Citrus Sinensis ID: 028060

---

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----
Protein Sequence
MDPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHcccccccccccccccccHHHcccccccccccccccccccc
Coil and Loop (DISEMBL)
mdpsdwddfinysfndqnasldfswpeqngsadndisstgvvppenentrkrarsdscsrpgskaCREKLRRERLndrfldlscilepgrpartdkpaILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMamptggympthpaayhAGLNkmavypsyglmpmwqylppslhdtsrdhelrppaa
Flexible Loop (DISEMBL)
MDPSDWDDFINYSFNDQNASLDFSWPEQNGSadndisstgvvppenentrkrarsdscsrpgskacreklrrerlndrfldlscilepgrpartdkpaiLDDAIRVLNQLRTesqelketnekLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDhelrppaa
Low Complexity Region (SEG)
MDPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA
Disordered region (IsUnstruct)
*******DFINYSFN*************************************************************DRFLDLSCILE***********ILDDAIRVL**************************************************VMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLP*****************
Disordered Region (DISOPRED)
***SDWDDFINYSF************************************************************LNDRFLDLSCILE*********PAILDDAIRVLNQLRT****************************************************************************LMPMWQYLPPSLHDTSRDH*LRPP**
Disordered Region (DISEMBL)
MDPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVP***********************REKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLH*************
Disordered Region (DISPRO)
****DWDDFINYSFNDQNASLDFSW****************************************CREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPP**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA
Positional Conservation
no confident homologs detected

---

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	214	2.2.26 [Sep-21-2011]
Q8L467	283	Transcription factor bHLH	yes	no	0.957	0.724	0.582	7e-67
Q9LTC7	320	Transcription factor bHLH	no	no	0.836	0.559	0.638	4e-59
Q9FH37	234	Transcription factor ILR3	no	no	0.897	0.820	0.502	4e-47
Q9C682	226	Transcription factor bHLH	no	no	0.948	0.898	0.451	2e-43
Q9LT23	337	Transcription factor bHLH	no	no	0.514	0.326	0.439	1e-15
Q8W2F2	286	Transcription factor bHLH	no	no	0.439	0.328	0.448	1e-12
Q9SN74	240	Transcription factor bHLH	no	no	0.588	0.525	0.307	8e-08
Q9FIP9	592	Transcription factor ATR2	no	no	0.439	0.158	0.316	1e-05
O49687	589	Transcription factor MYC4	no	no	0.537	0.195	0.290	0.0001
Q9CAD0	596	Transcription factor EGL1	no	no	0.397	0.142	0.370	0.0001

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

 Score =  253 bits (646), Expect = 7e-67,   Method: Compositional matrix adjust.
 Identities = 141/242 (58%), Positives = 167/242 (69%), Gaps = 37/242 (15%)

Query: 8   DFINYSFNDQN----------ASLDFSW--------PEQNGSAD-----------NDISS 38
           DF++Y  N Q           + LD S         PEQ G  D           N  SS
Sbjct: 44  DFVSYGVNLQQEPDEVFSIGASQLDLSSYNGVLSLEPEQVGQQDCEVVQEEEVEINSGSS 103

Query: 39  TGVVPPENEN-----TRKRARSDSCSRPG-SKACREKLRRERLNDRFLDLSCILEPGRPA 92
            G V  E E+     +RKRAR+ SCSR G +KACRE+LRRE+LN+RF+DLS +LEPGR  
Sbjct: 104 GGAVKEEQEHLDDDCSRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSSVLEPGRTP 163

Query: 93  RTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL 152
           +TDKPAILDDAIR+LNQLR E+ +L+ETN+KL EEIKSLKAEKNELREEKL+LKADKEK 
Sbjct: 164 KTDKPAILDDAIRILNQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLVLKADKEKT 223

Query: 153 EQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPP 212
           EQQLK M  P+ G++P  PAA++   NKMAVYPSYG MPMW Y+P S+ DTSRD ELRPP
Sbjct: 224 EQQLKSMTAPSSGFIPHIPAAFNH--NKMAVYPSYGYMPMWHYMPQSVRDTSRDQELRPP 281

Query: 213 AA 214
           AA
Sbjct: 282 AA 283

Arabidopsis thaliana (taxid: 3702)

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

 Score =  227 bits (579), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 120/188 (63%), Positives = 146/188 (77%), Gaps = 9/188 (4%)

Query: 34  NDISSTGVVPPE--NENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRP 91
           N  SS G V  E   E + KR R+ SCS+PG+KACREKLRRE+LND+F+DLS +LEPGR 
Sbjct: 135 NSSSSVGAVKEEFEEECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSVLEPGRT 194

Query: 92  ARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK 151
            +TDK AILDDAIRV+NQLR E+ EL+ETN+KL EEIKSLKA+KNELREEKL+LKA+KEK
Sbjct: 195 PKTDKSAILDDAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEK 254

Query: 152 LEQQLKVMAMPTGGYMPT-HPAAYHAGLNKMAVYPSYGL----MPMWQYLPPSLHDTSRD 206
           +EQQLK M +P+ G+MP+ HPAA+H+  +KMAV   YG     MPMW  LPP+  DTSRD
Sbjct: 255 MEQQLKSMVVPSPGFMPSQHPAAFHS--HKMAVAYPYGYYPPNMPMWSPLPPADRDTSRD 312

Query: 207 HELRPPAA 214
            +  PP A
Sbjct: 313 LKNLPPVA 320

Arabidopsis thaliana (taxid: 3702)

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

 Score =  187 bits (476), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 104/207 (50%), Positives = 131/207 (63%), Gaps = 15/207 (7%)

Query: 23  FSWPEQ-------NGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERL 75
           FSWP Q       N SA  D S+      +   ++KR R +S S   SKACREK RR+RL
Sbjct: 28  FSWPVQQPIGVSSNSSAGVDGSAGNSEASKEPGSKKRGRCESSSATSSKACREKQRRDRL 87

Query: 76  NDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEK 135
           ND+F++L  ILEPG P +TDK AIL DA+R++ QLR E+Q+LK++N  LQ++IK LK EK
Sbjct: 88  NDKFMELGAILEPGNPPKTDKAAILVDAVRMVTQLRGEAQKLKDSNSSLQDKIKELKTEK 147

Query: 136 NELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHP--------AAYHAGLNKMAVYPSY 187
           NELR+EK  LK +KEKLEQQLK M  P   + P  P        A   A  NKM    SY
Sbjct: 148 NELRDEKQRLKTEKEKLEQQLKAMNAPQPSFFPAPPMMPTAFASAQGQAPGNKMVPIISY 207

Query: 188 GLMPMWQYLPPSLHDTSRDHELRPPAA 214
             + MWQ++PP+  DTS+DH LRPP A
Sbjct: 208 PGVAMWQFMPPASVDTSQDHVLRPPVA 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 =  175 bits (444), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 97/215 (45%), Positives = 140/215 (65%), Gaps = 12/215 (5%)

Query: 9   FINYSFNDQNASLDFSWPEQNGSADNDISSTGVV----PPENENTRKRARSDSCSRPGSK 64
            I  +F+DQN +  F W + +GSA   +   G +      +  ++RKR +++SC+   SK
Sbjct: 15  LIEGAFSDQNPT--FPW-QIDGSATVSVEVDGFLCDADVIKEPSSRKRIKTESCTGSNSK 71

Query: 65  ACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKL 124
           ACREK RR+RLND+F +LS +LEPGR  +TDK AI++DAIR++NQ R E+Q+LK+ N  L
Sbjct: 72  ACREKQRRDRLNDKFTELSSVLEPGRTPKTDKVAIINDAIRMVNQARDEAQKLKDLNSSL 131

Query: 125 QEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAM---PTGGYMPTHPAAYHAGL--N 179
           QE+IK LK EKNELR+EK  LK +KE+++QQLK +     P   ++P       A    +
Sbjct: 132 QEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQPQPQPCFLPNPQTLSQAQAPGS 191

Query: 180 KMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           K+  + +Y    MWQ++PP+  DTS+DH LRPP A
Sbjct: 192 KLVPFTTYPGFAMWQFMPPAAVDTSQDHVLRPPVA 226

Arabidopsis thaliana (taxid: 3702)

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

 Score = 83.2 bits (204), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 51/116 (43%), Positives = 73/116 (62%), Gaps = 6/116 (5%)

Query: 56  DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 115
           D  +R   KA REKLRRE+LN+ F++L  +L+P RP + DK  IL D +++L +L +E  
Sbjct: 55  DVSARKSQKAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVN 113

Query: 116 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL----EQQLKVMAMPTGGYM 167
           +LK     L +E + L  EKN+LREEK  LK+D E L    +Q+L+ M+ P G  M
Sbjct: 114 KLKSEYTALTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMS-PWGAAM 168

Arabidopsis thaliana (taxid: 3702)

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

 Score = 73.2 bits (178), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 44/98 (44%), Positives = 63/98 (64%), Gaps = 4/98 (4%)

Query: 58  CSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQEL 117
           CS+   KA REKLRR++L ++FL+L   L+P RP ++DK ++L D I++L  +  +   L
Sbjct: 46  CSQ---KAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQVDRL 101

Query: 118 KETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ 155
           K   E L +E + L  EK+ELREEK  LK+D E L  Q
Sbjct: 102 KAEYETLSQESRELIQEKSELREEKATLKSDIEILNAQ 139

Arabidopsis thaliana (taxid: 3702)

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

 Score = 57.4 bits (137), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 39/127 (30%), Positives = 69/127 (54%), Gaps = 1/127 (0%)

Query: 46  NENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIR 105
           N    +R R     +  +KA RE+L+RE LN+ F++L+  LE  +   + K +IL +A R
Sbjct: 14  NATADERCRKGKVPKRINKAVRERLKREHLNELFIELADTLELNQ-QNSGKASILCEATR 72

Query: 106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGG 165
            L  +  + + L++ +  L  E   +  EKNEL+EE  +L+ +  KL+ +++  A  +  
Sbjct: 73  FLKDVFGQIESLRKEHASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEARANQSKP 132

Query: 166 YMPTHPA 172
            + T PA
Sbjct: 133 DLNTSPA 139

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FIP9|ATR2_ARATH Transcription factor ATR2 OS=Arabidopsis thaliana GN=ATR2 PE=1 SV=1

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 55/98 (56%), Gaps = 4/98 (4%)

Query: 41  VVPPENENTRKRARSDSCSR--PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPA 98
           VV P  +  RKR R  +  R  P +    E+ RRE+LN RF  L  ++     ++ DK +
Sbjct: 391 VVEPPEKKPRKRGRKPANGREEPLNHVEAERQRREKLNQRFYSLRAVVP--NVSKMDKAS 448

Query: 99  ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN 136
           +L DAI  +N+L+++ Q+ +   E++Q+++  +  E N
Sbjct: 449 LLGDAISYINELKSKLQQAESDKEEIQKKLDGMSKEGN 486

Involved in tryptophan and other stress-responsive gene regulation.

Arabidopsis thaliana (taxid: 3702)

>sp|O49687|BH004_ARATH Transcription factor MYC4 OS=Arabidopsis thaliana GN=BHLH4 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 68/124 (54%), Gaps = 9/124 (7%)

Query: 41  VVPPENENTRKRARSDSCSR--PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPA 98
           VV PE +  RKR R  +  R  P +    E+ RRE+LN RF  L  ++     ++ DK +
Sbjct: 393 VVEPEKK-PRKRGRKPANGREEPLNHVEAERQRREKLNQRFYSLRAVVP--NVSKMDKAS 449

Query: 99  ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE----KNELREEKLILKADKEKLEQ 154
           +L DAI  +++L+++ Q+ +   E+LQ++I  +  E    K+ +++ K + +     +E 
Sbjct: 450 LLGDAISYISELKSKLQKAESDKEELQKQIDVMNKEAGNAKSSVKDRKCLNQESSVLIEM 509

Query: 155 QLKV 158
           ++ V
Sbjct: 510 EVDV 513

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAD0|EGL1_ARATH Transcription factor EGL1 OS=Arabidopsis thaliana GN=BHLH2 PE=1 SV=1

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 48/89 (53%), Gaps = 4/89 (4%)

Query: 56  DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 115
           D+    G+ A  EK RRE+LN+RF+ L  I+     ++ DK +ILDD I  L  L+   Q
Sbjct: 398 DTPEETGNHALSEKKRREKLNERFMTLRSIIPS--ISKIDKVSILDDTIEYLQDLQKRVQ 455

Query: 116 ELKETNEKLQEE--IKSLKAEKNELREEK 142
           EL+   E    E  I  +K +K +  EE+
Sbjct: 456 ELESCRESADTETRITMMKRKKPDDEEER 484

Transcription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation but promotes trichome formation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Involved in seed mucilage production. Activates the transcription of GL2.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	214
224107875	221	predicted protein [Populus trichocarpa]	0.911	0.882	0.739	5e-77
356575261	220	PREDICTED: transcription factor bHLH104-	0.985	0.959	0.658	3e-72
296083619	248	unnamed protein product [Vitis vinifera]	0.995	0.858	0.637	4e-72
356534540	218	PREDICTED: transcription factor bHLH104-	0.995	0.977	0.643	5e-72
359477721	219	PREDICTED: transcription factor bHLH104-	0.995	0.972	0.631	3e-71
255637294	220	unknown [Glycine max]	0.985	0.959	0.649	3e-71
449432566	226	PREDICTED: transcription factor bHLH104-	0.990	0.938	0.626	4e-70
357439557	246	Transcription factor bHLH104 [Medicago t	1.0	0.869	0.595	3e-69
255576818	219	DNA binding protein, putative [Ricinus c	0.962	0.940	0.695	9e-69
313474112	219	bHLH transcriptional factor [Coptis japo	0.981	0.958	0.615	1e-66

>gi|224107875|ref|XP_002314636.1| predicted protein [Populus trichocarpa] gi|222863676|gb|EEF00807.1| predicted protein [Populus trichocarpa]

 Score =  292 bits (748), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 145/196 (73%), Positives = 162/196 (82%), Gaps = 1/196 (0%)

Query: 20  SLDFSWPEQNGSADNDISST-GVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDR 78
           SL  S     G  D D SS+ GVV    E +RKR RSD CSR G+KACREKLRRERLNDR
Sbjct: 26  SLTNSICSSGGVVDIDFSSSVGVVTQVKECSRKRERSDLCSRAGTKACREKLRRERLNDR 85

Query: 79  FLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL 138
           F DLS +LEPGRPA+TDKPAILDDAIRVLNQL+ E+QELKETNEKL EEI+SLKAEK EL
Sbjct: 86  FQDLSSVLEPGRPAKTDKPAILDDAIRVLNQLKNEAQELKETNEKLLEEIRSLKAEKTEL 145

Query: 139 REEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPP 198
           REEKL+LKADKEK+EQQLK +A+PT G+MPT+PAAYHA  NK+ V+P YGLMPMW YLPP
Sbjct: 146 REEKLMLKADKEKMEQQLKTLALPTSGFMPTYPAAYHAAANKIPVFPGYGLMPMWHYLPP 205

Query: 199 SLHDTSRDHELRPPAA 214
           +  DTSRDHELRPPAA
Sbjct: 206 TACDTSRDHELRPPAA 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575261|ref|XP_003555760.1| PREDICTED: transcription factor bHLH104-like [Glycine max]

 Score =  276 bits (707), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 143/217 (65%), Positives = 166/217 (76%), Gaps = 6/217 (2%)

Query: 2   DPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVPPENENTRKRARSDSCSRP 61
           D   WD F++YSF DQ A  DF W   N S   +I   G      ENT+KR R+DSC + 
Sbjct: 6   DSGCWD-FLDYSFIDQ-APPDFLWSNNNNSVSTEIDIPGDAVACQENTKKRGRTDSCFKA 63

Query: 62  GSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETN 121
           GSKACREKLRRERLN+RF DLS +LEPGRP RTDKPAILDDAIRVL+QL+TE+QELK+TN
Sbjct: 64  GSKACREKLRRERLNERFCDLSSVLEPGRPVRTDKPAILDDAIRVLSQLKTEAQELKKTN 123

Query: 122 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYM----PTHPAAYHAG 177
           EKL EEIK LKAEKNELREEKL+LKADKE++E+QLK + +   G+M        AAY AG
Sbjct: 124 EKLLEEIKCLKAEKNELREEKLVLKADKERIEKQLKALPVAPAGFMAPPVAAAAAAYQAG 183

Query: 178 LNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           +NKMAVYP+YG +PMWQYLP S+ DTS DHELRPPAA
Sbjct: 184 VNKMAVYPNYGYIPMWQYLPQSVRDTSHDHELRPPAA 220

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083619|emb|CBI23608.3| unnamed protein product [Vitis vinifera]

 Score =  276 bits (706), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 137/215 (63%), Positives = 163/215 (75%), Gaps = 2/215 (0%)

Query: 1   MDPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVPPENENTRKRARSDSCSR 60
            D   WD F+N+   D   S D SW       D D+S       ENE  +KR R+DS +R
Sbjct: 35  FDDDTWD-FLNHKLIDDVTSNDLSWINDGAGVDIDLSRICAASQENEGRQKRGRNDSSTR 93

Query: 61  PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKET 120
           PG+KACREKLRRERLNDRFLDLS ILEPG+ A+TDK AIL DAIRVLNQLR E+++L++ 
Sbjct: 94  PGTKACREKLRRERLNDRFLDLSSILEPGKSAKTDKLAILGDAIRVLNQLRNEAKDLEDA 153

Query: 121 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAA-YHAGLN 179
           NEKLQEEI+SLKAEKNELREEKL+LKADKE++EQQ+K ++ P  G+ PT+PAA +H G N
Sbjct: 154 NEKLQEEIRSLKAEKNELREEKLLLKADKERIEQQMKAISAPAAGFWPTYPAATHHTGAN 213

Query: 180 KMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           K AV+PSYGL PMWQY+P S  DTS DHELRPPAA
Sbjct: 214 KSAVFPSYGLFPMWQYIPSSALDTSHDHELRPPAA 248

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534540|ref|XP_003535811.1| PREDICTED: transcription factor bHLH104-like [Glycine max]

 Score =  276 bits (705), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 139/216 (64%), Positives = 167/216 (77%), Gaps = 3/216 (1%)

Query: 1   MDPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVPPENENTRKRARSDSCSR 60
           ++ S + DF++YSF DQ A  DF W     S + ++   G      ENT+KR  +DS  +
Sbjct: 4   LEDSGYWDFLDYSFIDQ-APPDFLWSNNTISVNTEVDIPGDAAACQENTKKRGHADSSCQ 62

Query: 61  PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKET 120
            GSKACREKLRRERLN+RF DLS +LEPGRP RTDKPAILDDAIRVL+QL+TE+QELK+T
Sbjct: 63  VGSKACREKLRRERLNERFCDLSSVLEPGRPVRTDKPAILDDAIRVLSQLKTEAQELKKT 122

Query: 121 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYM--PTHPAAYHAGL 178
           NEKL EEIK LKAEKNELREEKL+LKADKE++E+QLK + +   GYM  P   AAY AG+
Sbjct: 123 NEKLLEEIKCLKAEKNELREEKLVLKADKERIEKQLKALPVAPAGYMTPPVAAAAYQAGV 182

Query: 179 NKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           NKMA+YP+YG +PMWQYLP S+ DTS DHELRPPAA
Sbjct: 183 NKMALYPNYGYIPMWQYLPQSVRDTSHDHELRPPAA 218

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359477721|ref|XP_002280987.2| PREDICTED: transcription factor bHLH104-like [Vitis vinifera]

 Score =  273 bits (699), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 137/217 (63%), Positives = 163/217 (75%), Gaps = 4/217 (1%)

Query: 1   MDPSDWDDFINYSFNDQNASLDFSWPEQN--GSADNDISSTGVVPPENENTRKRARSDSC 58
            D   WD F+N+   D   S D SW         D D+S       ENE  +KR R+DS 
Sbjct: 4   FDDDTWD-FLNHKLIDDVTSNDLSWINDGYLAGVDIDLSRICAASQENEGRQKRGRNDSS 62

Query: 59  SRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELK 118
           +RPG+KACREKLRRERLNDRFLDLS ILEPG+ A+TDK AIL DAIRVLNQLR E+++L+
Sbjct: 63  TRPGTKACREKLRRERLNDRFLDLSSILEPGKSAKTDKLAILGDAIRVLNQLRNEAKDLE 122

Query: 119 ETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAA-YHAG 177
           + NEKLQEEI+SLKAEKNELREEKL+LKADKE++EQQ+K ++ P  G+ PT+PAA +H G
Sbjct: 123 DANEKLQEEIRSLKAEKNELREEKLLLKADKERIEQQMKAISAPAAGFWPTYPAATHHTG 182

Query: 178 LNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
            NK AV+PSYGL PMWQY+P S  DTS DHELRPPAA
Sbjct: 183 ANKSAVFPSYGLFPMWQYIPSSALDTSHDHELRPPAA 219

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637294|gb|ACU18977.1| unknown [Glycine max]

 Score =  273 bits (698), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 141/217 (64%), Positives = 164/217 (75%), Gaps = 6/217 (2%)

Query: 2   DPSDWDDFINYSFNDQNASLDFSWPEQNGSADNDISSTGVVPPENENTRKRARSDSCSRP 61
           D   WD F++YSF DQ A  DF W   N S   +I   G      ENT+KR R+DSC + 
Sbjct: 6   DSGCWD-FLDYSFIDQ-APPDFLWSNNNNSVSTEIDIPGDAVACQENTKKRGRTDSCFKA 63

Query: 62  GSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETN 121
           GSKACREKLRRERLN+RF DLS +LEPGRP RTDKPAILDDAIRVL+QL+TE+QELK+TN
Sbjct: 64  GSKACREKLRRERLNERFCDLSSVLEPGRPVRTDKPAILDDAIRVLSQLKTEAQELKKTN 123

Query: 122 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYM----PTHPAAYHAG 177
           EKL EEIK LKAEKNELREEKL+LKADKE++E+QLK + +   G+M        AAY AG
Sbjct: 124 EKLLEEIKCLKAEKNELREEKLVLKADKERIEKQLKALPVAPAGFMAPPVAAAAAAYQAG 183

Query: 178 LNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           +NKMAVYP+YG +PMWQY P  + DTS DHELRPPAA
Sbjct: 184 VNKMAVYPNYGYIPMWQYFPQFVRDTSHDHELRPPAA 220

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432566|ref|XP_004134070.1| PREDICTED: transcription factor bHLH104-like [Cucumis sativus] gi|449525932|ref|XP_004169970.1| PREDICTED: transcription factor bHLH104-like [Cucumis sativus]

 Score =  270 bits (689), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 139/222 (62%), Positives = 172/222 (77%), Gaps = 10/222 (4%)

Query: 2   DPSDWDDFINYSF-----NDQNASLDFSWP----EQNGSADNDISSTGVVPPENENTRKR 52
           D S WD F++ SF     N  N SL   WP     ++  AD D+S+  +   EN+ +RKR
Sbjct: 6   DSSCWD-FLDCSFFPDADNLINPSLHPFWPPNHSRRDSLADTDVSAGHLESEENDCSRKR 64

Query: 53  ARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRT 112
           AR  SC+   SKACRE+LRRE+LNDRFLDLS  LEP R  +T+KPAILDDAIRVLNQL+ 
Sbjct: 65  ARDGSCAGASSKACRERLRREKLNDRFLDLSIALEPSRHTKTNKPAILDDAIRVLNQLKN 124

Query: 113 ESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPA 172
           E++ELK+TNEKL+EE++SLKAEKN+LR+EK+ILK DKEK+EQQLK +A+P+ G +P HPA
Sbjct: 125 EAEELKQTNEKLREEVESLKAEKNDLRKEKIILKEDKEKMEQQLKSIAIPSPGLIPGHPA 184

Query: 173 AYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           AYHA   KMAV+P YGL+PMWQYLPPS+ DTS+DHELRPPAA
Sbjct: 185 AYHAASGKMAVFPGYGLIPMWQYLPPSIRDTSQDHELRPPAA 226

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357439557|ref|XP_003590056.1| Transcription factor bHLH104 [Medicago truncatula] gi|355479104|gb|AES60307.1| Transcription factor bHLH104 [Medicago truncatula] gi|356466277|gb|AET08955.1| basic helix-loop-helix transcription factor [Medicago truncatula]

 Score =  266 bits (681), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 143/240 (59%), Positives = 172/240 (71%), Gaps = 26/240 (10%)

Query: 1   MDPSDWDDFI-NYS-FNDQNASLDFSWPEQNGSADN--DISS------------------ 38
           ++ +D+ DF+ +YS F D +    F W   N S     DISS                  
Sbjct: 7   LENTDYLDFLGDYSPFIDPSPPTHFLWSNSNPSVSTEFDISSNVVACQEENTRKSVSTET 66

Query: 39  ---TGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTD 95
              +G V  + ENTRKR R++SC + G+KACREKLRRE+LN+RF DLS +LEPGRP RTD
Sbjct: 67  DIPSGAVVCQEENTRKRGRTESCYKAGTKACREKLRREKLNERFCDLSAVLEPGRPVRTD 126

Query: 96  KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ 155
           KPAILDDAIRVL+QL+TE+QELKE+NEKL EEIK LKAEKNELREEKL+LKADKEK+E+Q
Sbjct: 127 KPAILDDAIRVLSQLKTEAQELKESNEKLLEEIKCLKAEKNELREEKLVLKADKEKIEKQ 186

Query: 156 LKVMAMPTGGYMPTHP-AAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           LK M +   G+MP  P AAY A +NKMAVYP+YG +PMW YLP S  DTS+DHELRPPAA
Sbjct: 187 LKSMPVSPAGFMPPPPMAAYQASVNKMAVYPNYGYIPMWHYLPQSARDTSQDHELRPPAA 246

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255576818|ref|XP_002529295.1| DNA binding protein, putative [Ricinus communis] gi|223531219|gb|EEF33064.1| DNA binding protein, putative [Ricinus communis]

 Score =  265 bits (677), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 146/210 (69%), Positives = 172/210 (81%), Gaps = 4/210 (1%)

Query: 8   DFINYSFNDQNA-SLDFSWPEQNGS-ADNDISSTG-VVPPENENTRKRARSDSCSRPGSK 64
           DF++YSF ++   S D  WP  N + ++ D SS+G  V  E + +RKRAR DSCS+P +K
Sbjct: 11  DFLDYSFIEETTTSSDLLWPNSNNNLSEIDFSSSGGAVSEEKQCSRKRARGDSCSKPVTK 70

Query: 65  ACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKL 124
           ACREKLRRERLNDRF DLS +LEP RPARTDKP++LDDAIRVLNQL+TE+QELKETNEKL
Sbjct: 71  ACREKLRRERLNDRFQDLSSVLEPERPARTDKPSLLDDAIRVLNQLKTEAQELKETNEKL 130

Query: 125 QEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVY 184
            EEIK LKAEKNELREEKL LKADKE+ EQQLK+MA+   GYMP HPAAYHA +NKMA+Y
Sbjct: 131 LEEIKCLKAEKNELREEKLTLKADKERTEQQLKIMAVRPPGYMPAHPAAYHAAMNKMAIY 190

Query: 185 PSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
           PS+GL+PMWQ LPP+  DTS+DHE  PPAA
Sbjct: 191 PSFGLIPMWQ-LPPAAQDTSKDHEYWPPAA 219

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313474112|dbj|BAJ40866.1| bHLH transcriptional factor [Coptis japonica]

 Score =  258 bits (659), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 131/213 (61%), Positives = 160/213 (75%), Gaps = 3/213 (1%)

Query: 4   SDWDDFINYS-FNDQNASLDFSW-PEQNGSADNDISSTGVVPPENENTRKRARSDSCSRP 61
           S W+  I+Y+   +  +S D  W   Q+   + D+S+ G  P E    +KR R++SC   
Sbjct: 8   SPWN-LIDYTRLYEDPSSNDLLWCSNQSACTELDVSAAGAGPVEKGCAKKRGRNESCGGL 66

Query: 62  GSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETN 121
           GSKACREK+RR++LNDRF DLS  LEPGRPA+TDK AIL DAIRVLNQLRTESQELKE N
Sbjct: 67  GSKACREKMRRDKLNDRFADLSSALEPGRPAKTDKSAILSDAIRVLNQLRTESQELKEAN 126

Query: 122 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKM 181
           EKLQE+IK+LKAEKNELREEK +LKADKE++EQQ+K MA+  GG +P HPA Y AG+NK 
Sbjct: 127 EKLQEDIKNLKAEKNELREEKNLLKADKERIEQQMKAMAIVPGGIVPPHPATYQAGVNKF 186

Query: 182 AVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 214
             +PSYG  PMWQY+PP+  DTS+DH LRPP A
Sbjct: 187 MAFPSYGGYPMWQYIPPASLDTSQDHVLRPPVA 219

Source: Coptis japonica

Species: Coptis japonica

Genus: Coptis

Family: Ranunculaceae

Order: Ranunculales

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	214
TAIR|locus:2129710	283	bHLH104 "AT4G14410" [Arabidops	0.836	0.632	0.684	1.3e-63
TAIR|locus:2086198	320	bHLH34 "AT3G23210" [Arabidopsi	0.831	0.556	0.645	4.2e-56
TAIR|locus:2157538	234	ILR3 "AT5G54680" [Arabidopsis	0.897	0.820	0.502	1.2e-44
UNIPROTKB|Q6ZKI8	253	OJ1119_D01.9 "BHLH transcripti	0.822	0.695	0.487	1.6e-40
UNIPROTKB|Q6ZGM4	236	OJ1442_E05.19 "cDNA clone:006-	0.766	0.694	0.511	1.1e-39
TAIR|locus:2092216	337	bHLH121 "AT3G19860" [Arabidops	0.616	0.391	0.408	5.5e-18
UNIPROTKB|Q67U21	343	OSJNBa0065F08.2 "Basic helix-l	0.598	0.373	0.385	1.4e-17
TAIR|locus:2135169	286	bHLH11 "AT4G36060" [Arabidopsi	0.523	0.391	0.398	2.6e-15
TAIR|locus:2079102	240	PYE "AT3G47640" [Arabidopsis t	0.602	0.537	0.312	3.9e-12
UNIPROTKB|Q69V10	265	P0506F02.119 "cDNA clone:J0230	0.584	0.471	0.301	5.2e-12

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

 Score = 630 (226.8 bits), Expect = 1.3e-63, Sum P(2) = 1.3e-63
 Identities = 128/187 (68%), Positives = 151/187 (80%)

Query:    34 NDISSTGVVPPENEN-----TRKRARSDSCSRPG-SKACREKLRRERLNDRFLDLSCILE 87
             N  SS G V  E E+     +RKRAR+ SCSR G +KACRE+LRRE+LN+RF+DLS +LE
Sbjct:    99 NSGSSGGAVKEEQEHLDDDCSRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSSVLE 158

Query:    88 PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKA 147
             PGR  +TDKPAILDDAIR+LNQLR E+ +L+ETN+KL EEIKSLKAEKNELREEKL+LKA
Sbjct:   159 PGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLVLKA 218

Query:   148 DKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDH 207
             DKEK EQQLK M  P+ G++P  PAA++   NKMAVYPSYG MPMW Y+P S+ DTSRD 
Sbjct:   219 DKEKTEQQLKSMTAPSSGFIPHIPAAFNH--NKMAVYPSYGYMPMWHYMPQSVRDTSRDQ 276

Query:   208 ELRPPAA 214
             ELRPPAA
Sbjct:   277 ELRPPAA 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 = 578 (208.5 bits), Expect = 4.2e-56, P = 4.2e-56
 Identities = 122/189 (64%), Positives = 148/189 (78%)

Query:    34 NDISSTGVVPPENEN--TRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRP 91
             N  SS G V  E E   + KR R+ SCS+PG+KACREKLRRE+LND+F+DLS +LEPGR 
Sbjct:   135 NSSSSVGAVKEEFEEECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSVLEPGRT 194

Query:    92 ARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK 151
              +TDK AILDDAIRV+NQLR E+ EL+ETN+KL EEIKSLKA+KNELREEKL+LKA+KEK
Sbjct:   195 PKTDKSAILDDAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEK 254

Query:   152 LEQQLKVMAMPTGGYMPT-HPAAYHAGLNKMAV-YPSYGL----MPMWQYLPPSLHDTSR 205
             +EQQLK M +P+ G+MP+ HPAA+H+  +KMAV YP YG     MPMW  LPP+  DTSR
Sbjct:   255 MEQQLKSMVVPSPGFMPSQHPAAFHS--HKMAVAYP-YGYYPPNMPMWSPLPPADRDTSR 311

Query:   206 DHELRPPAA 214
             D +  PP A
Sbjct:   312 DLKNLPPVA 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

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

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 104/207 (50%), Positives = 132/207 (63%)

Query:    23 FSWPEQ-------NGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERL 75
             FSWP Q       N SA  D S+      +   ++KR R +S S   SKACREK RR+RL
Sbjct:    28 FSWPVQQPIGVSSNSSAGVDGSAGNSEASKEPGSKKRGRCESSSATSSKACREKQRRDRL 87

Query:    76 NDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEK 135
             ND+F++L  ILEPG P +TDK AIL DA+R++ QLR E+Q+LK++N  LQ++IK LK EK
Sbjct:    88 NDKFMELGAILEPGNPPKTDKAAILVDAVRMVTQLRGEAQKLKDSNSSLQDKIKELKTEK 147

Query:   136 NELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHP---AAY-----HAGLNKMAVYPSY 187
             NELR+EK  LK +KEKLEQQLK M  P   + P  P    A+      A  NKM    SY
Sbjct:   148 NELRDEKQRLKTEKEKLEQQLKAMNAPQPSFFPAPPMMPTAFASAQGQAPGNKMVPIISY 207

Query:   188 GLMPMWQYLPPSLHDTSRDHELRPPAA 214
               + MWQ++PP+  DTS+DH LRPP A
Sbjct:   208 PGVAMWQFMPPASVDTSQDHVLRPPVA 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 = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 96/197 (48%), Positives = 128/197 (64%)

Query:    36 ISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTD 95
             +++T  V  E   + KR RS SC RP SKA REK+RR+++NDRFL+L   LEPG+P ++D
Sbjct:    60 VNTTSYVLKE-PGSNKRVRSGSCGRPTSKASREKIRRDKMNDRFLELGTTLEPGKPVKSD 118

Query:    96 KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ 155
             K AIL DA R++ QLR E+++LK+TNE L+++IK LKAEK+ELR+EK  LK +KE LEQQ
Sbjct:   119 KAAILSDATRMVIQLRAEAKQLKDTNESLEDKIKELKAEKDELRDEKQKLKVEKETLEQQ 178

Query:   156 LKVMAMPTGGYMPTHP------------AAYH------AGLNKMAVYPSYGLMPMWQYLP 197
             +K++   T  YMP HP            A +H      AG   M  +  Y   PMWQ++P
Sbjct:   179 VKILTA-TPAYMP-HPTLMPAPYPQAPLAPFHHAQGQAAGQKLMMPFVGYPGYPMWQFMP 236

Query:   198 PSLHDTSRDHELRPPAA 214
             PS  DTS+D E  PP A
Sbjct:   237 PSEVDTSKDSEACPPVA 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 = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 92/180 (51%), Positives = 125/180 (69%)

