Citrus Sinensis ID: 028999

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
Protein Sequence
MPLIEFNFCVNAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccEEcccccccccccccccccccccccccccccccHcHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHcccccccccccccccccHHHcccccccccccccccccccc
Coil and Loop (DISEMBL)
mpliefnfcvnakisgsadndisstgvvppenentrkrarsdscsrpgskaCREKLRRERLndrfldlscilepgrpartdkpaILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMamptggympthpaayhAGLNkmavypsyglmpmwqylppslhdtsrdhelrppaa
Flexible Loop (DISEMBL)
MPLIEFNFCVNAkisgsadndisstgvvppenentrkrarsdscsrpgskacreklrrerlndrfldlscilepgrpartdkpaiLDDAIRVLNQLRTesqelketnekLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDhelrppaa
Low Complexity Region (SEG)
MPLIEFNFCVNAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA
Disordered region (IsUnstruct)
***IEFNFCVNAKI************************************************DRFLDLSCILE***********ILDDAIRVL**************************************************VMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLP*****************
Disordered Region (DISOPRED)
*P**********************************************************LNDRFLDLSCILEP****RTDKPAILDDAIRVLNQLR********************************************************************************************SRDH*LRPPA*
Disordered Region (DISEMBL)
MPLIEFNFCVNAKISGSADNDISSTGVV************************REKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLH*************
Disordered Region (DISPRO)
***IEFNFC******************************************CREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPP**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPLIEFNFCVNAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	200	2.2.26 [Sep-21-2011]
Q8L467	283	Transcription factor bHLH	yes	no	0.895	0.632	0.684	4e-66
Q9LTC7	320	Transcription factor bHLH	no	no	0.895	0.559	0.638	6e-59
Q9FH37	234	Transcription factor ILR3	no	no	0.92	0.786	0.505	5e-46
Q9C682	226	Transcription factor bHLH	no	no	0.985	0.871	0.446	3e-42
Q9LT23	337	Transcription factor bHLH	no	no	0.55	0.326	0.439	4e-16
Q8W2F2	286	Transcription factor bHLH	no	no	0.56	0.391	0.398	9e-13
Q9SN74	240	Transcription factor bHLH	no	no	0.63	0.525	0.307	8e-08
Q9FIP9	592	Transcription factor ATR2	no	no	0.47	0.158	0.326	2e-05
Q9CAD0	596	Transcription factor EGL1	no	no	0.425	0.142	0.370	0.0001
O49687	589	Transcription factor MYC4	no	no	0.455	0.154	0.333	0.0002

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

 Score =  250 bits (639), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 128/187 (68%), Positives = 151/187 (80%), Gaps = 8/187 (4%)

Query: 20  NDISSTGVVPPENEN-----TRKRARSDSCSRPG-SKACREKLRRERLNDRFLDLSCILE 73
           N  SS G V  E E+     +RKRAR+ SCSR G +KACRE+LRRE+LN+RF+DLS +LE
Sbjct: 99  NSGSSGGAVKEEQEHLDDDCSRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSSVLE 158

Query: 74  PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKA 133
           PGR  +TDKPAILDDAIR+LNQLR E+ +L+ETN+KL EEIKSLKAEKNELREEKL+LKA
Sbjct: 159 PGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLVLKA 218

Query: 134 DKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDH 193
           DKEK EQQLK M  P+ G++P  PAA++   NKMAVYPSYG MPMW Y+P S+ DTSRD 
Sbjct: 219 DKEKTEQQLKSMTAPSSGFIPHIPAAFNH--NKMAVYPSYGYMPMWHYMPQSVRDTSRDQ 276

Query: 194 ELRPPAA 200
           ELRPPAA
Sbjct: 277 ELRPPAA 283

Arabidopsis thaliana (taxid: 3702)

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

 Score =  226 bits (577), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 120/188 (63%), Positives = 146/188 (77%), Gaps = 9/188 (4%)

Query: 20  NDISSTGVVPPENEN--TRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRP 77
           N  SS G V  E E   + KR R+ SCS+PG+KACREKLRRE+LND+F+DLS +LEPGR 
Sbjct: 135 NSSSSVGAVKEEFEEECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSVLEPGRT 194

Query: 78  ARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK 137
            +TDK AILDDAIRV+NQLR E+ EL+ETN+KL EEIKSLKA+KNELREEKL+LKA+KEK
Sbjct: 195 PKTDKSAILDDAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVLKAEKEK 254

Query: 138 LEQQLKVMAMPTGGYMPT-HPAAYHAGLNKMAVYPSYGL----MPMWQYLPPSLHDTSRD 192
           +EQQLK M +P+ G+MP+ HPAA+H+  +KMAV   YG     MPMW  LPP+  DTSRD
Sbjct: 255 MEQQLKSMVVPSPGFMPSQHPAAFHS--HKMAVAYPYGYYPPNMPMWSPLPPADRDTSRD 312

Query: 193 HELRPPAA 200
            +  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 =  183 bits (465), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 100/198 (50%), Positives = 129/198 (65%), Gaps = 14/198 (7%)

Query: 11  NAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSC 70
           +A + GSA N  +S      +   ++KR R +S S   SKACREK RR+RLND+F++L  
Sbjct: 43  SAGVDGSAGNSEAS------KEPGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGA 96

Query: 71  ILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI 130
           ILEPG P +TDK AIL DA+R++ QLR E+Q+LK++N  LQ++IK LK EKNELR+EK  
Sbjct: 97  ILEPGNPPKTDKAAILVDAVRMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQR 156

Query: 131 LKADKEKLEQQLKVMAMPTGGYMPTHP--------AAYHAGLNKMAVYPSYGLMPMWQYL 182
           LK +KEKLEQQLK M  P   + P  P        A   A  NKM    SY  + MWQ++
Sbjct: 157 LKTEKEKLEQQLKAMNAPQPSFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFM 216

Query: 183 PPSLHDTSRDHELRPPAA 200
           PP+  DTS+DH LRPP A
Sbjct: 217 PPASVDTSQDHVLRPPVA 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 =  171 bits (432), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 91/204 (44%), Positives = 132/204 (64%), Gaps = 7/204 (3%)

Query: 2   PLIEFNFCVNAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERL 61
           P   +    +A +S   D  +    V+  +  ++RKR +++SC+   SKACREK RR+RL
Sbjct: 25  PTFPWQIDGSATVSVEVDGFLCDADVI--KEPSSRKRIKTESCTGSNSKACREKQRRDRL 82

Query: 62  NDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEK 121
           ND+F +LS +LEPGR  +TDK AI++DAIR++NQ R E+Q+LK+ N  LQE+IK LK EK
Sbjct: 83  NDKFTELSSVLEPGRTPKTDKVAIINDAIRMVNQARDEAQKLKDLNSSLQEKIKELKDEK 142

Query: 122 NELREEKLILKADKEKLEQQLKVMA---MPTGGYMPTHPAAYHAGL--NKMAVYPSYGLM 176
           NELR+EK  LK +KE+++QQLK +     P   ++P       A    +K+  + +Y   
Sbjct: 143 NELRDEKQKLKVEKERIDQQLKAIKTQPQPQPCFLPNPQTLSQAQAPGSKLVPFTTYPGF 202

Query: 177 PMWQYLPPSLHDTSRDHELRPPAA 200
            MWQ++PP+  DTS+DH LRPP A
Sbjct: 203 AMWQFMPPAAVDTSQDHVLRPPVA 226

Arabidopsis thaliana (taxid: 3702)

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

 Score = 84.3 bits (207), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 51/116 (43%), Positives = 73/116 (62%), Gaps = 6/116 (5%)

Query: 42  DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 101
           D  +R   KA REKLRRE+LN+ F++L  +L+P RP + DK  IL D +++L +L +E  
Sbjct: 55  DVSARKSQKAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVN 113

Query: 102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL----EQQLKVMAMPTGGYM 153
           +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 = 73.6 bits (179), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 47/118 (39%), Positives = 71/118 (60%), Gaps = 6/118 (5%)

Query: 44  CSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQEL 103
           CS+   KA REKLRR++L ++FL+L   L+P RP ++DK ++L D I++L  +  +   L
Sbjct: 46  CSQ---KAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQVDRL 101

Query: 104 KETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYH 161
           K   E L +E + L  EK+ELREEK  LK+D E L  Q +        ++P +  +YH
Sbjct: 102 KAEYETLSQESRELIQEKSELREEKATLKSDIEILNAQYQHRIKTMVPWVPHY--SYH 157

Arabidopsis thaliana (taxid: 3702)

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

 Score = 57.0 bits (136), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 39/127 (30%), Positives = 69/127 (54%), Gaps = 1/127 (0%)

Query: 32  NENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIR 91
           N    +R R     +  +KA RE+L+RE LN+ F++L+  LE  +   + K +IL +A R
Sbjct: 14  NATADERCRKGKVPKRINKAVRERLKREHLNELFIELADTLELNQ-QNSGKASILCEATR 72

Query: 92  VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGG 151
            L  +  + + L++ +  L  E   +  EKNEL+EE  +L+ +  KL+ +++  A  +  
Sbjct: 73  FLKDVFGQIESLRKEHASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEARANQSKP 132

Query: 152 YMPTHPA 158
            + 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 = 49.3 bits (116), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 32/98 (32%), Positives = 56/98 (57%), Gaps = 4/98 (4%)

Query: 27  VVPPENENTRKRARSDSCSR--PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPA 84
           VV P  +  RKR R  +  R  P +    E+ RRE+LN RF  L  ++ P   ++ DK +
Sbjct: 391 VVEPPEKKPRKRGRKPANGREEPLNHVEAERQRREKLNQRFYSLRAVV-P-NVSKMDKAS 448

Query: 85  ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN 122
           +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|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: 42  DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 101
           D+    G+ A  EK RRE+LN+RF+ L  I+     ++ DK +ILDD I  L  L+   Q
Sbjct: 398 DTPEETGNHALSEKKRREKLNERFMTLRSIIPS--ISKIDKVSILDDTIEYLQDLQKRVQ 455

Query: 102 ELKETNEKLQEE--IKSLKAEKNELREEK 128
           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)

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

 Score = 45.8 bits (107), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 55/96 (57%), Gaps = 5/96 (5%)

Query: 27  VVPPENENTRKRARSDSCSR--PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPA 84
           VV PE +  RKR R  +  R  P +    E+ RRE+LN RF  L  ++     ++ DK +
Sbjct: 393 VVEPEKK-PRKRGRKPANGREEPLNHVEAERQRREKLNQRFYSLRAVVP--NVSKMDKAS 449

Query: 85  ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE 120
           +L DAI  +++L+++ Q+ +   E+LQ++I  +  E
Sbjct: 450 LLGDAISYISELKSKLQKAESDKEELQKQIDVMNKE 485

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	200
224107875	221	predicted protein [Populus trichocarpa]	0.93	0.841	0.759	2e-76
357439557	246	Transcription factor bHLH104 [Medicago t	0.945	0.768	0.706	2e-69
359477721	219	PREDICTED: transcription factor bHLH104-	0.96	0.876	0.663	9e-69
449432566	226	PREDICTED: transcription factor bHLH104-	0.915	0.809	0.688	4e-68
296083619	248	unnamed protein product [Vitis vinifera]	0.93	0.75	0.679	4e-68
313474112	219	bHLH transcriptional factor [Coptis japo	0.955	0.872	0.652	2e-66
356534540	218	PREDICTED: transcription factor bHLH104-	0.92	0.844	0.682	2e-66
356575261	220	PREDICTED: transcription factor bHLH104-	0.93	0.845	0.678	6e-66
255637294	220	unknown [Glycine max]	0.93	0.845	0.668	6e-65
255576818	219	DNA binding protein, putative [Ricinus c	0.885	0.808	0.758	6e-65

