKDSN----SSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       109 K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n----~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +.+|-.++..=-+-|..|+.+++.++.+.    ..|...+..|..|..+-|..++....+.+.|..++..+
T Consensus        10 ~d~rD~~Ie~Lkreie~lk~ele~l~~E~q~~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~l   80 (120)
T 3i00_A           10 KDEKDHLIERLYREISGLKAQLENMKTESQRVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDEL   80 (120)
T ss_dssp             CCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555444444444555555555555432    34555566677777776666666777777777777764

>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=82.86  E-value=4.6  Score=30.31  Aligned_cols=36  Identities=33%  Similarity=0.470  Sum_probs=19.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          139 SLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       139 ~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .|-.++.+|+.|+.-|+.|...++.-+.+++..++.
T Consensus        34 DLI~rvdELt~E~e~l~~El~s~~~~~~r~~~ri~e   69 (77)
T 2w83_C           34 DLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRE   69 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445566666666666666666666666655544

>1lwu_C Fibrinogen gamma chain; heterotrimer, protein-peptide complex, blood clotting; HET: NDG MAN NAG BMA GAL; 2.80A {Petromyzon marinus} SCOP: d.171.1.1 h.1.8.1 PDB: 1n73_C*

Probab=82.86  E-value=2.6  Score=38.65  Aligned_cols=55  Identities=20%  Similarity=0.184  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          119 AVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       119 AI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      ++.=++.|++++.+|+.......++|+.|+.....++...+.|+.++..|+..+.
T Consensus         3 ~~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l~~~~~   57 (323)
T 1lwu_C            3 GQKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQTCS   57 (323)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4445667777777777776666777777777666666666666666666665543

>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=82.71  E-value=3  Score=30.84  Aligned_cols=35  Identities=20%  Similarity=0.169  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELR  155 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELr  155 (236)
                      +=|++..+.++.|+.+.....++|++|+.+.+.+|
T Consensus        33 eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfr   67 (72)
T 3nmd_A           33 EELRQRDALIDELELELDQKDELIQMLQNELDKYR   67 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            33444555555555555555555555555555443

>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=82.62  E-value=1.6  Score=30.98  Aligned_cols=33  Identities=18%  Similarity=0.369  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          141 QEKIKELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       141 ~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      ++.+.+|..+..+|..||..|+.+++.|.++|.
T Consensus        29 ~~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l~   61 (63)
T 2dgc_A           29 LQRMKQLEDKVEELLSKNYHLENEVARLKKLVG   61 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345667777777778888888888888877764

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

Probab=82.26  E-value=9.4  Score=32.22  Aligned_cols=42  Identities=21%  Similarity=0.455  Sum_probs=17.0

Q ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          130 AQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQ  171 (236)
Q Consensus       130 v~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~q  171 (236)
                      +.+|++.+..+...+..+....+||++-...|..++..|+++
T Consensus        29 ~~rlkK~~tEl~k~~~~~E~~~rELq~~~~~L~~~k~~Leke   70 (168)
T 3o0z_A           29 AVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKD   70 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444443333344444444444444444444444333

>2ocy_A RAB guanine nucleotide exchange factor SEC2; RAB, GEF, guanine exchange factor, coiled-coil, endocytosis/exocytosis complex; 3.30A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=82.21  E-value=6.3  Score=32.79  Aligned_cols=13  Identities=15%  Similarity=0.552  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHh
Q 026599          163 AEKEKIEQQLKAM  175 (236)
Q Consensus       163 ~ekekLe~qlk~~  175 (236)
                      .++.+++++|..+
T Consensus        79 ~~~~~ie~ElEeL   91 (154)
T 2ocy_A           79 EEADKLNKEVEDL   91 (154)
T ss_dssp             THHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            4455555655554

>2zvf_A Alanyl-tRNA synthetase; C-terminal, oligomerization domain, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase, nucleotide-binding; 3.20A {Archaeoglobus fulgidus}