Query:    51 KRARSDSCSR-PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ 109
             KR R +S S  P SKACREK+RR+RLNDRFL+LS ++ P + A+ DK  IL DA R+L +
Sbjct:    57 KRGRDESSSSGPKSKACREKIRRDRLNDRFLELSSVINPDKQAKLDKANILSDAARLLAE 116

Query:   110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMP- 168
             LR E+++LKE+NEKL+E IK LK EKNELR+EK+ LKA+KE+LEQQ+K +++   G++P 
Sbjct:   117 LRGEAEKLKESNEKLRETIKDLKVEKNELRDEKVTLKAEKERLEQQVKALSVAPTGFVPH 176

Query:   169 -THPAAYHAGL------------NKMAVYPS-YGLMPMWQYLPPSLHDTSRDHELRPPAA 214
               HPAA+H               NK A  P+ +  M MWQ+LPP+  DT++D +L PP A
Sbjct:   177 LPHPAAFHPAAFPPFIPPYQALGNKNAPTPAAFQGMAMWQWLPPTAVDTTQDPKLWPPNA 236

GO:0005634 "nucleus" evidence=IC

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

 Score = 219 (82.2 bits), Expect = 5.5e-18, P = 5.5e-18
 Identities = 60/147 (40%), Positives = 85/147 (57%)

Query:    56 DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 115
             D  +R   KA REKLRRE+LN+ F++L  +L+P RP + DK  IL D +++L +L +E  
Sbjct:    55 DVSARKSQKAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVN 113

Query:   116 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL----EQQLKVMAMPTGGYMPTHP 171
             +LK     L +E + L  EKN+LREEK  LK+D E L    +Q+L+ M+ P G  M    
Sbjct:   114 KLKSEYTALTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMS-PWGAAMD--- 169

Query:   172 AAYHAGLNKMAVYPSYGLMPMWQYLPP 198
                H  +  MA  PS+   PM   +PP
Sbjct:   170 ---HTVM--MAPPPSFPY-PMPIAMPP 190

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

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

 Score = 216 (81.1 bits), Expect = 1.4e-17, P = 1.4e-17
 Identities = 52/135 (38%), Positives = 79/135 (58%)

Query:    40 GVVPPENEN-TRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPA 98
             G  P ++   T  + +    +R   KA REK+RR+RLN++F +L   L+P RP R DK  
Sbjct:    19 GACPADSSGKTECKTQGSIATRKVQKADREKMRRDRLNEQFQELGSTLDPDRP-RNDKAT 77

Query:    99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL----EQ 154
             IL DAI++L  L ++  +LK     L EE + L  EKNELR+EK+ LK + + L    +Q
Sbjct:    78 ILSDAIQMLKDLTSQVNKLKAEYTSLSEEARELTQEKNELRDEKVSLKFEVDNLNTQYQQ 137

Query:   155 QLKVMAMPTGGYMPT 169
             +++V+  P  G  P+
Sbjct:   138 RMRVL-YPWTGMEPS 151

GO:0005634 "nucleus" evidence=IC

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

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 47/118 (39%), Positives = 71/118 (60%)

Query:    58 CSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQEL 117
             CS+   KA REKLRR++L ++FL+L   L+P RP ++DK ++L D I++L  +  +   L
Sbjct:    46 CSQ---KAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQVDRL 101

Query:   118 KETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYH 175
             K   E L +E + L  EK+ELREEK  LK+D E L  Q +        ++P +  +YH
Sbjct:   102 KAEYETLSQESRELIQEKSELREEKATLKSDIEILNAQYQHRIKTMVPWVPHY--SYH 157

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

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

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 41/131 (31%), Positives = 71/131 (54%)

Query:    46 NENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIR 105
             N    +R R     +  +KA RE+L+RE LN+ F++L+  LE  +   + K +IL +A R
Sbjct:    14 NATADERCRKGKVPKRINKAVRERLKREHLNELFIELADTLELNQQ-NSGKASILCEATR 72

Query:   106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGG 165
              L  +  + + L++ +  L  E   +  EKNEL+EE  +L+ +  KL+ +++  A  +  
Sbjct:    73 FLKDVFGQIESLRKEHASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEARANQSKP 132

Query:   166 YMPTHPAA-YH 175
              + T PA  YH
Sbjct:   133 DLNTSPAPEYH 143

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0055072 "iron ion homeostasis" evidence=IMP

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

 Score = 163 (62.4 bits), Expect = 5.2e-12, P = 5.2e-12
 Identities = 41/136 (30%), Positives = 73/136 (53%)

Query:    64 KACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEK 123
             K+ REKL+R++ ND F +L  +LEP R     K  +L +  R+L  L ++ + L++ N  
Sbjct:    40 KSEREKLKRDKQNDLFNELGNLLEPDRQ-NNGKACVLGETTRILKDLLSQVESLRKENSS 98

Query:   124 LQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM--AMPTGGYMPTHPAAYHAGLNKM 181
             L+ E   +  E+NEL ++  +L+ +  +L+ +L+      P   ++ T PA         
Sbjct:    99 LKNESHYVALERNELHDDNSMLRTEILELQNELRTRMEGNPVWSHVNTRPAL-------R 151

Query:   182 AVYPSYGLMPMWQYLP 197
               YP+ G+ P+ Q+LP
Sbjct:   152 VPYPTTGVFPV-QHLP 166

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)
Q8L467	BH104_ARATH	No assigned EC number	0.5826	0.9579	0.7243	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	214
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-06
smart00353	53	smart00353, HLH, helix loop helix domain	9e-06
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	1e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	1e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	1e-04
TIGR03346	852	TIGR03346, chaperone_ClpB, ATP-dependent chaperone	2e-04
pfam13870	177	pfam13870, DUF4201, Domain of unknown function (DU	2e-04
pfam06005	72	pfam06005, DUF904, Protein of unknown function (DU	5e-04
pfam07926	132	pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein	5e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	5e-04
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	0.001
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.001
TIGR02894	161	TIGR02894, DNA_bind_RsfA, transcription factor, Rs	0.002
TIGR00019	360	TIGR00019, prfA, peptide chain release factor 1	0.003
pfam03938	157	pfam03938, OmpH, Outer membrane protein (OmpH-like	0.003
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.004
PRK13922	276	PRK13922, PRK13922, rod shape-determining protein	0.004

>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 = 43.4 bits (103), Expect = 2e-06
 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 57  SCSRPGSKACREKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 115
             SR  +   RE+ RRER+ND F +L S +       +  K  IL  A+  +  L+   Q
Sbjct: 1   RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 41.4 bits (98), Expect = 9e-06
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 67  REKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQE 116
           RE+ RR ++N+ F +L S +    +  +  K  IL  AI  +  L+ E Q+
Sbjct: 3   RERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

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

 Score = 41.3 bits (98), Expect = 1e-05
 Identities = 16/49 (32%), Positives = 25/49 (51%)

Query: 63  SKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLR 111
           +   RE+ RR+R+ND F +L  +L      +  K  IL  AI  +  L+
Sbjct: 4   AHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

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

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 19/51 (37%), Positives = 34/51 (66%)

Query: 106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 156
            L +L+ E  EL+E   +LQE++  L+ E  EL++E   L+A+ E+L+++L
Sbjct: 67  RLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKEL 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|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score = 41.7 bits (99), Expect = 1e-04
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ 154
           L  L   + EL+E   +L+ +++ L+AE  +L  E   LK++ EKL+ 
Sbjct: 3   LEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS 50

Length = 389

>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 33/99 (33%), Positives = 47/99 (47%), Gaps = 23/99 (23%)

Query: 77  DRFL-----DLSCILEPGRPARTD---KPAILDDAIRVLNQLRTESQEL-KETN------ 121
           DRFL     DL  I E     R +   KP  LD+  R + QL  E + L KE +      
Sbjct: 378 DRFLPDKAIDL--IDEAAARIRMEIDSKPEELDELDRRIIQLEIEREALKKEKDEASKER 435

Query: 122 -EKLQEEIKSLKAEKNELREEKLILKADKEKLE--QQLK 157
            E L++E+  L+ E  +L E     KA+K  ++  QQ+K
Sbjct: 436 LEDLEKELAELEEEYADLEE---QWKAEKAAIQGIQQIK 471

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins [Protein fate, Protein folding and stabilization]. Length = 852

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 15/56 (26%), Positives = 32/56 (57%)

Query: 107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP 162
           L+ L  E + LK+  ++ +E +  L+ E  +++ E+  L+   +KL QQ  ++ +P
Sbjct: 86  LHMLEEELERLKKELKEKEERLAKLRKELYKVKLERDKLRKQNKKLRQQGGLLHVP 141

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

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

 Score = 37.3 bits (87), Expect = 5e-04
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ 155
           +L +L ++ Q+  ET   LQ EI+ LK E  +L EE   L+ + +KL+++
Sbjct: 5   LLEELESKIQQAVETIALLQMEIEELKEENEQLSEENEELEEENKKLKEE 54

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

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 4/60 (6%)

Query: 102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR----EEKLILKADKEKLEQQLK 157
           + I  L  LR +  ELK+   +L+ E +S +AE +E      E+K +L+ +  +LE++++
Sbjct: 56  EDIEELQALRKQLNELKKEIAQLKAEAESAQAELSEAEESWEEQKKMLEDELSELEKRIE 115

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

 Score = 40.0 bits (94), Expect = 5e-04
 Identities = 21/51 (41%), Positives = 33/51 (64%)

Query: 107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
           L +LR E  EL+E  E+LQ+E+ +L  E + L ++K IL+     LE+QL+
Sbjct: 269 LEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLE 319

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

>gnl|CDD|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA binding

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 19/48 (39%), Positives = 27/48 (56%)

Query: 109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 156
           QL  E ++L +   K    IK L+A+  EL +E   LK   EKLE++L
Sbjct: 16  QLMEEGEKLSKKELKHNNTIKKLRAKNKELEKEIAELKKKLEKLEKEL 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|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 24/67 (35%), Positives = 41/67 (61%), Gaps = 7/67 (10%)

Query: 100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK-------LILKADKEKL 152
           L++    L++L  E +EL+E  E+ ++EI+ LK+E  ELREE        L LK + E+L
Sbjct: 241 LEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEEL 300

Query: 153 EQQLKVM 159
           E ++ ++
Sbjct: 301 EGEISLL 307

Length = 1163

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

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 98  AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
           A L +  + LN+L  E + L++  ++LQE+   LK +   + +E   L   KE+LE++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|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family

 Score = 37.4 bits (87), Expect = 0.002
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL 152
           L         L+ E++ LK  NE LQ+  + L+ E  +LR+    ++ D + L
Sbjct: 92  LKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTL 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|129130 TIGR00019, prfA, peptide chain release factor 1

 Score = 37.4 bits (87), Expect = 0.003
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 5/64 (7%)

Query: 100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE-KNELREEKLILKADKEKLEQQLKV 158
           L++ +    + +   +++KE  E L+E    ++   K EL E    L+   E+LE+QLKV
Sbjct: 45  LEEIVDCYREYQQAQEDIKEAKEILEESDPEMREMAKEELEE----LEEKIEELEEQLKV 100

Query: 159 MAMP 162
           + +P
Sbjct: 101 LLLP 104

This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift [Protein synthesis, Translation factors]. Length = 360

>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like)

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 7/58 (12%)

Query: 102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM 159
           D  +VL++    S   K   ++L++E K L+AE  +  +E   L+ +++KL++Q   +
Sbjct: 22  DVQKVLSE----SPAGKAAQKQLEKEFKKLQAELQKKEKE---LQKEEQKLQKQAATL 72

This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery. Length = 157

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

 Score = 37.8 bits (88), Expect = 0.004
 Identities = 24/91 (26%), Positives = 42/91 (46%)

Query: 67  REKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 126
             +   E+L  R  +L   LE       +    L++    L  L     +LKE  E+L+E
Sbjct: 727 ALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEE 786

Query: 127 EIKSLKAEKNELREEKLILKADKEKLEQQLK 157
           + ++L+ E  EL EE    +   + LE++L+
Sbjct: 787 KRQALQEELEELEEELEEAERRLDALERELE 817

Length = 1163

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

 Score = 37.8 bits (88), Expect = 0.004
 Identities = 19/58 (32%), Positives = 34/58 (58%)

Query: 100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
           L      L QL++  +EL+E  E+L+EE++ L+    EL EE   L+    KL+++++
Sbjct: 725 LAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIE 782

Length = 1163

>gnl|CDD|237560 PRK13922, PRK13922, rod shape-determining protein MreC; Provisional

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 10/74 (13%)

Query: 102 DAIRVLNQLRTESQELKETNEKLQEEI---KSLKAEKNELREEKLILKADKEKLEQQL-- 156
           +++  L  LR E++ELK+   +L+  +   + L+AE   LRE    L   KE L+ Q   
Sbjct: 66  ESLASLFDLREENEELKKELLELESRLQELEQLEAENARLRE----LLNLKESLDYQFIT 121

Query: 157 -KVMAMPTGGYMPT 169
            +V++     +   
Sbjct: 122 ARVISRSPDPWSQQ 135

Length = 276

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	214
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.5
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.49
smart00353	53	HLH helix loop helix domain.	99.44
KOG1318	411	consensus Helix loop helix transcription factor EB	99.38
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.15
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	99.05
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.51
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.34
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.32
KOG0561	373	consensus bHLH transcription factor [Transcription	98.27
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.78
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.59
PLN03217	93	transcription factor ATBS1; Provisional	97.57
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.39
PRK15422	79	septal ring assembly protein ZapB; Provisional	97.34
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	97.15
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	96.94
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.8
PRK15422	79	septal ring assembly protein ZapB; Provisional	96.39
KOG3910	632	consensus Helix loop helix transcription factor [T	96.14
smart00338	65	BRLZ basic region leucin zipper.	95.97
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	95.87
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	95.77
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	95.71
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	95.7
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	95.49
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	95.32
PRK04406	75	hypothetical protein; Provisional	95.23
PRK13169	110	DNA replication intiation control protein YabA; Re	95.18
PRK00846	77	hypothetical protein; Provisional	95.11
PRK02119	73	hypothetical protein; Provisional	95.06
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	95.05
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	94.96
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	94.91
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	94.91
PRK11637	428	AmiB activator; Provisional	94.8
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	94.63
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	94.62
PRK02793	72	phi X174 lysis protein; Provisional	94.58
PRK00295	68	hypothetical protein; Provisional	94.53
PRK10884	206	SH3 domain-containing protein; Provisional	94.41
COG4026	290	Uncharacterized protein containing TOPRIM domain,	94.26
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	94.18
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	94.17
PRK00736	68	hypothetical protein; Provisional	94.03
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	93.99
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.6
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	93.59
PRK04325	74	hypothetical protein; Provisional	93.51
PRK10884	206	SH3 domain-containing protein; Provisional	93.47
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	93.41
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.33
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	93.32
PRK13169	110	DNA replication intiation control protein YabA; Re	93.31
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	93.21
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	93.17
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	93.05
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	92.99
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	92.82
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	92.8
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	92.57
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	92.56
PRK11637	428	AmiB activator; Provisional	92.56
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	92.47
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	92.44
PHA02562	562	46 endonuclease subunit; Provisional	92.43
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	92.37
KOG0996	1293	consensus Structural maintenance of chromosome pro	92.02
COG5570	57	Uncharacterized small protein [Function unknown]	91.99
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	91.9
KOG1962	216	consensus B-cell receptor-associated protein and r	91.85
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	91.85
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	91.72
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	91.71
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	91.64
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	91.62
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	91.47
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	91.34
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	91.32
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	91.27
smart00338	65	BRLZ basic region leucin zipper.	91.22
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	91.21
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	91.0
COG0216	363	PrfA Protein chain release factor A [Translation,	90.97
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	90.92
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	90.91
TIGR02231	525	conserved hypothetical protein. This family consis	90.83
KOG3582	856	consensus Mlx interactors and related transcriptio	90.75
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	90.73
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	90.72
PF14662	193	CCDC155: Coiled-coil region of CCDC155	90.69
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	90.67
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	90.64
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	90.37
COG2433	652	Uncharacterized conserved protein [Function unknow	90.33
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	90.31
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	90.29
PF12808	52	Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2	90.25
COG4467	114	Regulator of replication initiation timing [Replic	90.06
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	89.94
PRK09039	343	hypothetical protein; Validated	89.78
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	89.71
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	89.63
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	89.49
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	89.35
KOG3119	269	consensus Basic region leucine zipper transcriptio	89.18
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	89.01
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	89.01
PF11180	192	DUF2968: Protein of unknown function (DUF2968); In	88.97
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	88.97
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	88.74
PRK13922	276	rod shape-determining protein MreC; Provisional	88.72
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	88.65
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	88.64
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	88.62
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	88.61
KOG3898	254	consensus Transcription factor NeuroD and related	88.58
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	88.49
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	88.48
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	88.38
KOG3119	269	consensus Basic region leucine zipper transcriptio	88.22
PRK13922	276	rod shape-determining protein MreC; Provisional	88.04
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	87.99
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	87.77
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	87.7
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	87.61
COG0497	557	RecN ATPase involved in DNA repair [DNA replicatio	87.35
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	87.31
KOG4797	123	consensus Transcriptional regulator [Transcription	87.21
PF10186	302	Atg14: UV radiation resistance protein and autopha	87.17
COG1256	552	FlgK Flagellar hook-associated protein [Cell motil	87.11
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	87.07
KOG4343	655	consensus bZIP transcription factor ATF6 [Transcri	87.01
PRK09039	343	hypothetical protein; Validated	86.95
PF10018	188	Med4: Vitamin-D-receptor interacting Mediator subu	86.84
PF14282	106	FlxA: FlxA-like protein	86.76
PF15458	254	NTR2: Nineteen complex-related protein 2	86.62
PF00038	312	Filament: Intermediate filament protein; InterPro:	86.58
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	86.48
PRK00888	105	ftsB cell division protein FtsB; Reviewed	86.47
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	86.39
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	86.25
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	86.23
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	86.18
TIGR02492	322	flgK_ends flagellar hook-associated protein FlgK.	86.11
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	86.03
PHA02562	562	46 endonuclease subunit; Provisional	85.97
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	85.88
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	85.87
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	85.81
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	85.81
COG2433	652	Uncharacterized conserved protein [Function unknow	85.72
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	85.71
PF14662	193	CCDC155: Coiled-coil region of CCDC155	85.56
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	85.49
PRK10803	263	tol-pal system protein YbgF; Provisional	85.47
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	85.46
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	85.38
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	85.31
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	85.13
KOG0249	916	consensus LAR-interacting protein and related prot	85.08
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	85.06
COG4026	290	Uncharacterized protein containing TOPRIM domain,	85.06
KOG3650	120	consensus Predicted coiled-coil protein [General f	84.97
COG4942	420	Membrane-bound metallopeptidase [Cell division and	84.72
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	84.69
PF15397	258	DUF4618: Domain of unknown function (DUF4618)	84.68
PF14282	106	FlxA: FlxA-like protein	84.66
COG3937	108	Uncharacterized conserved protein [Function unknow	84.52
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	84.51
PF06637	442	PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 Th	84.47
PF14988	206	DUF4515: Domain of unknown function (DUF4515)	84.39
PRK03992	389	proteasome-activating nucleotidase; Provisional	84.3
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	84.29
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	84.27
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	84.27
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	84.26
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	84.2
PF13094	160	CENP-Q: CENP-Q, a CENPA-CAD centromere complex sub	84.16
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	84.12
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	84.01
PRK00888	105	ftsB cell division protein FtsB; Reviewed	83.98
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	83.97
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	83.87
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	83.83
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	83.7
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	83.68
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	83.46
COG2919	117	Septum formation initiator [Cell division and chro	83.44
PRK07739	507	flgK flagellar hook-associated protein FlgK; Valid	83.4
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	83.31
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	83.27
COG2900	72	SlyX Uncharacterized protein conserved in bacteria	83.18
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	83.01
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	82.82
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	82.81
KOG4395	285	consensus Transcription factor Atonal, contains HT	82.79
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	82.78
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	82.72
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	82.69
PRK10803	263	tol-pal system protein YbgF; Provisional	82.64
PF01166	59	TSC22: TSC-22/dip/bun family; InterPro: IPR000580	82.6
PF04999	97	FtsL: Cell division protein FtsL; InterPro: IPR007	82.59
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	82.56
PRK02224	880	chromosome segregation protein; Provisional	82.51
PRK07521	483	flgK flagellar hook-associated protein FlgK; Valid	82.48
PRK04406	75	hypothetical protein; Provisional	82.4
PRK05771	646	V-type ATP synthase subunit I; Validated	82.07
PRK07191	456	flgK flagellar hook-associated protein FlgK; Valid	82.05
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	82.05
PF11544	76	Spc42p: Spindle pole body component Spc42p; InterP	81.93
PRK14127	109	cell division protein GpsB; Provisional	81.83
PHA03011	120	hypothetical protein; Provisional	81.82
PRK03992	389	proteasome-activating nucleotidase; Provisional	81.8
PRK00409	782	recombination and DNA strand exchange inhibitor pr	81.78
KOG4571	294	consensus Activating transcription factor 4 [Trans	81.63
PRK05683	676	flgK flagellar hook-associated protein FlgK; Valid	81.51
PRK06665	627	flgK flagellar hook-associated protein FlgK; Valid	81.48
PF10458	66	Val_tRNA-synt_C: Valyl tRNA synthetase tRNA bindin	81.47
PF05837	106	CENP-H: Centromere protein H (CENP-H); InterPro: I	81.3
TIGR01554	378	major_cap_HK97 phage major capsid protein, HK97 fa	81.17
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	81.12
PF07334	76	IFP_35_N: Interferon-induced 35 kDa protein (IFP 3	81.1
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	81.05
PRK15396	78	murein lipoprotein; Provisional	81.01
PF10883	87	DUF2681: Protein of unknown function (DUF2681); In	80.88
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	80.85
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	80.83
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	80.8
PF05565	162	Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840	80.8
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	80.77
PRK04325	74	hypothetical protein; Provisional	80.38
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	80.06
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	80.02

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

Probab=99.50  E-value=1.6e-14  Score=99.33  Aligned_cols=51  Identities=33%  Similarity=0.483  Sum_probs=47.2

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHhhhcCCC---CCCCCChhhHHHHHHHHHHHHH
Q 028060           61 PGSKACREKLRRERLNDRFLDLSCILEPG---RPARTDKPAILDDAIRVLNQLR  111 (214)
Q Consensus        61 ~~sH~~~ERkRRdkLN~~F~~LrslLPP~---~~~K~DKasIL~dAI~yIk~Lr  111 (214)
                      +.+|+.+||+||++||++|.+|+.+||+.   ...|.||++||..||+||++|+
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            46799999999999999999999999885   4579999999999999999996

; 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 ....

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

Probab=99.49  E-value=4.1e-14  Score=97.33  Aligned_cols=55  Identities=31%  Similarity=0.442  Sum_probs=49.9

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTES  114 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~-~~K~DKasIL~dAI~yIk~Lr~~v  114 (214)
                      ++.+|+.+||+||++||++|.+|+++||+.. ..|.||++||..||+||+.|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4678999999999999999999999997752 469999999999999999999875

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=99.44  E-value=2.8e-13  Score=91.73  Aligned_cols=51  Identities=31%  Similarity=0.444  Sum_probs=46.1

Q ss_pred             hHHHHHHHHHHHHHHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHHH
Q 028060           65 ACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTESQ  115 (214)
Q Consensus        65 ~~~ERkRRdkLN~~F~~LrslLPP~~-~~K~DKasIL~dAI~yIk~Lr~~vq  115 (214)
                      +.+||+||++||++|..|+++||+.. ..|.||++||..||+||+.|+.+++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            46899999999999999999998653 5689999999999999999998875

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

Probab=99.38  E-value=1.1e-12  Score=123.32  Aligned_cols=84  Identities=23%  Similarity=0.347  Sum_probs=68.6

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRP--ARTDKPAILDDAIRVLNQLRTESQELK---ETNEKLQEEIKSLKAE  134 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~--~K~DKasIL~dAI~yIk~Lr~~vq~L~---~~n~~L~~ei~eL~~e  134 (214)
                      +|.+|++.||+||++||++|.+|+.|||.+..  .|..|.+||..+++||+.|++..++..   ...+.|+..+++|..+
T Consensus       233 Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~r  312 (411)
T KOG1318|consen  233 KRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRARELENRQKKLESTNQELALR  312 (411)
T ss_pred             HHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHH
Confidence            57899999999999999999999999987532  367899999999999999999877443   3345666777777777


Q ss_pred             HHHHHHHHH
Q 028060          135 KNELREEKL  143 (214)
Q Consensus       135 knELr~Ek~  143 (214)
                      +.||..+..
T Consensus       313 ieeLk~~~~  321 (411)
T KOG1318|consen  313 IEELKSEAG  321 (411)
T ss_pred             HHHHHHHHH
Confidence            777776665

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.15  E-value=1.2e-10  Score=100.55  Aligned_cols=80  Identities=21%  Similarity=0.342  Sum_probs=72.0

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCC-----CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRP-----ARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE  134 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~-----~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~e  134 (214)
                      |+.+|-.+|++|||.||..+..|..+||.+.+     .|++||.||.++|+||.+|..+..+-+++..+|+.++..|+.-
T Consensus        62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL~iI  141 (229)
T KOG1319|consen   62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTALKII  141 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999976543     3889999999999999999999999999999999999999888


Q ss_pred             HHHHH
Q 028060          135 KNELR  139 (214)
Q Consensus       135 knELr  139 (214)
                      +++..
T Consensus       142 k~~YE  146 (229)
T KOG1319|consen  142 KVNYE  146 (229)
T ss_pred             HHHHH
Confidence            88763

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

Probab=99.05  E-value=1.6e-09  Score=95.71  Aligned_cols=84  Identities=26%  Similarity=0.292  Sum_probs=70.3

Q ss_pred             CCCCCCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCC-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           56 DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTD-KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE  134 (214)
Q Consensus        56 ~~~~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~D-KasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~e  134 (214)
                      ...+.+.+||..||+||+.|.++|..|+..||.+...+.. -++||.+|++||+.|+.+........+.|..+-..|+++
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~r  134 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSRENRKLKAR  134 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456789999999999999999999999999886654444 589999999999999998888887777777777777777


Q ss_pred             HHHHH
Q 028060          135 KNELR  139 (214)
Q Consensus       135 knELr  139 (214)
                      +++|.
T Consensus       135 l~ql~  139 (232)
T KOG2483|consen  135 LEQLS  139 (232)
T ss_pred             HHHhc
Confidence            77664

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

Probab=98.51  E-value=6.3e-08  Score=86.29  Aligned_cols=59  Identities=29%  Similarity=0.342  Sum_probs=51.1

Q ss_pred             CCCCCchhHHHHHHHHHHHHHHHHHhhhcCC------CCCCCCChhhHHHHHHHHHHHHHHHHHH
Q 028060           58 CSRPGSKACREKLRRERLNDRFLDLSCILEP------GRPARTDKPAILDDAIRVLNQLRTESQE  116 (214)
Q Consensus        58 ~~~~~sH~~~ERkRRdkLN~~F~~LrslLPP------~~~~K~DKasIL~dAI~yIk~Lr~~vq~  116 (214)
                      +.+++.|-..||+||++||+++.+|+.+|+.      ...+|.+||-||.-|++|+++|+...+.
T Consensus        30 ~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   30 QYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             HHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            4578999999999999999999999999954      1237899999999999999999985433

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

Probab=98.34  E-value=5e-07  Score=91.42  Aligned_cols=52  Identities=25%  Similarity=0.397  Sum_probs=47.6

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHhhhcCCCCC---CCCChhhHHHHHHHHHHHHHHH
Q 028060           61 PGSKACREKLRRERLNDRFLDLSCILEPGRP---ARTDKPAILDDAIRVLNQLRTE  113 (214)
Q Consensus        61 ~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~---~K~DKasIL~dAI~yIk~Lr~~  113 (214)
                      +..|+..||+|||++|..+.||.++| |+..   .|+||-+||..||.+|+.+++.
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mv-p~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMV-PTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhh-hcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            67899999999999999999999999 4455   7999999999999999988875

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.32  E-value=5.7e-07  Score=91.77  Aligned_cols=77  Identities=26%  Similarity=0.348  Sum_probs=68.3

Q ss_pred             CCccCCCCCCCCCCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           48 NTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE  126 (214)
Q Consensus        48 ~~~kR~r~~~~~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~  126 (214)
                      .+.+|...+ ..+|..||..||+-|.-|||++.+|+.+||. ...|..|.+.|..||+||++|+...+.++.++..++.
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-GEKRTAHNIIEKRYRSSINDKIIELKDLVPG-TEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLRT  341 (953)
T ss_pred             CchhhcCCC-CcccchhhHHHHHhhcchhHHHHHHHHhcCc-cHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhhh
Confidence            456666655 5789999999999999999999999999954 6679999999999999999999999999999988773

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.27  E-value=6.4e-07  Score=82.29  Aligned_cols=70  Identities=23%  Similarity=0.279  Sum_probs=58.9

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           61 PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKS  130 (214)
Q Consensus        61 ~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~e  130 (214)
                      +.--|+-||+|=.-||-.|..||++||-...-|.+||+||..+.+||.+|+.+.-+|-.+|.+|+..+.+
T Consensus        61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~elKr~~~E  130 (373)
T KOG0561|consen   61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNGELKRLKLE  130 (373)
T ss_pred             HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccchHHHHHhh
Confidence            4456788999999999999999999987666799999999999999999999877777777666554433

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

Probab=97.78  E-value=5.9e-05  Score=67.94  Aligned_cols=62  Identities=29%  Similarity=0.345  Sum_probs=50.1

Q ss_pred             CCCCCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHH
Q 028060           57 SCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELK  118 (214)
Q Consensus        57 ~~~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~  118 (214)
                      ..+|+..--++||+|=.|+|+.|..|...-=+.-....-|+.||-.||+||..|+.-++++.
T Consensus       115 svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~  176 (284)
T KOG3960|consen  115 SVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQD  176 (284)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhh
Confidence            35677778899999999999999999876633223579999999999999999987655543

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

Probab=97.59  E-value=7.8e-05  Score=64.81  Aligned_cols=60  Identities=18%  Similarity=0.246  Sum_probs=50.9

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHH
Q 028060           59 SRPGSKACREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTESQELK  118 (214)
Q Consensus        59 ~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~--~~K~DKasIL~dAI~yIk~Lr~~vq~L~  118 (214)
                      ..+..++.+||.|=..+|..|.+||..||..-  ..|.+|+.+|--||.||+.|..-++.-.
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~  169 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQE  169 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccc
Confidence            35677888899999999999999999998644  3589999999999999999987655443

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.57  E-value=0.00019  Score=55.28  Aligned_cols=55  Identities=27%  Similarity=0.438  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHhhhcCCCCC-CCCChhh---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           72 RERLNDRFLDLSCILEPGRP-ARTDKPA---ILDDAIRVLNQLRTESQELKETNEKLQE  126 (214)
Q Consensus        72 RdkLN~~F~~LrslLPP~~~-~K~DKas---IL~dAI~yIk~Lr~~vq~L~~~n~~L~~  126 (214)
                      -|.||+.+..|+.+||..+. ...+|++   +|.+|+.||+.|+.+|..|.+...+|.+
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~   77 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLA   77 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            47899999999999976433 2345554   9999999999999999999887777654

>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=97.39  E-value=0.0021  Score=47.60  Aligned_cols=55  Identities=38%  Similarity=0.460  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ++.+.+|+.+++++-.....|+.++.+|+.+.++|.+++..|+.+.++|+++-.+
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~   57 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNA   57 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            4556667777777777777777777777777666666666666666666655444

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.

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=97.34  E-value=0.0024  Score=48.33  Aligned_cols=60  Identities=28%  Similarity=0.493  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +.-||+-|.=|+-++++|+++|..|.+++..++..+.+|++|+..||.|-...+.-|.++
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            456888888899999999999999999999988889999999999998888777777654

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.15  E-value=0.0053  Score=45.91  Aligned_cols=60  Identities=27%  Similarity=0.492  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +.-||+-|.-|+-++++|++.|.+|..+...+......|+.|+..||.|-...+.-++++
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            457899999999999999999999999999999999999999999999988877777664

>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=96.94  E-value=0.015  Score=43.15  Aligned_cols=57  Identities=32%  Similarity=0.492  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +..||+-|..|+.+++.|+.+|..|.++...|+.+...|++|....+.-+..|-..+
T Consensus        13 i~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~~LL~kl   69 (72)
T PF06005_consen   13 IQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLRSLLGKL   69 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            357889999999999999999988887777777777777766665555554444333

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=96.80  E-value=0.011  Score=50.25  Aligned_cols=60  Identities=30%  Similarity=0.486  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          100 LDDAIRVLNQLRTE---SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       100 L~dAI~yIk~Lr~~---vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      |.+.|.|+..|+..   .+.++.+|..|+.++.+|..+..+|..|+..|+.+..-++..++++
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            88999999999974   6677788888888888888888888888888888888777777664

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.