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

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 142/187 (75%), Positives = 159/187 (85%), Gaps = 1/187 (0%)

Query: 15  SGSADNDISST-GVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILE 73
            G  D D SS+ GVV    E +RKR RSD CSR G+KACREKLRRERLNDRF DLS +LE
Sbjct: 35  GGVVDIDFSSSVGVVTQVKECSRKRERSDLCSRAGTKACREKLRRERLNDRFQDLSSVLE 94

Query: 74  PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKA 133
           PGRPA+TDKPAILDDAIRVLNQL+ E+QELKETNEKL EEI+SLKAEK ELREEKL+LKA
Sbjct: 95  PGRPAKTDKPAILDDAIRVLNQLKNEAQELKETNEKLLEEIRSLKAEKTELREEKLMLKA 154

Query: 134 DKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDH 193
           DKEK+EQQLK +A+PT G+MPT+PAAYHA  NK+ V+P YGLMPMW YLPP+  DTSRDH
Sbjct: 155 DKEKMEQQLKTLALPTSGFMPTYPAAYHAAANKIPVFPGYGLMPMWHYLPPTACDTSRDH 214

Query: 194 ELRPPAA 200
           ELRPPAA
Sbjct: 215 ELRPPAA 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 135/191 (70%), Positives = 157/191 (82%), Gaps = 2/191 (1%)

Query: 11  NAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSC 70
           N + S S + DI S  VV  E ENTRKR R++SC + G+KACREKLRRE+LN+RF DLS 
Sbjct: 57  NTRKSVSTETDIPSGAVVCQE-ENTRKRGRTESCYKAGTKACREKLRREKLNERFCDLSA 115

Query: 71  ILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI 130
           +LEPGRP RTDKPAILDDAIRVL+QL+TE+QELKE+NEKL EEIK LKAEKNELREEKL+
Sbjct: 116 VLEPGRPVRTDKPAILDDAIRVLSQLKTEAQELKESNEKLLEEIKCLKAEKNELREEKLV 175

Query: 131 LKADKEKLEQQLKVMAMPTGGYMPTHP-AAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDT 189
           LKADKEK+E+QLK M +   G+MP  P AAY A +NKMAVYP+YG +PMW YLP S  DT
Sbjct: 176 LKADKEKIEKQLKSMPVSPAGFMPPPPMAAYQASVNKMAVYPNYGYIPMWHYLPQSARDT 235

Query: 190 SRDHELRPPAA 200
           S+DHELRPPAA
Sbjct: 236 SQDHELRPPAA 246

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  265 bits (677), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 128/193 (66%), Positives = 153/193 (79%), Gaps = 1/193 (0%)

Query: 9   CVNAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDL 68
            +N       D D+S       ENE  +KR R+DS +RPG+KACREKLRRERLNDRFLDL
Sbjct: 27  WINDGYLAGVDIDLSRICAASQENEGRQKRGRNDSSTRPGTKACREKLRRERLNDRFLDL 86

Query: 69  SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK 128
           S ILEPG+ A+TDK AIL DAIRVLNQLR E+++L++ NEKLQEEI+SLKAEKNELREEK
Sbjct: 87  SSILEPGKSAKTDKLAILGDAIRVLNQLRNEAKDLEDANEKLQEEIRSLKAEKNELREEK 146

Query: 129 LILKADKEKLEQQLKVMAMPTGGYMPTHPAA-YHAGLNKMAVYPSYGLMPMWQYLPPSLH 187
           L+LKADKE++EQQ+K ++ P  G+ PT+PAA +H G NK AV+PSYGL PMWQY+P S  
Sbjct: 147 LLLKADKERIEQQMKAISAPAAGFWPTYPAATHHTGANKSAVFPSYGLFPMWQYIPSSAL 206

Query: 188 DTSRDHELRPPAA 200
           DTS DHELRPPAA
Sbjct: 207 DTSHDHELRPPAA 219

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 126/183 (68%), Positives = 155/183 (84%)

Query: 18  ADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRP 77
           AD D+S+  +   EN+ +RKRAR  SC+   SKACRE+LRRE+LNDRFLDLS  LEP R 
Sbjct: 44  ADTDVSAGHLESEENDCSRKRARDGSCAGASSKACRERLRREKLNDRFLDLSIALEPSRH 103

Query: 78  ARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK 137
            +T+KPAILDDAIRVLNQL+ E++ELK+TNEKL+EE++SLKAEKN+LR+EK+ILK DKEK
Sbjct: 104 TKTNKPAILDDAIRVLNQLKNEAEELKQTNEKLREEVESLKAEKNDLRKEKIILKEDKEK 163

Query: 138 LEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRP 197
           +EQQLK +A+P+ G +P HPAAYHA   KMAV+P YGL+PMWQYLPPS+ DTS+DHELRP
Sbjct: 164 MEQQLKSIAIPSPGLIPGHPAAYHAASGKMAVFPGYGLIPMWQYLPPSIRDTSQDHELRP 223

Query: 198 PAA 200
           PAA
Sbjct: 224 PAA 226

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  263 bits (671), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 127/187 (67%), Positives = 151/187 (80%), Gaps = 1/187 (0%)

Query: 15  SGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEP 74
               D D+S       ENE  +KR R+DS +RPG+KACREKLRRERLNDRFLDLS ILEP
Sbjct: 62  GAGVDIDLSRICAASQENEGRQKRGRNDSSTRPGTKACREKLRRERLNDRFLDLSSILEP 121

Query: 75  GRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD 134
           G+ A+TDK AIL DAIRVLNQLR E+++L++ NEKLQEEI+SLKAEKNELREEKL+LKAD
Sbjct: 122 GKSAKTDKLAILGDAIRVLNQLRNEAKDLEDANEKLQEEIRSLKAEKNELREEKLLLKAD 181

Query: 135 KEKLEQQLKVMAMPTGGYMPTHPAA-YHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDH 193
           KE++EQQ+K ++ P  G+ PT+PAA +H G NK AV+PSYGL PMWQY+P S  DTS DH
Sbjct: 182 KERIEQQMKAISAPAAGFWPTYPAATHHTGANKSAVFPSYGLFPMWQYIPSSALDTSHDH 241

Query: 194 ELRPPAA 200
           ELRPPAA
Sbjct: 242 ELRPPAA 248

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  257 bits (656), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 126/193 (65%), Positives = 150/193 (77%), Gaps = 2/193 (1%)

Query: 8   FCVNAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLD 67
           +C N   S   + D+S+ G  P E    +KR R++SC   GSKACREK+RR++LNDRF D
Sbjct: 29  WCSNQ--SACTELDVSAAGAGPVEKGCAKKRGRNESCGGLGSKACREKMRRDKLNDRFAD 86

Query: 68  LSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREE 127
           LS  LEPGRPA+TDK AIL DAIRVLNQLRTESQELKE NEKLQE+IK+LKAEKNELREE
Sbjct: 87  LSSALEPGRPAKTDKSAILSDAIRVLNQLRTESQELKEANEKLQEDIKNLKAEKNELREE 146

Query: 128 KLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLH 187
           K +LKADKE++EQQ+K MA+  GG +P HPA Y AG+NK   +PSYG  PMWQY+PP+  
Sbjct: 147 KNLLKADKERIEQQMKAMAIVPGGIVPPHPATYQAGVNKFMAFPSYGGYPMWQYIPPASL 206

Query: 188 DTSRDHELRPPAA 200
           DTS+DH LRPP A
Sbjct: 207 DTSQDHVLRPPVA 219

Source: Coptis japonica

Species: Coptis japonica

Genus: Coptis

Family: Ranunculaceae

Order: Ranunculales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  256 bits (655), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 127/186 (68%), Positives = 150/186 (80%), Gaps = 2/186 (1%)

Query: 17  SADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGR 76
           S + ++   G      ENT+KR  +DS  + GSKACREKLRRERLN+RF DLS +LEPGR
Sbjct: 33  SVNTEVDIPGDAAACQENTKKRGHADSSCQVGSKACREKLRRERLNERFCDLSSVLEPGR 92

Query: 77  PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE 136
           P RTDKPAILDDAIRVL+QL+TE+QELK+TNEKL EEIK LKAEKNELREEKL+LKADKE
Sbjct: 93  PVRTDKPAILDDAIRVLSQLKTEAQELKKTNEKLLEEIKCLKAEKNELREEKLVLKADKE 152

Query: 137 KLEQQLKVMAMPTGGYM--PTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHE 194
           ++E+QLK + +   GYM  P   AAY AG+NKMA+YP+YG +PMWQYLP S+ DTS DHE
Sbjct: 153 RIEKQLKALPVAPAGYMTPPVAAAAYQAGVNKMALYPNYGYIPMWQYLPQSVRDTSHDHE 212

Query: 195 LRPPAA 200
           LRPPAA
Sbjct: 213 LRPPAA 218

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  255 bits (652), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 129/190 (67%), Positives = 151/190 (79%), Gaps = 4/190 (2%)

Query: 15  SGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEP 74
           + S   +I   G      ENT+KR R+DSC + GSKACREKLRRERLN+RF DLS +LEP
Sbjct: 31  NNSVSTEIDIPGDAVACQENTKKRGRTDSCFKAGSKACREKLRRERLNERFCDLSSVLEP 90

Query: 75  GRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD 134
           GRP RTDKPAILDDAIRVL+QL+TE+QELK+TNEKL EEIK LKAEKNELREEKL+LKAD
Sbjct: 91  GRPVRTDKPAILDDAIRVLSQLKTEAQELKKTNEKLLEEIKCLKAEKNELREEKLVLKAD 150

Query: 135 KEKLEQQLKVMAMPTGGYM----PTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTS 190
           KE++E+QLK + +   G+M        AAY AG+NKMAVYP+YG +PMWQYLP S+ DTS
Sbjct: 151 KERIEKQLKALPVAPAGFMAPPVAAAAAAYQAGVNKMAVYPNYGYIPMWQYLPQSVRDTS 210

Query: 191 RDHELRPPAA 200
            DHELRPPAA
Sbjct: 211 HDHELRPPAA 220

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  252 bits (644), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 127/190 (66%), Positives = 149/190 (78%), Gaps = 4/190 (2%)

Query: 15  SGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEP 74
           + S   +I   G      ENT+KR R+DSC + GSKACREKLRRERLN+RF DLS +LEP
Sbjct: 31  NNSVSTEIDIPGDAVACQENTKKRGRTDSCFKAGSKACREKLRRERLNERFCDLSSVLEP 90

Query: 75  GRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD 134
           GRP RTDKPAILDDAIRVL+QL+TE+QELK+TNEKL EEIK LKAEKNELREEKL+LKAD
Sbjct: 91  GRPVRTDKPAILDDAIRVLSQLKTEAQELKKTNEKLLEEIKCLKAEKNELREEKLVLKAD 150

Query: 135 KEKLEQQLKVMAMPTGGYM----PTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTS 190
           KE++E+QLK + +   G+M        AAY AG+NKMAVYP+YG +PMWQY P  + DTS
Sbjct: 151 KERIEKQLKALPVAPAGFMAPPVAAAAAAYQAGVNKMAVYPNYGYIPMWQYFPQFVRDTS 210