Probab=81.79  E-value=4  Score=32.51  Aligned_cols=46  Identities=20%  Similarity=0.275  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          119 AVRMVTQLRSEAQKLKDSN----SSLQEKIKELKAEKNELRDEKQRLKAE  164 (236)
Q Consensus       119 AI~ylkqLr~qv~~Lk~~n----~~L~eeik~Lk~EknELrdEk~~Lk~e  164 (236)
                      |++|+++.+..+.++....    ..|.+.+..|..|..+|+.|...|+.+
T Consensus         5 A~~~~~~~~~~l~~~a~~Lk~~~~~l~~~v~~l~~e~k~l~ke~~~l~~~   54 (171)
T 2zvf_A            5 AIEAVEEMERLLREASSILRVEPAKLPKTVERFFEEWKDQRKEIERLKSV   54 (171)
T ss_dssp             GTHHHHHHHHHHHHHHHTTTCCTTSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444443322    234444444444444444444444443

>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=81.77  E-value=12  Score=29.49  Aligned_cols=52  Identities=25%  Similarity=0.278  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKA-------EKNELRDEKQRLKAEKEKIEQQLKAMS  176 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~-------EknELrdEk~~Lk~ekekLe~qlk~~~  176 (236)
                      +|-.+--+|+...+.++++..-|+.       ...+|..|..+|++|..+|-++=+.+.
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            3444555566666666666555554       333445555555555555555544443

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

Probab=81.60  E-value=10  Score=30.05  Aligned_cols=19  Identities=26%  Similarity=0.562  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHh
Q 026599          157 EKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       157 Ek~~Lk~ekekLe~qlk~~  175 (236)
                      .-.++..+|+.|+.||..+
T Consensus        84 dREkl~~eKe~L~~ql~~L  102 (110)
T 2v4h_A           84 AREKLVEKKEYLQEQLEQL  102 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHhHHHHHHHHHHHH
Confidence            3346777888888888765

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

Probab=81.46  E-value=6.9  Score=33.65  Aligned_cols=22  Identities=14%  Similarity=0.243  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 026599          153 ELRDEKQRLKAEKEKIEQQLKA  174 (236)
Q Consensus       153 ELrdEk~~Lk~ekekLe~qlk~  174 (236)
                      .|..|...++.++..++.++..
T Consensus        94 aL~kEie~~~~~i~~lE~eile  115 (256)
T 3na7_A           94 SLNIEEDIAKERSNQANREIEN  115 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555566666666665555

>3m48_A General control protein GCN4; leucine zipper, synthetic peptide, alpha helix, activa amino-acid biosynthesis, DNA-binding, nucleus; 1.45A {Synthetic} PDB: 3i1g_A 2ahp_A* 2o7h_A

Probab=81.42  E-value=1.5  Score=28.13  Aligned_cols=21  Identities=24%  Similarity=0.442  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHHhhhhHHHHH
Q 026599          124 TQLRSEAQKLKDSNSSLQEKI  144 (236)
Q Consensus       124 kqLr~qv~~Lk~~n~~L~eei  144 (236)
                      +||..+|++|-.+|..|+.|+
T Consensus         3 ~QLE~kVEeLl~~n~~Le~EV   23 (33)
T 3m48_A            3 AQLEAKVEELLSKNWNLENEV   23 (33)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhHHHHHHH
Confidence            344444444444444444333

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=81.20  E-value=5.5  Score=36.43  Aligned_cols=58  Identities=14%  Similarity=0.249  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          118 DAVRMVTQLRSEAQKLKDSNSSLQ----EKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       118 dAI~ylkqLr~qv~~Lk~~n~~L~----eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      .++.+++....+.+++.++.+...    ...+....+.+.|++|+.+++.+++++..++...
T Consensus       407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  468 (487)
T 3oja_A          407 SPLQLLRAIVKRYEEMYVEQQSVQNNAIRDWDMYQHKETQLAEENARLKKLNGEADLALASA  468 (487)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhc
Confidence            445555555555555544433333    2334455566677777777777777777777654