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=96.39  E-value=0.035  Score=42.09  Aligned_cols=56  Identities=29%  Similarity=0.367  Sum_probs=45.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHh
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI-------LKADKEKLEQQLKVM  159 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~-------Lk~e~e~L~~qlk~~  159 (214)
                      .+.+.+|+.+|++.-+...-|+.+|++|+.+.+.|.+|...       |..+.+.|+++...+
T Consensus         3 ~EvleqLE~KIqqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~W   65 (79)
T PRK15422          3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGW   65 (79)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            36788999999999999999999999999998888888766       666666666665554

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.14  E-value=0.0037  Score=61.15  Aligned_cols=57  Identities=26%  Similarity=0.377  Sum_probs=43.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCC-C-CCCChhhHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGR-P-ARTDKPAILDDAIRVLNQLRTESQE  116 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~-~-~K~DKasIL~dAI~yIk~Lr~~vq~  116 (214)
                      ||+..+.|||.|=..||+.|.||..+.--.. . ....|..||..||..|-.|+++|.+
T Consensus       526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            4666777777777889999999999872211 0 1246788999999999999988754

>smart00338 BRLZ basic region leucin zipper

Probab=95.97  E-value=0.03  Score=39.65  Aligned_cols=38  Identities=29%  Similarity=0.521  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  142 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek  142 (214)
                      .||.+|+.+++.|+.+|..|..++..|..++..|++++
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       26 AEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68899999999999988888888888888777776654

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=95.87  E-value=0.073  Score=48.18  Aligned_cols=88  Identities=27%  Similarity=0.368  Sum_probs=66.6

Q ss_pred             CCch-hHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           61 PGSK-ACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  139 (214)
Q Consensus        61 ~~sH-~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr  139 (214)
                      +.+| ..-||.-|.||+++..+=-        ..-.|-+-..+-=..|++|.++.+.|..+|+.|++..+.|-.+.+||+
T Consensus        60 RL~HLS~EEK~~RrKLKNRVAAQt--------aRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~  131 (292)
T KOG4005|consen   60 RLDHLSWEEKVQRRKLKNRVAAQT--------ARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELD  131 (292)
T ss_pred             hhcccCHHHHHHHHHHHHHHHHhh--------hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            3445 4567778888888765422        223344444444466899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 028060          140 EEKLILKADKEKLEQQL  156 (214)
Q Consensus       140 ~Ek~~Lk~e~e~L~~ql  156 (214)
                      .+...+.+++-.|.+|-
T Consensus       132 ~~le~~~~~l~~~~~~~  148 (292)
T KOG4005|consen  132 SELELLRQELAELKQQQ  148 (292)
T ss_pred             HHHHHHHHHHHhhHHHH
Confidence            99999999888886554

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=95.77  E-value=0.11  Score=50.60  Aligned_cols=54  Identities=15%  Similarity=0.339  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      -+.+-+.++.+|+++.+.|+.+.+.+.+...++..+...|++|+..|+.|+++.
T Consensus        70 ALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~  123 (475)
T PRK13729         70 ATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKAL  123 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhh
Confidence            344455556666666666666666666666677666777777777777777653

>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=95.71  E-value=0.05  Score=38.45  Aligned_cols=37  Identities=32%  Similarity=0.575  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREE  141 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~E  141 (214)
                      .||.+|+.++..|+.+|..|..++..|+.+...|..+
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e   62 (64)
T PF00170_consen   26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLKSE   62 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            5666666666666666666665555555555554443

; 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=95.70  E-value=0.082  Score=41.88  Aligned_cols=53  Identities=28%  Similarity=0.410  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAM  161 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~  161 (214)
                      +|=..+.+|++....|.+++.+|+..+.+|-+||+.|+-|.+.|...|.....
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            34455666666777777777777777788888888888888877777766543

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

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=95.49  E-value=0.14  Score=51.50  Aligned_cols=60  Identities=27%  Similarity=0.308  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +...-.-+.+|+.+.|+|.++.+++..+|++|++++-.-+.|...||.++|.-|.|++.+
T Consensus        88 ~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El  147 (907)
T KOG2264|consen   88 LASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEEL  147 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHH
Confidence            333446688999999999999999999999999999999999999999999999999885

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=95.32  E-value=0.14  Score=49.96  Aligned_cols=61  Identities=25%  Similarity=0.355  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------HHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA----------------------EKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~----------------------eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      .|..-|.-+++||.+++.|..+|+.|.+|.+.|++                      +..+|.++.+.|+..+..|+.||
T Consensus        60 TlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l  139 (472)
T TIGR03752        60 TLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRL  139 (472)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445667788888888888888888877777765                      33444444455555555556666


Q ss_pred             HHh
Q 028060          157 KVM  159 (214)
Q Consensus       157 k~~  159 (214)
                      +.+
T Consensus       140 ~~~  142 (472)
T TIGR03752       140 AGV  142 (472)
T ss_pred             hhc
Confidence            544

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.

>PRK04406 hypothetical protein; Provisional

Probab=95.23  E-value=0.33  Score=36.14  Aligned_cols=54  Identities=13%  Similarity=0.121  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      +..|..++..|+....-++.-|++|...+.+...+...|+.++..|.++++.+.
T Consensus         6 ~~~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   59 (75)
T PRK04406          6 IEQLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNMD   59 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            346778888888888888888888889999999889999999999999998864

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=95.18  E-value=0.15  Score=40.65  Aligned_cols=51  Identities=25%  Similarity=0.398  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +|=..+.+|++....|..++.+|+..+.+|-+||+.|+.|.+.|..-|...
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            445566667777777777777788888888888888888888887777765

>PRK00846 hypothetical protein; Provisional

Probab=95.11  E-value=0.34  Score=36.54  Aligned_cols=52  Identities=13%  Similarity=0.045  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      .|..++..|+....-...-|++|...+.+.......|+.++..|..+|+.+.
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            4566777777777777777888888888888888899999999999999874

>PRK02119 hypothetical protein; Provisional

Probab=95.06  E-value=0.41  Score=35.36  Aligned_cols=54  Identities=15%  Similarity=0.067  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      +..+..++..|+....-.+.-|++|...+.+.+.+...|+.++..|.++++.+.
T Consensus         4 ~~~~e~Ri~~LE~rla~QE~tie~LN~~v~~Qq~~id~L~~ql~~L~~rl~~~~   57 (73)
T PRK02119          4 QQNLENRIAELEMKIAFQENLLEELNQALIEQQFVIDKMQVQLRYMANKLKDMQ   57 (73)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            456778888888888888888888899999999999999999999999998874

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.05  E-value=0.25  Score=37.08  Aligned_cols=52  Identities=31%  Similarity=0.415  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      .+.+.+|+.++++.-....-|+-+|++|+.+.|.|..|.+.++...|.|+.+
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            4667889999999999999999999999999998888888777666666543

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=94.96  E-value=0.017  Score=49.07  Aligned_cols=53  Identities=25%  Similarity=0.255  Sum_probs=45.4

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRT  112 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~  112 (214)
                      .++-|+.+||+|=.-||+.|..||.++|---..|.+|.-.|.-|.+||-.|-.
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~  130 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ  130 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence            45779999999999999999999999964333578888899999999998743

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

Probab=94.91  E-value=0.23  Score=39.37  Aligned_cols=50  Identities=34%  Similarity=0.419  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      +-|.+|+.++..|-.+...|+..+.+|-.|-++|+-||..|+..+..+++
T Consensus         8 ~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~   57 (107)
T PF06156_consen    8 DRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ   57 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            56778888999999999999999999999999999999999988888876

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

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

Probab=94.91  E-value=0.12  Score=42.88  Aligned_cols=55  Identities=38%  Similarity=0.527  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhcC
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEK--NELREEKLILKADKEKLEQQLKVMAM  161 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~ek--nELr~Ek~~Lk~e~e~L~~qlk~~~~  161 (214)
                      |.+|+.++..|+.++..|..++..|....  .||+++...|+.|++.|+..|..+..
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            88888888888888888888888887766  57888889999999999988887643

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 [].

>PRK11637 AmiB activator; Provisional

Probab=94.80  E-value=0.43  Score=44.93  Aligned_cols=59  Identities=14%  Similarity=0.161  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +.++...|..|..++..+..+...++.++..+..+++++..+...++.+++.++.+|+.
T Consensus        70 ~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~  128 (428)
T PRK11637         70 RASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAA  128 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444445555555555555555555555566666666666666665555555555544

>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=94.63  E-value=0.33  Score=39.20  Aligned_cols=42  Identities=36%  Similarity=0.551  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      ..|..|..++..++.+...|+.++..|..+++++++|...|-
T Consensus        16 ~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~   57 (120)
T PF12325_consen   16 QLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLM   57 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444445555555555555555555555555555444444433

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 [].

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

Probab=94.62  E-value=0.24  Score=35.92  Aligned_cols=52  Identities=17%  Similarity=0.177  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      +|+.++..|+....-+..-+++|...+.+...+...|+.++..|..+++.+.
T Consensus         1 ~le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen    1 MLEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3567777788777777788888888888888888888888888888888875

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.

>PRK02793 phi X174 lysis protein; Provisional

Probab=94.58  E-value=0.61  Score=34.35  Aligned_cols=52  Identities=19%  Similarity=0.151  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      .+..++..|+....-.+.-|++|...+.+.+.+...|+.++..|..+|+.+.
T Consensus         5 ~~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   56 (72)
T PRK02793          5 SLEARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLKASQ   56 (72)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3667777777777777777888888888888888889899999988888864

>PRK00295 hypothetical protein; Provisional

Probab=94.53  E-value=0.59  Score=34.05  Aligned_cols=51  Identities=18%  Similarity=0.141  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      +..++..|+....-++.-|++|...+.+...+...|+.++..|..+++.+.
T Consensus         3 ~e~Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00295          3 LEERVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEEMV   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            445566677666666777777778888888888888888888888888874

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.41  E-value=0.32  Score=42.49  Aligned_cols=78  Identities=13%  Similarity=0.109  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           69 KLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  148 (214)
Q Consensus        69 RkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e  148 (214)
                      |.|=.++...+.+|++-|.-          |-++.-....+|+.++++++.....|+++.++|+.+..+++.|+..|+++
T Consensus        92 ~~rlp~le~el~~l~~~l~~----------~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~  161 (206)
T PRK10884         92 RTRVPDLENQVKTLTDKLNN----------IDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQ  161 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHH----------HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34446778888888887721          11222344455555555555555555555555566666666666666666


Q ss_pred             HHHHHHHH
Q 028060          149 KEKLEQQL  156 (214)
Q Consensus       149 ~e~L~~ql  156 (214)
                      .+.++...
T Consensus       162 ~~~~~~~~  169 (206)
T PRK10884        162 LDDKQRTI  169 (206)
T ss_pred             HHHHHHHH
Confidence            66655444

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

Probab=94.26  E-value=0.4  Score=43.34  Aligned_cols=53  Identities=30%  Similarity=0.467  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ...+++.+.+.+.++++.|..+..+|..+.++++++..+|..|+.+|+..++.
T Consensus       136 ~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~  188 (290)
T COG4026         136 DYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKK  188 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33456666777777888888888888888888888888888888777766665

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=94.18  E-value=0.032  Score=55.38  Aligned_cols=60  Identities=28%  Similarity=0.344  Sum_probs=46.3

Q ss_pred             CccCCCCCCCCC----CCchhHHHHHHHHHHHHHHHHHhhhcC--CCCCCCCChhhHHHHHHHHHH
Q 028060           49 TRKRARSDSCSR----PGSKACREKLRRERLNDRFLDLSCILE--PGRPARTDKPAILDDAIRVLN  108 (214)
Q Consensus        49 ~~kR~r~~~~~~----~~sH~~~ERkRRdkLN~~F~~LrslLP--P~~~~K~DKasIL~dAI~yIk  108 (214)
                      +|||.|....-+    -.++.---|+-||+||.-+..|.++||  ++.++|.||.|||-=++.|++
T Consensus        10 srkRrrp~qk~rpp~~a~tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   10 SRKRRRPLQKQRPPPKALTKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hhhccCCccccCCCccccccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            455555543322    246666678899999999999999995  456789999999999999986

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

Probab=94.17  E-value=0.91  Score=41.58  Aligned_cols=16  Identities=19%  Similarity=0.491  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHhhhc
Q 028060           71 RRERLNDRFLDLSCIL   86 (214)
Q Consensus        71 RRdkLN~~F~~LrslL   86 (214)
                      |...|...+..|+.+.
T Consensus       185 ~~~~L~~e~~~Lk~~~  200 (325)
T PF08317_consen  185 RKAELEEELENLKQLV  200 (325)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4455555566666655

>PRK00736 hypothetical protein; Provisional

Probab=94.03  E-value=0.87  Score=33.17  Aligned_cols=51  Identities=12%  Similarity=0.144  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      +..++..|+....-++.-|++|...+.+...+...|+.++..|..+++.+.
T Consensus         3 ~e~Ri~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00736          3 AEERLTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSLE   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344555666666666666677777777777777888888888888888764

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=93.99  E-value=0.65  Score=34.02  Aligned_cols=53  Identities=23%  Similarity=0.309  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      |.+|-...++|+.+|..|.++...+..|...|.+.+..-.+.+|.+=..|++|
T Consensus         9 le~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEamI~RLk~l   61 (65)
T TIGR02449         9 VEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAMITRLKAL   61 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            44444455555555555555555555555555555555555555555555544

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.

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.60  E-value=0.62  Score=42.44  Aligned_cols=60  Identities=18%  Similarity=0.306  Sum_probs=34.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           98 AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus        98 sIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.|..+-.-.+.++.+++.|..+.+.++.++++++.+.+++..+...|+.+|+.|+..+.
T Consensus        38 s~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~   97 (265)
T COG3883          38 SKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIV   97 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555555555666666666666666666666666666666666666666655554443

>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=93.59  E-value=0.8  Score=33.84  Aligned_cols=56  Identities=32%  Similarity=0.416  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      =+-|.+|..+-+.|....-.+...|+.|++...++..+...|+..++.++.++..+
T Consensus        11 De~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l   66 (74)
T PF12329_consen   11 DEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESL   66 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36788999999999888877888888888888888887788877777777766654

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.

>PRK04325 hypothetical protein; Provisional

Probab=93.51  E-value=1.1  Score=33.06  Aligned_cols=53  Identities=19%  Similarity=0.165  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      ..+..++..|+....-++.-|++|...+.+...+...|+.++..|..+|+.+.
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            45667777777777777777888888888888888888888888888888874

>PRK10884 SH3 domain-containing protein; Provisional

Probab=93.47  E-value=1.8  Score=37.87  Aligned_cols=25  Identities=24%  Similarity=0.193  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          131 LKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus       131 L~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      +..+.++|+.|++.|+.|.+.++.+
T Consensus       130 ~~~~~~~L~~~n~~L~~~l~~~~~~  154 (206)
T PRK10884        130 SDSVINGLKEENQKLKNQLIVAQKK  154 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444444444444333333

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=93.41  E-value=0.67  Score=45.37  Aligned_cols=59  Identities=10%  Similarity=0.126  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      -|.+.=.-..+|+++++.|+.+.+.+..+.+++..++++|.+|+..|+.+.+-+-.+.-
T Consensus        70 ALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~~~  128 (475)
T PRK13729         70 ATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANPV  128 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCCC
Confidence            34445556778888888888888878888888888999999999999999876655543

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.33  E-value=0.48  Score=43.16  Aligned_cols=61  Identities=21%  Similarity=0.384  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      +...=.-|++|+.+.+.++.+.+.|..++.++..+.++++.+...+++++.+|+.+++.+.
T Consensus        33 i~~~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~   93 (265)
T COG3883          33 IQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELK   93 (265)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555667888999999999999999999999999999999999999999999999988763

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=93.32  E-value=1.5  Score=32.13  Aligned_cols=53  Identities=30%  Similarity=0.428  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ++.|..++.+|-.....|+++-..|+.+...+..|...|....+--.+.+.+|
T Consensus         2 L~~Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEam   54 (65)
T TIGR02449         2 LQALAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAM   54 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67889999999999999999999999999999999999988888888888876

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.

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=93.31  E-value=0.77  Score=36.68  Aligned_cols=50  Identities=26%  Similarity=0.298  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      +-|.+|..++..+-.+...|+..+.+|-.|..+|+-||..|+..++++++
T Consensus         8 d~l~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~   57 (110)
T PRK13169          8 DALDDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA   57 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            45677888888888899999999999999999999999999888888744

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

Probab=93.21  E-value=0.91  Score=38.56  Aligned_cols=82  Identities=24%  Similarity=0.331  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           70 LRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  149 (214)
Q Consensus        70 kRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~  149 (214)
                      +.|..+..++..+-.-+--       +-..+..--.-|..|+.++..|+.....|.+++++...-...|+||...|+.+.
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 RSKGELAQQLVELNDELQE-------LEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQL  160 (194)
T ss_dssp             ---------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccch-------hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555411       111223333445556666666666666666666666666666666666665555


Q ss_pred             HHHHHHHHH
Q 028060          150 EKLEQQLKV  158 (214)
Q Consensus       150 e~L~~qlk~  158 (214)
                      .-++..+..
T Consensus       161 ~~~e~k~~~  169 (194)
T PF08614_consen  161 NMLEEKLRK  169 (194)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555544443

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=93.17  E-value=1.5  Score=40.54  Aligned_cols=81  Identities=23%  Similarity=0.290  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           70 LRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  149 (214)
Q Consensus        70 kRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~  149 (214)
                      .|...|+..+..|+.+...-   ..-..+.|..+-+-|..+..++.....+...++.+..+++..+++..++++.+..+|
T Consensus       179 ~~~~~L~~e~~~L~~~~~e~---~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I  255 (312)
T smart00787      179 DRKDALEEELRQLKQLEDEL---EDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEI  255 (312)
T ss_pred             HHHHHHHHHHHHHHHhHHHH---HhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555666666666665331   112244444444444444444444444444444444444444444444444444333


Q ss_pred             HHHH
Q 028060          150 EKLE  153 (214)
Q Consensus       150 e~L~  153 (214)
                      ..++
T Consensus       256 ~~ae  259 (312)
T smart00787      256 AEAE  259 (312)
T ss_pred             HHHH
Confidence            3333

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

>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=93.05  E-value=1.3  Score=35.77  Aligned_cols=66  Identities=29%  Similarity=0.345  Sum_probs=46.5

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHh
Q 028060           94 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL---KADKEKLEQQLKVM  159 (214)
Q Consensus        94 ~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~L---k~e~e~L~~qlk~~  159 (214)
                      ..-++++..=-.-|+++..++..|+.++..|..+-+.+..|+-.|..++..+   ..++..|+.+++.+
T Consensus        12 ~~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~~~~~~~~~~L~~el~~l   80 (120)
T PF12325_consen   12 GPSVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEELRALKKEVEELEQELEEL   80 (120)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456677777777888888888888888888888778877777776666444   34555555555543

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 [].

>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=92.99  E-value=1.4  Score=37.77  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHhhhc
Q 028060           70 LRRERLNDRFLDLSCIL   86 (214)
Q Consensus        70 kRRdkLN~~F~~LrslL   86 (214)
                      -|++-.|.+|.+|-.=|
T Consensus        59 vr~~ly~~~F~ELIRQV   75 (189)
T PF10211_consen   59 VREELYSQCFDELIRQV   75 (189)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            35667777888777666

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 [].

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

Probab=92.82  E-value=0.55  Score=43.17  Aligned_cols=19  Identities=37%  Similarity=0.286  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 028060          140 EEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       140 ~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +|...++.+++...++|..
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            3333444444445555544

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.

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=92.80  E-value=1.6  Score=36.34  Aligned_cols=63  Identities=27%  Similarity=0.441  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  162 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  162 (214)
                      .+.++.-+..+++....+..++..+..++.........+|++...++.+.+++..+...+...
T Consensus        72 ~~~~v~~L~h~keKl~~~~~~~~~l~~~l~~~~~~~~~~r~~l~~~k~~r~k~~~~~~~l~~~  134 (177)
T PF13870_consen   72 IGKTVQILTHVKEKLHFLSEELERLKQELKDREEELAKLREELYRVKKERDKLRKQNKKLRQQ  134 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            456778888888888888899999999999999999999999999999999999999887655

>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=92.57  E-value=0.53  Score=31.93  Aligned_cols=36  Identities=31%  Similarity=0.462  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          119 ETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       119 ~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      ...+.|...-+.|+.+..-|..|+..|++|+..|..
T Consensus         5 ~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~   40 (45)
T PF02183_consen    5 RDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKE   40 (45)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333334444444444444444444444443

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

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

Probab=92.56  E-value=0.21  Score=42.55  Aligned_cols=14  Identities=29%  Similarity=0.249  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHH
Q 028060          101 DDAIRVLNQLRTES  114 (214)
Q Consensus       101 ~dAI~yIk~Lr~~v  114 (214)
                      ..||+.---|+.++
T Consensus        10 N~AIERnalLE~EL   23 (166)
T PF04880_consen   10 NQAIERNALLESEL   23 (166)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHH
Confidence            34444444444444

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.

>PRK11637 AmiB activator; Provisional

Probab=92.56  E-value=1  Score=42.45  Aligned_cols=39  Identities=23%  Similarity=0.235  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          120 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       120 ~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +...++.++..+..+++++..+...++.++..++.++..
T Consensus        83 qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~  121 (428)
T PRK11637         83 AISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAA  121 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333444444444444444444444444444444443

>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=92.47  E-value=1.4  Score=30.98  Aligned_cols=36  Identities=31%  Similarity=0.466  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          121 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       121 n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      ...|+.++..|..+...|+.+...|+.++..|..++
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            344455555555555555555555555555555443

; 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 ....

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=92.44  E-value=0.97  Score=38.49  Aligned_cols=54  Identities=26%  Similarity=0.328  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.....|+.+.+.|+.++..|+.+++.|..++..|..+...++.+.+-|-.-+.
T Consensus        96 ~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~Im~  149 (161)
T TIGR02894        96 NPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDIMD  149 (161)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677888888888888888888888888888888888888888877765553

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.

>PHA02562 46 endonuclease subunit; Provisional

Probab=92.43  E-value=1.3  Score=42.26  Aligned_cols=76  Identities=16%  Similarity=0.184  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           71 RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  150 (214)
Q Consensus        71 RRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e  150 (214)
                      ++..+..++.+|+..+.       .+-+-|...++-+..|+.++++|+.....+.+++++|..+++++..++..+..++.
T Consensus       331 ~~~~~~~~i~el~~~i~-------~~~~~i~~~~~~~~~l~~ei~~l~~~~~~~~~~l~~l~~~l~~~~~~~~~~~ke~~  403 (562)
T PHA02562        331 EFNEQSKKLLELKNKIS-------TNKQSLITLVDKAKKVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKY  403 (562)
T ss_pred             HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556666666666661       11222777888888999999999988888888888888888888888887776665


Q ss_pred             HHH
Q 028060          151 KLE  153 (214)
Q Consensus       151 ~L~  153 (214)
                      ..+
T Consensus       404 ~~~  406 (562)
T PHA02562        404 HRG  406 (562)
T ss_pred             HHH
Confidence            543

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

Probab=92.37  E-value=0.73  Score=43.56  Aligned_cols=44  Identities=45%  Similarity=0.453  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          117 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       117 L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      .+++.+.++.+...|++...||+.-++.|+.++|+|+||+..++
T Consensus       223 ~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~  266 (365)
T KOG2391|consen  223 REEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQ  266 (365)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence            34455555555666666666666666666666666666666543

>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=92.02  E-value=2.3  Score=45.81  Aligned_cols=83  Identities=24%  Similarity=0.341  Sum_probs=53.0

Q ss_pred             HHHHHHHHhhhcCCCCCCCCChhh-HHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHH
Q 028060           75 LNDRFLDLSCILEPGRPARTDKPA-ILDDAIRVLNQLRTESQELKET----------NEKLQEEIKSLKAEKNELREEKL  143 (214)
Q Consensus        75 LN~~F~~LrslLPP~~~~K~DKas-IL~dAI~yIk~Lr~~vq~L~~~----------n~~L~~ei~eL~~eknELr~Ek~  143 (214)
                      +++++.+||..+|.-. ....|.. =+.+.+..|..|..++.+++..          ...+++.|.+++.|++++.++..
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 LEERVRKLRERIPELE-NRLEKLTASVKRLAELIEYLESQIAELEAAVLKKVVDKKRLKELEEQIEELKKEVEELQEKAA  882 (1293)
T ss_pred             HHHHHHHHHHhhHHHH-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            5677777777774311 1122221 2345566677777777777643          24566778889999999885555


Q ss_pred             HHHHHHHHHHHHHHHh
Q 028060          144 ILKADKEKLEQQLKVM  159 (214)
Q Consensus       144 ~Lk~e~e~L~~qlk~~  159 (214)
                      . |++++.|+.++..+
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            5 78888888777654

>COG5570 Uncharacterized small protein [Function unknown]

Probab=91.99  E-value=0.52  Score=33.53  Aligned_cols=46  Identities=33%  Similarity=0.451  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLK-------AEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~-------~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      +...+..|++....|.++|++-.       ..+.+|.-.|.+||.|||+|..|
T Consensus         3 ieshl~eL~kkHg~le~ei~ea~n~Ps~dd~~i~eLKRrKL~lKeeIEkLka~   55 (57)
T COG5570           3 IESHLAELEKKHGNLEREIQEAMNSPSSDDLAIRELKRRKLRLKEEIEKLKAQ   55 (57)
T ss_pred             HHHHHHHHHHhhchHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHHHHhcc
Confidence            34556667777777777775543       25678888899999999999875

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=91.90  E-value=2  Score=31.50  Aligned_cols=52  Identities=29%  Similarity=0.349  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAE-------KNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~e-------knELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      |..|+.....+...++..+.+.+.|..|       +.....++..|+.|++.|.++++.
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            3445555555555544444444444444       445677777888888888887765

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

Probab=91.85  E-value=2.4  Score=37.67  Aligned_cols=62  Identities=26%  Similarity=0.292  Sum_probs=47.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           97 PAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus        97 asIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      .+=.....+=+..|++++++.+.+.+.++.+...|+.+..++.+|-.+|..|-++|+.|+..
T Consensus       150 ~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~  211 (216)
T KOG1962|consen  150 EEENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIES  211 (216)
T ss_pred             hhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhc
Confidence            33344555566777778888888888888888888888888888888888888888888764

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

Probab=91.85  E-value=1.5  Score=35.17  Aligned_cols=59  Identities=36%  Similarity=0.463  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHh
Q 028060          101 DDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN----ELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       101 ~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~ekn----ELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ..+|.-|..|+.+.+.++.....|+.+....+..+.    .+..++..|+.+++.++..+..+
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            356778888888888888777777766655444433    24445555555555555544444

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

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

Probab=91.72  E-value=1.2  Score=40.84  Aligned_cols=14  Identities=21%  Similarity=0.185  Sum_probs=5.4

Q ss_pred             HHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQEL  117 (214)
Q Consensus       104 I~yIk~Lr~~vq~L  117 (214)
                      ..+...|+.++..|
T Consensus       183 ~~~~~~L~~e~~~L  196 (325)
T PF08317_consen  183 RERKAELEEELENL  196 (325)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333344433333

>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=91.71  E-value=1.2  Score=39.17  Aligned_cols=6  Identities=67%  Similarity=1.769  Sum_probs=3.6

Q ss_pred             ccccCC
Q 028060          193 WQYLPP  198 (214)
Q Consensus       193 wq~~pp  198 (214)
                      |+|+|.
T Consensus       214 W~~l~~  219 (251)
T PF11932_consen  214 WQWLPD  219 (251)
T ss_pred             CeECCH
Confidence            666654

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.

>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=91.64  E-value=1.3  Score=37.37  Aligned_cols=30  Identities=37%  Similarity=0.423  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          125 QEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       125 ~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      .+|+++|+.|+.+...|...||.|.+.|+.
T Consensus       160 ~~ei~~lk~el~~~~~~~~~LkkQ~~~l~~  189 (192)
T PF05529_consen  160 SEEIEKLKKELEKKEKEIEALKKQSEGLQK  189 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344444444444444444444444444443

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

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

Probab=91.62  E-value=1.6  Score=34.44  Aligned_cols=55  Identities=22%  Similarity=0.292  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      ++.=+|+|+-..++   .|...+..|+++++.+..+..+++.+...++.++..|..++
T Consensus        63 LaQl~ieYLl~~q~---~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~  117 (118)
T PF13815_consen   63 LAQLSIEYLLHCQE---YLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKES  117 (118)
T ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            55677888776655   34445556666666666666666666666666666665554

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=91.47  E-value=3.3  Score=30.13  Aligned_cols=46  Identities=28%  Similarity=0.364  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      .+.....+..+...++.++++++.+.++|+.|...|.. .++++.--
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~-~~rIe~~A   67 (85)
T TIGR02209        22 AQHQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR-HERIEKIA   67 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-HHHHHHHH
Confidence            34445555555566666666666666666666665543 44444433

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.

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=91.34  E-value=2  Score=31.49  Aligned_cols=52  Identities=21%  Similarity=0.326  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      .+.+-+.--+.....|..+++.....+...-.+.++|++|+..|+.|++.+.
T Consensus        16 ~~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r   67 (69)
T PF14197_consen   16 SLTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELR   67 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3444444444555555556666666667777777777777777777766554

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

Probab=91.32  E-value=1  Score=40.37  Aligned_cols=53  Identities=23%  Similarity=0.411  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      .=+..+-+..+..|.+|++|...+..++..|+.|...|+++..+|...++-+.
T Consensus        82 pIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylq  134 (248)
T PF08172_consen   82 PIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQ  134 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34556677777777777788888888888888888888888888888877663

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

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=91.27  E-value=1.8  Score=35.90  Aligned_cols=42  Identities=31%  Similarity=0.458  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          115 QELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       115 q~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      .+|+.++..|..+++.|+.|..+++.|...++.-.+.|+.-.
T Consensus        77 ~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~  118 (135)
T KOG4196|consen   77 HELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSA  118 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            357777777888888888888888888888877777777643

>smart00338 BRLZ basic region leucin zipper

Probab=91.22  E-value=2.7  Score=29.57  Aligned_cols=34  Identities=32%  Similarity=0.537  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      ..|+.++..|..+..+|+.+...|..++..|.++
T Consensus        29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~   62 (65)
T smart00338       29 EELERKVEQLEAENERLKKEIERLRRELEKLKSE   62 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444443

>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=91.21  E-value=2.5  Score=35.11  Aligned_cols=43  Identities=35%  Similarity=0.467  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          117 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       117 L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      -+.++..|++++..|..+++.|..|...+..+++.|.++++.+
T Consensus        50 ~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~   92 (140)
T PF10473_consen   50 SKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKK   92 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3345556666666666666666666666666666666655543

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

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

Probab=91.00  E-value=2.5  Score=30.22  Aligned_cols=47  Identities=19%  Similarity=0.393  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      |.+|-.+|+.|.....+|..++..|+.+.....+|-.+-...++.+-
T Consensus         5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN~a   51 (56)
T PF04728_consen    5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDNIA   51 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            56677777777777777777777777776666666665555554443

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.

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

Probab=90.97  E-value=2.9  Score=39.67  Aligned_cols=90  Identities=29%  Similarity=0.418  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHhhhcC-CCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHH-HHHHHHHHH
Q 028060           73 ERLNDRFLDLSCILE-PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA----EKNE-LREEKLILK  146 (214)
Q Consensus        73 dkLN~~F~~LrslLP-P~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~----eknE-Lr~Ek~~Lk  146 (214)
                      +.|-++|.+|..+|- |...+..++..-|++-..+|..+-....++++..+.|..--.-|..    +..| ..+|...++
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            457789999999983 2222445666666666666666666665555554444432222222    2223 477889999


Q ss_pred             HHHHHHHHHHHHhcCC
Q 028060          147 ADKEKLEQQLKVMAMP  162 (214)
Q Consensus       147 ~e~e~L~~qlk~~~~~  162 (214)
                      .+++.|+.+|+.+-.|
T Consensus        90 ~~~~~le~~L~~lLlP  105 (363)
T COG0216          90 AKIEELEEELKILLLP  105 (363)
T ss_pred             HHHHHHHHHHHHhcCC
Confidence            9999999999988433

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

Probab=90.92  E-value=2.3  Score=36.72  Aligned_cols=59  Identities=24%  Similarity=0.372  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      |..+=+..|+.|+.++..++..-......+.++.+|...|.+-...+..+.+.|+.+|+
T Consensus        21 IT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~   79 (201)
T PF13851_consen   21 ITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLK   79 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            55566777888888777777554444444444444444444444444444444444443

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

Probab=90.91  E-value=1  Score=37.22  Aligned_cols=52  Identities=37%  Similarity=0.510  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK--LILKADKEKLEQQLKV  158 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek--~~Lk~e~e~L~~qlk~  158 (214)
                      +..|..++..|++++..|..+.+.|+.+++.|..+-  ..|..+++.|+.++..
T Consensus        74 l~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~  127 (169)
T PF07106_consen   74 LAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEE  127 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444444443332  3344444444444443

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 [].

>TIGR02231 conserved hypothetical protein

Probab=90.83  E-value=2.1  Score=41.39  Aligned_cols=86  Identities=20%  Similarity=0.254  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHH
Q 028060           71 RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRT---------------ESQELKETNEKLQEEIKSLKAEK  135 (214)
Q Consensus        71 RRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~---------------~vq~L~~~n~~L~~ei~eL~~ek  135 (214)
                      +...|.+.+.+|...+--    -.++.+.+..-+.+|..+..               .+.++.+......+++.++..++
T Consensus        72 ~~~~l~~~l~~l~~~~~~----~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (525)
T TIGR02231        72 RLAELRKQIRELEAELRD----LEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTED  147 (525)
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            445566677777766621    24677777777788877764               23445566666667777777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          136 NELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       136 nELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      .++..+...++.++++|+++|..++
T Consensus       148 ~~~~~~~~~~~~~l~~l~~~l~~l~  172 (525)
T TIGR02231       148 REAERRIRELEKQLSELQNELNALL  172 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            7777777778888888888777654

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.

>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]

Probab=90.75  E-value=0.11  Score=52.97  Aligned_cols=79  Identities=22%  Similarity=0.294  Sum_probs=60.7

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHhhhcCCCC----CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           59 SRPGSKACREKLRRERLNDRFLDLSCILEPGR----PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE  134 (214)
Q Consensus        59 ~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~----~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~e  134 (214)
                      .+.++|.-+|.+||..+.-+|..|-++. .+.    .-|+.++.-+..++.||.-+..+...+.++--.|..++.+|++-
T Consensus       650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~-Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr~~~s~~~A~  728 (856)
T KOG3582|consen  650 NRPITHISAEQKRRFNIKLQFDVLNSLS-SNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKEISELNAV  728 (856)
T ss_pred             CCcccCccHHHHHHhhHHhhhHhhhhhc-cCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhhhHHHHHH
Confidence            4689999999999999999999998887 422    13677778899999999988777766666666666666666665


Q ss_pred             HHHH
Q 028060          135 KNEL  138 (214)
Q Consensus       135 knEL  138 (214)
                      ++-+
T Consensus       729 ~~~~  732 (856)
T KOG3582|consen  729 ISAC  732 (856)
T ss_pred             HHHh
Confidence            5543

>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=90.73  E-value=0.77  Score=31.49  Aligned_cols=30  Identities=30%  Similarity=0.433  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          125 QEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       125 ~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      ...+.+|..++.+|..++..|+.++..|+.
T Consensus        24 k~~~~~le~~~~~L~~en~~L~~~i~~L~~   53 (54)
T PF07716_consen   24 KQREEELEQEVQELEEENEQLRQEIAQLER   53 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            444555555566666666666666655554

; 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 ....

>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=90.72  E-value=1.1  Score=30.46  Aligned_cols=34  Identities=29%  Similarity=0.419  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          125 QEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       125 ~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +..-..|+...+.|..+...|+.|++.|..++..
T Consensus         4 E~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~   37 (45)
T PF02183_consen    4 ERDYDALKASYDSLKAEYDSLKKENEKLRAEVQE   37 (45)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444444444444444444443

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

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=90.69  E-value=2.1  Score=37.47  Aligned_cols=49  Identities=33%  Similarity=0.408  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          112 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       112 ~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      ++..+|..++..+..+...|..++..|.+|+-.|..+.+.|+.+.+.++
T Consensus        81 E~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL~  129 (193)
T PF14662_consen   81 EENRSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKELA  129 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHH
Confidence            3333333444555566666667777777777777777777776666653

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

Probab=90.67  E-value=3.2  Score=34.85  Aligned_cols=22  Identities=45%  Similarity=0.599  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028060          136 NELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       136 nELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      ++++.+...|+.|+++|.++|+
T Consensus        76 ~~lr~~~e~L~~eie~l~~~L~   97 (177)
T PF07798_consen   76 AELRSENEKLQREIEKLRQELR   97 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444443

>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=90.64  E-value=2.4  Score=34.16  Aligned_cols=63  Identities=27%  Similarity=0.347  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  162 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  162 (214)
                      +......+..|..+...|.+.|-.++.++.+++.++.++.++...|+.+...+.++++.++.+
T Consensus        29 ~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~l~~~   91 (150)
T PF07200_consen   29 VQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEKEQQQDELSSN   91 (150)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            334445566677777777777777788888888888888888899999999998888887443

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.