Query: 191 RDHELRPPAA 200
            DHELRPPAA
Sbjct: 211 HDHELRPPAA 220

Source: Glycine max

Species: Glycine max

Genus: Glycine

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 =  252 bits (643), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 135/178 (75%), Positives = 153/178 (85%), Gaps = 1/178 (0%)

Query: 23  SSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDK 82
           SS G V  E + +RKRAR DSCS+P +KACREKLRRERLNDRF DLS +LEP RPARTDK
Sbjct: 43  SSGGAVSEEKQCSRKRARGDSCSKPVTKACREKLRRERLNDRFQDLSSVLEPERPARTDK 102

Query: 83  PAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 142
           P++LDDAIRVLNQL+TE+QELKETNEKL EEIK LKAEKNELREEKL LKADKE+ EQQL
Sbjct: 103 PSLLDDAIRVLNQLKTEAQELKETNEKLLEEIKCLKAEKNELREEKLTLKADKERTEQQL 162

Query: 143 KVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDHELRPPAA 200
           K+MA+   GYMP HPAAYHA +NKMA+YPS+GL+PMWQ LPP+  DTS+DHE  PPAA
Sbjct: 163 KIMAVRPPGYMPAHPAAYHAAMNKMAIYPSFGLIPMWQ-LPPAAQDTSKDHEYWPPAA 219

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	200
TAIR|locus:2129710	283	bHLH104 "AT4G14410" [Arabidops	0.895	0.632	0.684	1.3e-61
TAIR|locus:2086198	320	bHLH34 "AT3G23210" [Arabidopsi	0.915	0.571	0.635	3.3e-56
TAIR|locus:2157538	234	ILR3 "AT5G54680" [Arabidopsis	0.92	0.786	0.505	1.7e-43
UNIPROTKB|Q6ZKI8	253	OJ1119_D01.9 "BHLH transcripti	0.935	0.739	0.471	7.5e-41
UNIPROTKB|Q6ZGM4	236	OJ1442_E05.19 "cDNA clone:006-	0.82	0.694	0.511	1.1e-39
TAIR|locus:2092216	337	bHLH121 "AT3G19860" [Arabidops	0.66	0.391	0.408	5.5e-18
UNIPROTKB|Q67U21	343	OSJNBa0065F08.2 "Basic helix-l	0.64	0.373	0.385	1.4e-17
TAIR|locus:2135169	286	bHLH11 "AT4G36060" [Arabidopsi	0.56	0.391	0.398	2.6e-15
UNIPROTKB|Q69V10	265	P0506F02.119 "cDNA clone:J0230	0.785	0.592	0.282	2.2e-12
TAIR|locus:2079102	240	PYE "AT3G47640" [Arabidopsis t	0.645	0.537	0.312	3.9e-12

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

 Score = 630 (226.8 bits), Expect = 1.3e-61, P = 1.3e-61
 Identities = 128/187 (68%), Positives = 151/187 (80%)

Query:    20 NDISSTGVVPPENEN-----TRKRARSDSCSRPG-SKACREKLRRERLNDRFLDLSCILE 73
             N  SS G V  E E+     +RKRAR+ SCSR G +KACRE+LRRE+LN+RF+DLS +LE
Sbjct:    99 NSGSSGGAVKEEQEHLDDDCSRKRARTGSCSRGGGTKACRERLRREKLNERFMDLSSVLE 158

Query:    74 PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKA 133
             PGR  +TDKPAILDDAIR+LNQLR E+ +L+ETN+KL EEIKSLKAEKNELREEKL+LKA
Sbjct:   159 PGRTPKTDKPAILDDAIRILNQLRDEALKLEETNQKLLEEIKSLKAEKNELREEKLVLKA 218

Query:   134 DKEKLEQQLKVMAMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLPPSLHDTSRDH 193
             DKEK EQQLK M  P+ G++P  PAA++   NKMAVYPSYG MPMW Y+P S+ DTSRD 
Sbjct:   219 DKEKTEQQLKSMTAPSSGFIPHIPAAFNH--NKMAVYPSYGYMPMWHYMPQSVRDTSRDQ 276

Query:   194 ELRPPAA 200
             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 = 579 (208.9 bits), Expect = 3.3e-56, P = 3.3e-56
 Identities = 124/195 (63%), Positives = 151/195 (77%)

Query:    15 SGSAD-NDISSTGVVPPENEN--TRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCI 71
             SG  + N  SS G V  E E   + KR R+ SCS+PG+KACREKLRRE+LND+F+DLS +
Sbjct:   129 SGVVEINSSSSVGAVKEEFEEECSGKRRRTGSCSKPGTKACREKLRREKLNDKFMDLSSV 188

Query:    72 LEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL 131
             LEPGR  +TDK AILDDAIRV+NQLR E+ EL+ETN+KL EEIKSLKA+KNELREEKL+L
Sbjct:   189 LEPGRTPKTDKSAILDDAIRVVNQLRGEAHELQETNQKLLEEIKSLKADKNELREEKLVL 248

Query:   132 KADKEKLEQQLKVMAMPTGGYMPT-HPAAYHAGLNKMAV-YPSYGL----MPMWQYLPPS 185
             KA+KEK+EQQLK M +P+ G+MP+ HPAA+H+  +KMAV YP YG     MPMW  LPP+
Sbjct:   249 KAEKEKMEQQLKSMVVPSPGFMPSQHPAAFHS--HKMAVAYP-YGYYPPNMPMWSPLPPA 305

Query:   186 LHDTSRDHELRPPAA 200
               DTSRD +  PP A
Sbjct:   306 DRDTSRDLKNLPPVA 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 = 459 (166.6 bits), Expect = 1.7e-43, P = 1.7e-43
 Identities = 100/198 (50%), Positives = 130/198 (65%)

Query:    11 NAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSC 70
             +A + GSA N  +S      +   ++KR R +S S   SKACREK RR+RLND+F++L  
Sbjct:    43 SAGVDGSAGNSEAS------KEPGSKKRGRCESSSATSSKACREKQRRDRLNDKFMELGA 96

Query:    71 ILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI 130
             ILEPG P +TDK AIL DA+R++ QLR E+Q+LK++N  LQ++IK LK EKNELR+EK  
Sbjct:    97 ILEPGNPPKTDKAAILVDAVRMVTQLRGEAQKLKDSNSSLQDKIKELKTEKNELRDEKQR 156

Query:   131 LKADKEKLEQQLKVMAMPTGGYMPTHP---AAY-----HAGLNKMAVYPSYGLMPMWQYL 182
             LK +KEKLEQQLK M  P   + P  P    A+      A  NKM    SY  + MWQ++
Sbjct:   157 LKTEKEKLEQQLKAMNAPQPSFFPAPPMMPTAFASAQGQAPGNKMVPIISYPGVAMWQFM 216

Query:   183 PPSLHDTSRDHELRPPAA 200
             PP+  DTS+DH LRPP A
Sbjct:   217 PPASVDTSQDHVLRPPVA 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 = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 99/210 (47%), Positives = 133/210 (63%)

Query:     9 CVNAKISGSADNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDL 68
             C N  +  S+   +++T  V  E   + KR RS SC RP SKA REK+RR+++NDRFL+L
Sbjct:    49 CSNPSVEVSSY--VNTTSYVLKE-PGSNKRVRSGSCGRPTSKASREKIRRDKMNDRFLEL 105

Query:    69 SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK 128
                LEPG+P ++DK AIL DA R++ QLR E+++LK+TNE L+++IK LKAEK+ELR+EK
Sbjct:   106 GTTLEPGKPVKSDKAAILSDATRMVIQLRAEAKQLKDTNESLEDKIKELKAEKDELRDEK 165

Query:   129 LILKADKEKLEQQLKVMAMPTGGYMPTHP------------AAYH------AGLNKMAVY 170
               LK +KE LEQQ+K++   T  YMP HP            A +H      AG   M  +
Sbjct:   166 QKLKVEKETLEQQVKILTA-TPAYMP-HPTLMPAPYPQAPLAPFHHAQGQAAGQKLMMPF 223

Query:   171 PSYGLMPMWQYLPPSLHDTSRDHELRPPAA 200
               Y   PMWQ++PPS  DTS+D E  PP A
Sbjct:   224 VGYPGYPMWQFMPPSEVDTSKDSEACPPVA 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:    37 KRARSDSCSR-PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ 95
             KR R +S S  P SKACREK+RR+RLNDRFL+LS ++ P + A+ DK  IL DA R+L +
Sbjct:    57 KRGRDESSSSGPKSKACREKIRRDRLNDRFLELSSVINPDKQAKLDKANILSDAARLLAE 116

Query:    96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMP- 154
             LR E+++LKE+NEKL+E IK LK EKNELR+EK+ LKA+KE+LEQQ+K +++   G++P 
Sbjct:   117 LRGEAEKLKESNEKLRETIKDLKVEKNELRDEKVTLKAEKERLEQQVKALSVAPTGFVPH 176

Query:   155 -THPAAYHAGL------------NKMAVYPS-YGLMPMWQYLPPSLHDTSRDHELRPPAA 200
               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:    42 DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 101
             D  +R   KA REKLRRE+LN+ F++L  +L+P RP + DK  IL D +++L +L +E  
Sbjct:    55 DVSARKSQKAGREKLRREKLNEHFVELGNVLDPERP-KNDKATILTDTVQLLKELTSEVN 113

Query:   102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL----EQQLKVMAMPTGGYMPTHP 157
             +LK     L +E + L  EKN+LREEK  LK+D E L    +Q+L+ M+ P G  M    
Sbjct:   114 KLKSEYTALTDESRELTQEKNDLREEKTSLKSDIENLNLQYQQRLRSMS-PWGAAMD--- 169

Query:   158 AAYHAGLNKMAVYPSYGLMPMWQYLPP 184
                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:    26 GVVPPENEN-TRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPA 84
             G  P ++   T  + +    +R   KA REK+RR+RLN++F +L   L+P RP R DK  
Sbjct:    19 GACPADSSGKTECKTQGSIATRKVQKADREKMRRDRLNEQFQELGSTLDPDRP-RNDKAT 77

Query:    85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL----EQ 140
             IL DAI++L  L ++  +LK     L EE + L  EKNELR+EK+ LK + + L    +Q
Sbjct:    78 ILSDAIQMLKDLTSQVNKLKAEYTSLSEEARELTQEKNELRDEKVSLKFEVDNLNTQYQQ 137

Query:   141 QLKVMAMPTGGYMPT 155
             +++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:    44 CSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQEL 103
             CS+   KA REKLRR++L ++FL+L   L+P RP ++DK ++L D I++L  +  +   L
Sbjct:    46 CSQ---KAEREKLRRDKLKEQFLELGNALDPNRP-KSDKASVLTDTIQMLKDVMNQVDRL 101

Query:   104 KETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGYMPTHPAAYH 161
             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

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

 Score = 166 (63.5 bits), Expect = 2.2e-12, P = 2.2e-12
 Identities = 50/177 (28%), Positives = 90/177 (50%)

Query:    10 VNAKISGSA-DNDISSTGVVPPENENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDL 68
             VNA  +G   +  +  +G+V   N+   K+A      +   K+ REKL+R++ ND F +L
Sbjct:     7 VNAAAAGGGGEGRLVQSGIV---NKKCDKKA-----PKRIHKSEREKLKRDKQNDLFNEL 58