>3a2a_A Voltage-gated hydrogen channel 1; voltage-gated proton channel, alternative splicing, coiled C transport, ionic channel, membrane, transmembrane; 2.00A {Homo sapiens}

Probab=81.13  E-value=2.5  Score=30.10  Aligned_cols=44  Identities=25%  Similarity=0.336  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          125 QLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       125 qLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      +-..++.+|++-|.+|-+++..|+..+.+.       .+||+||...|+..
T Consensus         8 Rse~q~~kLKq~n~~L~~kv~~Le~~c~e~-------eQEieRL~~LLkqH   51 (58)
T 3a2a_A            8 RSERQLLRLKQMNVQLAAKIQHLEFSCSEK-------EQEIERLNKLLRQH   51 (58)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHc
Confidence            345678899999999999988887776664       45677777777754

>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=80.55  E-value=9.5  Score=32.79  Aligned_cols=52  Identities=17%  Similarity=0.259  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDEKQRLKAEKEKIEQQL  172 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdEk~~Lk~ekekLe~ql  172 (236)
                      +++.-+-..+..|+.+|..|+++...|..+.++|..+...+-.+|+.+|.+|
T Consensus       125 elfd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~v~~K~~~E~~L  176 (213)
T 1ik9_A          125 ELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDL  176 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555555566666666655555566666666555555555555555544

>2oxj_A Hybrid alpha/beta peptide based on the GCN4-P1 Se heptad positions B and F substituted...; helix bundle, foldamer, unknown function; HET: B3K B3D B3E B3S B3Y B3X B3A BAL; 2.00A {Synthetic} PDB: 2oxk_A*

Probab=80.47  E-value=2.2  Score=27.51  Aligned_cols=21  Identities=24%  Similarity=0.355  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHhhhhHHHH
Q 026599          123 VTQLRSEAQKLKDSNSSLQEK  143 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~ee  143 (236)
                      +.||..+|++|-.+|..|+.+
T Consensus         3 MnQLE~kVEeLl~~n~~Le~e   23 (34)
T 2oxj_A            3 MXQLEXKVXELLXKNXHLEXE   23 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhHHHH
Confidence            345555555444444444433

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

Probab=80.22  E-value=14  Score=27.84  Aligned_cols=41  Identities=20%  Similarity=0.288  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Q 026599          117 IDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNELRDE  157 (236)
Q Consensus       117 ~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknELrdE  157 (236)
                      ..|++...+++.++..++..+..+.+++..|+.....|.++
T Consensus        19 e~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~e   59 (101)
T 3u59_A           19 ENAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDE   59 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence            34555666666666666666555555555555444444433

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

Probab=80.03  E-value=15  Score=28.70  Aligned_cols=30  Identities=30%  Similarity=0.504  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHHHHHHH
Q 026599          117 IDAVRMVTQLRSEAQKLKDSNSSLQEKIKE  146 (236)
Q Consensus       117 ~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~  146 (236)
                      .+.-+-|..|+.+++.|+..+..|+..+.+
T Consensus        39 ~elrr~iq~L~~el~~l~~~~~~LE~~l~e   68 (129)
T 3tnu_B           39 SEMNRMIQRLRAEIDNVKKQCANLQNAIAD   68 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            334444555555555555555555544433

---

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	236
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	3e-18
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-15
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	9e-15
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	2e-13
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	7e-13
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	6e-09
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	9e-09
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	3e-06

>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 = 74.5 bits (183), Expect = 3e-18
 Identities = 16/73 (21%), Positives = 29/73 (39%)

Query: 83  REKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE 142
            E+ RRD + D F  L   +   +  K  +A IL  A   +  +R +    +     L+ 
Sbjct: 9   LERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR 68