>TIGR00219 mreC rod shape-determining protein MreC

Probab=90.37  E-value=1.9  Score=39.03  Aligned_cols=43  Identities=23%  Similarity=0.251  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          114 SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       114 vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ..+|++||++|++++.+|+++.+.+   ...|++|.++|+..|...
T Consensus        68 ~~~l~~EN~~Lr~e~~~l~~~~~~~---~~~l~~EN~rLr~LL~~~  110 (283)
T TIGR00219        68 VNNLEYENYKLRQELLKKNQQLEIL---TQNLKQENVRLRELLNSP  110 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCc
Confidence            3456667777777766664444432   223677777777766543

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.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.33  E-value=1.8  Score=43.72  Aligned_cols=44  Identities=25%  Similarity=0.335  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  145 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~L  145 (214)
                      .-.+-|+.|+..++.|+.+|..|+.++.+|+.++.+|+.+...+
T Consensus       419 ~~~~~i~~~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~  462 (652)
T COG2433         419 VYEKRIKKLEETVERLEEENSELKRELEELKREIEKLESELERF  462 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33455666777777788888777777777777777766665544

>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=90.31  E-value=6.1  Score=31.96  Aligned_cols=53  Identities=23%  Similarity=0.344  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          101 DDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       101 ~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      ...|..|..|-...+.-....+.|..++..+..+...|.....+|+.+++.++
T Consensus        34 ~~vin~i~~Ll~~~~r~~~~~e~l~~~~~~l~~d~~~l~~~~~rL~~~~~~~e   86 (151)
T PF11559_consen   34 VRVINCIYDLLQQRDRDMEQREDLSDKLRRLRSDIERLQNDVERLKEQLEELE   86 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            33445555444444444444444444444444444444333344433333333

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.

>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=90.29  E-value=1.4  Score=40.23  Aligned_cols=56  Identities=13%  Similarity=0.318  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCCCCC
Q 028060          111 RTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM-AMPTGGYM  167 (214)
Q Consensus       111 r~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~-~~~p~g~~  167 (214)
                      +..++.+..+.++++..+..|..+...|.....+-++|.||.+..|+++ ++-|+ ||
T Consensus       168 ~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPA-fm  224 (267)
T PF10234_consen  168 KEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPA-FM  224 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChH-HH
Confidence            3334444444444444444555555555555555566666666666665 34433 44

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 [].

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

Probab=90.25  E-value=1.1  Score=31.54  Aligned_cols=47  Identities=23%  Similarity=0.319  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      |..|++-+.+|+.+.+.-..+......++.+|+.||..|++++++++
T Consensus         3 ~~Rl~ELe~klkaerE~R~~d~~~a~~rl~~l~~EN~~Lr~eL~~~r   49 (52)
T PF12808_consen    3 LLRLEELERKLKAEREARSLDRSAARKRLSKLEGENRLLRAELERLR   49 (52)
T ss_pred             HHHHHHHHHHHHHhHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45566666677766654444556778888999999999998888775

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

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

Probab=90.06  E-value=2  Score=34.59  Aligned_cols=49  Identities=29%  Similarity=0.353  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +=.++..|+.....|-.++..|++.+.+|-+||..|+-|.++|..-|-.
T Consensus         6 iFd~v~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~   54 (114)
T COG4467           6 IFDQVDNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE   54 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence            4456677777888888889999999999999999999999999876643

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

Probab=89.94  E-value=3.2  Score=36.46  Aligned_cols=16  Identities=25%  Similarity=0.264  Sum_probs=7.3

Q ss_pred             HHHHHHHHHHHHHHHH
Q 028060          143 LILKADKEKLEQQLKV  158 (214)
Q Consensus       143 ~~Lk~e~e~L~~qlk~  158 (214)
                      ..++++++.|++|+..
T Consensus        80 ~~q~~el~~L~~qi~~   95 (251)
T PF11932_consen   80 ASQEQELASLEQQIEQ   95 (251)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3334444445444444

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.

>PRK09039 hypothetical protein; Validated

Probab=89.78  E-value=2.4  Score=39.40  Aligned_cols=54  Identities=11%  Similarity=0.109  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      +.+++-.-|..|+.+++.|+.+...|+.++..++.+..+.+.....|+.+++.+
T Consensus       131 ~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a  184 (343)
T PRK09039        131 VSARALAQVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVA  184 (343)
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566667777778888877777777777777766666666666665555544

>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=89.71  E-value=2.8  Score=29.71  Aligned_cols=42  Identities=38%  Similarity=0.518  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          116 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       116 ~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +++.+...|+.++++++.+..+|+.+...|+...+.++...+
T Consensus        21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR   62 (80)
T PF04977_consen   21 QLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAR   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            333444444444444445555555555555444555554444

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

>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=89.63  E-value=3.5  Score=36.68  Aligned_cols=27  Identities=26%  Similarity=0.369  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKS  130 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~e  130 (214)
                      -.+|.+++++.+.|..+.....++++.
T Consensus        31 e~~L~e~~kE~~~L~~Er~~h~eeLrq   57 (230)
T PF10146_consen   31 EKCLEEYRKEMEELLQERMAHVEELRQ   57 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356666666666665554444433333

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.

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

Probab=89.49  E-value=2.6  Score=37.78  Aligned_cols=61  Identities=26%  Similarity=0.324  Sum_probs=54.2

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           94 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus        94 ~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      .+-.+||.=.+.-=...|.++.+|++++..++.++..|+.|++.|+.+|..|-..+--|+.
T Consensus        75 ~~~~siLpIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqS  135 (248)
T PF08172_consen   75 GGDSSILPIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQS  135 (248)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4667788888888888999999999999999999999999999999999999877777765

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

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

Probab=89.35  E-value=2.4  Score=33.17  Aligned_cols=48  Identities=29%  Similarity=0.349  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          109 QLRTESQELKETNEKL--QEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L--~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      .+..+++.++.+.+.|  ..++..|+.++.+++-+...+.++++-+.+++
T Consensus        46 ~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~~   95 (106)
T PF10805_consen   46 EHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSHQL   95 (106)
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            3445555555555555  44455555555555555555555555444443

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

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

Probab=89.18  E-value=2.1  Score=38.66  Aligned_cols=54  Identities=17%  Similarity=0.326  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +|....+.....++++..+-+....++...+.+|..||..|+.+++.|++++..
T Consensus       194 ~y~err~rNN~A~~kSR~~~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~  247 (269)
T KOG3119|consen  194 EYKERRRRNNEAVRKSRDKRKQKEDEMAHRVAELEKENEALRTQVEQLKKELAT  247 (269)
T ss_pred             HHHHHHHhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444434444444444445555555555555555544444

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

Probab=89.01  E-value=3.7  Score=30.56  Aligned_cols=26  Identities=23%  Similarity=0.247  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKA  133 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~  133 (214)
                      ++....+..|+.+|=.|.=+|..|..
T Consensus         3 rEqe~~i~~L~KENF~LKLrI~fLee   28 (75)
T PF07989_consen    3 REQEEQIDKLKKENFNLKLRIYFLEE   28 (75)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            44555555555555544444444433

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

Probab=89.01  E-value=2.4  Score=45.22  Aligned_cols=51  Identities=27%  Similarity=0.440  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +|..+|++++..+..|.++.++++.+.-+-++|+...+.++..|...+...
T Consensus       405 ~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~  455 (1074)
T KOG0250|consen  405 QLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENI  455 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333334444444444444444433

>PF11180 DUF2968: Protein of unknown function (DUF2968); InterPro: IPR021350 This family of proteins has no known function

Probab=88.97  E-value=5  Score=35.13  Aligned_cols=60  Identities=15%  Similarity=0.268  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTG  164 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p~  164 (214)
                      .....|+..++--...-......-++.+.|...|+.|+...+.++..|+.|+..+..+-.
T Consensus       126 ~ra~~LqaDl~~~~~Q~~~va~~Q~q~r~ea~aL~~e~~aaqaQL~~lQ~qv~~Lq~q~~  185 (192)
T PF11180_consen  126 ARANRLQADLQIARQQQQQVAARQQQARQEAQALEAERRAAQAQLRQLQRQVRQLQRQAN  185 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            445556665555555555555556667777777788888888888888888887755433

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

Probab=88.97  E-value=1.9  Score=40.78  Aligned_cols=53  Identities=19%  Similarity=0.195  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPT  163 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p  163 (214)
                      .--.+.|......++.++..|+.+.+.+..+.+       .++.|+++++.+++.+..+|
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~   66 (398)
T PTZ00454         14 THTERDLYEKLKELEKELEFLDIQEEYIKEEQK-------NLKRELIRAKEEVKRIQSVP   66 (398)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHhCCC
Confidence            334444555555554455554444444444444       44455555555565555554

>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=88.74  E-value=7  Score=29.64  Aligned_cols=42  Identities=26%  Similarity=0.366  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          117 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       117 L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      |..+...||..+..|...+.+.++|+..|++|.+-|++=+..
T Consensus        21 Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~n   62 (80)
T PF10224_consen   21 LIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGN   62 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333334444444444444444444455555555555444443

The exact function is unknown.

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=88.72  E-value=2.5  Score=37.32  Aligned_cols=39  Identities=33%  Similarity=0.563  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          116 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       116 ~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ++.++|+.|++|+.+|+.+..++    ..++.|.++|...|..
T Consensus        73 ~l~~en~~L~~e~~~l~~~~~~~----~~l~~en~~L~~lL~~  111 (276)
T PRK13922         73 DLREENEELKKELLELESRLQEL----EQLEAENARLRELLNL  111 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhcC
Confidence            34444444444444444444433    1456677777776654

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

Probab=88.65  E-value=0.32  Score=49.55  Aligned_cols=51  Identities=25%  Similarity=0.358  Sum_probs=41.0

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHhhhcCC--CCCCCCChhhHHHHHHHHHHHHHH
Q 028060           61 PGSKACREKLRRERLNDRFLDLSCILEP--GRPARTDKPAILDDAIRVLNQLRT  112 (214)
Q Consensus        61 ~~sH~~~ERkRRdkLN~~F~~LrslLPP--~~~~K~DKasIL~dAI~yIk~Lr~  112 (214)
                      |.+-.-+-|-||.|=|+-|.+|..+||-  +..+..|||||+-=||-|++ ||+
T Consensus        47 kEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR-lrk   99 (768)
T KOG3558|consen   47 KEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR-LRK   99 (768)
T ss_pred             hhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH-HHH
Confidence            3334456788999999999999999962  33467999999999999998 554

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

Probab=88.64  E-value=3.8  Score=31.22  Aligned_cols=62  Identities=34%  Similarity=0.466  Sum_probs=31.5

Q ss_pred             hhHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           97 PAILDDAIRVL---NQLRTESQELKETNEKLQEEIKSLKA---EKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus        97 asIL~dAI~yI---k~Lr~~vq~L~~~n~~L~~ei~eL~~---eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ...+.+.++.-   ++|+.+++.|+.+...+..+|..++.   +..+|..+...++.++..++.+++.
T Consensus        25 ~~~vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~   92 (108)
T PF02403_consen   25 EEDVDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKE   92 (108)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444443   34445566666666666666555554   2344555555555555555444443

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 ....

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

Probab=88.62  E-value=6.6  Score=33.64  Aligned_cols=76  Identities=29%  Similarity=0.411  Sum_probs=41.4

Q ss_pred             HhhhcCCCCCCCCChhh-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHH
Q 028060           82 LSCILEPGRPARTDKPA-----------ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA------EKNELREEKLI  144 (214)
Q Consensus        82 LrslLPP~~~~K~DKas-----------IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~------eknELr~Ek~~  144 (214)
                      |.+||.-|. -.++|.+           ....--.-+..|+.+++.++.....|+.++..++.      +..++-.+...
T Consensus        36 lq~LvDDgl-V~~EKiGssn~YWsFps~~~~~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~~~~r~~~~eR~~~l~~l~~  114 (188)
T PF03962_consen   36 LQSLVDDGL-VHVEKIGSSNYYWSFPSQAKQKRQNKLEKLQKEIEELEKKIEELEEKIEEAKKGREESEEREELLEELEE  114 (188)
T ss_pred             HHHHhcccc-chhhhccCeeEEEecChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHH
Confidence            444554444 3566654           22333444556666666666666666666655543      22334455556


Q ss_pred             HHHHHHHHHHHHHH
Q 028060          145 LKADKEKLEQQLKV  158 (214)
Q Consensus       145 Lk~e~e~L~~qlk~  158 (214)
                      |+.+++.|+.+|..
T Consensus       115 l~~~~~~l~~el~~  128 (188)
T PF03962_consen  115 LKKELKELKKELEK  128 (188)
T ss_pred             HHHHHHHHHHHHHH
Confidence            66666666666664

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

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

Probab=88.61  E-value=4.3  Score=37.34  Aligned_cols=32  Identities=34%  Similarity=0.450  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNE  137 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknE  137 (214)
                      -+..|+.+...|.++...|+.+..+|.+|+.+
T Consensus        51 el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~   82 (314)
T PF04111_consen   51 ELEKLEQEEEELLQELEELEKEREELDQELEE   82 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333333333333333

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.

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

Probab=88.58  E-value=0.35  Score=43.35  Aligned_cols=53  Identities=26%  Similarity=0.318  Sum_probs=44.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRT  112 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr~  112 (214)
                      ++..=|.+||.|=-.||+.|..||.+||.. ...|..|...|.-|-.||..|..
T Consensus        72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~  125 (254)
T KOG3898|consen   72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE  125 (254)
T ss_pred             hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence            567778999999999999999999999732 34689999999888888887743

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

Probab=88.49  E-value=4  Score=35.22  Aligned_cols=14  Identities=21%  Similarity=0.354  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHHh
Q 028060          146 KADKEKLEQQLKVM  159 (214)
Q Consensus       146 k~e~e~L~~qlk~~  159 (214)
                      +.+++..+.+++..
T Consensus       172 ~~~~~~~e~~F~~~  185 (190)
T PF05266_consen  172 KEEIENAELEFQSV  185 (190)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33333344444433

>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=88.48  E-value=4.7  Score=36.81  Aligned_cols=59  Identities=22%  Similarity=0.303  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHh
Q 028060          101 DDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK-------ADKEKLEQQLKVM  159 (214)
Q Consensus       101 ~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk-------~e~e~L~~qlk~~  159 (214)
                      ..+..-|.+++..+..+......|..+|+.-+.|+...+.+...|+       .|-|+|+.+|+.+
T Consensus       172 ~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmdEyEklE~EL~~l  237 (267)
T PF10234_consen  172 KAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMDEYEKLEEELQKL  237 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHH
Confidence            3444455566666666667777788888888888887777777776       6888888888774

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 [].

>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=88.38  E-value=7.2  Score=36.48  Aligned_cols=66  Identities=20%  Similarity=0.357  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHhhh--------cCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           71 RRERLNDRFLDLSCI--------LEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNE  137 (214)
Q Consensus        71 RRdkLN~~F~~Lrsl--------LPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknE  137 (214)
                      |...++....+|--.        ++|.. .+.+=+.+|.++-+-.+.|+.++..|+.....++.+++-|+...+.
T Consensus        38 r~q~LKkk~~el~~~~~~~~d~~~~~~~-~~~~La~lL~~sre~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~la~  111 (319)
T PF09789_consen   38 RYQALKKKYRELIQEAAGFGDPSIPPEK-ENKNLAQLLSESREQNKKLKEEVEELRQKLNEAQGDIKLLREKLAR  111 (319)
T ss_pred             HHHHHHHHHHHhhhhhcccCCccCCccc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHh
Confidence            446666666555511        22221 2334455889999999999999888887766666666666654443

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

Probab=88.22  E-value=11  Score=34.12  Aligned_cols=33  Identities=30%  Similarity=0.511  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      .+++.++..|+.+|+.|+.++.+|+.|+.-|++
T Consensus       218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~~~  250 (269)
T KOG3119|consen  218 DEMAHRVAELEKENEALRTQVEQLKKELATLRR  250 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566677777777777777777777777766655

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=88.04  E-value=4.3  Score=35.87  Aligned_cols=27  Identities=30%  Similarity=0.470  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEI  128 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei  128 (214)
                      +.+..+.+|+++.++|++++..|+.+.
T Consensus        66 ~~~~~~~~l~~en~~L~~e~~~l~~~~   92 (276)
T PRK13922         66 ESLASLFDLREENEELKKELLELESRL   92 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555555555544

>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=87.99  E-value=8.2  Score=27.87  Aligned_cols=54  Identities=24%  Similarity=0.377  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      |..=|+--..|+.++.+.+..|-.+...+++-.....+|..+...|+.+++.++
T Consensus         6 L~~EirakQ~~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r   59 (61)
T PF08826_consen    6 LEAEIRAKQAIQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEELR   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            444455556667777777777777776666666666666666666666666554

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

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

Probab=87.77  E-value=3.2  Score=39.48  Aligned_cols=71  Identities=21%  Similarity=0.275  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhcCCCCCCCCCCC
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL---EQQLKVMAMPTGGYMPTHP  171 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L---~~qlk~~~~~p~g~~p~~p  171 (214)
                      ++.++=..+++|++-+..++++|..|+-+.+++.+|.+|..+|.+.|..|....   ++.|..-...  -|.++|.
T Consensus       121 vf~k~k~~~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~layqq~L~~eyQa--tf~eq~~  194 (401)
T PF06785_consen  121 VFMKTKGDIQHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAEALAYQQELNDEYQA--TFVEQHS  194 (401)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHHHHHHHHHHhhc--ccccchh
Confidence            555666678889999999999999999999999999999999999997766553   3444332222  1666653

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

Probab=87.70  E-value=3.7  Score=41.38  Aligned_cols=45  Identities=29%  Similarity=0.395  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          115 QELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       115 q~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +.|+.+...++.++.+|..+++.|+.|+......+..|+.+|..+
T Consensus        18 ~~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eL   62 (617)
T PF15070_consen   18 QQLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSEL   62 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555555555555555555555555554443

>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=87.61  E-value=3.1  Score=29.47  Aligned_cols=32  Identities=38%  Similarity=0.442  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNEL  138 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknEL  138 (214)
                      +.+++.+++.|+.+++.++.+.++|+.++..|
T Consensus        19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l   50 (80)
T PF04977_consen   19 YYQLNQEIAELQKEIEELKKENEELKEEIERL   50 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34555556666666666666666666666655

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

>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=87.35  E-value=9.1  Score=38.37  Aligned_cols=92  Identities=26%  Similarity=0.436  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCCCCCChhhH-HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           69 KLRRERLNDRFLDLSCILEPGRPARTDKPAI-LDDAIRVLNQLRTESQELKE---TNEKLQEEIKSLKAEKNELREEKLI  144 (214)
Q Consensus        69 RkRRdkLN~~F~~LrslLPP~~~~K~DKasI-L~dAI~yIk~Lr~~vq~L~~---~n~~L~~ei~eL~~eknELr~Ek~~  144 (214)
                      -.|=+++.+|+..|+.+-   +     |-.. +.+.++|..+++.+.+.|..   ..++|+.++..+..+..+.-...+.
T Consensus       296 p~~L~~ve~Rl~~L~~l~---R-----KY~~~~~~l~~~~~~~~~el~~L~~~~~~~~~Le~~~~~l~~~~~~~A~~Ls~  367 (557)
T COG0497         296 PNRLEEVEERLFALKSLA---R-----KYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSA  367 (557)
T ss_pred             HHHHHHHHHHHHHHHHHH---H-----HhCCCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345567777777777776   2     3333 78999999999999999875   4678888888888888777666665


Q ss_pred             HHHHH-----HHHHHHHHHhcCCCCCCCC
Q 028060          145 LKADK-----EKLEQQLKVMAMPTGGYMP  168 (214)
Q Consensus       145 Lk~e~-----e~L~~qlk~~~~~p~g~~p  168 (214)
                      .+...     ..+.++|+.++...+-|.-
T Consensus       368 ~R~~~A~~L~~~v~~eL~~L~Me~a~F~v  396 (557)
T COG0497         368 IRKKAAKELEKEVTAELKALAMEKARFTV  396 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCceEEE
Confidence            54332     2356777777766655554

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

Probab=87.31  E-value=4.2  Score=40.79  Aligned_cols=59  Identities=34%  Similarity=0.463  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ....-.-+.+|+.+++.|..+.+.+..+++.|+.+..++.+|....+.+.++|+++++-
T Consensus       323 ~~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l  381 (594)
T PF05667_consen  323 QEEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKL  381 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34667788899999999999999999999999999999999999999999999998875

>KOG4797 consensus Transcriptional regulator [Transcription]

Probab=87.21  E-value=3.4  Score=33.47  Aligned_cols=31  Identities=32%  Similarity=0.543  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          117 LKETNEKLQEEIKSLKAEKNELREEKLILKA  147 (214)
Q Consensus       117 L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~  147 (214)
                      .+++.+.|+++|++|....+.|+.||..||.
T Consensus        65 VREEVe~Lk~qI~eL~er~~~Le~EN~lLk~   95 (123)
T KOG4797|consen   65 VREEVEVLKEQIRELEERNSALERENSLLKT   95 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3456677788888888888889999988874

>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=87.17  E-value=6  Score=34.31  Aligned_cols=13  Identities=31%  Similarity=0.322  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHH
Q 028060          146 KADKEKLEQQLKV  158 (214)
Q Consensus       146 k~e~e~L~~qlk~  158 (214)
                      +.....++.++..
T Consensus       132 ~~~l~~l~~~l~~  144 (302)
T PF10186_consen  132 KQRLSQLQSQLAR  144 (302)
T ss_pred             HHHHHHHHHHHHH
Confidence            3444444444443

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

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

Probab=87.11  E-value=5.2  Score=39.81  Aligned_cols=81  Identities=22%  Similarity=0.277  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           71 RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  150 (214)
Q Consensus        71 RRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e  150 (214)
                      =+..||+-|..|..+.-- -..-.-|.+||++|=..+.++...-..|+........+|...-.++|.|-.+...|..+|-
T Consensus       109 l~~~L~~ff~s~q~la~~-P~~~a~r~~vl~~a~~l~~~in~~~~~L~~l~~~i~~~I~~~V~~vNsLl~qIa~lN~qI~  187 (552)
T COG1256         109 LSTLLNDFFNSLQELASN-PSDTAARQAVLSKAQTLVNQINNTYEQLTDLRKDINAEIAATVDEVNSLLKQIADLNKQIR  187 (552)
T ss_pred             HHHHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356678888888887721 1123677889999988888888888888877777777777777788877776666665555


Q ss_pred             HH
Q 028060          151 KL  152 (214)
Q Consensus       151 ~L  152 (214)
                      +.
T Consensus       188 ~~  189 (552)
T COG1256         188 KV  189 (552)
T ss_pred             Hh
Confidence            43

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

Probab=87.07  E-value=6.7  Score=35.30  Aligned_cols=46  Identities=35%  Similarity=0.361  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      +..|..+++.+++...+|..++.+|..++.+|.++...|+.++.++
T Consensus        91 ~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~~  136 (239)
T COG1579          91 LRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERL  136 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444444444443333333

>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]

Probab=87.01  E-value=0.84  Score=45.56  Aligned_cols=60  Identities=22%  Similarity=0.304  Sum_probs=29.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           97 PAILDDAIRVLNQLRTESQELK---ETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus        97 asIL~dAI~yIk~Lr~~vq~L~---~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      ..||.+--++|+--+...+.=+   +....|+..+++|.+|...||.|+..||.+++-|..+=
T Consensus       277 ~kv~krqQRmIKNResA~~SRkKKKEy~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En  339 (655)
T KOG4343|consen  277 IKVLKRQQRMIKNRESACQSRKKKKEYMLGLEARLQALLSENEQLKKENATLKRQLDELVSEN  339 (655)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcC
Confidence            3455554455554333322221   22345555555555555556666666665555555533

>PRK09039 hypothetical protein; Validated

Probab=86.95  E-value=5.2  Score=37.25  Aligned_cols=49  Identities=16%  Similarity=0.203  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      .+.+|..|..+.+.|+.++..|..++.+...+....+.+++.|++.|..
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            3334555555666666666666666666666666666666666666654

>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes

Probab=86.84  E-value=11  Score=31.85  Aligned_cols=41  Identities=24%  Similarity=0.326  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  145 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~L  145 (214)
                      .-+.+++.+++.|+.+...|.++++.+-.++.+.+.+...+
T Consensus        22 ~~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~   62 (188)
T PF10018_consen   22 QEHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTL   62 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33456777888888888888888888888888888777544

Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex

>PF14282 FlxA: FlxA-like protein

Probab=86.76  E-value=4.5  Score=31.60  Aligned_cols=55  Identities=18%  Similarity=0.238  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEE----IKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~e----i~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      -..|..|+.++..|.++...|...    .++-......|..+...|.++|..|+.+...
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~   76 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAE   76 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567788888888888777777652    1333444445566666666666666555443

>PF15458 NTR2: Nineteen complex-related protein 2

Probab=86.62  E-value=8.2  Score=34.53  Aligned_cols=20  Identities=20%  Similarity=0.380  Sum_probs=14.9

Q ss_pred             CchhHHHHHHHHHHHHHHHH
Q 028060           62 GSKACREKLRRERLNDRFLD   81 (214)
Q Consensus        62 ~sH~~~ERkRRdkLN~~F~~   81 (214)
                      .......++||..|-+.+..
T Consensus       141 ka~~~~~~~rR~~i~e~I~~  160 (254)
T PF15458_consen  141 KAEREQKRRRREEIEEAIND  160 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHh
Confidence            34566677888888888877

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

Probab=86.58  E-value=5  Score=35.69  Aligned_cols=24  Identities=33%  Similarity=0.400  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQ  125 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~  125 (214)
                      .+-.-+..++..++.|..+...|+
T Consensus       213 ~~~~E~~~~r~~~~~l~~el~~l~  236 (312)
T PF00038_consen  213 SAKEELKELRRQIQSLQAELESLR  236 (312)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhHHHHHHhhhhHhhhhhhccc
Confidence            333334444444444443333333

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

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

Probab=86.48  E-value=16  Score=31.24  Aligned_cols=68  Identities=22%  Similarity=0.340  Sum_probs=33.5

Q ss_pred             CCCchhHHHHH-----HHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKL-----RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRV---LNQLRTESQELKETNEKLQEEIKSL  131 (214)
Q Consensus        60 ~~~sH~~~ERk-----RRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~y---Ik~Lr~~vq~L~~~n~~L~~ei~eL  131 (214)
                      |-+|=.|.||-     =|+.+...|.+...+..      ...+-.+.+++..   ..+|+.++..|+.++..|..++.+|
T Consensus        73 RQVTi~C~ERGlLL~rvrde~~~~l~~y~~l~~------s~~~f~~rk~l~~e~~~~~l~~~i~~L~~e~~~L~~~~~~l  146 (189)
T PF10211_consen   73 RQVTIDCPERGLLLLRVRDEYRMTLDAYQTLYE------SSIAFGMRKALQAEQGKQELEEEIEELEEEKEELEKQVQEL  146 (189)
T ss_pred             HHHHhCcHHHhHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44566678873     36666666776666552      2222233333322   2344444444544444444444444


Q ss_pred             HH
Q 028060          132 KA  133 (214)
Q Consensus       132 ~~  133 (214)
                      +.
T Consensus       147 ~~  148 (189)
T PF10211_consen  147 KN  148 (189)
T ss_pred             HH
Confidence            33

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 [].

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=86.47  E-value=3  Score=32.69  Aligned_cols=32  Identities=25%  Similarity=0.331  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELR  139 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr  139 (214)
                      .+|+.+++.++.+++.|+.+.+.|+.+++.|+
T Consensus        30 ~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~   61 (105)
T PRK00888         30 WRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK   61 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34555555555555555554444444444443

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

Probab=86.39  E-value=7  Score=32.44  Aligned_cols=50  Identities=26%  Similarity=0.454  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLK-------AEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~-------~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +..+.+++.++.....+.+++.++.       .+..+++.+...++.+.+++++.++
T Consensus       126 ~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  182 (191)
T PF04156_consen  126 KSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERLQENLQQLEEKIQ  182 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444       4444444555555555555544444

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 [].

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

Probab=86.25  E-value=2.4  Score=40.15  Aligned_cols=43  Identities=30%  Similarity=0.302  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      ..++..|+.+++.|+.++..|..+.+.++.++..+++|...|+
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (398)
T PTZ00454         21 YEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQ   63 (398)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3566778889999999999999999999998888877766664

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

Probab=86.23  E-value=4.8  Score=28.96  Aligned_cols=58  Identities=16%  Similarity=0.310  Sum_probs=33.5

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           94 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus        94 ~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      .+|-+.|.++-.+|.+....+.+++-+...+..      .+++.+.......++++.+|+.+|+
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            466666666666666666666666555444321      4555555555566666666666654

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.

>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=86.18  E-value=7.2  Score=31.25  Aligned_cols=34  Identities=32%  Similarity=0.413  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEK  142 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek  142 (214)
                      +|+..++.|+.++..+...+.+|.++++|++...
T Consensus        41 ~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~l   74 (107)
T PF09304_consen   41 QLRNALQSLQAQNASRNQRIAELQAKIDEARRNL   74 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555555555555555555555555555544433

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.

>TIGR02492 flgK_ends flagellar hook-associated protein FlgK

Probab=86.11  E-value=8.4  Score=35.17  Aligned_cols=78  Identities=26%  Similarity=0.356  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHhhhc-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           73 ERLNDRFLDLSCIL-EPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  151 (214)
Q Consensus        73 dkLN~~F~~LrslL-PP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~  151 (214)
                      ..||+-|..|.++- .|.  ...-+.++|..|-..+..++.--.+|.........+|+..-.++|.|-++...|..+|..
T Consensus       107 ~~l~~ff~a~~~ls~~P~--~~~~r~~vl~~a~~l~~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~~Ia~lN~~I~~  184 (322)
T TIGR02492       107 TYLNNFFNALQELAKNPD--SEALRQAVLESAQALANSFNQTSNELQDLRKGINAEIKSAVTEINSLLKQIASLNKEIQQ  184 (322)
T ss_pred             HHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566666666665 121  235678889988888888888888888777777778877778888887777777766654


Q ss_pred             H
Q 028060          152 L  152 (214)
Q Consensus       152 L  152 (214)
                      .
T Consensus       185 ~  185 (322)
T TIGR02492       185 V  185 (322)
T ss_pred             H
Confidence            3

The flagellar hook-associated protein FlgK of bacterial flagella has conserved N- and C-terminal domains. The central region is highly variable in length and sequence, and often contains substantial runs of low-complexity sequence. This model is built from an alignment of FlgK sequences with the central region excised. Note that several other proteins of the flagellar apparatus also are homologous in the N- and C-terminal regions to FlgK, but are excluded from this model.

>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=86.03  E-value=11  Score=30.50  Aligned_cols=21  Identities=29%  Similarity=0.385  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhhc
Q 028060           66 CREKLRRERLNDRFLDLSCIL   86 (214)
Q Consensus        66 ~~ERkRRdkLN~~F~~LrslL   86 (214)
                      .++...|+.+++.+..|++-+
T Consensus        48 ~r~~~~~e~l~~~~~~l~~d~   68 (151)
T PF11559_consen   48 DRDMEQREDLSDKLRRLRSDI   68 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHhHH
Confidence            346666777777777776655

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.

>PHA02562 46 endonuclease subunit; Provisional

Probab=85.97  E-value=5.2  Score=38.24  Aligned_cols=16  Identities=13%  Similarity=0.266  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHhhhc
Q 028060           71 RRERLNDRFLDLSCIL   86 (214)
Q Consensus        71 RRdkLN~~F~~LrslL   86 (214)
                      .+..|+..+..|...+
T Consensus       307 ~i~~l~~~l~~l~~~i  322 (562)
T PHA02562        307 KLKELQHSLEKLDTAI  322 (562)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444444444444444

>smart00787 Spc7 Spc7 kinetochore protein

Probab=85.88  E-value=5.5  Score=36.83  Aligned_cols=18  Identities=22%  Similarity=0.187  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 028060          101 DDAIRVLNQLRTESQELK  118 (214)
Q Consensus       101 ~dAI~yIk~Lr~~vq~L~  118 (214)
                      .+..++...|+.++..|+
T Consensus       175 ~~l~~~~~~L~~e~~~L~  192 (312)
T smart00787      175 PKLRDRKDALEEELRQLK  192 (312)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            334445555555555444

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

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

Probab=85.87  E-value=0.65  Score=36.18  Aligned_cols=50  Identities=36%  Similarity=0.478  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          101 DDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  150 (214)
Q Consensus       101 ~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e  150 (214)
                      .+.=.||..|...+..|..++..|+.++.+|..++.+++.+...|+..+.
T Consensus        21 ~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~~l~   70 (131)
T PF05103_consen   21 DEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQRALI   70 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT----------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHhhh
Confidence            34558899999999999888888888888888888888777666665443

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

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

Probab=85.81  E-value=8.5  Score=31.94  Aligned_cols=45  Identities=29%  Similarity=0.356  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          112 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       112 ~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +..+..++....+.+..+.+..+..+++++...++.+.+.+..++
T Consensus       123 ~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~  167 (191)
T PF04156_consen  123 ELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQL  167 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455555556666666666666633333334444443333

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 [].

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

Probab=85.81  E-value=8  Score=30.19  Aligned_cols=54  Identities=17%  Similarity=0.324  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSL--KAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL--~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      |..|+.++...+.....++.+++.|  +.+.++|+-+...++.++..+..+++.++
T Consensus        37 ~~~l~~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~   92 (106)
T PF10805_consen   37 IEKLEERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVS   92 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            3445555555566666677777777  66777777777777777777777777664

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

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=85.72  E-value=3.6  Score=41.65  Aligned_cols=37  Identities=32%  Similarity=0.480  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          103 AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  139 (214)
Q Consensus       103 AI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr  139 (214)
                      --+.|..|+.+++.|+.++++++.++..|+.++.+++
T Consensus       427 ~~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~  463 (652)
T COG2433         427 LEETVERLEEENSELKRELEELKREIEKLESELERFR  463 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344555566666666666666555555555555443

>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=85.71  E-value=5.8  Score=31.76  Aligned_cols=27  Identities=22%  Similarity=0.187  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          117 LKETNEKLQEEIKSLKAEKNELREEKL  143 (214)
Q Consensus       117 L~~~n~~L~~ei~eL~~eknELr~Ek~  143 (214)
                      |+..+..|+.+...+...++||+.+..
T Consensus        42 L~~~l~~L~~q~~s~~qr~~eLqaki~   68 (107)
T PF09304_consen   42 LRNALQSLQAQNASRNQRIAELQAKID   68 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333444433333

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.