Query:    69 SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK 128
               +LEP R     K  +L +  R+L  L ++ + L++ N  L+ E   +  E+NEL ++ 
Sbjct:    59 GNLLEPDRQ-NNGKACVLGETTRILKDLLSQVESLRKENSSLKNESHYVALERNELHDDN 117

Query:   129 LILKADKEKLEQQLKVM--AMPTGGYMPTHPAAYHAGLNKMAVYPSYGLMPMWQYLP 183
              +L+ +  +L+ +L+      P   ++ T PA           YP+ G+ P+ Q+LP
Sbjct:   118 SMLRTEILELQNELRTRMEGNPVWSHVNTRPAL-------RVPYPTTGVFPV-QHLP 166

GO:0005634 "nucleus" evidence=IC

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:    32 NENTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIR 91
             N    +R R     +  +KA RE+L+RE LN+ F++L+  LE  +   + K +IL +A R
Sbjct:    14 NATADERCRKGKVPKRINKAVRERLKREHLNELFIELADTLELNQQ-NSGKASILCEATR 72

Query:    92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGG 151
              L  +  + + L++ +  L  E   +  EKNEL+EE  +L+ +  KL+ +++  A  +  
Sbjct:    73 FLKDVFGQIESLRKEHASLLSESSYVTTEKNELKEETSVLETEISKLQNEIEARANQSKP 132

Query:   152 YMPTHPAA-YH 161
              + 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

---

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	0.6844	0.895	0.6325	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	200
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	5e-06
smart00353	53	smart00353, HLH, helix loop helix domain	2e-05
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	8e-05
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	1e-04
TIGR03346	852	TIGR03346, chaperone_ClpB, ATP-dependent chaperone	3e-04
pfam13870	177	pfam13870, DUF4201, Domain of unknown function (DU	4e-04
pfam07926	132	pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein	5e-04
pfam06005	72	pfam06005, DUF904, Protein of unknown function (DU	6e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	6e-04
TIGR02894	161	TIGR02894, DNA_bind_RsfA, transcription factor, Rs	0.001
TIGR02169	1164	TIGR02169, SMC_prok_A, chromosome segregation prot	0.002
pfam12329	74	pfam12329, TMF_DNA_bd, TATA element modulatory fac	0.002
COG1196	1163	COG1196, Smc, Chromosome segregation ATPases [Cell	0.002
TIGR00019	360	TIGR00019, prfA, peptide chain release factor 1	0.003
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.004
pfam03938	157	pfam03938, OmpH, Outer membrane protein (OmpH-like	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 = 42.2 bits (100), Expect = 5e-06
 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 43  SCSRPGSKACREKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQ 101
             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 = 40.3 bits (95), Expect = 2e-05
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 53  REKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQE 102
           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 = 40.1 bits (95), Expect = 2e-05
 Identities = 16/49 (32%), Positives = 25/49 (51%)

Query: 49 SKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLR 97
          +   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 = 41.5 bits (98), Expect = 8e-05
 Identities = 19/51 (37%), Positives = 34/51 (66%)

Query: 92  VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 142
            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 = 41.4 bits (98), Expect = 1e-04
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 93  LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ 140
           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 = 40.7 bits (96), Expect = 3e-04
 Identities = 33/99 (33%), Positives = 47/99 (47%), Gaps = 23/99 (23%)

Query: 63  DRFL-----DLSCILEPGRPARTD---KPAILDDAIRVLNQLRTESQEL-KETN------ 107
           DRFL     DL  I E     R +   KP  LD+  R + QL  E + L KE +      
Sbjct: 378 DRFLPDKAIDL--IDEAAARIRMEIDSKPEELDELDRRIIQLEIEREALKKEKDEASKER 435

Query: 108 -EKLQEEIKSLKAEKNELREEKLILKADKEKLE--QQLK 143
            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 = 39.1 bits (92), Expect = 4e-04
 Identities = 15/56 (26%), Positives = 32/56 (57%)

Query: 93  LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP 148
           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|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: 88  DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR----EEKLILKADKEKLEQQLK 143
           + 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|203371 pfam06005, DUF904, Protein of unknown function (DUF904)

 Score = 36.9 bits (86), Expect = 6e-04
 Identities = 18/50 (36%), Positives = 31/50 (62%)

Query: 92  VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ 141
           +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|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 39.7 bits (93), Expect = 6e-04
 Identities = 21/51 (41%), Positives = 33/51 (64%)

Query: 93  LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
           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|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 86  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL 138
           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|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC, primarily archaeal type

 Score = 38.5 bits (90), Expect = 0.002
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 84  AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
           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|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA binding

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 19/48 (39%), Positives = 27/48 (56%)

Query: 95  QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 142
           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 = 38.2 bits (89), Expect = 0.002
 Identities = 24/67 (35%), Positives = 41/67 (61%), Gaps = 7/67 (10%)

Query: 86  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK-------LILKADKEKL 138
           L++    L++L  E +EL+E  E+ ++EI+ LK+E  ELREE        L LK + E+L
Sbjct: 241 LEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQEELLELKEEIEEL 300

Query: 139 EQQLKVM 145
           E ++ ++
Sbjct: 301 EGEISLL 307

Length = 1163

>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: 86  LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE-KNELREEKLILKADKEKLEQQLKV 144
           L++ +    + +   +++KE  E L+E    ++   K EL E    L+   E+LE+QLKV
Sbjct: 45  LEEIVDCYREYQQAQEDIKEAKEILEESDPEMREMAKEELEE----LEEKIEELEEQLKV 100

Query: 145 MAMP 148
           + +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|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 36.5 bits (85), Expect = 0.004
 Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 93  LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK---LILKADKEKLEQQLKVM 145
           L +L+ E+QELK+    L+ E++ L+ E   +++     + L  +  +L ++L  +
Sbjct: 89  LAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEENRELREELAEL 144

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 7/58 (12%)

Query: 88  DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM 145
           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|237560 PRK13922, PRK13922, rod shape-determining protein MreC; Provisional

 Score = 36.9 bits (86), Expect = 0.004
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 10/74 (13%)

Query: 88  DAIRVLNQLRTESQELKETNEKLQEEI---KSLKAEKNELREEKLILKADKEKLEQQL-- 142
           +++  L  LR E++ELK+   +L+  +   + L+AE   LRE    L   KE L+ Q   
Sbjct: 66  ESLASLFDLREENEELKKELLELESRLQELEQLEAENARLRE----LLNLKESLDYQFIT 121

Query: 143 -KVMAMPTGGYMPT 155
            +V++     +   
Sbjct: 122 ARVISRSPDPWSQQ 135