Query: 143 KIKELKAEKNELR 155
           +   L+ +   L 
Sbjct: 69  QNALLEQQVRALG 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 = 68.0 bits (166), Expect = 1e-15
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 83  REKLRRDRLNDKFVELASIL-EPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQ 141
            E+ RR+ L   F  L   + E     K  K  IL  A   +  +++E QKL      L+
Sbjct: 13  LERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR 72

Query: 142 EKIKELKAEKNELR 155
           ++ ++LK +  +L 
Sbjct: 73  KRREQLKHKLEQLG 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 = 65.0 bits (158), Expect = 9e-15
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 83  REKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQE 142
            EK  R  +NDK +EL   L  G   K +K+A+L  A+  +  L+   QKLK  N SL+ 
Sbjct: 13  IEKRYRSSINDKIIELKD-LVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT 71

Query: 143 KIKELKAEK 151
            + + K+ K
Sbjct: 72  AVHKSKSLK 80

>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 = 61.5 bits (149), Expect = 2e-13
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 1/72 (1%)

Query: 83  REKLRRDRLNDKFVELASILEPGRP-PKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQ 141
            EK RR  L     +L  ++  G    +    ++L  A   + +L    +K       LQ
Sbjct: 8   MEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ 67

Query: 142 EKIKELKAEKNE 153
            + + LK +  +
Sbjct: 68  REQRHLKRQLEK 79

>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 = 59.7 bits (145), Expect = 7e-13
 Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 88  RDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKEL 147
           R  +NDK +EL  ++  G   K  K+ +L  A+  +  L+    KL+  N  L+   ++ 
Sbjct: 1   RSSINDKIIELKDLV-MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKN 59

Query: 148 K 148
           K
Sbjct: 60  K 60

>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 = 49.0 bits (117), Expect = 6e-09
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 83  REKLRRDRLNDKFVELASIL----EPGRPPKTDKAAILIDAVRMVTQLRSEAQK 132
            E+ RRD++N+  V+L+ I+             K  IL  A   + +LR    +
Sbjct: 12  VERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65

>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 = 48.3 bits (115), Expect = 9e-09
 Identities = 14/70 (20%), Positives = 30/70 (42%), Gaps = 3/70 (4%)

Query: 66  KKRVRSESCGSSSSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQ 125
           + + ++ +     +   RE+ R  ++N+ F  L          +  K  IL +A+R +  
Sbjct: 2   ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEG 61

Query: 126 LRSEAQKLKD 135
           L+     L+D
Sbjct: 62  LQ---ALLRD 68

>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 = 41.4 bits (97), Expect = 3e-06
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 5/54 (9%)

Query: 83  REKLRRDRLNDKFVELASIL-----EPGRPPKTDKAAILIDAVRMVTQLRSEAQ 131
            E+ RR+RL     ELAS++     +        KA  +  A R +  L+    
Sbjct: 9   AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	236
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.65
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.63
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.44
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.37
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.31
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	88.99
d1lrza1	65	Methicillin resistance protein FemA probable tRNA-	84.84
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	84.27

>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=99.69  E-value=4.5e-17  Score=119.70  Aligned_cols=70  Identities=33%  Similarity=0.476  Sum_probs=63.0

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELK  148 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk  148 (236)
                      ..|+..||+||++||+.|.+|+++| |+...|+||++||..||+||++|+.+++.|++++..|..++..++
T Consensus         8 ~~H~~~Er~RR~~in~~~~~L~~ll-P~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~~~~~~   77 (80)
T d1am9a_           8 TAHNAIEKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-TCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcC-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            3699999999999999999999999 876679999999999999999999999999988888877765543

>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=1.7e-16  Score=116.82  Aligned_cols=74  Identities=22%  Similarity=0.325  Sum_probs=61.5

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCCCC-CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEPGR-PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNE  153 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P~~-~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknE  153 (236)
                      .|+.+||+||++||+.|.+|+++| |+. ..|++|++||..||.||++|+.+++.|.++...|..+...|..+...
T Consensus         5 ~Hn~~Er~RR~~in~~f~~L~~ll-P~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~   79 (83)
T d1nkpb_           5 HHNALERKRRDHIKDSFHSLRDSV-PSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRA   79 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTS-GGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999999999999 653 35899999999999999999999988887766666555555544443