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=85.56  E-value=7.9  Score=33.92  Aligned_cols=61  Identities=30%  Similarity=0.386  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ++..|...=+-|.+++..|+.....|+++.+.|-++..++..|+..|-++++.|+.+-..+
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            4455555555566666666666666666666666666666666666666666666555443

>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=85.49  E-value=7.1  Score=29.62  Aligned_cols=48  Identities=25%  Similarity=0.329  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      =..|..++..|+.....|-..++.++.|..-|+.||..|+.=|..|-.
T Consensus        18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~   65 (80)
T PF10224_consen   18 KEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMS   65 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356788888899999999999999999999999999999999998855

The exact function is unknown.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=85.47  E-value=7.1  Score=34.92  Aligned_cols=48  Identities=17%  Similarity=0.239  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      +-+|+.+++.|+.+...|+-+++++.-+++++.++...+..+++++..
T Consensus        56 ~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r~~  103 (263)
T PRK10803         56 LTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSS  103 (263)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345566666666666666666666666666666666666666666544

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

Probab=85.46  E-value=5.3  Score=37.57  Aligned_cols=45  Identities=22%  Similarity=0.374  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKL  143 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~  143 (214)
                      +|+-++.-+..|+.+++.|..+|+.|+.+...+..++.++-.+|.
T Consensus       131 l~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE~~v~~K~  175 (342)
T PF06632_consen  131 LFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLEKFVNAKE  175 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566667777778888888888887777777777666666555444

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.

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=85.38  E-value=8.7  Score=32.96  Aligned_cols=60  Identities=27%  Similarity=0.414  Sum_probs=44.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           98 AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus        98 sIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      .=|.+++..+.+=+.+...|..-|.-|+++.+..+.....|.++..+|..+-+++..+|.
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            346666666666666677777788888888888888888888888888888777766654

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=85.31  E-value=5.4  Score=40.63  Aligned_cols=42  Identities=24%  Similarity=0.254  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  151 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~  151 (214)
                      |..+++++....++|+..|..-+.|+..|+-+....+.+.+.
T Consensus       105 l~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~E  146 (907)
T KOG2264|consen  105 LNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEE  146 (907)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHH
Confidence            444444444444444444444444444444444333333333

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

Probab=85.13  E-value=9.8  Score=25.96  Aligned_cols=29  Identities=41%  Similarity=0.569  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKA  133 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~  133 (214)
                      .++.+|+.+++.|+.+|..|..++..|+.
T Consensus        25 ~~~~~le~~~~~L~~en~~L~~~i~~L~~   53 (54)
T PF07716_consen   25 QREEELEQEVQELEEENEQLRQEIAQLER   53 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45556666666666666666555555544

; 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 ....

>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]

Probab=85.08  E-value=4.7  Score=41.76  Aligned_cols=47  Identities=28%  Similarity=0.437  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          114 SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       114 vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      ..+-.+..+.|.++.+.++..+.+++.++.+|..++|+|.++++.+-
T Consensus       211 rmaAle~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~  257 (916)
T KOG0249|consen  211 RMAALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLR  257 (916)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            33334556678889999999999999999999999999998888763

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=85.06  E-value=4.9  Score=39.46  Aligned_cols=36  Identities=36%  Similarity=0.460  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      +-|+.|-.++.+++.+..+|..+-+.|+.|.++||.
T Consensus        59 DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~   94 (472)
T TIGR03752        59 DTLRTLVAEVKELRKRLAKLISENEALKAENERLQK   94 (472)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455555555555555555555555555555544

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.

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

Probab=85.06  E-value=16  Score=33.31  Aligned_cols=89  Identities=21%  Similarity=0.156  Sum_probs=43.7

Q ss_pred             CchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           62 GSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREE  141 (214)
Q Consensus        62 ~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~E  141 (214)
                      +.|...|--|.+-=|-...+--..| .+.+.-+|=-.-+.+--+-+.+++++...|.++++.|+.+..++..++.+|+-|
T Consensus       100 vEhiD~elvrkEl~nAlvRAGLktL-~~v~~~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E  178 (290)
T COG4026         100 VEHIDVELVRKELKNALVRAGLKTL-QRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVE  178 (290)
T ss_pred             ccccCHHHHHHHHHHHHHHHHHHHH-hccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4466666555544444443322222 111122343333333334455555666666666666666666666666666555


Q ss_pred             HHHHHHHHHH
Q 028060          142 KLILKADKEK  151 (214)
Q Consensus       142 k~~Lk~e~e~  151 (214)
                      ++.|.....+
T Consensus       179 ~s~LeE~~~~  188 (290)
T COG4026         179 NSRLEEMLKK  188 (290)
T ss_pred             HHHHHHHHHh
Confidence            5555443333

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

Probab=84.97  E-value=4.7  Score=32.29  Aligned_cols=41  Identities=34%  Similarity=0.448  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          112 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       112 ~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      .+|-+|+...+.|-..++.++.|.=.||.|++.|-+=||.|
T Consensus        63 tQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL  103 (120)
T KOG3650|consen   63 TQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL  103 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence            34444555555555555555555555666666665555554

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

Probab=84.72  E-value=16  Score=35.57  Aligned_cols=17  Identities=24%  Similarity=0.389  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHhhh
Q 028060           69 KLRRERLNDRFLDLSCI   85 (214)
Q Consensus        69 RkRRdkLN~~F~~Lrsl   85 (214)
                      |.||..|-..+..+.-.
T Consensus       111 r~qr~~La~~L~A~~r~  127 (420)
T COG4942         111 REQRRRLAEQLAALQRS  127 (420)
T ss_pred             HHHHHHHHHHHHHHHhc
Confidence            67888888888877663

>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=84.69  E-value=12  Score=31.07  Aligned_cols=14  Identities=29%  Similarity=0.330  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHhhhc
Q 028060           73 ERLNDRFLDLSCIL   86 (214)
Q Consensus        73 dkLN~~F~~LrslL   86 (214)
                      +-|.+++..|-+-|
T Consensus        20 dsle~~v~~LEreL   33 (140)
T PF10473_consen   20 DSLEDHVESLEREL   33 (140)
T ss_pred             hhHHHHHHHHHHHH
Confidence            44556666666655

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

>PF15397 DUF4618: Domain of unknown function (DUF4618)

Probab=84.68  E-value=5.1  Score=36.44  Aligned_cols=83  Identities=25%  Similarity=0.289  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           73 ERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ-LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  151 (214)
Q Consensus        73 dkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~-Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~  151 (214)
                      +.+++.+...+.-+.- . -...|-.||+.++.-+.. .+..+-+.-.+|..++.++..-+.++++|.++...|++|++.
T Consensus       141 del~e~~~~el~~l~~-~-~q~k~~~il~~~~~k~~~~~~~~l~~~~~~N~~m~kei~~~re~i~el~e~I~~L~~eV~~  218 (258)
T PF15397_consen  141 DELNEMRQMELASLSR-K-IQEKKEEILSSAAEKTQSPMQPALLQRTLENQVMQKEIVQFREEIDELEEEIPQLRAEVEQ  218 (258)
T ss_pred             HHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666655555521 1 134566788876655444 566666666788888888888888999999999999999998


Q ss_pred             HHHHHH
Q 028060          152 LEQQLK  157 (214)
Q Consensus       152 L~~qlk  157 (214)
                      |+.+..
T Consensus       219 L~~~~~  224 (258)
T PF15397_consen  219 LQAQAQ  224 (258)
T ss_pred             HHHhhc
Confidence            888766

>PF14282 FlxA: FlxA-like protein

Probab=84.66  E-value=3.8  Score=31.99  Aligned_cols=59  Identities=24%  Similarity=0.375  Sum_probs=40.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           97 PAILDDAIRVLNQLRTESQELKE----TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus        97 asIL~dAI~yIk~Lr~~vq~L~~----~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      .+.+..--+-|..|+.++..|..    ..+.-+..++.|..++..|......|+.++..-..+
T Consensus        18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~~~~~   80 (106)
T PF14282_consen   18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAEQQQQ   80 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            55566666677778888888776    225556777777777777777777776666555443

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=84.52  E-value=7.7  Score=31.14  Aligned_cols=58  Identities=26%  Similarity=0.381  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETN-EKLQEEIKSLKAEKN--------ELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n-~~L~~ei~eL~~ekn--------ELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      ...|-+|+.+|-.+++.-..+. +..+.+++.+....+        +|+.+...|+.++.+|+.+++
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            4678888888888777544332 234555555554443        667777777777777777664

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

Probab=84.51  E-value=15  Score=31.18  Aligned_cols=48  Identities=29%  Similarity=0.433  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      |++|..++..+...++.|+.|+..|..+.|-+.+....|+.|...|-+
T Consensus       132 ~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~  179 (194)
T PF08614_consen  132 IKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLEEENRELVE  179 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555556666777777777777777777777777666643

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.

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

Probab=84.47  E-value=14  Score=35.87  Aligned_cols=24  Identities=33%  Similarity=0.459  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          134 EKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       134 eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      ||+-||.|+..|..|.|..+.++.
T Consensus       350 EKaaLrkerd~L~keLeekkrele  373 (442)
T PF06637_consen  350 EKAALRKERDSLAKELEEKKRELE  373 (442)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555566666666666555544443

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

>PF14988 DUF4515: Domain of unknown function (DUF4515)

Probab=84.39  E-value=9.1  Score=33.38  Aligned_cols=58  Identities=28%  Similarity=0.381  Sum_probs=35.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           96 KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus        96 KasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      |+-.|.-|.  ++.|-.-...+..+|..|+.++..|..+...|+..+..|..++..|.++
T Consensus       142 k~~ale~~A--~~~l~e~~~~i~~EN~~L~k~L~~l~~e~~~L~~~~~~Le~qk~~L~~e  199 (206)
T PF14988_consen  142 KAQALELAA--KKSLDEFTRSIKRENQQLRKELLQLIQEAQKLEARKSQLEKQKQQLQQE  199 (206)
T ss_pred             HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444332  3444555556666777777777777777777777777776666666554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=84.30  E-value=4.3  Score=37.97  Aligned_cols=48  Identities=25%  Similarity=0.396  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPT  163 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p  163 (214)
                      .|++.+.+++.++++|++       .+.+|..+...++.++++++.+++.+..+|
T Consensus         5 ~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   52 (389)
T PRK03992          5 ALEERNSELEEQIRQLEL-------KLRDLEAENEKLERELERLKSELEKLKSPP   52 (389)
T ss_pred             HHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Confidence            344444444444444444       444444444455555566666666555443

>TIGR00219 mreC rod shape-determining protein MreC

Probab=84.29  E-value=4.4  Score=36.70  Aligned_cols=45  Identities=18%  Similarity=0.301  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  149 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~  149 (214)
                      +-+..+.+|+++.++|++++.+|..+.   .....+++.||.+|+.-.
T Consensus        63 ~~~~~~~~l~~EN~~Lr~e~~~l~~~~---~~~~~~l~~EN~rLr~LL  107 (283)
T TIGR00219        63 ENLKDVNNLEYENYKLRQELLKKNQQL---EILTQNLKQENVRLRELL  107 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHh
Confidence            334445567788888988887774443   334455777777776543

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.

>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=84.27  E-value=8.7  Score=36.13  Aligned_cols=38  Identities=21%  Similarity=0.332  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  142 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek  142 (214)
                      .-+.+|..+.+.|+.+...+..+++++..+|.++..+.
T Consensus       144 ~~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~L  181 (342)
T PF06632_consen  144 AENEHLQKENERLESEANKLLKQLEKFVNAKEEHEEDL  181 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34456778888888888888888888888888876665

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.

>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=84.27  E-value=7.1  Score=31.40  Aligned_cols=52  Identities=33%  Similarity=0.417  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ++.++..++.+..+|..|-+..-.+..++.++|++...+..+...|+.++..
T Consensus        29 ~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~   80 (150)
T PF07200_consen   29 VQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQE   80 (150)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555555555555555555555555555555555555555443

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.

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

Probab=84.26  E-value=12  Score=30.85  Aligned_cols=27  Identities=30%  Similarity=0.475  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSL  131 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL  131 (214)
                      .-+..|+.++..|+..+..+..+|..|
T Consensus        14 ~r~e~~e~~~K~le~~~~~~E~EI~sL   40 (143)
T PF12718_consen   14 DRAEELEAKVKQLEQENEQKEQEITSL   40 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344444444444444433333333

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 [].

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

Probab=84.20  E-value=1.2  Score=37.97  Aligned_cols=46  Identities=35%  Similarity=0.478  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      |.+++.+..+--+.|.-|++|+    .||..|+.+.++||-|+-+|.+++
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            4566666666667777777777    556666666666666666666666

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.

>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit

Probab=84.16  E-value=15  Score=30.07  Aligned_cols=64  Identities=19%  Similarity=0.101  Sum_probs=41.4

Q ss_pred             ChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           95 DKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus        95 DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +...-...+++....|+.++.........|+++++........-......|+..+..++.+++.
T Consensus        17 ~~~~~~e~ll~~~~~LE~qL~~~~~~l~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~   80 (160)
T PF13094_consen   17 EDSFDYEQLLDRKRALERQLAANLHQLELLQEEIEKEEAALERDYEYLQELEKNAKALEREREE   80 (160)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445567778888888888887777777777777666555554444445555555555555544

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=84.12  E-value=1.1  Score=43.63  Aligned_cols=46  Identities=26%  Similarity=0.395  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHH
Q 028060           66 CREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRT  112 (214)
Q Consensus        66 ~~ERkRRdkLN~~F~~LrslLPP~~--~~K~DKasIL~dAI~yIk~Lr~  112 (214)
                      .+-|.||++=|--|.+|..+||-..  .+..||++|+-=|+.||| |+.
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlK-mr~   54 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLK-MRN   54 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHH-HHH
Confidence            3468999999999999999997422  246999999999999998 443

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

Probab=84.01  E-value=7.4  Score=28.14  Aligned_cols=48  Identities=17%  Similarity=0.272  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      .|.+|+.++.-++...++|...+-....++..|+.+...|...+..++
T Consensus         5 Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen    5 RIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            455555555555555555555555555555555555555555555554

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.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=83.98  E-value=5  Score=31.43  Aligned_cols=46  Identities=22%  Similarity=0.229  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          113 ESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       113 ~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ...+++++.+.++.++++|+++..+|+.|...|+...+-++.....
T Consensus        28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe~AR~   73 (105)
T PRK00888         28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEERARN   73 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHH
Confidence            4555666666666666666666666666666666655555555544

>TIGR00606 rad50 rad50

Probab=83.97  E-value=8.6  Score=41.51  Aligned_cols=82  Identities=17%  Similarity=0.173  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           69 KLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  148 (214)
Q Consensus        69 RkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e  148 (214)
                      ...++++++.+..|...+.- .  +..|.. |..++.-..+|+.++..|..++..+.+++++++.++..|..+...++++
T Consensus       849 ~~e~e~~~~eI~~Lq~ki~e-l--~~~klk-l~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~  924 (1311)
T TIGR00606       849 RKLIQDQQEQIQHLKSKTNE-L--KSEKLQ-IGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQE  924 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-H--HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            44556667777777666621 1  223333 3337777788888888888888888888877777777777777766666


Q ss_pred             HHHHHH
Q 028060          149 KEKLEQ  154 (214)
Q Consensus       149 ~e~L~~  154 (214)
                      .+++..
T Consensus       925 ~~~~~~  930 (1311)
T TIGR00606       925 KEELIS  930 (1311)
T ss_pred             HHHHHH
Confidence            655543

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

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

Probab=83.87  E-value=9.7  Score=35.34  Aligned_cols=53  Identities=25%  Similarity=0.497  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      .-++.|+.+++.|.++...+.+++.+|+.+.+++....+.|.++...+.....
T Consensus        48 ~kvrE~~e~~~elr~~rdeineev~elK~kR~ein~kl~eL~~~~~~l~e~~~  100 (294)
T COG1340          48 AKVRELREKAQELREERDEINEEVQELKEKRDEINAKLQELRKEYRELKEKRN  100 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            55667777777777777777777777777777776666666666655554443

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=83.83  E-value=5  Score=42.10  Aligned_cols=28  Identities=21%  Similarity=0.164  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHhhhcCCCCCCCCChhhHHH
Q 028060           73 ERLNDRFLDLSCILEPGRPARTDKPAILD  101 (214)
Q Consensus        73 dkLN~~F~~LrslLPP~~~~K~DKasIL~  101 (214)
                      |.+|++|.-|.+.+-. .....==.|||+
T Consensus       382 Dd~~~~f~lL~n~vkd-T~aE~yfLSILQ  409 (1102)
T KOG1924|consen  382 DDANEVFELLANTVKD-TGAEPYFLSILQ  409 (1102)
T ss_pred             ccHHHHHHHHHHhhhh-ccccchHHHHHH
Confidence            5678888888888733 222333445554

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

Probab=83.70  E-value=19  Score=36.97  Aligned_cols=18  Identities=28%  Similarity=0.399  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHHhhhc
Q 028060           69 KLRRERLNDRFLDLSCIL   86 (214)
Q Consensus        69 RkRRdkLN~~F~~LrslL   86 (214)
                      |.||..|..-+..|+.-|
T Consensus       544 r~r~~~lE~E~~~lr~el  561 (697)
T PF09726_consen  544 RQRRRQLESELKKLRREL  561 (697)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            444445555555555544

; GO: 0016021 integral to membrane

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

Probab=83.68  E-value=13  Score=39.87  Aligned_cols=88  Identities=24%  Similarity=0.339  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHHHHhhhcCCCC----CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           69 KLRRERLNDRFLDLSCILEPGR----PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI  144 (214)
Q Consensus        69 RkRRdkLN~~F~~LrslLPP~~----~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~  144 (214)
                      |.+.+.++..+..+..-+--..    ..--+|..-|...|+   .|+..+.+|.++...+.+++.....++...+.+...
T Consensus       371 k~~~d~l~k~I~~~~~~~~~~~~~~~~e~e~k~~~L~~eve---k~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~  447 (1074)
T KOG0250|consen  371 KKEVDRLEKQIADLEKQTNNELGSELEERENKLEQLKKEVE---KLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQ  447 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            4455566666666655551100    012345555555443   455677778877777777777777777777777777


Q ss_pred             HHHHHHHHHHHHHHh
Q 028060          145 LKADKEKLEQQLKVM  159 (214)
Q Consensus       145 Lk~e~e~L~~qlk~~  159 (214)
                      |+..++....+|+.+
T Consensus       448 l~k~i~~~~~~l~~l  462 (1074)
T KOG0250|consen  448 LRKKIENISEELKDL  462 (1074)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            776666666555553

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=83.46  E-value=11  Score=31.21  Aligned_cols=38  Identities=18%  Similarity=0.382  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .+|+.+-.+|.+++..|+.|++.+..|.+-+...++++
T Consensus        77 ~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l  114 (135)
T KOG4196|consen   77 HELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEAL  114 (135)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444445544444444444444433

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

Probab=83.44  E-value=8.5  Score=30.51  Aligned_cols=34  Identities=26%  Similarity=0.320  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREE  141 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~E  141 (214)
                      ..|..+++.++.+++.|..+...|+++++.|++.
T Consensus        53 ~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          53 LQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            3355555566666666666555555555555554

>PRK07739 flgK flagellar hook-associated protein FlgK; Validated

Probab=83.40  E-value=12  Score=36.35  Aligned_cols=77  Identities=19%  Similarity=0.203  Sum_probs=56.2

Q ss_pred             HHHHHHHHHhhhcC-CCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           74 RLNDRFLDLSCILE-PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        74 kLN~~F~~LrslLP-P~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      .|++-|..|..+-- |.  ...-+..+|..|-.....++.-..+|+.....+..+|+..-.++|.|-.+...|..+|...
T Consensus       120 ~l~~ff~a~~~la~~P~--~~~~r~~vl~~a~~La~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~~Ia~LN~~I~~~  197 (507)
T PRK07739        120 VLDQFWNSLQELSKNPE--NLGARSVVRQRAQALAETFNYLSQSLTDIQNDLKSEIDVTVKEINSLASQISDLNKQIAKV  197 (507)
T ss_pred             HHHHHHHHHHHHHhCcC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35566666666551 21  2456788999998888888888888887777778888888888888888888887777553

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

Probab=83.31  E-value=7  Score=39.47  Aligned_cols=55  Identities=24%  Similarity=0.316  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .|..+|+.+...++..+..+.+++..|+.++.........|...+.+|+.|+...
T Consensus        15 ~ya~~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eLk~q~~~~   69 (617)
T PF15070_consen   15 QYAQQLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSELKNQMAEP   69 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            5999999999999999999999999999999999999999999999998887754

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

Probab=83.27  E-value=11  Score=32.50  Aligned_cols=17  Identities=29%  Similarity=0.460  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 028060          141 EKLILKADKEKLEQQLK  157 (214)
Q Consensus       141 Ek~~Lk~e~e~L~~qlk  157 (214)
                      |..+|+++.+.+.+++.
T Consensus       160 ei~~lks~~~~l~~~~~  176 (190)
T PF05266_consen  160 EISRLKSEAEALKEEIE  176 (190)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            34444444444455444

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

Probab=83.18  E-value=17  Score=27.24  Aligned_cols=52  Identities=21%  Similarity=0.129  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ..|+.++..|+....--..-|.+|...+.|.+-...+++.+...|-..++.+
T Consensus         4 ~~lE~Ri~eLE~r~AfQE~tieeLn~~laEq~~~i~k~q~qlr~L~~kl~~~   55 (72)
T COG2900           4 MELEARIIELEIRLAFQEQTIEELNDALAEQQLVIDKLQAQLRLLTEKLKDL   55 (72)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4567777777766655555678888888888888888888888888888876

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

Probab=83.01  E-value=7.5  Score=40.77  Aligned_cols=61  Identities=25%  Similarity=0.340  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      |..+=-..|+.|..+++.|++...+|+-+.++|..++.++-.+.+.|+.+.+.|+.||.-.
T Consensus       658 ~~~kyK~lI~~lD~~~e~lkQ~~~~l~~e~eeL~~~vq~~~s~hsql~~q~~~Lk~qLg~~  718 (970)
T KOG0946|consen  658 IQQKYKGLIRELDYQIENLKQMEKELQVENEELEEEVQDFISEHSQLKDQLDLLKNQLGII  718 (970)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            4444455566666666677777777777777777777777777888888888888888743

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=82.82  E-value=4.8  Score=29.21  Aligned_cols=33  Identities=39%  Similarity=0.461  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      .++..+++.++.+.+.++.+..+|+.|.+.|.+
T Consensus        27 ~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~   59 (85)
T TIGR02209        27 RQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR   59 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            345555555555555555555555555555433

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.

>TIGR01069 mutS2 MutS2 family protein

Probab=82.81  E-value=8.8  Score=39.55  Aligned_cols=10  Identities=20%  Similarity=0.368  Sum_probs=4.4

Q ss_pred             HHHHHHHHHH
Q 028060           99 ILDDAIRVLN  108 (214)
Q Consensus        99 IL~dAI~yIk  108 (214)
                      |+.+|-+++.
T Consensus       498 ii~~A~~~~~  507 (771)
T TIGR01069       498 IIEQAKTFYG  507 (771)
T ss_pred             HHHHHHHHHH
Confidence            4444444443

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

>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]

Probab=82.79  E-value=2  Score=39.27  Aligned_cols=52  Identities=25%  Similarity=0.245  Sum_probs=43.5

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLR  111 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr  111 (214)
                      ++..-+.+||+|=..||..|..||..+|.+ ...|.+|-..|.-|-.||--|-
T Consensus       174 rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~  226 (285)
T KOG4395|consen  174 RRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALG  226 (285)
T ss_pred             hhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhH
Confidence            566778999999999999999999999753 3357888889999988887663

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

Probab=82.78  E-value=9.3  Score=31.39  Aligned_cols=42  Identities=29%  Similarity=0.404  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          117 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       117 L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ++..+..|..+...+..++..|...+..|..++++++.+|+.
T Consensus        19 ~e~~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~   60 (143)
T PF12718_consen   19 LEAKVKQLEQENEQKEQEITSLQKKNQQLEEELDKLEEQLKE   60 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333334444444444444444444444444444443

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 [].

>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans

Probab=82.72  E-value=12  Score=31.57  Aligned_cols=48  Identities=25%  Similarity=0.432  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      -.++|+.++++|+.+|..|....+.+......|.+....|+.+...+.
T Consensus        90 e~k~L~~~v~~Le~e~r~L~~~~~~~~~q~~rlee~e~~l~~e~~~l~  137 (158)
T PF09744_consen   90 ERKDLQSQVEQLEEENRQLELKLKNLSDQSSRLEEREAELKKEYNRLH  137 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhhhhccccchhHHHHHHHHHHHH
Confidence            345566666666666666665555544444445444444444444443

Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.

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

Probab=82.69  E-value=13  Score=26.49  Aligned_cols=47  Identities=19%  Similarity=0.334  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          112 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       112 ~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      .++.+|.....+|..++..|..+++-+|.+....|.|-.|--+-|..
T Consensus         3 akid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN   49 (56)
T PF04728_consen    3 AKIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDN   49 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46788888888888888888888888888888888887776665543

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.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=82.64  E-value=8  Score=34.61  Aligned_cols=44  Identities=16%  Similarity=0.212  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          116 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       116 ~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +|..+.+.|+.|+.+|+-++.++..+...++..--.+.++|..+
T Consensus        58 ~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r  101 (263)
T PRK10803         58 QLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSL  101 (263)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555555555555444555555554

>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation

Probab=82.60  E-value=2.1  Score=30.92  Aligned_cols=29  Identities=34%  Similarity=0.475  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          126 EEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       126 ~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      +|++.|+..+.||.+++..|+.|...|.+
T Consensus        14 EEVevLK~~I~eL~~~n~~Le~EN~~Lk~   42 (59)
T PF01166_consen   14 EEVEVLKEQIAELEERNSQLEEENNLLKQ   42 (59)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444445555555555555555555544

These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.

>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum

Probab=82.59  E-value=18  Score=27.07  Aligned_cols=36  Identities=33%  Similarity=0.404  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  145 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~L  145 (214)
                      ...+...+..+...++.+.+.|..|...|+-|.+.|
T Consensus        33 ~~~~~~~~~~~l~~l~~~~~~l~~e~~~L~lE~~~l   68 (97)
T PF04999_consen   33 SRHQSRQLFYELQQLEKEIDQLQEENERLRLEIATL   68 (97)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            333444444444444444444444444444444444

One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane

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

Probab=82.56  E-value=9.5  Score=31.17  Aligned_cols=50  Identities=20%  Similarity=0.296  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +|..+++.|....++..+-++..+.+.++++......+.+++.+++-+..
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            45566777777766666667777777777777777777777766655443

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

>PRK02224 chromosome segregation protein; Provisional

Probab=82.51  E-value=15  Score=37.37  Aligned_cols=50  Identities=24%  Similarity=0.425  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +..|...+..++.....+..++..+...++.++.+...++.+++.++.++
T Consensus       351 ~~~le~~~~~l~~~~~~l~~~~~~~~~~l~~~~~~l~~l~~el~el~~~l  400 (880)
T PRK02224        351 ADDLEERAEELREEAAELESELEEAREAVEDRREEIEELEEEIEELRERF  400 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333444444444444444444444444444443

>PRK07521 flgK flagellar hook-associated protein FlgK; Validated

Probab=82.48  E-value=11  Score=36.36  Aligned_cols=77  Identities=21%  Similarity=0.137  Sum_probs=56.0

Q ss_pred             HHHHHHHHHhhhcC-CCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           74 RLNDRFLDLSCILE-PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        74 kLN~~F~~LrslLP-P~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      .|++-|..|.++-- |.  ...-+..+|+.|-..+..++.-..+|+.....+..+|+..-.++|.+-++...|..+|-..
T Consensus       103 ~l~~ff~a~~~la~~P~--~~~~R~~vl~~a~~L~~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~l~~~Ia~LN~~I~~~  180 (483)
T PRK07521        103 RLSDFQAALQTAASSPD--NTTLAQAAVDAAQDLANSLNDASDAVQSARADADAEIADSVDTLNDLLAQFEDANNAVVSG  180 (483)
T ss_pred             HHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35566666666551 21  2355778999998888888888888888777788888888888888888777777776553

>PRK04406 hypothetical protein; Provisional

Probab=82.40  E-value=10  Score=28.11  Aligned_cols=47  Identities=11%  Similarity=0.165  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  151 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~  151 (214)
                      ..|.+|+.++.-++...+.|...+-+..+++..|+.+...|...+..
T Consensus        11 ~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~   57 (75)
T PRK04406         11 ERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKN   57 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46777777777777777777777766667777776666666544443

>PRK05771 V-type ATP synthase subunit I; Validated

Probab=82.07  E-value=5.1  Score=39.87  Aligned_cols=80  Identities=25%  Similarity=0.306  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           69 KLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  148 (214)
Q Consensus        69 RkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e  148 (214)
                      .++.+++++.+..|+...+...   ..+..  ...+++. .+.+-.+..+...+++.+++.++..++++|++|...++.+
T Consensus        49 ~~~~~~~~~~l~~L~~~~~~~~---~~~~~--~~~~~~~-~~~e~~~~~~~~~~~~~~~i~~l~~~~~~L~~~~~~l~~~  122 (646)
T PRK05771         49 RSLLTKLSEALDKLRSYLPKLN---PLREE--KKKVSVK-SLEELIKDVEEELEKIEKEIKELEEEISELENEIKELEQE  122 (646)
T ss_pred             HHHHHHHHHHHHHHHHhccccc---cchhh--hcccccc-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566678888888887774311   11000  0011111 0111122333344555555666666666666666666666


Q ss_pred             HHHHHH
Q 028060          149 KEKLEQ  154 (214)
Q Consensus       149 ~e~L~~  154 (214)
                      ++.|+.
T Consensus       123 ~~~l~~  128 (646)
T PRK05771        123 IERLEP  128 (646)
T ss_pred             HHHhhh
Confidence            665553

>PRK07191 flgK flagellar hook-associated protein FlgK; Validated

Probab=82.05  E-value=13  Score=35.67  Aligned_cols=77  Identities=12%  Similarity=0.098  Sum_probs=56.6

Q ss_pred             HHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           75 LNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        75 LN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      |++-|..|.++--. -....-+..+|..|-..+..++.-...|.+....+..+|...-.++|.+-++...|..+|.+.
T Consensus       109 l~~ff~a~~~la~~-P~~~~~r~~vl~~a~~la~~~n~~~~~l~~~~~~~~~~i~~~V~~iN~ll~~Ia~LN~~I~~~  185 (456)
T PRK07191        109 LNNFFSALSAATQL-PDSPPMRQQVIESANAMALRFNNVNNFIVQQKKSIGQQRDATVKQINSLTRSIADYNQKILKN  185 (456)
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            67777777776621 112456788999998888888888888887777777777777788888888777777777543

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

Probab=82.05  E-value=14  Score=31.43  Aligned_cols=54  Identities=20%  Similarity=0.376  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      +--.|+.-+.+++.++..|+.....+...+..|+..+.+|......++.+.+-|
T Consensus        85 LAr~al~~k~~~e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l  138 (221)
T PF04012_consen   85 LAREALQRKADLEEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREEL  138 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555666666666666665555555555555555444444444444444444

The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].

>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S

Probab=81.93  E-value=12  Score=28.24  Aligned_cols=50  Identities=18%  Similarity=0.219  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      |+.-++|+.++...+++.+.|..-+..|+..+--.-+-+..|+.+...++
T Consensus         4 i~qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLiKYt~LnkkLq~~~~~~~   53 (76)
T PF11544_consen    4 IKQNKELKKKLNDKQEEIDRLNILVGSLRGKLIKYTELNKKLQDQLLNLQ   53 (76)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445555555554444444444444444444444444444444444433

cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.

>PRK14127 cell division protein GpsB; Provisional

Probab=81.83  E-value=9.8  Score=30.38  Aligned_cols=29  Identities=34%  Similarity=0.510  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          130 SLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       130 eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      .|..|+.+|++++..|+.+++.++.++..
T Consensus        41 ~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~   69 (109)
T PRK14127         41 AFQKEIEELQQENARLKAQVDELTKQVSV   69 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            33344444444555555555555555543

>PHA03011 hypothetical protein; Provisional

Probab=81.82  E-value=17  Score=29.21  Aligned_cols=58  Identities=24%  Similarity=0.420  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      ...-++-+.+|+.+-..|-.+..-+..+++.+..-..+-.+|.--|.+|++||..++.
T Consensus        59 ~Nai~e~ldeL~~qYN~L~dEYn~i~Ne~k~~~~iIQdn~d~I~~LraeIDkLK~nia  116 (120)
T PHA03011         59 INAIIEILDELIAQYNELLDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENIA  116 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHh
Confidence            3444566777777777777777777778888877777777788888888888887664

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=81.80  E-value=6.1  Score=36.94  Aligned_cols=44  Identities=23%  Similarity=0.230  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKA  147 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~  147 (214)
                      .++++.|+.++++|+..+..|..+.+.++.++.+++.++..|+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   50 (389)
T PRK03992          7 EERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS   50 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            45677788899999999999998888888888888877766653

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=81.78  E-value=7.9  Score=39.90  Aligned_cols=7  Identities=43%  Similarity=0.591  Sum_probs=3.6

Q ss_pred             CCCCccc
Q 028060          188 GLMPMWQ  194 (214)
Q Consensus       188 ~~~~mwq  194 (214)
                      |+|-||-
T Consensus       668 g~~k~~v  674 (782)
T PRK00409        668 GIMKMKV  674 (782)
T ss_pred             CCEEEEE
Confidence            4555653

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=81.63  E-value=19  Score=33.43  Aligned_cols=49  Identities=24%  Similarity=0.343  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      -|++|=+.=|.+-+.|       ..|++.|..+..+|++....|..||..|.|-+-
T Consensus       238 AAtRYRqKkRae~E~l-------~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~  286 (294)
T KOG4571|consen  238 AATRYRQKKRAEKEAL-------LGELEGLEKRNEELKDQASELEREIRYLKQLIL  286 (294)
T ss_pred             HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5667755444444333       334444444444555555555555555555443

>PRK05683 flgK flagellar hook-associated protein FlgK; Validated

Probab=81.51  E-value=12  Score=38.08  Aligned_cols=78  Identities=13%  Similarity=0.211  Sum_probs=57.0

Q ss_pred             HHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           74 RLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        74 kLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      .|++-|..|.++.- .-..-.-+..+|+.|-..+.+++.-...|......+..+|+..-.++|.|-++...|..+|.+.
T Consensus       108 ~L~~Ff~alq~la~-~P~s~aaRq~vl~~A~~La~~fn~~~~~L~~l~~~vn~qI~~~V~~IN~l~~qIA~LN~qI~~~  185 (676)
T PRK05683        108 ALQRFFTALQTAAA-NPTDTAARQLLLTQAQGLSKRFNSLSSQLNQQNSNINSQLSAMTDQVNNLTTSIASYNKQIAQA  185 (676)
T ss_pred             HHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35555555555551 0112356788999998888888888888888888888888888888888888888887777653

>PRK06665 flgK flagellar hook-associated protein FlgK; Validated

Probab=81.48  E-value=14  Score=37.10  Aligned_cols=76  Identities=16%  Similarity=0.190  Sum_probs=53.5

Q ss_pred             HHHHHHHHhhhc-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           75 LNDRFLDLSCIL-EPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        75 LN~~F~~LrslL-PP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      |++-|..|..+- .|.  .-.-+.++|..|-....+++.-..+|+.....+..+|+..-.++|.|-++.+.|..+|-..
T Consensus       121 l~~ff~al~~ls~~P~--~~a~R~~vl~~A~~La~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~qIa~LN~qI~~~  197 (627)
T PRK06665        121 LDDFWDSWQDLSNYPE--GLAERQVVLERAQSLGERIHDRYRSLERIRDMANDEIEITVEEINNILRNIADLNEQIVKS  197 (627)
T ss_pred             HHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444444454444 111  2356778999998888888888888887777777788777788888888777777777653

>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6

Probab=81.47  E-value=14  Score=26.20  Aligned_cols=50  Identities=32%  Similarity=0.438  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHh
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKN--------------ELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~ekn--------------ELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +..++.+|..+.+.++.++..+...++              .-+.....++.++++|+..|..|
T Consensus         2 ~~~E~~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~~~l~~~l~~L   65 (66)
T PF10458_consen    2 VEAEIERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEELEKLEEALEQL   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344555555555555555554444333              23455567778888888777654

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 C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.