Length = 276

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	200
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.53
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.51
KOG1318	411	consensus Helix loop helix transcription factor EB	99.5
smart00353	53	HLH helix loop helix domain.	99.46
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.18
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	99.08
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.55
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.44
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.35
KOG0561	373	consensus bHLH transcription factor [Transcription	98.26
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.06
PLN03217	93	transcription factor ATBS1; Provisional	97.76
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.72
PRK15422	79	septal ring assembly protein ZapB; Provisional	97.45
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	97.35
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.29
PF06005	72	DUF904: Protein of unknown function (DUF904); Inte	97.2
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	96.82
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	96.54
KOG3910	632	consensus Helix loop helix transcription factor [T	96.43
PRK15422	79	septal ring assembly protein ZapB; Provisional	96.11
smart00338	65	BRLZ basic region leucin zipper.	96.03
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	95.85
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	95.77
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	95.75
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	95.75
PRK13169	110	DNA replication intiation control protein YabA; Re	95.31
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	95.31
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	95.2
PRK11637	428	AmiB activator; Provisional	95.18
PRK04406	75	hypothetical protein; Provisional	94.97
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	94.79
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	94.7
PF06156	107	DUF972: Protein of unknown function (DUF972); Inte	94.65
PRK02119	73	hypothetical protein; Provisional	94.65
KOG0996	1293	consensus Structural maintenance of chromosome pro	94.56
PRK00846	77	hypothetical protein; Provisional	94.5
COG3074	79	Uncharacterized protein conserved in bacteria [Fun	94.44
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	94.37
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	94.29
PF08317	325	Spc7: Spc7 kinetochore protein; InterPro: IPR01325	94.28
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	94.16
COG4026	290	Uncharacterized protein containing TOPRIM domain,	94.16
PRK10884	206	SH3 domain-containing protein; Provisional	94.13
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	94.06
PRK00295	68	hypothetical protein; Provisional	94.0
PRK02793	72	phi X174 lysis protein; Provisional	93.97
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	93.95
PRK10884	206	SH3 domain-containing protein; Provisional	93.95
PF12329	74	TMF_DNA_bd: TATA element modulatory factor 1 DNA b	93.57
TIGR02449	65	conserved hypothetical protein TIGR02449. Members	93.56
PRK11637	428	AmiB activator; Provisional	93.55
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.42
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	93.42
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	93.41
PRK04325	74	hypothetical protein; Provisional	93.36
PRK00736	68	hypothetical protein; Provisional	93.34
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	93.3
COG3883	265	Uncharacterized protein conserved in bacteria [Fun	93.22
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	93.07
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	92.92
PF00170	64	bZIP_1: bZIP transcription factor cAMP response el	92.88
PRK13169	110	DNA replication intiation control protein YabA; Re	92.86
PRK13729	475	conjugal transfer pilus assembly protein TraB; Pro	92.85
PHA02562	562	46 endonuclease subunit; Provisional	92.82
PF13815	118	Dzip-like_N: Iguana/Dzip1-like DAZ-interacting pro	92.51
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	92.47
PF12325	120	TMF_TATA_bd: TATA element modulatory factor 1 TATA	92.28
PF13870	177	DUF4201: Domain of unknown function (DUF4201)	92.15
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	92.14
PF02183	45	HALZ: Homeobox associated leucine zipper; InterPro	92.14
TIGR02894	161	DNA_bind_RsfA transcription factor, RsfA family. I	92.09
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	92.05
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	91.93
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	91.87
smart00338	65	BRLZ basic region leucin zipper.	91.68
PF07798	177	DUF1640: Protein of unknown function (DUF1640); In	91.49
COG4467	114	Regulator of replication initiation timing [Replic	91.43
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	91.42
PF14197	69	Cep57_CLD_2: Centrosome localisation domain of PPC	91.37
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	91.33
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	91.26
TIGR02231	525	conserved hypothetical protein. This family consis	91.23
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	91.22
COG5570	57	Uncharacterized small protein [Function unknown]	91.17
KOG3119	269	consensus Basic region leucine zipper transcriptio	90.86
KOG1962	216	consensus B-cell receptor-associated protein and r	90.85
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	90.81
COG0216	363	PrfA Protein chain release factor A [Translation,	90.72
PF07106	169	TBPIP: Tat binding protein 1(TBP-1)-interacting pr	90.65
KOG2391	365	consensus Vacuolar sorting protein/ubiquitin recep	90.61
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	90.6
PF12808	52	Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2	90.48
KOG3119	269	consensus Basic region leucine zipper transcriptio	90.46
KOG3898	254	consensus Transcription factor NeuroD and related	90.41
PF11932	251	DUF3450: Protein of unknown function (DUF3450); In	90.38
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	90.34
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	90.22
COG2433	652	Uncharacterized conserved protein [Function unknow	90.22
KOG3582	856	consensus Mlx interactors and related transcriptio	90.11
PF08172	248	CASP_C: CASP C terminal; InterPro: IPR012955 This	90.06
PF14662	193	CCDC155: Coiled-coil region of CCDC155	89.88
PF10146	230	zf-C4H2: Zinc finger-containing protein ; InterPro	89.76
PF04111	314	APG6: Autophagy protein Apg6; InterPro: IPR007243	89.63
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	89.48
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	89.44
TIGR00219	283	mreC rod shape-determining protein MreC. MreC (mur	89.42
PRK09039	343	hypothetical protein; Validated	89.27
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	89.19
PF04977	80	DivIC: Septum formation initiator; InterPro: IPR00	88.98
PF11559	151	ADIP: Afadin- and alpha -actinin-Binding; InterPro	88.89
PRK00888	105	ftsB cell division protein FtsB; Reviewed	88.78
PF07989	75	Microtub_assoc: Microtubule associated; InterPro:	88.75
PRK13922	276	rod shape-determining protein MreC; Provisional	88.69
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	88.67
PF05667	594	DUF812: Protein of unknown function (DUF812); Inte	88.63
PF09789	319	DUF2353: Uncharacterized coiled-coil protein (DUF2	88.33
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	88.33
PRK10803	263	tol-pal system protein YbgF; Provisional	88.29
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	88.25
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	88.11
PF10234	267	Cluap1: Clusterin-associated protein-1; InterPro:	87.87
PRK09039	343	hypothetical protein; Validated	87.75
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	87.64
PRK13922	276	rod shape-determining protein MreC; Provisional	87.64
PF11180	192	DUF2968: Protein of unknown function (DUF2968); In	87.61
PF15035	182	Rootletin: Ciliary rootlet component, centrosome c	87.59
COG0497	557	RecN ATPase involved in DNA repair [DNA replicatio	87.48
COG4942	420	Membrane-bound metallopeptidase [Cell division and	87.41
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	87.35
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	87.14
PF09304	107	Cortex-I_coil: Cortexillin I, coiled coil; InterPr	87.04
PF00038	312	Filament: Intermediate filament protein; InterPro:	87.04
PF05529	192	Bap31: B-cell receptor-associated protein 31-like	86.98
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	86.94
COG2433	652	Uncharacterized conserved protein [Function unknow	86.94
PF04156	191	IncA: IncA protein; InterPro: IPR007285 Chlamydia	86.84
TIGR02492	322	flgK_ends flagellar hook-associated protein FlgK.	86.78
PF15458	254	NTR2: Nineteen complex-related protein 2	86.76
KOG4395	285	consensus Transcription factor Atonal, contains HT	86.72
KOG4343	655	consensus bZIP transcription factor ATF6 [Transcri	86.7
KOG0612	1317	consensus Rho-associated, coiled-coil containing p	86.65
PF04728	56	LPP: Lipoprotein leucine-zipper; InterPro: IPR0068	86.47
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	86.46
PF14662	193	CCDC155: Coiled-coil region of CCDC155	86.43
COG1256	552	FlgK Flagellar hook-associated protein [Cell motil	86.4
PF14282	106	FlxA: FlxA-like protein	86.38
PHA03011	120	hypothetical protein; Provisional	86.33
COG4942	420	Membrane-bound metallopeptidase [Cell division and	86.29
PF15397	258	DUF4618: Domain of unknown function (DUF4618)	86.2
PF08826	61	DMPK_coil: DMPK coiled coil domain like; InterPro:	86.14
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	86.12
PF04102	69	SlyX: SlyX; InterPro: IPR007236 The SlyX protein h	86.0
PF10224	80	DUF2205: Predicted coiled-coil protein (DUF2205);	85.95
PRK00888	105	ftsB cell division protein FtsB; Reviewed	85.93
PHA02562	562	46 endonuclease subunit; Provisional	85.9
KOG0250	1074	consensus DNA repair protein RAD18 (SMC family pro	85.88
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	85.75
PF05103	131	DivIVA: DivIVA protein; InterPro: IPR007793 The Ba	85.64
PRK04406	75	hypothetical protein; Provisional	85.52
KOG2264	907	consensus Exostosin EXT1L [Signal transduction mec	85.49
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	85.42
TIGR03752	472	conj_TIGR03752 integrating conjugative element pro	85.39
PRK10803	263	tol-pal system protein YbgF; Provisional	85.36
PF13094	160	CENP-Q: CENP-Q, a CENPA-CAD centromere complex sub	85.3
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	85.29
PF10211	189	Ax_dynein_light: Axonemal dynein light chain; Inte	85.26
COG4026	290	Uncharacterized protein containing TOPRIM domain,	85.24
COG2919	117	Septum formation initiator [Cell division and chro	85.07
PF08614	194	ATG16: Autophagy protein 16 (ATG16); InterPro: IPR	85.05
PF07200	150	Mod_r: Modifier of rudimentary (Mod(r)) protein; I	85.03
COG2900	72	SlyX Uncharacterized protein conserved in bacteria	85.02
PF07716	54	bZIP_2: Basic region leucine zipper; InterPro: IPR	84.96
COG3937	108	Uncharacterized conserved protein [Function unknow	84.87
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	84.82
COG1340	294	Uncharacterized archaeal coiled-coil protein [Func	84.75
KOG4360	596	consensus Uncharacterized coiled coil protein [Fun	84.73
TIGR00606	1311	rad50 rad50. This family is based on the phylogeno	84.65
smart00787	312	Spc7 Spc7 kinetochore protein. This domain is foun	84.57
PF09726	697	Macoilin: Transmembrane protein; InterPro: IPR0191	84.4
PRK15396	78	murein lipoprotein; Provisional	84.32
PF06810	155	Phage_GP20: Phage minor structural protein GP20; I	84.22
PF10018	188	Med4: Vitamin-D-receptor interacting Mediator subu	84.17
PRK02224	880	chromosome segregation protein; Provisional	84.12
PF05266	190	DUF724: Protein of unknown function (DUF724); Inte	84.11
PF06785	401	UPF0242: Uncharacterised protein family (UPF0242);	83.86
PF10473	140	CENP-F_leu_zip: Leucine-rich repeats of kinetochor	83.74
KOG3650	120	consensus Predicted coiled-coil protein [General f	83.7
PRK07739	507	flgK flagellar hook-associated protein FlgK; Valid	83.55
PF10805	106	DUF2730: Protein of unknown function (DUF2730); In	83.55
TIGR02209	85	ftsL_broad cell division protein FtsL. This model	83.49
TIGR02169	1164	SMC_prok_A chromosome segregation protein SMC, pri	83.49
KOG4797	123	consensus Transcriptional regulator [Transcription	83.48
PRK02224	880	chromosome segregation protein; Provisional	83.46
PF12709	87	Kinetocho_Slk19: Central kinetochore-associated; I	83.42
KOG0249	916	consensus LAR-interacting protein and related prot	83.41
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	83.4
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	83.27
PF04880	166	NUDE_C: NUDE protein, C-terminal conserved region;	83.2
PF12718	143	Tropomyosin_1: Tropomyosin like; InterPro: IPR0005	83.12
PRK07191	456	flgK flagellar hook-associated protein FlgK; Valid	82.87
PRK04325	74	hypothetical protein; Provisional	82.8
PF09744	158	Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; Inte	82.74
PRK07521	483	flgK flagellar hook-associated protein FlgK; Valid	82.39
KOG4196	135	consensus bZIP transcription factor MafK [Transcri	82.38
PF14988	206	DUF4515: Domain of unknown function (DUF4515)	82.37
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	82.34
KOG3156	220	consensus Uncharacterized membrane protein [Functi	82.34
PF14282	106	FlxA: FlxA-like protein	82.27
PF07888	546	CALCOCO1: Calcium binding and coiled-coil domain (	82.2
KOG0946	970	consensus ER-Golgi vesicle-tethering protein p115	82.01
PF13851	201	GAS: Growth-arrest specific micro-tubule binding	81.96
KOG1962	216	consensus B-cell receptor-associated protein and r	81.94
KOG1029	1118	consensus Endocytic adaptor protein intersectin [S	81.93
PF04999	97	FtsL: Cell division protein FtsL; InterPro: IPR007	81.79
PF04012	221	PspA_IM30: PspA/IM30 family; InterPro: IPR007157 T	81.78
PF05008	79	V-SNARE: Vesicle transport v-SNARE protein N-termi	81.74
KOG4005	292	consensus Transcription factor XBP-1 [Transcriptio	81.69
PRK05771	646	V-type ATP synthase subunit I; Validated	81.68
PF09738	302	DUF2051: Double stranded RNA binding protein (DUF2	81.68
PRK06665	627	flgK flagellar hook-associated protein FlgK; Valid	81.51
PF01166	59	TSC22: TSC-22/dip/bun family; InterPro: IPR000580	81.41
KOG0995	581	consensus Centromere-associated protein HEC1 [Cell	81.41
KOG4571	294	consensus Activating transcription factor 4 [Trans	81.36
PF15070	617	GOLGA2L5: Putative golgin subfamily A member 2-lik	81.34
TIGR01554	378	major_cap_HK97 phage major capsid protein, HK97 fa	81.29
PRK05683	676	flgK flagellar hook-associated protein FlgK; Valid	81.17
PRK03992	389	proteasome-activating nucleotidase; Provisional	81.17
PRK10869	553	recombination and repair protein; Provisional	80.99
PF10186	302	Atg14: UV radiation resistance protein and autopha	80.95
PF02403	108	Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal dom	80.94
PF00769	246	ERM: Ezrin/radixin/moesin family; InterPro: IPR011	80.86
PRK03992	389	proteasome-activating nucleotidase; Provisional	80.86
PF10458	66	Val_tRNA-synt_C: Valyl tRNA synthetase tRNA bindin	80.77
PF06120	301	Phage_HK97_TLTM: Tail length tape measure protein;	80.7
PF07926	132	TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro:	80.64
PF06103	90	DUF948: Bacterial protein of unknown function (DUF	80.56
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	80.54
PRK00409	782	recombination and DNA strand exchange inhibitor pr	80.28
PF07889	126	DUF1664: Protein of unknown function (DUF1664); In	80.25
KOG0977	546	consensus Nuclear envelope protein lamin, intermed	80.23
PRK03918	880	chromosome segregation protein; Provisional	80.22
PF04325	49	DUF465: Protein of unknown function (DUF465); Inte	80.16
PF00038	312	Filament: Intermediate filament protein; InterPro:	80.15

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

Probab=99.53  E-value=6.7e-15  Score=100.17  Aligned_cols=51  Identities=33%  Similarity=0.483  Sum_probs=47.2

Q ss_pred             CCchhHHHHHHHHHHHHhHHHHhhhcCCC---CCCCCChhhHHHHHHHHHHHHH
Q 028999           47 PGSKACREKLRRERLNDRFLDLSCILEPG---RPARTDKPAILDDAIRVLNQLR   97 (200)
Q Consensus        47 ~~sH~~~ER~RRekiNe~F~~Lr~lLpP~---~~~K~dKasIL~dAI~YIk~L~   97 (200)
                      +.+|+.+||+||++||++|.+|+.+||++   ...|.||++||..||+||++|+
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            56899999999999999999999999876   4578999999999999999996

; 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=99.51  E-value=2.6e-14  Score=97.35  Aligned_cols=56  Identities=32%  Similarity=0.447  Sum_probs=50.3