>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=99.63  E-value=5.5e-16  Score=113.07  Aligned_cols=71  Identities=21%  Similarity=0.273  Sum_probs=60.9

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAE  150 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~E  150 (236)
                      .|+..||+||++||+.|.+|+++| |..  ..|++|++||..||+||++|+.+++.|..+...|..+...|+..
T Consensus         4 ~Hn~~Er~RR~~in~~f~~L~~ll-P~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~~~~L~~~   76 (79)
T d1nlwa_           4 THNEMEKNRRAHLRLSLEKLKGLV-PLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQ   76 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSS-CCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhC-ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999 642  35899999999999999999999988888777777666665543

>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=4.8e-16  Score=115.44  Aligned_cols=75  Identities=27%  Similarity=0.403  Sum_probs=61.9

Q ss_pred             cchhHHHHHHHHHHHhHHHHhhhcCCCC--CCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Q 026599           79 SKACREKLRRDRLNDKFVELASILEPGR--PPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKNEL  154 (236)
Q Consensus        79 ~ka~rER~RRdkLNerF~eL~slL~P~~--~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~EknEL  154 (236)
                      .|+.+||+||++||+.|.+|+++| |+.  ..|++|++||..||+||+.|+.++++|+.+.+.|..+...|..+.++|
T Consensus         9 ~Hn~~Er~RR~~in~~f~~Lr~ll-P~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~L   85 (88)
T d1nkpa_           9 THNVLERQRRNELKRSFFALRDQI-PELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTC-GGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhC-CCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            599999999999999999999999 643  258999999999999999999999888877666665555555544443

>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=99.55  E-value=2.2e-15  Score=106.03  Aligned_cols=56  Identities=29%  Similarity=0.451  Sum_probs=51.1

Q ss_pred             HHHHHHhHHHHhhhcCCCCCCCCchhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Q 026599           88 RDRLNDKFVELASILEPGRPPKTDKAAILIDAVRMVTQLRSEAQKLKDSNSSLQEKI  144 (236)
Q Consensus        88 RdkLNerF~eL~slL~P~~~~K~DKAsIL~dAI~ylkqLr~qv~~Lk~~n~~L~eei  144 (236)
                      |++||++|.+|+++| |+..+|+|||+||.+||+||+.|+.+++.|++++..|..+.
T Consensus         1 R~~in~~f~~L~~lv-P~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   56 (61)
T d1uklc_           1 RSSINDKIIELKDLV-MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLAN   56 (61)
T ss_dssp             CCCHHHHHHHHHHHH-SCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhC-CCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999 87657999999999999999999999999999888887653

>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=99.44  E-value=3.2e-14  Score=100.25  Aligned_cols=52  Identities=31%  Similarity=0.441  Sum_probs=46.7

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCC------CCCCCchhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPG------RPPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~------~~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      ..|+..||+||++||+.|.+|+++| |+      ...|++|++||..||+||++|++++
T Consensus         4 ~~H~~~Er~RR~~in~~~~~L~~ll-P~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           4 ESHKHAEQARRNRLAVALHELASLI-PAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TGGGGGTHHHHHHHHHHHHHHHHTS-CHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHC-CCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            4699999999999999999999999 62      2369999999999999999998764

>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=1.5e-13  Score=98.51  Aligned_cols=53  Identities=25%  Similarity=0.407  Sum_probs=47.4

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCCC-CCCchhhhHHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGRP-PKTDKAAILIDAVRMVTQLRSEAQ  131 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~~-~K~DKAsIL~dAI~ylkqLr~qv~  131 (236)
                      ..|+.+||+||++||+.|.+|+++| |+.+ .|+||++||..||+||+.|+..++
T Consensus        14 ~~hn~~Er~Rr~~in~~~~~L~~ll-P~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          14 KAATMRERRRLSKVNEAFETLKRST-SSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTS-CSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            4699999999999999999999999 7642 589999999999999999997654