>PF05837 CENP-H: Centromere protein H (CENP-H); InterPro: IPR008426 Chromosome segregation in eukaryotes requires the kinetochore, a multi-protein structure that assembles on centromeric DNA, and which acts to link chromosomes to spindle microtubules

Probab=81.30  E-value=15  Score=28.70  Aligned_cols=53  Identities=30%  Similarity=0.412  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +-|..++.+.-.++..|.+|-.++.+|+.+....+. ...++.++++++..++.
T Consensus        17 ~~L~~v~~~~l~l~~~n~el~~el~~l~~~~~~~~~-~~~~~~~l~~~~~~lk~   69 (106)
T PF05837_consen   17 EKLSDVEKKRLRLKRRNQELAQELLELAEKQKSQRE-DEELSEKLEKLEKELKK   69 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc-chHHHHHHHHHHHHHHH
Confidence            444444555555555555555666555555554433 34456677777776665

Kinetochore structure and composition is highly conserved among vertebrates. The inner kinetochore is essential for kinetochore assembly, and is involved in chromosome segregation via regulation of the spindle. Inner kinetochore components include the multi-subunit CENP-H/I complex, which may function, in part, in directing centromere protein A (CENP-A) deposition to centromeres, where CENP-A is a centromere-specific histone H3 variant required for the organisation of centromeric chromatin during interphase. The CENP-H/I complex contains three functional classes of proteins [, ]: CENP-H class (includes CENP-H, -I, -K, -L) CENP-M class (includes CENP-M) CENP-O class (includes CENP-O, -P, -Q, -R, -50) CENP-H is required for the localisation of CENP-C, but not CENP-A, to the centromere. However, it may be involved in the incorporation of newly synthesised CENP-A into centromeres via its interaction with the CENP-A/CENP-HI complex. CENP-H contains a coiled-coil structure and a nuclear localisation signal. CENP-H is specifically and constitutively localised in kinetochores throughout the cell cycle, and may play a role in kinetochore organisation and function throughout the cell cycle []. Studies show that CENP-H may be associated with certain human cancers [, ]. This entry also includes Kinetochore protein Fta3 which is a subunit of the Sim4 complex. This complex is required for loading the DASH complex onto the kinetochore via interaction with dad1. Fta2, Fta3 and Fta4 associate with the central core and inner repeat region of the centromere [].; GO: 0043515 kinetochore binding, 0007059 chromosome segregation, 0051301 cell division, 0000777 condensed chromosome kinetochore, 0005634 nucleus

>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family

Probab=81.17  E-value=7.6  Score=35.80  Aligned_cols=59  Identities=20%  Similarity=0.282  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           72 RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE  134 (214)
Q Consensus        72 RdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~e  134 (214)
                      |++++..=.+.++++..    +..+..=+.+.-.-+++|+.+.++++.+.+.+..+++++...
T Consensus         5 ~~~~~~~~~~~r~l~~~----~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   63 (378)
T TIGR01554         5 KEQREEIVAEIRSLLDK----AEKLEKELTAAALEKEELETDVEKLKEEIKLLEDAIADLEKV   63 (378)
T ss_pred             HHHHHHHHHHHHHHHhh----hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            66777777777777731    111111122222234455555555555555555555444443

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.

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

Probab=81.12  E-value=11  Score=37.65  Aligned_cols=9  Identities=11%  Similarity=0.172  Sum_probs=3.4

Q ss_pred             HHHHHHhhh
Q 028060           77 DRFLDLSCI   85 (214)
Q Consensus        77 ~~F~~Lrsl   85 (214)
                      +-+.+|+..
T Consensus       120 ~e~~elr~~  128 (546)
T KOG0977|consen  120 EELKELRKK  128 (546)
T ss_pred             HHHHHHHHH
Confidence            333333333

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

Probab=81.10  E-value=2.3  Score=32.07  Aligned_cols=24  Identities=38%  Similarity=0.516  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          136 NELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       136 nELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +|+.+|+..||.++.+|+.+|+.+
T Consensus         3 ~ei~eEn~~Lk~eiqkle~ELq~~   26 (76)
T PF07334_consen    3 HEIQEENARLKEEIQKLEAELQQN   26 (76)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455566666666666666555554

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

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

Probab=81.05  E-value=15  Score=36.92  Aligned_cols=29  Identities=17%  Similarity=0.407  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          129 KSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       129 ~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.+..|+++|..+...++.++++|.+.+.
T Consensus       335 e~mn~Er~~l~r~l~~i~~~~d~l~k~vw  363 (581)
T KOG0995|consen  335 ERMNLERNKLKRELNKIQSELDRLSKEVW  363 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44455666666666666666666654443

>PRK15396 murein lipoprotein; Provisional

Probab=81.01  E-value=13  Score=28.05  Aligned_cols=47  Identities=11%  Similarity=0.324  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      -|.+|..+|+.|..+.++|...+..++.....-.+|-.+-.+.++..
T Consensus        26 kvd~LssqV~~L~~kvdql~~dv~~~~~~~~~a~~eA~raN~RlDn~   72 (78)
T PRK15396         26 KIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNQ   72 (78)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566667776666666666666666666665555555544444433

>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function

Probab=80.88  E-value=11  Score=29.06  Aligned_cols=35  Identities=14%  Similarity=0.217  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN  136 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~ekn  136 (214)
                      -+.=-+++++.++++|.++|++|+.|+....++++
T Consensus        20 y~~~k~~ka~~~~~kL~~en~qlk~Ek~~~~~qvk   54 (87)
T PF10883_consen   20 YLWWKVKKAKKQNAKLQKENEQLKTEKAVAETQVK   54 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333455666666666666666555544444443

>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=80.85  E-value=20  Score=26.40  Aligned_cols=54  Identities=30%  Similarity=0.404  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      ..--..|-....++...+..|+..+.++..++.+|......+..+++.|+..++
T Consensus        18 ~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~l~   71 (74)
T PF12329_consen   18 MEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESLEERLK   71 (74)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            333445555555666666666666666666666666666666667777666554

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.

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

Probab=80.83  E-value=9.2  Score=34.01  Aligned_cols=56  Identities=27%  Similarity=0.369  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          103 AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       103 AI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      |-..+..|+.+......+...|..++.++..++..|.++...-..|.++|+.++..
T Consensus        59 aee~~~rL~~~~~~~~eEk~~Le~e~~e~~~~i~~l~ee~~~ke~Ea~~lq~el~~  114 (246)
T PF00769_consen   59 AEEEKQRLEEEAEMQEEEKEQLEQELREAEAEIARLEEESERKEEEAEELQEELEE  114 (246)
T ss_dssp             HHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444445555555555566677777777777777777777777777777776655

Ezrin was first identified as a constituent of microvilli [], radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions [], and moesin as a heparin binding protein []. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain; an extended alpha-helical domain; and a charged C-terminal domain []. Ezrin, radixin and merlin also contain a polyproline region between the helical and C-terminal domains. The N-terminal domain is highly conserved, and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily. ERM proteins crosslink actin filaments with plasma membranes. They co-localise with CD44 at actin filament-plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains [].; GO: 0008092 cytoskeletal protein binding, 0005737 cytoplasm, 0019898 extrinsic to membrane; PDB: 2I1J_A 2I1K_A 1E5W_A 1EF1_C.

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

Probab=80.80  E-value=12  Score=28.51  Aligned_cols=57  Identities=35%  Similarity=0.474  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          103 AIRVLNQLRTESQELKETNEKLQE---EIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       103 AI~yIk~Lr~~vq~L~~~n~~L~~---ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ++.-+..|+.+...+.++...+..   +..+|..+..++.++...+..+...++.++..+
T Consensus        41 l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e~~l~~~  100 (108)
T PF02403_consen   41 LQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKELEEELNEL  100 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566667776666666665554   467777888888888888888888888887764

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 ....

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

Probab=80.80  E-value=31  Score=28.65  Aligned_cols=81  Identities=22%  Similarity=0.430  Sum_probs=60.9

Q ss_pred             HHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           74 RLNDRFLDLSCILEPGRPARTDKPAILDDAIRVL-NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus        74 kLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yI-k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      .|++.|..|-.++..+   . .....+.++++-| .++...+...-.-...++.+++.++.|...|.+.+.+.+..+++|
T Consensus         5 el~~~~~~l~~~~e~~---~-~d~e~~~dtLe~i~~~~~~K~~~~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~L   80 (162)
T PF05565_consen    5 ELTDEYLELLELLEEG---D-LDEEAIADTLESIEDEIEEKADNIAKVIKNLEADIEAIKAEIKRLQERKKSIENRIDRL   80 (162)
T ss_pred             HHHHHHHHHHHHHhcC---C-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4788899999988542   2 3345666777663 346666777777778888889999999999999998888888888


Q ss_pred             HHHHHH
Q 028060          153 EQQLKV  158 (214)
Q Consensus       153 ~~qlk~  158 (214)
                      .+-|..
T Consensus        81 k~yL~~   86 (162)
T PF05565_consen   81 KEYLLD   86 (162)
T ss_pred             HHHHHH
Confidence            776654

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

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=80.77  E-value=10  Score=37.87  Aligned_cols=49  Identities=27%  Similarity=0.299  Sum_probs=31.0

Q ss_pred             CChhhHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           94 TDKPAIL----DDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  142 (214)
Q Consensus        94 ~DKasIL----~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek  142 (214)
                      ++++.++    ..-+.-+.+++++..+|..+...++.+++++..|++|+..-.
T Consensus       211 N~q~~s~~eel~~kt~el~~q~Ee~skLlsql~d~qkk~k~~~~Ekeel~~~L  263 (596)
T KOG4360|consen  211 NTQARSGQEELQSKTKELSRQQEENSKLLSQLVDLQKKIKYLRHEKEELDEHL  263 (596)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            4555555    233334445566666777777777888888888888764443

>PRK04325 hypothetical protein; Provisional

Probab=80.38  E-value=11  Score=27.78  Aligned_cols=49  Identities=8%  Similarity=0.093  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      +.|.+|+.++.-++...+.|...+-+-..++.+|+.+...|...+..++
T Consensus         9 ~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~~   57 (74)
T PRK04325          9 DRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDAN   57 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4577777777777777777777777777777777766666655544443

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

Probab=80.06  E-value=20  Score=31.02  Aligned_cols=41  Identities=29%  Similarity=0.419  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  139 (214)
Q Consensus        99 IL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr  139 (214)
                      .|..+-.-++.++.++..|+-+++.|......|..|+++|.
T Consensus        87 ~L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~  127 (201)
T PF13851_consen   87 SLQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELY  127 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444445555555666666666666655555555555554

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

Probab=80.02  E-value=9.1  Score=38.29  Aligned_cols=37  Identities=32%  Similarity=0.463  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          123 KLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       123 ~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .|+.++..++..+.-|.+|+..|++|+.+|..+|+.+
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            4456666777777778888888888888887777664

---

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	214
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	6e-11
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-10
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	1e-09
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	2e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	1e-06
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	3e-05
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	6e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	7e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	5e-05
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	1e-04
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	7e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	3e-04
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	7e-04
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	8e-04

>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 = 55.8 bits (135), Expect = 6e-11
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 68  EKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 126
           E+ RR  L   F  L   I E     +  K  IL  A   +  ++ E Q+L    + L++
Sbjct: 14  ERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK 73

Query: 127 EIKSLKAEKNELR 139
             + LK +  +L 
Sbjct: 74  RREQLKHKLEQLG 86

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

 Score = 54.3 bits (131), Expect = 2e-10
 Identities = 14/72 (19%), Positives = 32/72 (44%)

Query: 68  EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE 127
           E+ RR+ + D F  L   +   +  +  +  ILD A   +  +R ++   ++  + L+ +
Sbjct: 10  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 69

Query: 128 IKSLKAEKNELR 139
              L+ +   L 
Sbjct: 70  NALLEQQVRALG 81

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

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 68  EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE 127
           EK  R  +ND+ ++L  ++  G  A+ +K A+L  AI  +  L+  +Q+LK+ N  L+  
Sbjct: 14  EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72

Query: 128 IKSLKAEK 135
           +   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 = 46.6 bits (111), Expect = 2e-07
 Identities = 12/60 (20%), Positives = 28/60 (46%)

Query: 68  EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE 127
           E+ RR+ + D F  L   +   +  +  +  ILD A   +  +R ++   ++  + L+ +
Sbjct: 20  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 79

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

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 1/72 (1%)

Query: 68  EKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 126
           EK RR  L      L   +      +R    ++L  A   + +L    ++     ++LQ 
Sbjct: 9   EKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR 68

Query: 127 EIKSLKAEKNEL 138
           E + LK +  +L
Sbjct: 69  EQRHLKRQLEKL 80

>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 = 43.3 bits (102), Expect = 3e-05
 Identities = 18/108 (16%), Positives = 45/108 (41%)

Query: 50  RKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ 109
             +A+ +   R   +  + +   + L  +   L       +     +  +  +A  +  +
Sbjct: 858 EMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVR 917

Query: 110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
           L  + QEL+E   +++  I+  +    +L+ EK  ++     LE+QL+
Sbjct: 918 LAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLE 965

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 100  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 156
            L+D     N    + +EL+     LQE+++S KA +N+  ++K  L  + E L+ +L
Sbjct: 1104 LEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEELEALKTEL 1160

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 19/96 (19%), Positives = 45/96 (46%), Gaps = 7/96 (7%)

Query: 64  KACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEK 123
                +  R RL  +  +L  IL        +  A +++      QL+ E +++++    
Sbjct: 907 LYAEAEEMRVRLAAKKQELEEILH-------EMEARIEEEEERSQQLQAEKKKMQQQMLD 959

Query: 124 LQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM 159
           L+E+++  +A + +L+ EK+      +K+E  + +M
Sbjct: 960 LEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIM 995

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 10/54 (18%), Positives = 26/54 (48%)

Query: 107  LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA 160
            L       ++         ++I+ L++  ++L+E+    KA + K E+Q + ++
Sbjct: 1097 LQAALARLEDETSQKNNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLS 1150

>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 = 40.6 bits (95), Expect = 2e-04
 Identities = 16/62 (25%), Positives = 30/62 (48%)

Query: 98   AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
            +++ +    L +     QEL++   KL+ E   L  +  EL+ +   LKA   K E++L+
Sbjct: 1039 SMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQ 1098

Query: 158  VM 159
              
Sbjct: 1099 AA 1100

>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 = 39.4 bits (92), Expect = 6e-04
 Identities = 12/58 (20%), Positives = 24/58 (41%)

Query: 100  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
              D    + +L+ +  ELK    K +EE+++  A   +   +K        +LE  + 
Sbjct: 1069 SSDLHEQIAELQAQIAELKAQLAKKEEELQAALARLEDETSQKNNALKKIRELESHIS 1126

>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 = 39.0 bits (91), Expect = 7e-04
 Identities = 11/58 (18%), Positives = 28/58 (48%)

Query: 100  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
            L++      +L+ E        +K++++I  ++ + N+L +E+ +L+     L   L 
Sbjct: 964  LEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLA 1021

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

 Score = 42.4 bits (100), Expect = 5e-05
 Identities = 16/58 (27%), Positives = 35/58 (60%), Gaps = 3/58 (5%)

Query: 100  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
            +    + L+Q +TE + ++E  +K + E + L +E   L+E+  +LK +KE+L +++ 
Sbjct: 993  IAKLRKELHQTQTEKKTIEEWADKYKHETEQLVSE---LKEQNTLLKTEKEELNRRIH 1047

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

 Score = 41.6 bits (98), Expect = 1e-04
 Identities = 13/58 (22%), Positives = 26/58 (44%)

Query: 100  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
            L   +  L     E++        LQEEI  L+ E ++ + EK  ++   +K + + +
Sbjct: 965  LRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETE 1022

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

 Score = 39.3 bits (92), Expect = 7e-04
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 103 AIRVLNQLRTES---QELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 157
           A R L +L+ E+   +  K+ +  L+ +I  L+ + +E  +E   L      LE    
Sbjct: 902 AKRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYS 959

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

 Score = 39.4 bits (91), Expect = 3e-04
 Identities = 9/51 (17%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ 154
           I   ++L  E + +++  E+ ++ ++      +++ E++   KA K+  E 
Sbjct: 74  IAQADRLTQEPESIRKWREEQRKRLQE-LDAASKVMEQEWREKAKKDLEEW 123

>3iv1_A Tumor susceptibility gene 101 protein; coiled_COIL, tumorigenesis, CELL_cycle regulation, alternative splicing, cell cycle, cell division; HET: MSE; 2.50A {Homo sapiens} Length = 78

 Score = 36.4 bits (84), Expect = 7e-04
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 156
           LN L+   ++LK+ ++KL+E +  L  E  E+ +   +LK   E+L   L
Sbjct: 27  LNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELSSAL 76

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 Length = 854

 Score = 39.1 bits (92), Expect = 8e-04
 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 17/96 (17%)

Query: 77  DRFL-----DLSCILEPGRPARTD---KPAILDDAIRVLNQLRTESQEL-KETNEKLQEE 127
           +R L     DL  I E     R      P  +D   R   QL  E + L KE +   QE 
Sbjct: 374 ERRLPDKAIDL--IDEAAARLRMALESAPEEIDALERKKLQLEIEREALKKEKDPDSQER 431

Query: 128 IKSLKAEKNELREEKLILKA----DKEKLE--QQLK 157
           +K+++AE  +L EE   L+A    ++E L   ++ +
Sbjct: 432 LKAIEAEIAKLTEEIAKLRAEWEREREILRKLREAQ 467

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	214
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.77
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.76
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.75
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.74
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.69
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.67
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.6
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.59
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.55
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.49
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.46
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.31
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.19
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.09
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.08
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.84
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.69
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.86
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	97.57
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	96.92
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	96.49
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.47
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	96.21
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	95.8
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	95.67
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	95.46
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	95.37
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	95.2
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	95.19
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	94.81
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	94.64
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	94.13
2oqq_A	42	Transcription factor HY5; homodimer leucine zipper	94.11
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	93.89
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	93.89
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	93.65
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	93.51
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	93.42
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	93.4
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	93.28
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	92.87
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	92.53
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	92.32
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.12
3he5_B	52	Synzip2; heterodimeric coiled-coil, de novo protei	92.03
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	91.8
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	91.8
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	91.79
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	91.75
2wt7_B	90	Transcription factor MAFB; transcription, transcri	91.66
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	91.47
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	91.33
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	91.3
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	91.26
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	91.24
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	91.23
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	91.21
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	90.86
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	90.85
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	90.76
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	90.74
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	90.71
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	90.57
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	90.51
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	90.36
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	90.11
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	90.1
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	90.02
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	89.94
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	89.91
2w6a_A	63	ARF GTPase-activating protein GIT1; PIX, zinc, sig	89.53
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	89.18
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	88.98
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	88.91
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	88.89
3swf_A	74	CGMP-gated cation channel alpha-1; coiled-coil, as	88.88
3htk_A	60	Structural maintenance of chromosomes protein 5; S	88.67
3swy_A	46	Cyclic nucleotide-gated cation channel alpha-3; co	88.66
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	88.58
3htk_A	60	Structural maintenance of chromosomes protein 5; S	88.58
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	88.44
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	88.2
3u06_A	412	Protein claret segregational; motor domain, stalk	88.18
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	88.18
1dip_A	78	Delta-sleep-inducing peptide immunoreactive peptid	87.98
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	87.61
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	87.54
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	87.34
1kd8_A	36	GABH AIV, GCN4 acid base heterodimer acid-D12IA16V	86.94
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	86.84
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	86.83
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	86.78
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	86.72
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	86.65
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	86.44
1m1j_C	409	Fibrinogen gamma chain; coiled coils, disulfide ri	86.39
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	86.38
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	86.36
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	85.91
3m48_A	33	General control protein GCN4; leucine zipper, synt	85.9
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	85.78
2wt7_B	90	Transcription factor MAFB; transcription, transcri	85.76
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	85.12
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	84.99
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	84.96
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	84.38
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	84.33
3v86_A	27	De novo design helix; computational design of A pr	84.25
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	84.23
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	84.18
3gpv_A	148	Transcriptional regulator, MERR family; protein st	84.17
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	84.13
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	83.93
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	83.9
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	83.87
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	83.87
1gk6_A	59	Vimentin; intermediate filament, dimer, parallel c	83.85
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	83.33
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	83.13
2d4y_A	463	HAP1, flagellar HOOK-associated protein 1; multi-d	83.05
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	82.74
2v4h_A	110	NF-kappa-B essential modulator; transcription, met	82.7
3c3g_A	33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	82.64
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	82.54
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	82.47
3vmx_A	48	Voltage-gated hydrogen channel 1; coiled-coil, ION	82.25
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	82.11
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	82.01
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	81.9
3m48_A	33	General control protein GCN4; leucine zipper, synt	81.68
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	81.65
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	81.44
2wq1_A	33	General control protein GCN4; TAA, nucleus, coiled	81.44
3c3g_A	33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	81.26
1uix_A	71	RHO-associated kinase; coiled-coil, transferase; H	81.05
3c3f_A	34	Alpha/beta peptide with the GCN4-PLI SIDE chain S	80.89
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	80.65
1deq_A	390	Fibrinogen (alpha chain); coiled-coil, blood clott	80.56
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	80.45
3d5a_X	354	RF1, peptide chain release factor 1; ribosome, rib	80.33
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	80.11

>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=99.77  E-value=4.6e-19  Score=131.12  Aligned_cols=77  Identities=17%  Similarity=0.304  Sum_probs=63.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN  136 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~ekn  136 (214)
                      ++.+|+.+||+||+.||++|.+|+++||.....|.||++||..||+||++|+.+++.|+.+.+.|..+...|++++.
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~~L~~~l~   78 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVR   78 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999986555799999999999999999999988887666655555555544443

>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=99.76  E-value=1.1e-18  Score=129.73  Aligned_cols=72  Identities=26%  Similarity=0.393  Sum_probs=64.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLK  132 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~  132 (214)
                      ++.+|+.+||+||++||++|.+|+++||+ ...|+||++||.+||+||++|+.+++.|+.++..|+.++++..
T Consensus         6 rr~~H~~~ErrRR~~in~~f~~L~~lvP~-~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~~~~   77 (82)
T 1am9_A            6 KRTAHNAIEKRYRSSINDKIIELKDLVVG-TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTC-SSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHhccC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            36789999999999999999999999975 4479999999999999999999999999999998888775543

>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=99.75  E-value=2.5e-18  Score=129.55  Aligned_cols=79  Identities=22%  Similarity=0.300  Sum_probs=67.6

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL  138 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknEL  138 (214)
                      ++.+|+.+||+||+.||++|..|+++||.. ...|.||++||.+||+||++|+.+.+.+..+.+.|+.+...|+.++.+|
T Consensus         6 ~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~n~~L~~rl~~L   85 (88)
T 1nkp_A            6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999653 2369999999999999999999999998888777777776666666655

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

Probab=99.74  E-value=5.7e-18  Score=125.76  Aligned_cols=77  Identities=21%  Similarity=0.261  Sum_probs=68.2

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           61 PGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNE  137 (214)
Q Consensus        61 ~~sH~~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknE  137 (214)
                      +.+|+..||+||+.||++|..|+++||.. ...|.+|++||.+|++||++|+.+.++|..+++.|+.+..+|+++++.
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e~~~L~~~L~~   79 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLEK   79 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            46899999999999999999999999743 346899999999999999999999999999888888888877777654

>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=99.69  E-value=2.8e-17  Score=121.03  Aligned_cols=68  Identities=18%  Similarity=0.344  Sum_probs=61.3

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE  127 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~e  127 (214)
                      ++.+|+.+||+||+.||++|.+|+++||.....|.+|++||..||+||++|+.+++.|+.+++.|+.+
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~~   79 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   79 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999999976545699999999999999999999999998888877653

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=99.67  E-value=8.5e-17  Score=126.96  Aligned_cols=61  Identities=25%  Similarity=0.392  Sum_probs=51.7

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTESQELKET  120 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~--~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~  120 (214)
                      ++.+|+..||+||++||++|.+|+++||++.  ..|++|++||.+||+||+.|+.+++.|+++
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4788999999999999999999999998654  248999999999999999999999999864

>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=99.60  E-value=3.4e-16  Score=110.88  Aligned_cols=57  Identities=25%  Similarity=0.373  Sum_probs=50.5

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHhhhcCCCCC----CCCChhhHHHHHHHHHHHHHHHHH
Q 028060           59 SRPGSKACREKLRRERLNDRFLDLSCILEPGRP----ARTDKPAILDDAIRVLNQLRTESQ  115 (214)
Q Consensus        59 ~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~----~K~DKasIL~dAI~yIk~Lr~~vq  115 (214)
                      .++.+|+..||+||++||++|.+|+++||++..    .|+||++||..||+||++|+.+.+
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999987543    378999999999999999987653

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.59  E-value=7.7e-16  Score=112.43  Aligned_cols=58  Identities=24%  Similarity=0.346  Sum_probs=51.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELK  118 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~  118 (214)
                      ++.+|+..||+||++||++|.+|+++||. ...|+||++||..||+||++|+.++.=|+
T Consensus         8 kR~~Hn~iErrRRd~IN~~i~eL~~LvP~-~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            8 KRVSRNKSEKKRRDQFNVLIKELGSMLPG-NARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSSS-CCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HhhhhhHHHhhHHHHHHHHHHHHHHhCCC-CCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            36789999999999999999999999964 45699999999999999999999876553

>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=99.55  E-value=1e-15  Score=108.95  Aligned_cols=55  Identities=22%  Similarity=0.354  Sum_probs=48.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCC-----CCCCChhhHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGR-----PARTDKPAILDDAIRVLNQLRTES  114 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~-----~~K~DKasIL~dAI~yIk~Lr~~v  114 (214)
                      ++.+|+.+||+||++||++|.+|+++||++.     ..+.+||+||..||+||++|+.++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999999997531     357899999999999999998765

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=99.49  E-value=9.5e-15  Score=107.61  Aligned_cols=60  Identities=22%  Similarity=0.350  Sum_probs=48.7

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHhhhcCC-CCCCCC-ChhhHHHHHHHHHHHHHHHHHHHH
Q 028060           59 SRPGSKACREKLRRERLNDRFLDLSCILEP-GRPART-DKPAILDDAIRVLNQLRTESQELK  118 (214)
Q Consensus        59 ~~~~sH~~~ERkRRdkLN~~F~~LrslLPP-~~~~K~-DKasIL~dAI~yIk~Lr~~vq~L~  118 (214)
                      .++.+|+.+||+||+.||++|.+|+.+||+ ....|. +|++||..||+||+.|+.++++++
T Consensus         4 ~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            467889999999999999999999999974 233455 799999999999999999988764

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.46  E-value=8.7e-15  Score=107.15  Aligned_cols=53  Identities=23%  Similarity=0.327  Sum_probs=47.3

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCC--CCCCCChhhHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPG--RPARTDKPAILDDAIRVLNQLRT  112 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~--~~~K~DKasIL~dAI~yIk~Lr~  112 (214)
                      ++.+|+..||+||++||++|.+|+++||.+  ..+|+||++||..||+||+.|+.
T Consensus         9 rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            367899999999999999999999999753  23699999999999999999975

>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=99.31  E-value=4.7e-13  Score=96.72  Aligned_cols=57  Identities=26%  Similarity=0.328  Sum_probs=50.0

Q ss_pred             CCCCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHH
Q 028060           58 CSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTES  114 (214)
Q Consensus        58 ~~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~v  114 (214)
                      ..++..|+.+||+|+..||+.|..|+.+||.....|.+|+.||..||+||..|+..+
T Consensus        10 ~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            345788999999999999999999999997543468999999999999999998754

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=99.19  E-value=1.3e-11  Score=86.99  Aligned_cols=55  Identities=20%  Similarity=0.109  Sum_probs=48.1

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRTES  114 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr~~v  114 (214)
                      ++..|+.+||+|+..||+.|..|+..||.. ...|.+|+.||..||+||..|+..+
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L   57 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEIL   57 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHT
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHH
Confidence            356799999999999999999999999742 2358999999999999999998765

>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=7.8e-11  Score=105.05  Aligned_cols=53  Identities=26%  Similarity=0.433  Sum_probs=42.5

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTE  113 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~  113 (214)
                      ++.+|+..||+||++||..|.+|+++|| +...|+||++||..||.||+.|+..
T Consensus        12 ~~~~~~~~e~~rr~~~n~~~~~l~~~~p-~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           12 KRVSRNKSEKKRRDQFNVLIKELGSMLP-GNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTCC-SSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHhCC-CCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            3678999999999999999999999997 4557999999999999999998754

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=99.08  E-value=1.4e-09  Score=81.56  Aligned_cols=51  Identities=25%  Similarity=0.418  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHhhhcCCC--CCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           72 RERLNDRFLDLSCILEPG--RPARTDKPAILDDAIRVLNQLRTESQELKETNE  122 (214)
Q Consensus        72 RdkLN~~F~~LrslLPP~--~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~  122 (214)
                      |..||++|.+|+.+||++  ...|.+|++||..||+||+.|+.+++++.++..
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~   56 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN   56 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999863  336899999999999999999999988876543

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.84  E-value=1.3e-09  Score=98.55  Aligned_cols=53  Identities=23%  Similarity=0.331  Sum_probs=47.1

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHhhhcCCC--CCCCCChhhHHHHHHHHHHHHHHH
Q 028060           61 PGSKACREKLRRERLNDRFLDLSCILEPG--RPARTDKPAILDDAIRVLNQLRTE  113 (214)
Q Consensus        61 ~~sH~~~ERkRRdkLN~~F~~LrslLPP~--~~~K~DKasIL~dAI~yIk~Lr~~  113 (214)
                      +.+|+..||+||++||+.|.+|+++||..  ...|+||++||..||.||+.|+..
T Consensus        14 ~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           14 REAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            67899999999999999999999999731  236999999999999999999753

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.69  E-value=6e-09  Score=75.50  Aligned_cols=49  Identities=16%  Similarity=0.150  Sum_probs=42.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHH
Q 028060           64 KACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRT  112 (214)
Q Consensus        64 H~~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr~  112 (214)
                      =+.+||+|+..||+.|..||.+||.. ...|.+|+.||.-||+||..|+.
T Consensus        18 a~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           18 AAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CBCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            34779999999999999999999642 22589999999999999999974

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=97.86  E-value=3.3e-05  Score=59.32  Aligned_cols=51  Identities=16%  Similarity=0.134  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHHHHHH
Q 028060           66 CREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRTESQE  116 (214)
Q Consensus        66 ~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr~~vq~  116 (214)
                      ..||.|=..||+.|..||..||.. ...|.+|..||.-||+||..|+..++.
T Consensus        31 ~~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           31 DDPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            345778889999999999999642 225899999999999999999876653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=97.57  E-value=0.00072  Score=50.33  Aligned_cols=60  Identities=28%  Similarity=0.493  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +..||+-|.-|+-+++.|+.+|..|.++..+++.....|+.|+..|+.|....+..|.++
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            457888888888888888888888888888888888888888888888887777766653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=96.92  E-value=0.0069  Score=45.04  Aligned_cols=55  Identities=29%  Similarity=0.357  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHh
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI-------LKADKEKLEQQLKVM  159 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~-------Lk~e~e~L~~qlk~~  159 (214)
                      +.+.+|+.+|+++-+...-|+.++++|+.+.+.|.+++..       |..|+++|+++...+
T Consensus         6 ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~w   67 (81)
T 2jee_A            6 EVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGW   67 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence            6788899999998888888888888888888777777766       667888887777665

>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=96.49  E-value=0.02  Score=39.95  Aligned_cols=58  Identities=28%  Similarity=0.387  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           68 EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus        68 ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      ||++|-+..++..+-++--               +-..|+.+|+.++..|+.+|..|..++..|..++..|+.
T Consensus         1 Ekr~rrrerNR~AA~rcR~---------------rKk~~~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~   58 (63)
T 2wt7_A            1 EKRRIRRERNKMAAAKCRN---------------RRRELTDTLQAETDQLEDEKSALQTEIANLLKEKEKLEF   58 (63)
T ss_dssp             CHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHhHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566666666766666643               234788899999999999998888888777777766654

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

Probab=96.47  E-value=0.029  Score=44.94  Aligned_cols=81  Identities=15%  Similarity=0.096  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHhhh--cCCCCCCCCChhhHHHH--HHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHH
Q 028060           73 ERLNDRFLDLSCI--LEPGRPARTDKPAILDD--AIRVLNQLRTESQELKETNEKLQ--------------EEIKSLKAE  134 (214)
Q Consensus        73 dkLN~~F~~Lrsl--LPP~~~~K~DKasIL~d--AI~yIk~Lr~~vq~L~~~n~~L~--------------~ei~eL~~e  134 (214)
                      ..+|+++.+++..  -|-   --.++.+||.-  .++=+-+++.+.+.|+.+.+.+.              .++++++.+
T Consensus        35 ~~vd~km~ei~~~~~~~~---l~~~r~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~k~e~~~~e  111 (138)
T 3hnw_A           35 SYINNKITEFNKEESYRR---MSAELRTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQIKAESSAKE  111 (138)
T ss_dssp             HHHHHHHHHHTTCHHHHT---SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5689999999966  632   24788888862  22222234444444444444333              334444444


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028060          135 KNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       135 knELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +.+|++++..|+.++-+|+..+
T Consensus       112 ~~~l~~~~~~l~~~~~~le~~~  133 (138)
T 3hnw_A          112 IKELKSEINKYQKNIVKLETEL  133 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444444444

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1

Probab=96.21  E-value=0.0081  Score=43.33  Aligned_cols=42  Identities=31%  Similarity=0.298  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  145 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~L  145 (214)
                      -.||++|+.++..|+..+..|..+...|+.++..|+.|+..|
T Consensus        28 ~~~i~~LE~~v~~le~~~~~l~~en~~Lr~~i~~L~~El~~l   69 (70)
T 1gd2_E           28 EDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL   69 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            478888888888888877776666666666666666555443

>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=95.80  E-value=0.013  Score=40.06  Aligned_cols=39  Identities=18%  Similarity=0.291  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRT-------ESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus       102 dAI~yIk~Lr~-------~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      +|++||++--.       .++.|+.+|..|+.++.+|+.+..||+.
T Consensus         2 ~AlefIk~~LG~~~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el~~   47 (53)
T 2yy0_A            2 SALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKLKA   47 (53)
T ss_dssp             --------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68889887633       4555555555555555555555555443

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

Probab=95.67  E-value=0.058  Score=43.15  Aligned_cols=45  Identities=24%  Similarity=0.303  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  150 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e  150 (214)
                      -|..|+.++..++..++.+..++.+|+.++++|+.++..|.++.+
T Consensus        90 E~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~  134 (138)
T 3hnw_A           90 EIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELN  134 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555556666666666666666666666666665554