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTES  100 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~-~~K~dKasIL~dAI~YIk~L~~~v  100 (200)
                      .++.+|+.+||+||++||+.|.+|+++||+.. ..|.||++||..||+||+.|+.++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            35788999999999999999999999996652 479999999999999999999875

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

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

Probab=99.50  E-value=5.5e-14  Score=130.74  Aligned_cols=85  Identities=24%  Similarity=0.340  Sum_probs=70.3

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTESQELKE---TNEKLQEEIKSLKAE  120 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~--~~K~dKasIL~dAI~YIk~L~~~v~~L~~---~~~~L~~ei~~L~~e  120 (200)
                      +|..|+++|||||++||++|.+|+.|||.+.  ..|..|.+||..+++||+.|++..++..+   ....|+..+++|..+
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            6799999999999999999999999997764  24778999999999999999998774333   445677777888888


Q ss_pred             HHHHHHHHHH
Q 028999          121 KNELREEKLI  130 (200)
Q Consensus       121 knELr~Ek~~  130 (200)
                      +.||..+...
T Consensus       313 ieeLk~~~~~  322 (411)
T KOG1318|consen  313 IEELKSEAGR  322 (411)
T ss_pred             HHHHHHHHHH
Confidence            8887776653

>smart00353 HLH helix loop helix domain

Probab=99.46  E-value=1.4e-13  Score=92.17  Aligned_cols=51  Identities=31%  Similarity=0.444  Sum_probs=46.1

Q ss_pred             hHHHHHHHHHHHHhHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHHH
Q 028999           51 ACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTESQ  101 (200)
Q Consensus        51 ~~~ER~RRekiNe~F~~Lr~lLpP~~-~~K~dKasIL~dAI~YIk~L~~~v~  101 (200)
                      +..||+||++||++|..|+++||++. ..|.||++||..||+||+.|+.+++
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            46899999999999999999997653 5789999999999999999998875

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.18  E-value=7.1e-11  Score=100.91  Aligned_cols=80  Identities=21%  Similarity=0.342  Sum_probs=71.6

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCC-----CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRP-----ARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE  120 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~-----~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~e  120 (200)
                      |+..|-..|++|||.||..+..|..|||-|.+     .|++||.||.++|+||.+|+.+..+-+++..+|+.++..|+.=
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            57899999999999999999999999976642     3889999999999999999999999999999999998888887


Q ss_pred             HHHHH
Q 028999          121 KNELR  125 (200)
Q Consensus       121 knELr  125 (200)
                      +++..
T Consensus       142 k~~YE  146 (229)
T KOG1319|consen  142 KVNYE  146 (229)
T ss_pred             HHHHH
Confidence            77753

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

Probab=99.08  E-value=1e-09  Score=95.90  Aligned_cols=84  Identities=26%  Similarity=0.292  Sum_probs=70.4

Q ss_pred             CCCCCCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCC-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           42 DSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTD-KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE  120 (200)
Q Consensus        42 ~~~~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~d-KasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~e  120 (200)
                      .+.+.+.+||.-||+||+.|.++|..|+..||.+...+.. -++||.+|++||+.|+..........+.|..+-..|+++
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            4456789999999999999999999999999776654444 599999999999999998888877777777777777777


Q ss_pred             HHHHH
Q 028999          121 KNELR  125 (200)
Q Consensus       121 knELr  125 (200)
                      +++|.
T Consensus       135 l~ql~  139 (232)
T KOG2483|consen  135 LEQLS  139 (232)
T ss_pred             HHHhc
Confidence            77665

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

Probab=98.55  E-value=3.6e-08  Score=86.92  Aligned_cols=60  Identities=28%  Similarity=0.344  Sum_probs=51.5

Q ss_pred             CCCCCCCchhHHHHHHHHHHHHhHHHHhhhcCCC------CCCCCChhhHHHHHHHHHHHHHHHHH
Q 028999           42 DSCSRPGSKACREKLRRERLNDRFLDLSCILEPG------RPARTDKPAILDDAIRVLNQLRTESQ  101 (200)
Q Consensus        42 ~~~~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~------~~~K~dKasIL~dAI~YIk~L~~~v~  101 (200)
                      ..+.|+..|-..||+||++||+++.+|+.||+-.      ..+|.+||-||.-|++|+++|+....
T Consensus        28 ~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   28 TRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             hHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            3356899999999999999999999999999432      23689999999999999999998543

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

Probab=98.44  E-value=2.2e-07  Score=92.95  Aligned_cols=52  Identities=25%  Similarity=0.397  Sum_probs=48.2

Q ss_pred             CCchhHHHHHHHHHHHHhHHHHhhhcCCCCC---CCCChhhHHHHHHHHHHHHHHH
Q 028999           47 PGSKACREKLRRERLNDRFLDLSCILEPGRP---ARTDKPAILDDAIRVLNQLRTE   99 (200)
Q Consensus        47 ~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~---~K~dKasIL~dAI~YIk~L~~~   99 (200)
                      +..|+..||||||++|.-|+||+++| |.+.   .|.||-+||..||.+|+.+++.
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            78999999999999999999999999 5555   7999999999999999998885

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.35  E-value=4.7e-07  Score=91.46  Aligned_cols=76  Identities=29%  Similarity=0.424  Sum_probs=68.2

Q ss_pred             CCccCCCCCCCCCCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           34 NTRKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQ  111 (200)
Q Consensus        34 ~~~kR~r~~~~~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~  111 (200)
                      -+.+|..+| ..+|..||..||+=|..|||++.+|+.+| |+...|..|.+.|..||+||++|+...+.++.++..++
T Consensus       265 ~Pi~rl~~G-~~kRtAHN~IEKRYRsSINDKI~eLk~lV-~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  265 KPIKRLLPG-GEKRTAHNIIEKRYRSSINDKIIELKDLV-PGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             CchhhcCCC-CcccchhhHHHHHhhcchhHHHHHHHHhc-CccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            456777666 67899999999999999999999999999 54567999999999999999999999999999888776

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.26  E-value=7.3e-07  Score=81.10  Aligned_cols=69  Identities=25%  Similarity=0.315  Sum_probs=56.3

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEI  114 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei  114 (200)
                      |+.--|+-||+|=.-||-.|..||+|||-...-|.+||+||..+.+||.+|+.+--+|--+|.+|+..+
T Consensus        60 RReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~elKr~~  128 (373)
T KOG0561|consen   60 RREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNGELKRLK  128 (373)
T ss_pred             HHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccchHHHHH
Confidence            455678899999999999999999999554457899999999999999999987666665555544433

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

Probab=98.06  E-value=1e-05  Score=71.97  Aligned_cols=64  Identities=30%  Similarity=0.346  Sum_probs=51.1

Q ss_pred             CCCCCCCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHH
Q 028999           41 SDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELK  104 (200)
Q Consensus        41 ~~~~~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~  104 (200)
                      .-..+|+..--.+||+|=.|+|+.|+.|.----+.-....-|+.||-.||+||..|+.-++++.
T Consensus       113 s~svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~  176 (284)
T KOG3960|consen  113 STSVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQD  176 (284)
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3345677788899999999999999999877633223578999999999999999987655433

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.76  E-value=6.8e-05  Score=57.15  Aligned_cols=56  Identities=21%  Similarity=0.373  Sum_probs=45.3

Q ss_pred             HHHHHHhHHHHhhhcCCCCC----CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           58 RERLNDRFLDLSCILEPGRP----ARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE  113 (200)
Q Consensus        58 RekiNe~F~~Lr~lLpP~~~----~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~e  113 (200)
                      -|.|||.+..|+.+||..+.    .|.+-+-+|.+++.||+.|+.+|+.|.+...+|.+-
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t   78 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN   78 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            47899999999999966432    334444599999999999999999999888777643

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

Probab=97.72  E-value=3.7e-05  Score=66.09  Aligned_cols=58  Identities=19%  Similarity=0.256  Sum_probs=50.0

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTESQE  102 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~--~~K~dKasIL~dAI~YIk~L~~~v~~  102 (200)
                      ..+..++.+||.|=..+|..|.+||..||..-  ..|.+|+.+|.-||.||..|..-++.
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~  167 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLAT  167 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcc
Confidence            35677888899999999999999999997654  35799999999999999999886543

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=97.45  E-value=0.0015  Score=48.87  Aligned_cols=60  Identities=28%  Similarity=0.493  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +..||+-|.=|+-++++|+..|..|.+++..++....+|.+|+..||.|-...+..|.++
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            467899999999999999999999999999999999999999999999988888777764

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=97.35  E-value=0.0026  Score=47.11  Aligned_cols=60  Identities=27%  Similarity=0.492  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +..||+-|.=|+-++++|++.|.+|..+..++......|+.|+..||.|-...+..++++
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            567999999999999999999999999999999999999999999999988888777764

>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=97.29  E-value=0.0034  Score=46.00  Aligned_cols=45  Identities=36%  Similarity=0.567  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      .||+-|..|+.++++|+.+|..|.++...|+.+.+.|++|....+
T Consensus        15 ~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~   59 (72)
T PF06005_consen   15 QAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQ   59 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444455555555555444444444444444444444443333

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.

>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=97.20  E-value=0.0062  Score=44.64  Aligned_cols=56  Identities=38%  Similarity=0.446  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ++.+.+|+.+++.+-.++..|+.++.+|+.+.++|.+++..|+.+.++|+++-..+
T Consensus         3 ~E~l~~LE~ki~~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~   58 (72)
T PF06005_consen    3 LELLEQLEEKIQQAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAW   58 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            57788999999999999999999999999998888888888888888888766553

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=96.82  E-value=0.01  Score=49.73  Aligned_cols=61  Identities=30%  Similarity=0.475  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           85 ILDDAIRVLNQLRTE---SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        85 IL~dAI~YIk~L~~~---v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      -|.+.|.|+..|+..   .+.++.++..|+.++.+|..++.+|..|+..|+.+...++..++++
T Consensus        81 tl~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L  144 (161)
T TIGR02894        81 TLQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTL  144 (161)
T ss_pred             CHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            388999999999974   6677788888888888888888888888888888888887777764

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.