>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=99.31  E-value=4.4e-13  Score=94.83  Aligned_cols=52  Identities=29%  Similarity=0.469  Sum_probs=46.3

Q ss_pred             CcchhHHHHHHHHHHHhHHHHhhhcCCCC-----CCCCchhhhHHHHHHHHHHHHHHH
Q 026599           78 SSKACREKLRRDRLNDKFVELASILEPGR-----PPKTDKAAILIDAVRMVTQLRSEA  130 (236)
Q Consensus        78 ~~ka~rER~RRdkLNerF~eL~slL~P~~-----~~K~DKAsIL~dAI~ylkqLr~qv  130 (236)
                      ..|+.+||+||++||+.|.+|+++| |..     ..|++|++||..||+||++|+++.
T Consensus         7 ~~H~~~Er~RR~~in~~f~~L~~lv-P~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           7 AQHNEVERRRRDKINNWIVQLSKII-PDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHS-CCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHc-ccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            4699999999999999999999999 742     349999999999999999998653

>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=88.99  E-value=2.3  Score=30.40  Aligned_cols=53  Identities=23%  Similarity=0.391  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHhhhhHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026599          123 VTQLRSEAQKLKDSNSSLQEK--------IKELKAEKNELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       123 lkqLr~qv~~Lk~~n~~L~ee--------ik~Lk~EknELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      .++|+.+++.|+.+...+..+        ..+|..+..+|+++...|..+...++.++..+
T Consensus        37 rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~   97 (110)
T d1seta1          37 VQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEAL   97 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444433333333        34455555566666666666666666666664

>d1lrza1 a.2.7.4 (A:245-309) Methicillin resistance protein FemA probable tRNA-binding arm {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: tRNA-binding arm
family: Methicillin resistance protein FemA probable tRNA-binding arm
domain: Methicillin resistance protein FemA probable tRNA-binding arm
species: Staphylococcus aureus [TaxId: 1280]

Probab=84.84  E-value=3.2  Score=28.20  Aligned_cols=53  Identities=11%  Similarity=0.197  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHhhhhHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026599          121 RMVTQLRSEAQKLKDSNSSLQEKIK------ELKAEKNELRDEKQRLKAEKEKIEQQLK  173 (236)
Q Consensus       121 ~ylkqLr~qv~~Lk~~n~~L~eeik------~Lk~EknELrdEk~~Lk~ekekLe~qlk  173 (236)
                      +||..|+.+...|...+..+...+.      .-+..+.+|......+...|...+..+.
T Consensus         3 eYl~~L~~~~~~L~~~i~k~~~~leknP~skK~~nk~~el~~Q~~s~~~ki~Ea~~li~   61 (65)
T d1lrza1           3 EYIKELNEERDILNKDLNKALKDIEKRPENKKAHNKRDNLQQQLDANEQKIEEGKRLQE   61 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6999999999999999888877652      3444445555555555555555555443

>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=84.27  E-value=1.7  Score=31.16  Aligned_cols=56  Identities=20%  Similarity=0.281  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHh
Q 026599          120 VRMVTQLRSEAQKLKDSNSSLQEKIKELKAEKN--------ELRDEKQRLKAEKEKIEQQLKAM  175 (236)
Q Consensus       120 I~ylkqLr~qv~~Lk~~n~~L~eeik~Lk~Ekn--------ELrdEk~~Lk~ekekLe~qlk~~  175 (236)
                      ++.|-+|-.+..+|..+.+.|+.+.+.+..+..        +|..+...|+.++..++.+++.+
T Consensus        27 ld~i~~ld~~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~   90 (110)
T d1seta1          27 LEALLALDREVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREK   90 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666667777777777777777666654442        33444455666666666666654