>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=95.46  E-value=0.039  Score=38.03  Aligned_cols=35  Identities=26%  Similarity=0.428  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  139 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr  139 (214)
                      .|+.+|+.++..|+.+|..|..++..|+.|+..|+
T Consensus        22 ~~~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk   56 (61)
T 1t2k_D           22 VWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLK   56 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56677777777777766666666555555555443

>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=95.37  E-value=0.14  Score=39.39  Aligned_cols=63  Identities=24%  Similarity=0.317  Sum_probs=41.7

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060           93 RTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus        93 K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .++|..++.+   ||. |+..+..+++++..|+...+..-..+.||..|..+|+.|..+|.++-+.+
T Consensus        29 ~mSKqELIqE---Yl~-LE~~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~~   91 (104)
T 3s9g_A           29 NMSKQELIKE---YLE-LEKSLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENELH   91 (104)
T ss_dssp             TSCHHHHHHH---HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHH---HHH-HHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4788888774   554 88888888888888887555555555555555555555555555554444

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=95.20  E-value=0.16  Score=41.67  Aligned_cols=91  Identities=16%  Similarity=0.136  Sum_probs=35.9

Q ss_pred             HHHHH-HHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           66 CREKL-RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI  144 (214)
Q Consensus        66 ~~ERk-RRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~  144 (214)
                      ..+|. =|+.+-.+|.+|-.-+ .+-+.. .=+|=+..-+.-|..|+.+...|+..+..|.+++++-......++||...
T Consensus        30 l~~rL~~Rd~~E~~~~~l~~e~-~~~~~~-~~vs~~~~~~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~a  107 (152)
T 3a7p_A           30 LIRRLTDRNDKEAHLNELFQDN-SGAIGG-NIVSHDDALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALIS  107 (152)
T ss_dssp             ----------------------------C-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHhh-ccCCCc-ccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44443 4777777777776665 222111 11222333345666666666666666666666555555555566666666


Q ss_pred             HHHHHHHHHHHHHH
Q 028060          145 LKADKEKLEQQLKV  158 (214)
Q Consensus       145 Lk~e~e~L~~qlk~  158 (214)
                      |+.+..-+++.++.
T Consensus       108 Lqlq~n~lE~kl~k  121 (152)
T 3a7p_A          108 GTIENNVLQQKLSD  121 (152)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            66655555554443

>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=95.19  E-value=0.1  Score=40.11  Aligned_cols=55  Identities=33%  Similarity=0.480  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------------HHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKN----------------------------ELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~ekn----------------------------ELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +-+..|+.+++.|+.+++.|.+++..|..++.                            ..+.+...|++|+++|...+
T Consensus        12 e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~Gd~~~~~TKVlH~~~NPa~~a~~~~~~~~e~Lq~E~erLr~~v   91 (100)
T 1go4_E           12 EEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAECERLRGLL   91 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCCSCCCTTTEEEEEESSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCccCeeeeecCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556777777777777777777766665443                            34556677888888888877


Q ss_pred             HHh
Q 028060          157 KVM  159 (214)
Q Consensus       157 k~~  159 (214)
                      +.|
T Consensus        92 ~~l   94 (100)
T 1go4_E           92 RAM   94 (100)
T ss_dssp             TTC
T ss_pred             HHH
Confidence            765

>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=94.81  E-value=0.1  Score=37.94  Aligned_cols=49  Identities=22%  Similarity=0.204  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      -|.+|+..+++..++....++.|++|..++.|..++...|+.++++++.
T Consensus        20 ti~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDKfrS   68 (72)
T 3nmd_A           20 SLRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYRS   68 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3888999888888888888899999999999999999999988888743

>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=94.64  E-value=0.041  Score=38.10  Aligned_cols=34  Identities=21%  Similarity=0.348  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL  138 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknEL  138 (214)
                      +|+.+|+.++..|+.+|..|..++..|..|+..|
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            5667777777777766666666555555554444

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

Probab=94.13  E-value=0.13  Score=35.79  Aligned_cols=29  Identities=38%  Similarity=0.463  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEK  135 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~ek  135 (214)
                      +..|+.+++.|+.+|..|..++..|+.|+
T Consensus        25 ~~~le~~~~~L~~~N~~L~~~i~~L~~E~   53 (63)
T 1ci6_A           25 QEALTGECKELEKKNEALKERADSLAKEI   53 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444333333333

>2oqq_A Transcription factor HY5; homodimer leucine zipper; 2.00A {Arabidopsis thaliana}

Probab=94.11  E-value=0.16  Score=33.39  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      .|+.+|+.++..|+..|.+|.+.+..|..|-.=||+
T Consensus         3 aYl~eLE~r~k~le~~naeLEervstLq~EN~mLRq   38 (42)
T 2oqq_A            3 AYLSELENRVKDLENKNSELEERLSTLQNENQMLRH   38 (42)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            489999999999998888888877776666655554

>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=93.89  E-value=0.51  Score=34.46  Aligned_cols=55  Identities=15%  Similarity=0.166  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +|...-+......+.+.+.-.....++..+..+|..||..|+.+++.|+.++..+
T Consensus        15 ~Y~~rR~rNN~AakrSR~krk~r~~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~L   69 (78)
T 1gu4_A           15 EYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTL   69 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5665555545555555555556666677777777777777777777777777665

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=93.89  E-value=0.31  Score=35.29  Aligned_cols=50  Identities=14%  Similarity=0.250  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.+..+++.++..|..|+..++.|...+.+-+.+...++.|+.++.++|.
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            35667788888899999999999999999988888888888888877664

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=93.65  E-value=0.79  Score=34.19  Aligned_cols=54  Identities=19%  Similarity=0.375  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKL------------QEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L------------~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +-|+.|+.+...|+.+...+            +.+|.+|+..+.++..++..|..|+..|+..+..
T Consensus        23 dKVR~LEqqN~~Le~~i~~l~~~~~~~~~~~ye~~i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~~   88 (93)
T 3s4r_A           23 DKVRFLEQQNKILLAELEQLKGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMR   88 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555443333            3566777777777777777777777777766544

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=93.51  E-value=0.63  Score=34.47  Aligned_cols=57  Identities=26%  Similarity=0.415  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +-|.-|++|+-+|..|+.+.-+-..+++.-+.|+..|+.....-.+++++|+.||.+
T Consensus        23 ~L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~~   79 (81)
T 3qh9_A           23 ELLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLSR   79 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHhh
Confidence            446778999999999998887777777888888888888888888999999988753

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=93.42  E-value=0.66  Score=34.55  Aligned_cols=54  Identities=15%  Similarity=0.151  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +|...-+.....-+.+.+.-.....++..+..+|..||..|+.+++.|+.++..
T Consensus        15 ~Y~~rR~rNN~AarrSR~krk~r~~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~   68 (87)
T 1hjb_A           15 EYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELST   68 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            354443333333444444444444555556666666666666666666655554

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=93.40  E-value=0.064  Score=36.65  Aligned_cols=30  Identities=30%  Similarity=0.401  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAE  134 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~e  134 (214)
                      .||.+|+.+|..|+.+|..|..++..|..+
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~   51 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALKDL   51 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            577777777777776666666666555543

>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=93.28  E-value=0.44  Score=44.01  Aligned_cols=34  Identities=18%  Similarity=0.263  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          126 EEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       126 ~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .++.+++....+.++....+++|...+.++++.+
T Consensus       544 ~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l  577 (597)
T 3oja_B          544 QENIALEKQLDNKRAKQAELRQETSLKRQKVKQL  577 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444445555555555555553

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=92.87  E-value=0.46  Score=32.48  Aligned_cols=37  Identities=22%  Similarity=0.350  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          120 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       120 ~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      ....|+.++..|..+..+|+.+...|+.|+..|.++|
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            3455666666666666666666666666666666544

>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=92.53  E-value=0.16  Score=35.57  Aligned_cols=31  Identities=19%  Similarity=0.369  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          126 EEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       126 ~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +.+.+|..+..+|..+|..|+.+++.|.++|
T Consensus        30 ~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l   60 (63)
T 2dgc_A           30 QRMKQLEDKVEELLSKNYHLENEVARLKKLV   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444555555555555555443

>3cvf_A Homer-3, homer protein homolog 3; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, phosphoprotein, polymorphism; 2.90A {Homo sapiens}

Probab=92.32  E-value=0.55  Score=34.56  Aligned_cols=48  Identities=21%  Similarity=0.362  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +..+++.++..|..|+..++.|...+.+-+.+...++.|+.++.++|.
T Consensus        11 ~~~klq~~E~rN~~Le~~v~~le~~Le~s~~~q~~~~~Elk~l~e~Ld   58 (79)
T 3cvf_A           11 TQQKVQDLETRNAELEHQLRAMERSLEEARAERERARAEVGRAAQLLD   58 (79)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            445677778888888888888888888888888888888887776664

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

Probab=92.12  E-value=1.1  Score=31.06  Aligned_cols=43  Identities=26%  Similarity=0.340  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      .+|=..=+.+.+.|+.+.+.|..+..+|+.+++.|+.|+..|+
T Consensus        15 ~R~R~KKk~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk   57 (63)
T 1ci6_A           15 TRYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYLK   57 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444554444444444444444444444444443

>3he5_B Synzip2; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=92.03  E-value=0.53  Score=31.45  Aligned_cols=41  Identities=27%  Similarity=0.342  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  149 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~  149 (214)
                      .|++++..|++.|-+|+..-+.|..-+..||+|.++|..|.
T Consensus         7 ylrkkiarlkkdnlqlerdeqnlekiianlrdeiarlenev   47 (52)
T 3he5_B            7 YLRKKIARLKKDNLQLERDEQNLEKIIANLRDEIARLENEV   47 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHHHHHHHHH
Confidence            47888889999888888777777777788888777776554

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=91.80  E-value=0.9  Score=29.99  Aligned_cols=44  Identities=25%  Similarity=0.251  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  148 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e  148 (214)
                      ..+.||+.++..|+.+|++|..+--.-+.-+.-|..|.+.|+..
T Consensus         3 nlvaqlenevaslenenetlkkknlhkkdliaylekeianlrkk   46 (49)
T 3he5_A            3 NLVAQLENEVASLENENETLKKKNLHKKDLIAYLEKEIANLRKK   46 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhhcccHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999988765433333333344444444433

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=91.80  E-value=2.2  Score=33.34  Aligned_cols=67  Identities=18%  Similarity=0.294  Sum_probs=33.5

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060           93 RTDKPAILDDAIRVLNQLRTESQELKET----NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus        93 K~DKasIL~dAI~yIk~Lr~~vq~L~~~----n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +.+|-.++..=-.-|..|+.+++.++.+    ..+|+..+.+|..++.+-+..++....|.+.|..++..+
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            3444433333333334444444444322    234455555555566665555555566666666666654

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=91.79  E-value=0.59  Score=33.99  Aligned_cols=52  Identities=13%  Similarity=0.058  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      +|..++..|+....-+..-|++|...+.+...+...|+.++..|..+++.+.
T Consensus        11 ~le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L~~rl~~~~   62 (78)
T 3efg_A           11 ELEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR   62 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4566666676666666666777777777777777777777777777776653

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

Probab=91.75  E-value=1  Score=33.81  Aligned_cols=45  Identities=27%  Similarity=0.426  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      ..|+.+++.|+.+-..|..++..|..+..++..+...++.+.++|
T Consensus         7 ~~l~~eL~~l~~eE~~L~~eL~~lEke~~~l~~el~~le~E~~~L   51 (96)
T 3q8t_A            7 EQLQRELKELALEEERLIQELEDVEKNRKVVAENLEKVQAEAERL   51 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            344445555554444444445555554444444444444444444

>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=91.66  E-value=1.4  Score=33.00  Aligned_cols=40  Identities=15%  Similarity=0.272  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          120 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       120 ~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      +...|+.+...|..++..|+.|+..+..|++.+.+.+.++
T Consensus        49 q~~~LE~e~~~L~~e~~~L~~e~~~~~~e~d~~k~k~~~L   88 (90)
T 2wt7_B           49 QKHHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEKL   88 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4566777777777777777777777777777777777655

>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=91.47  E-value=0.96  Score=31.22  Aligned_cols=36  Identities=42%  Similarity=0.469  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          121 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       121 n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      ...|+.++..|..+..+|+.+...|+.|+..|...|
T Consensus        25 ~~~Le~~v~~L~~~n~~L~~ei~~L~~e~~~Lk~~l   60 (63)
T 2wt7_A           25 TDTLQAETDQLEDEKSALQTEIANLLKEKEKLEFIL   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555555555555555555555555555544

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=91.33  E-value=0.98  Score=35.37  Aligned_cols=49  Identities=22%  Similarity=0.164  Sum_probs=35.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           97 PAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  145 (214)
Q Consensus        97 asIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~L  145 (214)
                      -.|..++=.||.+|+.++..|+.+++.-+...+....+...||.++..|
T Consensus        32 e~l~~E~q~~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~l   80 (120)
T 3i00_A           32 ENMKTESQRVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDEL   80 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3578899999999999999999988776655555555555555555444

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

Probab=91.30  E-value=1.3  Score=34.35  Aligned_cols=32  Identities=16%  Similarity=0.410  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNEL  138 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknEL  138 (214)
                      |..|+.++..|...+..|+..+++|.+...+|
T Consensus        37 ~~~Lq~El~~lr~~~~~l~~~iReLEq~NDDL   68 (111)
T 2v66_B           37 VSVLEDDLSQTRAIKEQLHKYVRELEQANDDL   68 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhchHH
Confidence            33334444444444444444444433333333

>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=91.26  E-value=2.2  Score=33.08  Aligned_cols=62  Identities=18%  Similarity=0.248  Sum_probs=41.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060           98 AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus        98 sIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ..+.+|-+....|...-..|+.....+.+.+.+.....++|..++-.|..+++.|..++...
T Consensus        62 ~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~Lk~~led~  123 (129)
T 2fxo_A           62 DNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSELKRDIDDL  123 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35666667777777766677766666666666666666666666667777777777666554

>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=91.24  E-value=1  Score=30.49  Aligned_cols=39  Identities=28%  Similarity=0.448  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      +.+|+.++..|...|+.|.       ..+.+.|++...|+.++++|
T Consensus        11 ~~~l~~~l~~L~~rN~rL~-------~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           11 IHQLEARIDSLAARNSKLM-------ETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHh
Confidence            4455666666666665554       45556666666666676665

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=91.23  E-value=0.62  Score=42.74  Aligned_cols=53  Identities=25%  Similarity=0.322  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      |..|+.++..|+++..+|++++++++.+..++.++........-+|..+++.+
T Consensus         5 ~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~rr~l~n~~~el   57 (403)
T 4etp_A            5 IAALKEKIAALKEKIAALKEKIKDTELGMKELNEILIKEETVRRTLHNELQEL   57 (403)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            45788888888888888888888888888888887777777777787777774

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=91.21  E-value=2.1  Score=33.35  Aligned_cols=16  Identities=38%  Similarity=0.459  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHHh
Q 028060          144 ILKADKEKLEQQLKVM  159 (214)
Q Consensus       144 ~Lk~e~e~L~~qlk~~  159 (214)
                      ++..+|+.|+.||..+
T Consensus        87 kl~~eKe~L~~ql~~L  102 (110)
T 2v4h_A           87 KLVEKKEYLQEQLEQL  102 (110)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHH
Confidence            4455666666665554

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=90.86  E-value=0.27  Score=43.15  Aligned_cols=38  Identities=24%  Similarity=0.338  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          117 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       117 L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      |+.++..|..+.+.|+.+++++++|...||.|+++|.+
T Consensus        59 L~~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~s   96 (251)
T 3m9b_A           59 LEARIDSLAARNSKLMETLKEARQQLLALREEVDRLGQ   96 (251)
T ss_dssp             HHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            33333444444444445555555555555555555443

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=90.85  E-value=0.47  Score=35.36  Aligned_cols=33  Identities=30%  Similarity=0.445  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      .+++.++..|+.+|..|+.+|..|+.|+..|+.
T Consensus        39 ~e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~Lr~   71 (87)
T 1hjb_A           39 LETQHKVLELTAENERLQKKVEQLSRELSTLRN   71 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445666666666776666666666555555443

>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=90.76  E-value=5.4  Score=36.68  Aligned_cols=46  Identities=24%  Similarity=0.444  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          113 ESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       113 ~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +.++++++...++..+++.+....|+++|++.+++|+..|++.+..
T Consensus       538 ~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~~  583 (597)
T 3oja_B          538 ETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKNR  583 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             chhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3444446666777777777777888888887777777777776543

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=90.74  E-value=2.5  Score=32.12  Aligned_cols=52  Identities=21%  Similarity=0.256  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          103 AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       103 AI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      +-+-|.+|+.++...+.+...|..++.+-+...-+...++..+.+|+|.|-.
T Consensus        10 lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLTa   61 (97)
T 2eqb_B           10 LKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTA   61 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444433333344444444444555555443

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A

Probab=90.71  E-value=0.39  Score=33.01  Aligned_cols=30  Identities=20%  Similarity=0.304  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          128 IKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       128 i~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.+|..+..+|..++..|+.++..|+.++.
T Consensus        24 ~~~Le~~v~~L~~~n~~L~~~v~~L~~e~~   53 (62)
T 1jnm_A           24 IARLEEKVKTLKAQNSELASTANMLREQVA   53 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444443

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

Probab=90.57  E-value=2.1  Score=36.03  Aligned_cols=20  Identities=30%  Similarity=0.333  Sum_probs=8.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQ  125 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~  125 (214)
                      -+++|+.++..|..+.+.++
T Consensus        57 ~~~~L~~~~~~L~~E~e~~k   76 (189)
T 2v71_A           57 RNRDLQADNQRLKYEVEALK   76 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444443333

>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=90.51  E-value=0.63  Score=33.35  Aligned_cols=39  Identities=21%  Similarity=0.309  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          120 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       120 ~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      ....|+.++.+|......|..|+..|+.+++.|..+++.
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            445566666666666666777777777777777777654

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=90.36  E-value=1.6  Score=33.24  Aligned_cols=53  Identities=21%  Similarity=0.356  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  160 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  160 (214)
                      ..|+.++.+|+.++.....++..|..++.+-+........++.+++++|..++
T Consensus         8 e~lre~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLT   60 (97)
T 2eqb_B            8 NQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLT   60 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34556666666666666666666665555555555555566666666666553

>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=90.11  E-value=1.5  Score=33.73  Aligned_cols=50  Identities=28%  Similarity=0.460  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      .+.+|+.+...|+......-..+++|..++..|+.||+.|..|.+-..++
T Consensus        45 ~~s~le~e~~rlr~~~~~~~~~v~eLe~everL~~ENq~L~~e~~~~~~~   94 (104)
T 3s9g_A           45 SLSRMEDENNRLRLESKRLDARVRELELELDRLRAENLQLLTENELHRQQ   94 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            34556677767776666677888999999999999999999888877665

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=90.10  E-value=0.31  Score=42.81  Aligned_cols=44  Identities=20%  Similarity=0.271  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 028060          121 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTG  164 (214)
Q Consensus       121 n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p~  164 (214)
                      ...|+.++..|......|.++...++.|+++|+.|++.+..||.
T Consensus        56 l~eL~~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~sPPL   99 (251)
T 3m9b_A           56 IHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLGQPPS   99 (251)
T ss_dssp             HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            45667777777666666788888888888888888888877765

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=90.02  E-value=2.5  Score=35.06  Aligned_cols=75  Identities=19%  Similarity=0.341  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           72 RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  151 (214)
Q Consensus        72 RdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~  151 (214)
                      |+.|-.-+..|.+.|...   +.    -...+-+.|.+|+.+++.|..+.+.+......+..++..|.+....|..++..
T Consensus        64 k~~Leke~~~LQa~L~qE---r~----~r~q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~  136 (168)
T 3o0z_A           64 KSQTDKDYYQLQAILEAE---RR----DRGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNN  136 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHH---HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH---HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444555555555555221   11    12334466667777777777766666666666666666666666666665555


Q ss_pred             HH
Q 028060          152 LE  153 (214)
Q Consensus       152 L~  153 (214)
                      ++
T Consensus       137 ~e  138 (168)
T 3o0z_A          137 LE  138 (168)
T ss_dssp             HH
T ss_pred             hh
Confidence            55

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

Probab=89.94  E-value=0.89  Score=46.70  Aligned_cols=16  Identities=44%  Similarity=0.785  Sum_probs=7.5

Q ss_pred             HHHHHHHHHHHHHHHH
Q 028060          138 LREEKLILKADKEKLE  153 (214)
Q Consensus       138 Lr~Ek~~Lk~e~e~L~  153 (214)
                      |++|++.|+++++.|+
T Consensus      1028 L~~e~~~L~qq~~~l~ 1043 (1080)
T 2dfs_A         1028 LKEQNTLLKTEKEELN 1043 (1080)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4444444444444444

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=89.91  E-value=2  Score=33.05  Aligned_cols=53  Identities=17%  Similarity=0.197  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      |.-|+..+..+++.+.+++.+.++...+...++.....|+.++..|+.||+..
T Consensus        32 VdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~lk~~L~qR   84 (103)
T 4h22_A           32 VDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEVKEALKQR   84 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55667777777788888888888888888888888888888888888888873

>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=89.53  E-value=0.67  Score=32.64  Aligned_cols=36  Identities=31%  Similarity=0.529  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          111 RTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       111 r~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      +.++|+|-+-|..|.+|++-|..+++.|+.|+..|+
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            456777777777888888888888888888877765

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A

Probab=89.18  E-value=1.5  Score=29.61  Aligned_cols=37  Identities=22%  Similarity=0.275  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          123 KLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       123 ~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .|+.++..|......|-+-....+.++++|..+|..+
T Consensus        13 ~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           13 QLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4455555555555556666666666666666666554

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=88.98  E-value=2.1  Score=31.84  Aligned_cols=18  Identities=28%  Similarity=0.383  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 028060          114 SQELKETNEKLQEEIKSL  131 (214)
Q Consensus       114 vq~L~~~n~~L~~ei~eL  131 (214)
                      |..|+.+|..|..+++.+
T Consensus        25 VR~LEqqN~~Le~~i~~l   42 (93)
T 3s4r_A           25 VRFLEQQNKILLAELEQL   42 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            444444555554444443

>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=88.91  E-value=1.2  Score=32.54  Aligned_cols=34  Identities=29%  Similarity=0.374  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  139 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr  139 (214)
                      -..+++.++..|+.+|..|+.++..|+.|+..|+
T Consensus        37 r~~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~Lr   70 (78)
T 1gu4_A           37 RNLETQHKVLELTAENERLQKKVEQLSRELSTLR   70 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455677777788888777777777766666554

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=88.89  E-value=2.7  Score=28.65  Aligned_cols=46  Identities=24%  Similarity=0.315  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      .||-.+|+.|+.+|..|+.|.+.=...++.|..|...+|.=...|+
T Consensus         6 dQL~~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKevlk~lq   51 (54)
T 1deb_A            6 DQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQ   51 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHc
Confidence            4678889999999998888887777777777777776665444443

>3swf_A CGMP-gated cation channel alpha-1; coiled-coil, assembly domain, transport protein; 2.14A {Bos taurus}

Probab=88.88  E-value=1.6  Score=31.71  Aligned_cols=49  Identities=22%  Similarity=0.239  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .+|+++|.+|+...+.|+.....|-+|.+   .-..+||+-+.+|+.+++..
T Consensus         3 ~dlEEKv~~LE~sld~LQTrfARLLaEy~---ssQ~KLKqRit~LE~~~~~~   51 (74)
T 3swf_A            3 MGLEEKVTRMESSVDLLQTRFARILAEYE---SMQQKLKQRLTKVEKFLKPL   51 (74)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhccc
Confidence            35889999999999999998877766655   45678999999999999874

>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=88.67  E-value=3.9  Score=27.26  Aligned_cols=51  Identities=22%  Similarity=0.208  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +..|+..+..++.....+..+...++...+++..+......+|..++.|+.
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            344444444444444444444455555555555555555555555554443

>3swy_A Cyclic nucleotide-gated cation channel alpha-3; coiled-coil, assembly domain, transport protein; 1.90A {Homo sapiens}

Probab=88.66  E-value=2.1  Score=28.45  Aligned_cols=44  Identities=27%  Similarity=0.356  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          109 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      +|++.|.+|+...+.|+.....|-+|.+   .-..+||+-+.+|+.+
T Consensus         2 dlEekv~~Le~~ld~LqTr~ArLlae~~---ssq~KlKqRit~lE~~   45 (46)
T 3swy_A            2 ALEEKVEQLGSSLDTLQTRFARLLAEYN---ATQMKMKQRLSQLESQ   45 (46)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhc
Confidence            5788999999999999988877766555   4567889999999876

>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=88.58  E-value=4.6  Score=31.27  Aligned_cols=55  Identities=20%  Similarity=0.278  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .-+.+.......|......|...+.++...+.+..+.+..|.+++.+|++++..+
T Consensus        62 ~~l~e~EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~L  116 (129)
T 2fxo_A           62 DNLADAEERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSEL  116 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444445555566667777777777777777777777777777777766543

>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=88.58  E-value=3.1  Score=27.74  Aligned_cols=51  Identities=18%  Similarity=0.190  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      ..-+++..+...+..++.+...+...+..+...++..+++...++.+++.+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~l~~~~~~I~~~k~qi~~y   59 (60)
T 3htk_A            9 TLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYY   59 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            344677777778888888888889999999999999999999998888653

>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=88.44  E-value=3  Score=35.36  Aligned_cols=41  Identities=12%  Similarity=0.276  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  140 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~  140 (214)
                      +.=++.-+..|+.++..|..+++.|+.++..|..+..++-.
T Consensus       127 fd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~v~  167 (213)
T 1ik9_A          127 IAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVS  167 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56566665566666666666655555555555555444433

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

Probab=88.20  E-value=2.1  Score=44.04  Aligned_cols=22  Identities=14%  Similarity=0.080  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHh
Q 028060          138 LREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       138 Lr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      |++....|+.|+.+|++|+..+
T Consensus      1021 L~~kv~~L~~e~~~L~qq~~~l 1042 (1080)
T 2dfs_A         1021 TEQLVSELKEQNTLLKTEKEEL 1042 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3344455667777777777654

>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=88.18  E-value=1.9  Score=39.70  Aligned_cols=52  Identities=19%  Similarity=0.243  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ..|+.++..|++..++|++++++++.+..++.++......+.-+|..++..+
T Consensus         6 ~~l~~el~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~rr~l~n~~~~l   57 (412)
T 3u06_A            6 AALSTEVVHLRQRTEELLRCNEQQAAELETCKEQLFQSNMERKELHNTVMDL   57 (412)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5688888888888888888888888888888888777777777788888775

>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=88.18  E-value=0.94  Score=30.69  Aligned_cols=29  Identities=28%  Similarity=0.432  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          128 IKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       128 i~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      ++.|+.|..+|+.+...|+.+++.|..+|
T Consensus        21 ~eaLk~E~~eLk~k~~~L~~~~~el~~~l   49 (53)
T 2yy0_A           21 IELLRLELAEMKEKYEAIVEENKKLKAKL   49 (53)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444443

>1dip_A Delta-sleep-inducing peptide immunoreactive peptide; structure, leucine zipper, PIG, acetylation; NMR {Sus scrofa} SCOP: h.1.12.1

Probab=87.98  E-value=0.052  Score=39.82  Aligned_cols=25  Identities=36%  Similarity=0.587  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      +.|+++|.+|....++|..||..||
T Consensus        18 evLKe~I~EL~e~~~qLE~EN~~Lk   42 (78)
T 1dip_A           18 EILKEQIRELVEKNSQLERENTLLK   42 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555554

>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=87.61  E-value=0.76  Score=32.00  Aligned_cols=32  Identities=28%  Similarity=0.391  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEK  135 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~ek  135 (214)
                      ..|+.+|+.++..|+.+|..|..++..|+.++
T Consensus        29 ~~~~~~Le~~v~~L~~eN~~L~~ev~~Lr~~l   60 (63)
T 2dgc_A           29 LQRMKQLEDKVEELLSKNYHLENEVARLKKLV   60 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36888888888888888888777777766554

>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=87.54  E-value=1  Score=32.29  Aligned_cols=32  Identities=22%  Similarity=0.338  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          128 IKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       128 i~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      |+.|..+..+|..|+..|+.+++.|+++|.++
T Consensus        49 I~~L~~~~~~l~~e~~~L~~~~~~L~~~l~~L   80 (83)
T 1nkp_B           49 IQYMRRKNHTHQQDIDDLKRQNALLEQQVRAL   80 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34444455555555555555666666666554

>3mq7_A Bone marrow stromal antigen 2; HIV, antiviral protein; 2.28A {Homo sapiens} PDB: 3mqc_A 3mqb_A 3mkx_A 3nwh_A 2xg7_A* 2x7a_A

Probab=87.34  E-value=4  Score=32.17  Aligned_cols=34  Identities=24%  Similarity=0.304  Sum_probs=16.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          121 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       121 n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      .+.|+.||+.|++++.+...|..+|+.+++.|..
T Consensus        73 vqeLqgEI~~Lnq~Lq~a~ae~erlr~~~~~~~~  106 (121)
T 3mq7_A           73 VEELEGEITTLNHKLQDASAEVERLRRENQVLSV  106 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhchhhhh
Confidence            4444445555555444444444444444444433

>1kd8_A GABH AIV, GCN4 acid base heterodimer acid-D12IA16V; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kdd_A 1kd9_A

Probab=86.94  E-value=1.2  Score=28.32  Aligned_cols=26  Identities=27%  Similarity=0.413  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQEEIKSLKA  133 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~~ei~eL~~  133 (214)
                      +||+.+|++|..++..|+.++..|+.
T Consensus         4 nQLE~kVEeLl~~~~~Le~EV~RL~~   29 (36)
T 1kd8_A            4 KQLEAEVEEIESEVWHLENEVARLEK   29 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            45555555555555444444444433

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=86.84  E-value=2.7  Score=28.40  Aligned_cols=32  Identities=22%  Similarity=0.264  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          125 QEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       125 ~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +.-+.+|..++..|..||..|+.+++.|++++
T Consensus        21 k~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~~   52 (55)
T 1dh3_A           21 KEYVKSLENRVAVLENQNKTLIEELKALKDLY   52 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45567777778888888888888888877644

>1kd8_B GABH BLL, GCN4 acid base heterodimer base-D12LA16L; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kd9_B 1kdd_B

Probab=86.83  E-value=1.7  Score=27.51  Aligned_cols=26  Identities=31%  Similarity=0.465  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLK  132 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~  132 (214)
                      ++||+.+|++|..++..|+.++..|+
T Consensus         3 MnQLE~KVEeLl~~~~~Le~eV~RLk   28 (36)
T 1kd8_B            3 VKQLKAKVEELKSKLWHLKNKVARLK   28 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            34555555555554444444443333

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=86.78  E-value=6.8  Score=30.15  Aligned_cols=58  Identities=24%  Similarity=0.356  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA-----------EKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~-----------eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.+.-+-|..|+.+++.++..+..|+..+.++..           .+.+|..+...++.+.++.-++++
T Consensus        38 i~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~e~~~ql~EYq  106 (129)
T 3tnu_B           38 ISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAELEEALQKAKQDMARLLREYQ  106 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            3444455566666666666666666555544432           333444455555555554444433

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=86.72  E-value=5.1  Score=32.72  Aligned_cols=79  Identities=24%  Similarity=0.206  Sum_probs=41.1

Q ss_pred             HHHHHHHHhhhcCCCCCC--CCChhhHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           75 LNDRFLDLSCILEPGRPA--RTDKPAILDDAIRVLNQLRTESQELK-------ETNEKLQEEIKSLKAEKNELREEKLIL  145 (214)
Q Consensus        75 LN~~F~~LrslLPP~~~~--K~DKasIL~dAI~yIk~Lr~~vq~L~-------~~n~~L~~ei~eL~~eknELr~Ek~~L  145 (214)
                      +++.|.++....++...+  ++... .+..--.-+..|+.++..|+       ..++.|+.|+..|..+.|.+.+....|
T Consensus        44 ~~~l~~e~~~~~~~~~vs~~~~~~~-~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~kL  122 (152)
T 3a7p_A           44 LNELFQDNSGAIGGNIVSHDDALLN-TLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSDL  122 (152)
T ss_dssp             -------------CHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccCCCcccccchhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666555430000  11111 33333344455555555555       556788899999999999999999999


Q ss_pred             HHHHHHHHH
Q 028060          146 KADKEKLEQ  154 (214)
Q Consensus       146 k~e~e~L~~  154 (214)
                      +.|...|-+
T Consensus       123 q~EN~~LV~  131 (152)
T 3a7p_A          123 KKEHSQLVA  131 (152)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988877643

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.65  E-value=1.2  Score=41.12  Aligned_cols=44  Identities=18%  Similarity=0.318  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 028060          120 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPT  163 (214)
Q Consensus       120 ~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p  163 (214)
                      ....|+.+++.|..+.+.++++...++.|..+++.+++.+..+|
T Consensus        50 ~lk~le~~~~~L~~e~e~l~~~~~~~~~e~~~~~ee~~~l~~~~   93 (428)
T 4b4t_K           50 KLKKLEKEYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVP   93 (428)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            33445555566666667777777778888888888888776554

>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=86.44  E-value=3.1  Score=40.12  Aligned_cols=51  Identities=18%  Similarity=0.145  Sum_probs=36.2

Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           99 ILDDAIRVLN-QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  149 (214)
Q Consensus        99 IL~dAI~yIk-~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~  149 (214)
                      =+..++.-|. +|+.+++-|+++...--..|+.|+.-+.+++.+.++|..+|
T Consensus       103 dNdNtynE~S~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDI  154 (562)
T 3ghg_A          103 NRDNTYNRVSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDI  154 (562)
T ss_dssp             HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444444 88888888888766555778888888888888888887444

>1m1j_C Fibrinogen gamma chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_C

Probab=86.39  E-value=5.4  Score=36.97  Aligned_cols=59  Identities=15%  Similarity=0.112  Sum_probs=42.5

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           96 KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus        96 KasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      +......++++++.+..++.+|+.......++|+.|...++.++...+.|+..+..|+.
T Consensus        75 ~~d~~e~~tq~skkml~~~~~~e~~~~~~~~~i~~l~~~~~~~~~~i~~l~~~i~~l~~  133 (409)
T 1m1j_C           75 LPQSIEQLTQKSKKIIEEIIRYENTILAHENTIQQLTDMHIMNSNKITQLKQKIAQLES  133 (409)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            34445666899999999999998877777777888877777766655666555555544

>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=86.38  E-value=1.3  Score=33.78  Aligned_cols=37  Identities=35%  Similarity=0.452  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028060          126 EEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  162 (214)
Q Consensus       126 ~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  162 (214)
                      +++..|+.++.+|+.|+..|+.+++.|+-+|.....+
T Consensus        12 e~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~l~   48 (100)
T 1go4_E           12 EEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQ   48 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3556666677777777777777777777777665443

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=86.36  E-value=5.7  Score=29.10  Aligned_cols=39  Identities=13%  Similarity=0.189  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  148 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e  148 (214)
                      |..+++.|+.+...|+-.++++.-+++++..+...+..+
T Consensus        25 Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~rQrd~Y~d   63 (83)
T 2xdj_A           25 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQ   63 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444443333333333