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=96.54  E-value=0.036  Score=49.61  Aligned_cols=88  Identities=26%  Similarity=0.360  Sum_probs=67.2

Q ss_pred             CCch-hHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           47 PGSK-ACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        47 ~~sH-~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr  125 (200)
                      +..| ..-||.-|.||+.+..+=-+        .-.|-+-..+-=..|++|.++.+.|..+|+.|++..+.|-.+.+||+
T Consensus        60 RL~HLS~EEK~~RrKLKNRVAAQta--------RDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~  131 (292)
T KOG4005|consen   60 RLDHLSWEEKVQRRKLKNRVAAQTA--------RDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELD  131 (292)
T ss_pred             hhcccCHHHHHHHHHHHHHHHHhhh--------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            3455 67888889899888765322        23344444454566899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 028999          126 EEKLILKADKEKLEQQL  142 (200)
Q Consensus       126 ~Ek~~Lk~e~e~L~~ql  142 (200)
                      .+...+..++-.|.+|-
T Consensus       132 ~~le~~~~~l~~~~~~~  148 (292)
T KOG4005|consen  132 SELELLRQELAELKQQQ  148 (292)
T ss_pred             HHHHHHHHHHHhhHHHH
Confidence            99888888888886543

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.43  E-value=0.0024  Score=61.77  Aligned_cols=72  Identities=25%  Similarity=0.350  Sum_probs=51.0

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN  122 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~--~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~ekn  122 (200)
                      ||...+.+||.|=..||+.|.||+.+.=-..  .....|..||..|+..|-.|+++|.+-     .|.-+...|+...+
T Consensus       526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER-----NLNPKaaclkRRee  599 (632)
T KOG3910|consen  526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER-----NLNPKAACLKRREE  599 (632)
T ss_pred             HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc-----cCChhhhhhhccch
Confidence            5677788888888899999999999862211  112568889999999999999988531     23344445554433

>PRK15422 septal ring assembly protein ZapB; Provisional

Probab=96.11  E-value=0.064  Score=40.30  Aligned_cols=56  Identities=29%  Similarity=0.367  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHh
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI-------LKADKEKLEQQLKVM  145 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~-------Lk~e~e~L~~qlk~~  145 (200)
                      .+.+.+|+.+|+..-++..-|+.+|++|+.+.+.|.+|...       |..+.+.|+++...+
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            46788999999999999999999999999999988888766       666666666665544

>smart00338 BRLZ basic region leucin zipper

Probab=96.03  E-value=0.028  Score=39.36  Aligned_cols=38  Identities=29%  Similarity=0.521  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  128 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek  128 (200)
                      .||..|+.+++.|+.+|..|..++..|..++..|++++
T Consensus        26 ~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~   63 (65)
T smart00338       26 AEIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL   63 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68888888888888888888888877777777776643

>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=95.85  E-value=0.042  Score=38.39  Aligned_cols=37  Identities=32%  Similarity=0.575  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREE  127 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~E  127 (200)
                      .||.+|+.++..|+.+|..|..++..|+.+...|..+
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=95.77  E-value=0.077  Score=41.55  Aligned_cols=52  Identities=29%  Similarity=0.424  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      +|=..+.+|+.....|..++.+|+..+.+|-+||+.|+.|.+.|...|....
T Consensus         5 ~l~~~l~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~   56 (107)
T PF06156_consen    5 ELFDRLDQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELE   56 (107)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3445566667777777777778888888888888888888888887777653

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

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=95.75  E-value=0.0095  Score=49.99  Aligned_cols=53  Identities=25%  Similarity=0.255  Sum_probs=45.5

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRT   98 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~   98 (200)
                      .+.-|+.+||+|=..||+.|..|+.++|---..|.+|.-.|.-|..||-.|-.
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~  130 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ  130 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence            45679999999999999999999999954334688899999999999998854

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=95.75  E-value=0.12  Score=49.89  Aligned_cols=55  Identities=15%  Similarity=0.336  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .-+.+-+..+.+|+++.+.|+.+.+.|.+...++.++...|+.|+..|+.|++.+
T Consensus        69 SALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~  123 (475)
T PRK13729         69 HATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKAL  123 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhh
Confidence            3444555566667777777777766666777777777778888888888888654

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=95.31  E-value=0.14  Score=40.49  Aligned_cols=51  Identities=25%  Similarity=0.398  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +|=..+.+|+.....|..++.+|+..+.+|-+||..|+.|.+.|...|...
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            344566677777777778888888888888888888888888888877765

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=95.31  E-value=0.18  Score=50.23  Aligned_cols=61  Identities=28%  Similarity=0.324  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      |+...-.-+.+|+.+.++|.++.+++...+++|++++..-+.|...||.++|..+.|++++
T Consensus        87 I~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~~~El  147 (907)
T KOG2264|consen   87 ILASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQLEEL  147 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHHHHHH
Confidence            3333445677888888889999999999999999999988999999999999999999886

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=95.20  E-value=0.16  Score=48.92  Aligned_cols=60  Identities=25%  Similarity=0.365  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------HHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA----------------------EKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~----------------------eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      |..-|--+++|+.+++.|..+|+.|.+|.+.|++                      +..+|.+|.+.|+..+..|+.||+
T Consensus        61 lrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l~  140 (472)
T TIGR03752        61 LRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRLA  140 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4444566778888888888888777777766655                      445555556666666666667775


Q ss_pred             Hh
Q 028999          144 VM  145 (200)
Q Consensus       144 ~~  145 (200)
                      .+
T Consensus       141 ~~  142 (472)
T TIGR03752       141 GV  142 (472)
T ss_pred             hc
Confidence            54

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.

>PRK11637 AmiB activator; Provisional

Probab=95.18  E-value=0.33  Score=45.23  Aligned_cols=60  Identities=13%  Similarity=0.148  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      -+.++...|..|..++..+......++.++..+..+++++..+...++.+++.++.+|+.
T Consensus        69 ~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~~~~~l~~  128 (428)
T PRK11637         69 QRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAAQERLLAA  128 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555555556666666666666666666666666666666666666666555554

>PRK04406 hypothetical protein; Provisional

Probab=94.97  E-value=0.47  Score=34.95  Aligned_cols=54  Identities=13%  Similarity=0.121  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      +..|..++..|+....-++.-|.+|...+.+.+.+...|+.++..|.++++++.
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            346777888888888888888888888888888888888889999988888874

>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=94.79  E-value=0.13  Score=42.20  Aligned_cols=54  Identities=39%  Similarity=0.545  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEK--NELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~ek--nELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      |.+|+.++..|+.++..|..++..|....  .||+++...|+.+++.|+..|..+.
T Consensus        81 i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~  136 (169)
T PF07106_consen   81 IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLR  136 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888888888888888777765  6788888899999999998888764

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 [].

>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=94.70  E-value=0.32  Score=38.84  Aligned_cols=47  Identities=34%  Similarity=0.564  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  136 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e  136 (200)
                      +..|..|..++..++.+...|+.++..|..+++++++|...|-.+.+
T Consensus        15 ~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e   61 (120)
T PF12325_consen   15 VQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENE   61 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555555555555555555555554443333

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 [].

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

Probab=94.65  E-value=0.3  Score=38.24  Aligned_cols=50  Identities=34%  Similarity=0.419  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      +-|.+|..++..|-.+...|+..+.+|-.|..+|+-|+..|+..+..+++
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            56778888888888888889999999999999999999999888887766

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

>PRK02119 hypothetical protein; Provisional

Probab=94.65  E-value=0.65  Score=33.96  Aligned_cols=54  Identities=15%  Similarity=0.067  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      +..+..++..|+....-.+.-+.+|...+.+.+.+...|+.++..|.++++.+.
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            456777888888888888888888888888888888899999999999998874

>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=94.56  E-value=0.58  Score=49.61  Aligned_cols=83  Identities=27%  Similarity=0.385  Sum_probs=52.8

Q ss_pred             HHHhHHHHhhhcCCCCCCCCChh-hHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHH
Q 028999           61 LNDRFLDLSCILEPGRPARTDKP-AILDDAIRVLNQLRTESQELKET----------NEKLQEEIKSLKAEKNELREEKL  129 (200)
Q Consensus        61 iNe~F~~Lr~lLpP~~~~K~dKa-sIL~dAI~YIk~L~~~v~~L~~~----------~~~L~~ei~~L~~eknELr~Ek~  129 (200)
                      +++++.+||..+ +..-....|. +=+.+.+..|..|..++.+++..          ...+++.|.+++.|+++++++..
T Consensus       804 ~ee~~~~lr~~~-~~l~~~l~~~~~~~k~~~~~~~~l~~~i~~~E~~~~k~~~d~~~l~~~~~~ie~l~kE~e~~qe~~~  882 (1293)
T KOG0996|consen  804 LEERVRKLRERI-PELENRLEKLTASVKRLAELIEYLESQIAELEAAVLKKVVDKKRLKELEEQIEELKKEVEELQEKAA  882 (1293)
T ss_pred             HHHHHHHHHHhh-HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCcHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            566677777777 3221111222 12345566777777777777754          24456778889999999886556


Q ss_pred             HHHHHHHHHHHHHHHh
Q 028999          130 ILKADKEKLEQQLKVM  145 (200)
Q Consensus       130 ~Lk~e~e~L~~qlk~~  145 (200)
                      . |++++.|+.++..+
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            6 78888888777654

>PRK00846 hypothetical protein; Provisional

Probab=94.50  E-value=0.64  Score=34.69  Aligned_cols=52  Identities=13%  Similarity=0.045  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      .|..++..|+....-.+.-|.+|...+.+.+.+...|+.++..|..+|+++.
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            4556677777777777777778888888888888888888888888898873

>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.44  E-value=0.46  Score=35.35  Aligned_cols=51  Identities=31%  Similarity=0.412  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      .+.+.+|+..+++.-....-|+-+|.+|+...|.|..|.+.++...|.|++
T Consensus         3 lEv~ekLE~KiqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~   53 (79)
T COG3074           3 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALER   53 (79)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHH
Confidence            356778888888888888889999999998888888888766666666653

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

Probab=94.37  E-value=0.31  Score=34.96  Aligned_cols=51  Identities=18%  Similarity=0.187  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      |...+.+|+....-++..+.+|...+.+...+...|+.++..|..+++.+.
T Consensus         2 le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen    2 LEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            566677777777777777777777888888888888888888888888875

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.

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=94.29  E-value=0.54  Score=34.06  Aligned_cols=53  Identities=23%  Similarity=0.309  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      |.+|-...++|+.+|..|.++...+..|...|.+.+....+.+|.+=..|++|
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            33444444555555555555555555555555555555555555555555544

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

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

Probab=94.28  E-value=0.89  Score=41.18  Aligned_cols=17  Identities=18%  Similarity=0.407  Sum_probs=11.3

Q ss_pred             HHHHHHHHhHHHHhhhc
Q 028999           56 LRRERLNDRFLDLSCIL   72 (200)
Q Consensus        56 ~RRekiNe~F~~Lr~lL   72 (200)
                      .|...|...+..|+.+.
T Consensus       184 ~~~~~L~~e~~~Lk~~~  200 (325)
T PF08317_consen  184 ERKAELEEELENLKQLV  200 (325)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            45666667777777766

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

Probab=94.16  E-value=0.51  Score=39.63  Aligned_cols=82  Identities=24%  Similarity=0.336  Sum_probs=36.1

Q ss_pred             HHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           56 LRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  135 (200)
Q Consensus        56 ~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~  135 (200)
                      +.+..+..++..+..-+ -      .+-..+..--.-|..|+.++..|+..+..|..++++....+..|+||...|+.+.
T Consensus        88 r~~~el~~~L~~~~~~l-~------~l~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~  160 (194)
T PF08614_consen   88 RSKGELAQQLVELNDEL-Q------ELEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDELQALQLQL  160 (194)
T ss_dssp             ---------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccc-c------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444555555555444 1      1112233333456666666777776666666666666666666677766666666


Q ss_pred             HHHHHHHHH
Q 028999          136 EKLEQQLKV  144 (200)
Q Consensus       136 e~L~~qlk~  144 (200)
                      .-++..+..
T Consensus       161 ~~~e~k~~~  169 (194)
T PF08614_consen  161 NMLEEKLRK  169 (194)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            666555544

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.