>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=85.90  E-value=0.97  Score=28.22  Aligned_cols=15  Identities=33%  Similarity=0.351  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHHHHHH
Q 028060          109 QLRTESQELKETNEK  123 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~  123 (214)
                      ||+.+|++|-.+|..
T Consensus         4 QLE~kVEeLl~~n~~   18 (33)
T 3m48_A            4 QLEAKVEELLSKNWN   18 (33)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHH
Confidence            333333333333333

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

Probab=85.78  E-value=3.9  Score=34.36  Aligned_cols=28  Identities=25%  Similarity=0.319  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNE  137 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknE  137 (214)
                      |..++..++..+..|+.....|+.+..+
T Consensus        47 LE~eL~~~Ek~~~~L~~~~~~L~~E~e~   74 (189)
T 2v71_A           47 LEAQLVQAEQRNRDLQADNQRLKYEVEA   74 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333444444444444444444333

>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=85.76  E-value=3.5  Score=30.91  Aligned_cols=38  Identities=29%  Similarity=0.440  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          115 QELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       115 q~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      ..|+.++..|+.+++.|+.|..++..|...+|+..+.|
T Consensus        51 ~~LE~e~~~L~~e~~~L~~e~~~~~~e~d~~k~k~~~L   88 (90)
T 2wt7_B           51 HHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEKL   88 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44445555555555555555555555555555544443

>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=85.12  E-value=5.2  Score=32.65  Aligned_cols=23  Identities=13%  Similarity=0.120  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 028060          100 LDDAIRVLNQLRTESQELKETNE  122 (214)
Q Consensus       100 L~dAI~yIk~Lr~~vq~L~~~n~  122 (214)
                      |-.||++...|...+..+..+++
T Consensus         8 LI~Ain~qs~LeD~L~~~R~el~   30 (154)
T 2ocy_A            8 LIESVDKQSHLEEQLNKSLKTIA   30 (154)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHH
Confidence            44566666666665555555444

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

Probab=84.99  E-value=4.8  Score=34.18  Aligned_cols=51  Identities=14%  Similarity=0.167  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      |..|+.++..++.....++.++.+++.++..+..+...+++.+++.+.++.
T Consensus        34 l~~le~~~~~l~~~~~~~~~~l~d~~~~~~~~e~~i~~~~~ri~~~~~~l~   84 (256)
T 3na7_A           34 LDKALNDKEAKNKAILNLEEEKLALKLQVSKNEQTLQDTNAKIASIQKKMS   84 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444444444444444444444444444444444444444444555554444

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=84.96  E-value=18  Score=32.53  Aligned_cols=37  Identities=14%  Similarity=0.068  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          121 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       121 n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      .+..+++++.|+.+++.++.+...+..+++...+.++
T Consensus       437 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  473 (487)
T 3oja_A          437 WDMYQHKETQLAEENARLKKLNGEADLALASANATLQ  473 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhcccHHH
Confidence            3344444444444444444444444444444444443

>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=84.38  E-value=2  Score=26.92  Aligned_cols=18  Identities=33%  Similarity=0.374  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQ  125 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~  125 (214)
                      .||+.+|++|-.+|..|+
T Consensus         4 nQLE~kVEeLl~~n~~Le   21 (34)
T 2oxj_A            4 XQLEXKVXELLXKNXHLE   21 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhHH
Confidence            344444444433333333

>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor 1 (RF-1), structural joint center for structural genomics, JCSG; 2.34A {Streptococcus mutans}

Probab=84.33  E-value=3.9  Score=37.61  Aligned_cols=88  Identities=19%  Similarity=0.333  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHhhhc-CCCCCCCCCh-------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHH
Q 028060           71 RRERLNDRFLDLSCIL-EPGRPARTDK-------PAILDDAIRVLNQLRTESQELKETNEKLQE-E-IKSLKAEKNELRE  140 (214)
Q Consensus        71 RRdkLN~~F~~LrslL-PP~~~~K~DK-------asIL~dAI~yIk~Lr~~vq~L~~~n~~L~~-e-i~eL~~eknELr~  140 (214)
                      +-+.+.++|.+|...+ .|+.....++       .+-|...++.+..++...+.++.-.+-+.+ + -.+   -+.+..+
T Consensus        18 ~l~~~~~r~~el~~~l~~p~~~~d~~~~~~~~ke~~~l~~~v~~~~~~~~~~~d~~~~~el~~~~e~D~e---~~~~a~~   94 (371)
T 1zbt_A           18 QLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAVYREYKQVVQNIADAQEMIKDASGDPE---LEEMAKE   94 (371)
T ss_dssp             HHHHHHHHHHHC--------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CH---HHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhcCCcchhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHH---HHHHHHH
Confidence            4556788999998877 2322112223       345666666666666665555544433322 1 111   1234577


Q ss_pred             HHHHHHHHHHHHHHHHHHhcC
Q 028060          141 EKLILKADKEKLEQQLKVMAM  161 (214)
Q Consensus       141 Ek~~Lk~e~e~L~~qlk~~~~  161 (214)
                      |...|+.+++.|+.+|+.+-.
T Consensus        95 e~~~l~~~l~~le~~l~~lLl  115 (371)
T 1zbt_A           95 ELKNSKVAKEEYEEKLRFLLL  115 (371)
T ss_dssp             HHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHHHHHHHhcC
Confidence            788999999999999997643

>3v86_A De novo design helix; computational design of A protein crystal, helical coil, DE designed helix, de novo protein; 2.91A {Synthetic}

Probab=84.25  E-value=1  Score=26.42  Aligned_cols=25  Identities=36%  Similarity=0.489  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          106 VLNQLRTESQELKETNEKLQEEIKS  130 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei~e  130 (214)
                      |+-||+.++-+|+-+...|..+++.
T Consensus         1 yvyqlkdevgelkgevralkdevkd   25 (27)
T 3v86_A            1 YVYQLKDEVGELKGEVRALKDEVKD   25 (27)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchhhHHHHHHHhHHHHHHHHHhc
Confidence            3445555555555444444444433

>3iv1_A Tumor susceptibility gene 101 protein; coiled_COIL, tumorigenesis, CELL_cycle regulation, alternative splicing, cell cycle, cell division; HET: MSE; 2.50A {Homo sapiens}

Probab=84.23  E-value=10  Score=27.74  Aligned_cols=43  Identities=30%  Similarity=0.484  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      |+..-+.|.+-...|..-+..|..|.+++......|+...+.|
T Consensus        30 LrrT~~EL~~G~~KL~~mi~~l~~E~~~l~~ni~~lk~K~~EL   72 (78)
T 3iv1_A           30 LKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEEL   72 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444445555555444444444444433

>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=84.18  E-value=2  Score=26.94  Aligned_cols=25  Identities=24%  Similarity=0.356  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      .+|+.++++|-.++.+|.+|..+|+
T Consensus         4 nQLE~kVEeLl~~n~~Le~eV~rLk   28 (34)
T 2oxj_A            4 XQLEXKVXELLXKNXHLEXEVXRLK   28 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            4555666666666666655555543

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=84.17  E-value=2.3  Score=33.42  Aligned_cols=41  Identities=5%  Similarity=0.081  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  162 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  162 (214)
                      ..|.+.+.+|..++.+|+.-...|...++.+++.+..-...
T Consensus        98 ~~l~~~~~~l~~~i~~L~~~~~~L~~~i~~~~~~~~~~~~~  138 (148)
T 3gpv_A           98 KLMKQQEANVLQLIQDTEKNLKKIQQKIAKYEDEISSANAT  138 (148)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence            34455555555566666555556666666666655544333

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=84.13  E-value=6.2  Score=35.68  Aligned_cols=47  Identities=15%  Similarity=0.121  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          113 ESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       113 ~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      ..++++.+.+......+....+.+.|++|+.+++.+++.+..++...
T Consensus       422 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  468 (487)
T 3oja_A          422 MYVEQQSVQNNAIRDWDMYQHKETQLAEENARLKKLNGEADLALASA  468 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcchhhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhc
Confidence            33444444455556666677777888888888888888888877654

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

Probab=83.93  E-value=11  Score=29.12  Aligned_cols=22  Identities=32%  Similarity=0.448  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEI  128 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei  128 (214)
                      +++|+..+..|..+++.++.+.
T Consensus         5 ~rdL~~~~~~L~~E~e~~k~K~   26 (111)
T 2v66_B            5 NRDLQADNQRLKYEVEALKEKL   26 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555555555554444443

>3mq7_A Bone marrow stromal antigen 2; HIV, antiviral protein; 2.28A {Homo sapiens} PDB: 3mqc_A 3mqb_A 3mkx_A 3nwh_A 2xg7_A* 2x7a_A

Probab=83.90  E-value=12  Score=29.44  Aligned_cols=34  Identities=24%  Similarity=0.332  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          125 QEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       125 ~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +.++++|.-|+..|.++.....+++|+|..+...
T Consensus        70 q~~vqeLqgEI~~Lnq~Lq~a~ae~erlr~~~~~  103 (121)
T 3mq7_A           70 QKKVEELEGEITTLNHKLQDASAEVERLRRENQV  103 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchh
Confidence            4445555555555555555555666666555443

>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=83.87  E-value=2.8  Score=37.73  Aligned_cols=54  Identities=11%  Similarity=0.083  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          104 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       104 I~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.=++.|..++.+|+.......++|+.|+..+..++...+.|+.++..|+..+.
T Consensus         4 ~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l~~~~~   57 (323)
T 1lwu_C            4 QKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQTCS   57 (323)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344556666666666666666666777776666666666666666666665443

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

Probab=83.87  E-value=11  Score=27.80  Aligned_cols=42  Identities=17%  Similarity=0.391  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      +.+++.+.+..|..++.+.++....       +..|..|+++|+.+++.
T Consensus        29 i~EELs~vr~~ni~~eskL~eae~r-------n~eL~~e~~~l~~~~ee   70 (81)
T 1wt6_A           29 LSREMEAIRTDNQNFASQLREAEAR-------NRDLEAHVRQLQERMEL   70 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444       44444455555555444

>1gk6_A Vimentin; intermediate filament, dimer, parallel coiled coil, heptad repeat, leucine zipper, fusion protein; 1.9A {Saccharomyces cerevisiae} SCOP: h.1.20.1

Probab=83.85  E-value=3  Score=28.47  Aligned_cols=50  Identities=26%  Similarity=0.354  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      +++++..+..|+.+...++.++.....+..+|.+=|..|..||.--..-|
T Consensus         2 l~~~q~~i~~le~el~~~r~e~~~q~~eYq~LlniK~~Le~EIatYRkLL   51 (59)
T 1gk6_A            2 MKQLEDKVEELLSKNYHLENEVARLKKLVGDLLNVKMALDIEIATYRKLL   51 (59)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            34677788888888888888888888899999999999988887654433

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

Probab=83.33  E-value=12  Score=27.87  Aligned_cols=41  Identities=15%  Similarity=0.324  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  142 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek  142 (214)
                      .|++-..+++.++..++..+.++..++..|...+..+.++.
T Consensus        20 ~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~el   60 (101)
T 3u1c_A           20 NALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSR   60 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555555555555555544444444443

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=83.13  E-value=3.4  Score=29.88  Aligned_cols=44  Identities=20%  Similarity=0.141  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          114 SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       114 vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      +.+|+.......++++.....+.+|..+......++..|+.+|.
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLD   64 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELD   64 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444555555555555555555555553

>2d4y_A HAP1, flagellar HOOK-associated protein 1; multi-domain protein, alpha-helical bundle, complex all- beta folds, structural protein; 2.10A {Salmonella typhimurium}

Probab=83.05  E-value=5.4  Score=36.56  Aligned_cols=78  Identities=19%  Similarity=0.300  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHhhhc-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           73 ERLNDRFLDLSCIL-EPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  151 (214)
Q Consensus        73 dkLN~~F~~LrslL-PP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~  151 (214)
                      ..|++-|..|..+- -|.  .-.-+..+|..|-.....++.--+.|+.....+..+|+..-.++|.|-.+.+.|..+|-+
T Consensus        44 ~~l~~ff~alq~la~~P~--~~~~R~~vl~~a~~La~~~n~~~~~L~~~~~~~n~~i~~~V~~iN~l~~qIa~LN~qI~~  121 (463)
T 2d4y_A           44 GSLQSFFTSLQTLVSNAE--DPAARQALIGKAEGLVNQFKTTDQYLRDQDKQVNIAIGSSVAQINNYAKQIANLNDQISR  121 (463)
T ss_dssp             HHHHHHHHHHHHHHHTTT--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46888899998888 222  235678899999988888888888888877778888888888888887777777766654


Q ss_pred             H
Q 028060          152 L  152 (214)
Q Consensus       152 L  152 (214)
                      .
T Consensus       122 ~  122 (463)
T 2d4y_A          122 M  122 (463)
T ss_dssp             H
T ss_pred             h
Confidence            3

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=82.74  E-value=12  Score=27.60  Aligned_cols=43  Identities=19%  Similarity=0.264  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          102 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI  144 (214)
Q Consensus       102 dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~  144 (214)
                      .|++-..+++.++..++..+..+.+++..|...+.-+.++...
T Consensus        20 ~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~   62 (101)
T 3u59_A           20 NAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEK   62 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            4555555666666666655555555555555555544444433

>2v4h_A NF-kappa-B essential modulator; transcription, metal-binding, NEMO - IKK gamma - NFKB pathwa darpin, transcription regulation; 2.9A {Mus musculus}

Probab=82.70  E-value=12  Score=29.04  Aligned_cols=22  Identities=27%  Similarity=0.412  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028060          137 ELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       137 ELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      .+..||..|+.+++.|+.|+..
T Consensus        87 kl~~eKe~L~~ql~~Lq~q~~~  108 (110)
T 2v4h_A           87 KLVEKKEYLQEQLEQLQREFNK  108 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHhHHHHHHHHHHHHHHHHHh
Confidence            4667777888888888777654

>3c3g_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-beta) backbone; helix bundle, foldamer, unknown function protein; HET: HMR B3Q B3D B3E B3L BIL B3K BAL GOL; 1.80A {Synthetic} PDB: 3heu_A* 3het_A* 3hev_A* 3hew_A* 3hey_A* 3hex_A* 3c3h_A*

Probab=82.64  E-value=2.5  Score=26.30  Aligned_cols=17  Identities=6%  Similarity=0.073  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 028060          109 QLRTESQELKETNEKLQ  125 (214)
Q Consensus       109 ~Lr~~vq~L~~~n~~L~  125 (214)
                      ||+.+|++|-.+|..|+
T Consensus         4 QLEdKvEeLl~~~~~Le   20 (33)
T 3c3g_A            4 XIEXKLXEIXSKXYHXE   20 (33)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHH
Confidence            44444444433333333

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

Probab=82.54  E-value=7.8  Score=32.87  Aligned_cols=15  Identities=20%  Similarity=0.266  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHHHHHH
Q 028060          141 EKLILKADKEKLEQQ  155 (214)
Q Consensus       141 Ek~~Lk~e~e~L~~q  155 (214)
                      |...++.++..|+.+
T Consensus        98 Eie~~~~~i~~lE~e  112 (256)
T 3na7_A           98 EEDIAKERSNQANRE  112 (256)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            333333333333333

>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=82.47  E-value=6.5  Score=26.60  Aligned_cols=35  Identities=6%  Similarity=0.287  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREE  141 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~E  141 (214)
                      |.+|-.+|+.|..+..+|..++..|+.+...-.+|
T Consensus         6 i~~Lss~V~~L~~kVdqLssdV~al~~~v~~ak~e   40 (52)
T 1jcd_A            6 ADQASSDAQTANAKADQASNDANAARSDAQAAKDD   40 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555544444444433333

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}

Probab=82.25  E-value=5  Score=26.92  Aligned_cols=40  Identities=25%  Similarity=0.248  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          112 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  158 (214)
Q Consensus       112 ~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~  158 (214)
                      .++.+|++.|..|-.++.       +|...-..+.+||++|..-|+.
T Consensus         4 q~l~kLKe~n~~L~~kv~-------~Le~~c~~~eQEieRL~~LLkq   43 (48)
T 3vmx_A            4 RQILRLKQINIQLATKIQ-------HLEFSCSEKEQEIERLNKLLKQ   43 (48)
T ss_dssp             HHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH-------HHHHHccHHHHHHHHHHHHHHH
Confidence            355667777776655554       4444445556788888777764

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=82.11  E-value=5.2  Score=28.89  Aligned_cols=44  Identities=14%  Similarity=0.139  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          116 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       116 ~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      .|+.....|+.++.....-+.+|-+.......+|++|+.+++.+
T Consensus        11 ~le~Ri~~LE~klAfqE~tIeeLn~~v~~Qq~~Id~L~~ql~~L   54 (78)
T 3efg_A           11 ELEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHL   54 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555555555555555555555555555555554

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=82.01  E-value=10  Score=29.30  Aligned_cols=56  Identities=18%  Similarity=0.258  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHH
Q 028060          101 DDAIRVLNQLRTESQELKETNEKLQEEIKSLKA-----------EKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       101 ~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~-----------eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      .+.-+-|..|+.+++.++..+..|+..+.++..           .+.+|..+...++.+.++.-+++
T Consensus        41 ~elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~em~~ql~EY  107 (131)
T 3tnu_A           41 SELRRTMQNLEIELQSQLSMKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEY  107 (131)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334445555666666665555555554443333           33344444444554444443333

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

Probab=81.90  E-value=9.5  Score=27.89  Aligned_cols=51  Identities=31%  Similarity=0.388  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          107 LNQLRTESQELKETNEKL-------QEEIKSLKAEKNELREEKLILKADKEKLEQQLK  157 (214)
Q Consensus       107 Ik~Lr~~vq~L~~~n~~L-------~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk  157 (214)
                      |..|-.+..+|......|       -.++++|.-|+.-|+.|...+++-+.+++..++
T Consensus        11 vEnLi~EN~eLl~TKNaLnvvk~DLI~rvdELt~E~e~l~~El~s~~~~~~r~~~ri~   68 (77)
T 2w83_C           11 VENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNR   68 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444433333       334444444444444444444444444444433

>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=81.68  E-value=2.4  Score=26.42  Aligned_cols=24  Identities=25%  Similarity=0.382  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          131 LKAEKNELREEKLILKADKEKLEQ  154 (214)
Q Consensus       131 L~~eknELr~Ek~~Lk~e~e~L~~  154 (214)
                      |.....||..+|..|+.|++||..
T Consensus         5 LE~kVEeLl~~n~~Le~EV~RLk~   28 (33)
T 3m48_A            5 LEAKVEELLSKNWNLENEVARLKK   28 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHH
Confidence            344445555555555666666554

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

Probab=81.65  E-value=11  Score=28.06  Aligned_cols=27  Identities=26%  Similarity=0.367  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSL  131 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL  131 (214)
                      .-|..|..+...+..+...++.+...|
T Consensus        25 ~eL~~lEke~~~l~~el~~le~E~~~L   51 (96)
T 3q8t_A           25 QELEDVEKNRKVVAENLEKVQAEAERL   51 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444333

>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=81.44  E-value=3.7  Score=30.05  Aligned_cols=32  Identities=31%  Similarity=0.323  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          121 NEKLQEEIKSLKAEKNELREEKLILKADKEKL  152 (214)
Q Consensus       121 n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L  152 (214)
                      ...|+.+...+..++++|+.++..|+.+++.|
T Consensus        54 I~~L~~~~~~l~~~~~~L~~~n~~L~~rl~~L   85 (88)
T 1nkp_A           54 ILSVQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33444444455555556666666666555544

>2wq1_A General control protein GCN4; TAA, nucleus, coiled coil, DNA-binding, protein export, ION coordination, polar core residues; 1.08A {Saccharomyces cerevisiae} PDB: 2wq0_A 2wq2_A 2wq3_A 2wpz_A 2wpy_A 1ij0_A 1ij1_A 1gcm_A 1rb5_A 1rb6_A 1rb1_A 1rb4_A 1swi_A 3k7z_A 1zii_A 1zij_A 1ij2_A 1ij3_A 1zil_A 1zim_A ...

Probab=81.44  E-value=3  Score=25.98  Aligned_cols=20  Identities=15%  Similarity=0.157  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 028060          124 LQEEIKSLKAEKNELREEKL  143 (214)
Q Consensus       124 L~~ei~eL~~eknELr~Ek~  143 (214)
                      |+.++++|..++.+|.+|..
T Consensus         5 LEdKVEell~~~~~le~EV~   24 (33)
T 2wq1_A            5 LEDKIEENTSKIYHNTNEIA   24 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHH
Confidence            33444444444444443333

>3c3g_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-beta) backbone; helix bundle, foldamer, unknown function protein; HET: HMR B3Q B3D B3E B3L BIL B3K BAL GOL; 1.80A {Synthetic} PDB: 3heu_A* 3het_A* 3hev_A* 3hew_A* 3hey_A* 3hex_A* 3c3h_A*

Probab=81.26  E-value=3.1  Score=25.89  Aligned_cols=25  Identities=4%  Similarity=0.181  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      .+|+.++++|-.++.+|.+|..+||
T Consensus         3 nQLEdKvEeLl~~~~~Le~EV~RLk   27 (33)
T 3c3g_A            3 KXIEXKLXEIXSKXYHXENXLARIK   27 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            3555666666666666655555554

>1uix_A RHO-associated kinase; coiled-coil, transferase; HET: MSE; 1.80A {Bos taurus} SCOP: h.1.27.1

Probab=81.05  E-value=11  Score=27.01  Aligned_cols=47  Identities=23%  Similarity=0.402  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          110 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  156 (214)
Q Consensus       110 Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~ql  156 (214)
                      |...++.|..+++.|..+++.+..+...+++|-....+.+..|+.+|
T Consensus         2 ~~k~v~~l~~E~eel~~klk~~~ee~~~~~eee~~~~~~k~~lek~L   48 (71)
T 1uix_A            2 STSDVANLANEKEELNNKLKEAQEQLSRLKDEEISAAAIKAQFEKQL   48 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555555555555555555555555444444333333443333

>3c3f_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-alpha-beta) backbone...; helix bundle, foldamer, unknown function, de novo protein; HET: B3K B3D B3E BIL B3L BAL; 2.00A {Synthetic} SCOP: h.1.3.1

Probab=80.89  E-value=3.2  Score=26.00  Aligned_cols=18  Identities=6%  Similarity=-0.056  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q 028060          108 NQLRTESQELKETNEKLQ  125 (214)
Q Consensus       108 k~Lr~~vq~L~~~n~~L~  125 (214)
                      +||+.+|++|-.++..|+
T Consensus         4 nQLEdKVEeLl~~~~~Le   21 (34)
T 3c3f_A            4 XQIEXKLEXILSXLYHXE   21 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhHHH
Confidence            344444444333333333

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=80.65  E-value=15  Score=26.98  Aligned_cols=40  Identities=23%  Similarity=0.341  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAM  161 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~  161 (214)
                      ..|...++.+..++..|......+..+.+.|+.+|..+-.
T Consensus        73 ~~L~~~~e~ie~~i~~le~~~~~l~~~l~~lk~~l~~~~~  112 (117)
T 2zqm_A           73 AELKEKIETLEVRLNALERQEKKLNEKLKELTAQIQSALR  112 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3444445555555555555555556666666666666533

>1kd8_B GABH BLL, GCN4 acid base heterodimer base-D12LA16L; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kd9_B 1kdd_B

Probab=80.45  E-value=3.2  Score=26.27  Aligned_cols=25  Identities=24%  Similarity=0.385  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          122 EKLQEEIKSLKAEKNELREEKLILK  146 (214)
Q Consensus       122 ~~L~~ei~eL~~eknELr~Ek~~Lk  146 (214)
                      .+|+.++++|..++.+|.+|-.+|+
T Consensus         4 nQLE~KVEeLl~~~~~Le~eV~RLk   28 (36)
T 1kd8_B            4 KQLKAKVEELKSKLWHLKNKVARLK   28 (36)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            3455555555555555555444443

>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein, ribosomal protein, RNA-binding, binding, metal-binding, zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y 3d5c_X 3mr8_V 3ms0_V

Probab=80.33  E-value=15  Score=33.53  Aligned_cols=92  Identities=23%  Similarity=0.333  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHhhhcC-CCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH-HHHHHHHHHHHHH
Q 028060           71 RRERLNDRFLDLSCILE-PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSL-KAE-KNELREEKLILKA  147 (214)
Q Consensus        71 RRdkLN~~F~~LrslLP-P~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL-~~e-knELr~Ek~~Lk~  147 (214)
                      |=+.+.++|.+|...+- |+.....+++.-|.+-...|+.+-.....++...+.+.+-.+-+ -.+ +.+..+|...|+.
T Consensus         4 ~l~~~~~r~~el~~~~~~p~~~~d~~~~~~~~ke~~~l~~~v~~~~~~~~~~~~~~~~~el~~D~e~~~~a~~e~~~l~~   83 (354)
T 3d5a_X            4 KLDRLEEEYRELEALLSDPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLEDLEQAESLLDDPELKEMAKAEREALLA   83 (354)
T ss_dssp             HHHHHTHHHHHHHHHTTSTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCchhhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence            33567789999998772 32222334444444443333333333333333333332211111 122 2345778888999


Q ss_pred             HHHHHHHHHHHhcCC
Q 028060          148 DKEKLEQQLKVMAMP  162 (214)
Q Consensus       148 e~e~L~~qlk~~~~~  162 (214)
                      +++.|+.+|+.+-.|
T Consensus        84 ~~~~le~~l~~lLlp   98 (354)
T 3d5a_X           84 RKEALEKELERHLLP   98 (354)
T ss_dssp             HHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHhcCC
Confidence            999999999887444

>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=80.11  E-value=8.9  Score=32.42  Aligned_cols=49  Identities=24%  Similarity=0.213  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  153 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknELr~Ek~~Lk~e~e~L~  153 (214)
                      +++..+-..+..++.++..|.++...|..+.++|..+...+-.+++.+|
T Consensus       125 elfd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~v~~K~~~E  173 (213)
T 1ik9_A          125 ELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALE  173 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444444444444444444444444444443333

---

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	214
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	8e-16
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-13
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	3e-12
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-11
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	5e-11
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	5e-08
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	5e-06
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	3e-04

>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 = 67.6 bits (165), Expect = 8e-16
 Identities = 14/73 (19%), Positives = 32/73 (43%)

Query: 67  REKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 126
            E+ RR+ + D F  L   +   +  +  +  ILD A   +  +R ++   ++  + L+ 
Sbjct: 9   LERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR 68

Query: 127 EIKSLKAEKNELR 139
           +   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 = 61.8 bits (150), Expect = 2e-13
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 67  REKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQ 125
            E+ RR  L   F  L   I E     +  K  IL  A   +  ++ E Q+L    + L+
Sbjct: 13  LERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR 72

Query: 126 EEIKSLKAEKNELR 139
           +  + 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 = 58.0 bits (140), Expect = 3e-12
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 67  REKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 126
            EK  R  +ND+ ++L   L  G  A+ +K A+L  AI  +  L+  +Q+LK+ N  L+ 
Sbjct: 13  IEKRYRSSINDKIIELKD-LVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT 71

Query: 127 EIKSLKAEK 135
            +   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 = 56.1 bits (135), Expect = 1e-11
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 67  REKLRRERLNDRFLDLSCILEPGRPA-RTDKPAILDDAIRVLNQLRTESQELKETNEKLQ 125
            EK RR  L      L  ++  G  + R    ++L  A   + +L    ++     ++LQ
Sbjct: 8   MEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ 67

Query: 126 EEIKSLKAEKNE 137
            E + 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 = 54.4 bits (131), Expect = 5e-11
 Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 72  RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSL 131
           R  +ND+ ++L  ++  G  A+  K  +L  AI  +  L+  + +L++ N  L+   +  
Sbjct: 1   RSSINDKIIELKDLV-MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKN 59

Query: 132 K 132
           K
Sbjct: 60  K 60

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.0 bits (109), Expect = 5e-08
 Identities = 15/67 (22%), Positives = 29/67 (43%)

Query: 50  RKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ 109
             + ++ +  R  +   RE+ R  ++N+ F  L          R  K  IL +AIR +  
Sbjct: 2   ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEG 61

Query: 110 LRTESQE 116
           L+   ++
Sbjct: 62  LQALLRD 68

>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 = 40.5 bits (95), Expect = 5e-06
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 67  REKLRRERLNDRFLDLSCIL----EPGRPARTDKPAILDDAIRVLNQLRTESQ 115
            E+ RR+++N+  + LS I+         +   K  IL  A   + +LR  + 
Sbjct: 12  VERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

>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 = 36.0 bits (83), Expect = 3e-04
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 5/50 (10%)

Query: 67  REKLRRERLNDRFLDL-----SCILEPGRPARTDKPAILDDAIRVLNQLR 111
            E+ RR RL     +L     +   +    A   K   ++ A R +  L+
Sbjct: 9   AEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 58

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	214
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.76
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.74
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.73
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.59
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.56
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.49
d1lrza1	65	Methicillin resistance protein FemA probable tRNA-	85.15
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	84.16

>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=99.76  E-value=3.8e-19  Score=129.66  Aligned_cols=79  Identities=18%  Similarity=0.313  Sum_probs=66.7

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL  138 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknEL  138 (214)
                      ++.+|+.+||+||++||+.|.+|+++||+....|++|++||..||+||++|+.+++.|..+.+.|..+...|..++++|
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~L   80 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRAL   80 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3578999999999999999999999998655568999999999999999999999888877777666666666555543

>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=99.75  E-value=1.7e-18  Score=125.07  Aligned_cols=76  Identities=21%  Similarity=0.257  Sum_probs=66.8

Q ss_pred             CCchhHHHHHHHHHHHHHHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           61 PGSKACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN  136 (214)
Q Consensus        61 ~~sH~~~ERkRRdkLN~~F~~LrslLPP~~-~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~ekn  136 (214)
                      +.+|+..||+||++||++|.+|+++||++. ..|.+|++||..||+||++|+.+++.|..+.+.|..+...|+.++.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~~~~L~~~l~   78 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQRHLKRQLE   78 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            457999999999999999999999998643 4589999999999999999999999998888888877777766554

>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=99.74  E-value=1.5e-18  Score=127.72  Aligned_cols=79  Identities=22%  Similarity=0.300  Sum_probs=67.9

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL  138 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~-~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~~eknEL  138 (214)
                      ++.+|+.+||+||++||++|..|+++||+. ...|.+|++||..||+||++|+.+++.|..+.+.|..+...|..++++|
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~L   85 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            356899999999999999999999999763 2357999999999999999999999999888877777777776666655

>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=99.73  E-value=3.4e-18  Score=124.20  Aligned_cols=72  Identities=26%  Similarity=0.393  Sum_probs=63.4

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLK  132 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei~eL~  132 (214)
                      ++.+|+..||+||++||++|.+|+++||+ ...|+||++||..||+||++|+.+++.|..++..|+.++..++
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~llP~-~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~~~~~~   77 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLVVG-TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKSK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTC-SSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            35789999999999999999999999965 4569999999999999999999999999888888777665543

>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=99.59  E-value=5e-16  Score=108.17  Aligned_cols=55  Identities=22%  Similarity=0.358  Sum_probs=49.4

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCC-----CCCCCCChhhHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEP-----GRPARTDKPAILDDAIRVLNQLRTES  114 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP-----~~~~K~DKasIL~dAI~yIk~Lr~~v  114 (214)
                      ++.+|+.+||+||++||++|.+|+++||+     +...|.||++||..||+||++|+.++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            47889999999999999999999999974     33469999999999999999998764

>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=99.56  E-value=3e-16  Score=111.16  Aligned_cols=57  Identities=26%  Similarity=0.334  Sum_probs=51.2

Q ss_pred             CCCCchhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHH
Q 028060           59 SRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ  115 (214)
Q Consensus        59 ~~~~sH~~~ERkRRdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq  115 (214)
                      .++.+|+.+||+||++||++|..|+++||+....|.||++||..||+||++|+..++
T Consensus        11 ~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            456789999999999999999999999987655689999999999999999987653

>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=99.54  E-value=3.2e-15  Score=103.65  Aligned_cols=56  Identities=23%  Similarity=0.386  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060           72 RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEI  128 (214)
Q Consensus        72 RdkLN~~F~~LrslLPP~~~~K~DKasIL~dAI~yIk~Lr~~vq~L~~~n~~L~~ei  128 (214)
                      |++||++|.+|+++||. ...|+|||+||.+||+||++|+.+++.|++++..|+.+.
T Consensus         1 R~~in~~f~~L~~lvP~-~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   56 (61)
T d1uklc_           1 RSSINDKIIELKDLVMG-TDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLAN   56 (61)
T ss_dssp             CCCHHHHHHHHHHHHSC-SSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999965 346999999999999999999999999999888887654

>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=99.49  E-value=4.7e-15  Score=103.75  Aligned_cols=55  Identities=25%  Similarity=0.390  Sum_probs=48.8

Q ss_pred             CCCchhHHHHHHHHHHHHHHHHHhhhcCCC----CCCCCChhhHHHHHHHHHHHHHHHH
Q 028060           60 RPGSKACREKLRRERLNDRFLDLSCILEPG----RPARTDKPAILDDAIRVLNQLRTES  114 (214)
Q Consensus        60 ~~~sH~~~ERkRRdkLN~~F~~LrslLPP~----~~~K~DKasIL~dAI~yIk~Lr~~v  114 (214)
                      ++.+|+.+||+||++||++|.+|+++||..    ...|.+|++||..||+||++|+++.
T Consensus         5 rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            467899999999999999999999999753    2358999999999999999998654

>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=85.15  E-value=3.7  Score=27.21  Aligned_cols=51  Identities=16%  Similarity=0.210  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028060          105 RVLNQLRTESQELKETNEKLQEEI------KSLKAEKNELREEKLILKADKEKLEQQ  155 (214)
Q Consensus       105 ~yIk~Lr~~vq~L~~~n~~L~~ei------~eL~~eknELr~Ek~~Lk~e~e~L~~q  155 (214)
                      +||..|+.+...|......+...+      +--+..+.+|.+...++..-|+..++.
T Consensus         3 eYl~~L~~~~~~L~~~i~k~~~~leknP~skK~~nk~~el~~Q~~s~~~ki~Ea~~l   59 (65)
T d1lrza1           3 EYIKELNEERDILNKDLNKALKDIEKRPENKKAHNKRDNLQQQLDANEQKIEEGKRL   59 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999888887665      334556666777776666666655543

>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=84.16  E-value=4.1  Score=28.48  Aligned_cols=54  Identities=20%  Similarity=0.329  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028060          106 VLNQLRTESQELKETNEKLQEEI--------KSLKAEKNELREEKLILKADKEKLEQQLKVM  159 (214)
Q Consensus       106 yIk~Lr~~vq~L~~~n~~L~~ei--------~eL~~eknELr~Ek~~Lk~e~e~L~~qlk~~  159 (214)
                      -.++|+.+++.|+.+...+..++        .+|..+..+|.++...|..+...++.++..+
T Consensus        36 ~rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~   97 (110)
T d1seta1          36 EVQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEAL   97 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445555555655544444333        4455555555555556666666666666553