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

Probab=94.16  E-value=0.45  Score=42.58  Aligned_cols=52  Identities=31%  Similarity=0.495  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ..+++...+++..+++.|..+..+|..+.++++++...|..|+.+|+..++.
T Consensus       137 ~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~  188 (290)
T COG4026         137 YEELKEKLEELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKK  188 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3455666777777888888888888888888888888888887777766654

>PRK10884 SH3 domain-containing protein; Provisional

Probab=94.13  E-value=0.41  Score=41.33  Aligned_cols=78  Identities=13%  Similarity=0.107  Sum_probs=43.4

Q ss_pred             HHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           55 KLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  134 (200)
Q Consensus        55 R~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e  134 (200)
                      |.|=.++...+.+|++-| -.         |-++.-+...+|+..+++.+.....|+++.++|+.++.+++.|+..|+++
T Consensus        92 ~~rlp~le~el~~l~~~l-~~---------~~~~~~~~~~~l~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~  161 (206)
T PRK10884         92 RTRVPDLENQVKTLTDKL-NN---------IDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQ  161 (206)
T ss_pred             HHHHHHHHHHHHHHHHHH-HH---------HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344467788888888777 21         11222344445555555555555555555555555555555555555555


Q ss_pred             HHHHHHHH
Q 028999          135 KEKLEQQL  142 (200)
Q Consensus       135 ~e~L~~ql  142 (200)
                      ++.++...
T Consensus       162 ~~~~~~~~  169 (206)
T PRK10884        162 LDDKQRTI  169 (206)
T ss_pred             HHHHHHHH
Confidence            55555443

>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=94.06  E-value=0.23  Score=33.35  Aligned_cols=39  Identities=31%  Similarity=0.484  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          103 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus       103 L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      |+...+.|...-+.|+.+..-|..|+..|++++..|...
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~k   41 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEK   41 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344444444444455555555555555555555555443

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

>PRK00295 hypothetical protein; Provisional

Probab=94.00  E-value=0.94  Score=32.64  Aligned_cols=51  Identities=18%  Similarity=0.141  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      |..++..|+....-++.-|.+|...+.+.+.+...|+.++..|..+++.+.
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            445566666666666667777777777777777888888888888888774

>PRK02793 phi X174 lysis protein; Provisional

Probab=93.97  E-value=1  Score=32.73  Aligned_cols=52  Identities=19%  Similarity=0.151  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      .+..++..|+....-.+.-|.+|...+.+.+.+...|+.++..|..+++.+.
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            3666777777777777777788888888888888888888888888888873

>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=93.95  E-value=0.85  Score=38.66  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=12.1

Q ss_pred             HHHHHHHHhHHHHhhhc
Q 028999           56 LRRERLNDRFLDLSCIL   72 (200)
Q Consensus        56 ~RRekiNe~F~~Lr~lL   72 (200)
                      -|++-.|.+|.+|---|
T Consensus        59 vr~~ly~~~F~ELIRQV   75 (189)
T PF10211_consen   59 VREELYSQCFDELIRQV   75 (189)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            45677777888876666

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 [].

>PRK10884 SH3 domain-containing protein; Provisional

Probab=93.95  E-value=1.4  Score=38.09  Aligned_cols=27  Identities=22%  Similarity=0.407  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          117 LKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus       117 L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      |+.+..+|++|...++++.+.|++++.
T Consensus       137 L~~~n~~L~~~l~~~~~~~~~l~~~~~  163 (206)
T PRK10884        137 LKEENQKLKNQLIVAQKKVDAANLQLD  163 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333433333

>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=93.57  E-value=0.84  Score=33.34  Aligned_cols=55  Identities=33%  Similarity=0.447  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +-|.+|..+-+.|....-.+...|+.|++...++..+...|+..++.++..+..+
T Consensus        12 e~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~l   66 (74)
T PF12329_consen   12 EQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELESL   66 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6788999999999888777778888888888887777777777777777666554

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.

>TIGR02449 conserved hypothetical protein TIGR02449

Probab=93.56  E-value=1.3  Score=32.01  Aligned_cols=53  Identities=30%  Similarity=0.428  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ++.|..+++.|-..++.|+.+...|+.+...+..|...|....+--.+.+.+|
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            67889999999999999999999999999999999999988888888888887

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.

>PRK11637 AmiB activator; Provisional

Probab=93.55  E-value=0.9  Score=42.31  Aligned_cols=43  Identities=23%  Similarity=0.248  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       102 ~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      .+..+...++.++..+..+++++..+...++.++..++.++..
T Consensus        79 ~l~~qi~~~~~~i~~~~~~i~~~~~ei~~l~~eI~~~q~~l~~  121 (428)
T PRK11637         79 KQEEAISQASRKLRETQNTLNQLNKQIDELNASIAKLEQQQAA  121 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333344444444444444444444444555555544443

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.42  E-value=0.76  Score=41.44  Aligned_cols=63  Identities=17%  Similarity=0.286  Sum_probs=37.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           82 KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        82 KasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +-+.|.++-.-.+.++.+++.|....+.++.++.+++.+++++..|...|+.+|+.|+..+..
T Consensus        36 ~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~   98 (265)
T COG3883          36 QDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVE   98 (265)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334555555555566666666666666666666666666666666666666666665544443

>smart00787 Spc7 Spc7 kinetochore protein

Probab=93.42  E-value=1.3  Score=40.37  Aligned_cols=83  Identities=23%  Similarity=0.300  Sum_probs=43.6

Q ss_pred             HHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           55 KLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  134 (200)
Q Consensus        55 R~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e  134 (200)
                      +.|.+.|+..+..|+.+....   ..-..+.|..+-+=|..+..++.........++.+..+++..+++..++++.+..+
T Consensus       178 ~~~~~~L~~e~~~L~~~~~e~---~~~d~~eL~~lk~~l~~~~~ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~  254 (312)
T smart00787      178 RDRKDALEEELRQLKQLEDEL---EDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESKIEDLTNKKSELNTE  254 (312)
T ss_pred             HHHHHHHHHHHHHHHHhHHHH---HhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666777777777776332   12235555555555555555555555555555555555555555555555544444


Q ss_pred             HHHHHH
Q 028999          135 KEKLEQ  140 (200)
Q Consensus       135 ~e~L~~  140 (200)
                      |..++.
T Consensus       255 I~~ae~  260 (312)
T smart00787      255 IAEAEK  260 (312)
T ss_pred             HHHHHH
Confidence            444443

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

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

Probab=93.41  E-value=0.14  Score=43.18  Aligned_cols=43  Identities=35%  Similarity=0.466  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      ++....+--+.|.-|+.|+    .|++.|+.+.++||-|+.+|.+++
T Consensus         5 ~EsklN~AIERnalLE~EL----dEKE~L~~~~QRLkDE~RDLKqEl   47 (166)
T PF04880_consen    5 FESKLNQAIERNALLESEL----DEKENLREEVQRLKDELRDLKQEL   47 (166)
T ss_dssp             HHHHHHHHHHHHHHHHHHH----HHHHHHHHCH--------------
T ss_pred             HHHHHHHHHHHhHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333444444444    334444444444444444443333

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.

>PRK04325 hypothetical protein; Provisional

Probab=93.36  E-value=1.3  Score=32.39  Aligned_cols=53  Identities=19%  Similarity=0.165  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      ..+..++..|+....-++.-|.+|...+.+.+.+...|+.++..|..+++.+.
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            45666677777777777777888888888888888888888888888888874

>PRK00736 hypothetical protein; Provisional

Probab=93.34  E-value=1.4  Score=31.69  Aligned_cols=50  Identities=12%  Similarity=0.155  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           97 RTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        97 ~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      ..++..|+....-++.-|++|...+.+...+...|+.++..|..+++.+.
T Consensus         4 e~Ri~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~~   53 (68)
T PRK00736          4 EERLTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSLE   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34455556555566666666666777777777777778888888887763

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=93.30  E-value=0.056  Score=53.20  Aligned_cols=60  Identities=30%  Similarity=0.385  Sum_probs=44.8

Q ss_pred             CccCCCCCCCCCC----CchhHHHHHHHHHHHHhHHHHhhhcC--CCCCCCCChhhHHHHHHHHHH
Q 028999           35 TRKRARSDSCSRP----GSKACREKLRRERLNDRFLDLSCILE--PGRPARTDKPAILDDAIRVLN   94 (200)
Q Consensus        35 ~~kR~r~~~~~r~----~sH~~~ER~RRekiNe~F~~Lr~lLp--P~~~~K~dKasIL~dAI~YIk   94 (200)
                      +|||.|....-++    .++.-=-||-||+||.-+.-|.+|||  ++.++|.||.|||-=++.|++
T Consensus        10 srkRrrp~qk~rpp~~a~tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   10 SRKRRRPLQKQRPPPKALTKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hhhccCCccccCCCccccccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            3555554443332    34444557889999999999999994  345689999999999999986

>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.22  E-value=0.53  Score=42.44  Aligned_cols=60  Identities=22%  Similarity=0.393  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +...=.-|..|+.+...++.+.+.|..++.++-.+.++++.+...+++++.+|+.+++..
T Consensus        33 i~~~ds~l~~~~~~~~~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~eik~l~~eI~~~   92 (265)
T COG3883          33 IQNQDSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAEL   92 (265)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444555677788888888888888888888888888888888888888888888887765

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

Probab=93.07  E-value=1  Score=38.52  Aligned_cols=60  Identities=23%  Similarity=0.354  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      |..+=++.|+.|+.++.+++..-......+.++.+|...|.+-...+..+++.|+.+|+.
T Consensus        21 IT~~NL~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~epL~~a~~e~~eL~k~L~~   80 (201)
T PF13851_consen   21 ITLNNLELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSEPLKKAEEEVEELRKQLKN   80 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            666778899999999998887766666666667777666666666666666666666554

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=92.92  E-value=1.2  Score=36.56  Aligned_cols=50  Identities=26%  Similarity=0.424  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      ++.++. -.+|+.++..|..+++.|+.|..+++.|...++...+.|..-.-
T Consensus        70 ~KRv~Q-k~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~~  119 (135)
T KOG4196|consen   70 VKRVQQ-KHELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSAV  119 (135)
T ss_pred             HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            344443 34677888888888888888888888888888888888877443

>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=92.88  E-value=1.2  Score=31.00  Aligned_cols=34  Identities=32%  Similarity=0.550  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      +.|+..+..|..+...|+.++..|+.++..|..+
T Consensus        29 ~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e   62 (64)
T PF00170_consen   29 EELEEKVEELESENEELKKELEQLKKEIQSLKSE   62 (64)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3444444444444445555555555555555443

; 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 ....

>PRK13169 DNA replication intiation control protein YabA; Reviewed

Probab=92.86  E-value=1  Score=35.57  Aligned_cols=50  Identities=26%  Similarity=0.298  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      +-|.+|..++..|-.+...|+..+.+|-.|...|+-||..|+..++.+++
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            55677888888888888888888888888888899999888888887744

>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional

Probab=92.85  E-value=0.95  Score=43.85  Aligned_cols=59  Identities=10%  Similarity=0.126  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      -|.+.=.-..+|+++++.|+.+.+.+..+..++...+++|.+|+..|+.+.+-+..+.-
T Consensus        70 ALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a~~~~~~  128 (475)
T PRK13729         70 ATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANPV  128 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCCC
Confidence            34555566778888888888888877788888888899999999999988876665543

>PHA02562 46 endonuclease subunit; Provisional

Probab=92.82  E-value=1.2  Score=42.00  Aligned_cols=75  Identities=16%  Similarity=0.190  Sum_probs=54.4

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           57 RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  136 (200)
Q Consensus        57 RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e  136 (200)
                      ++..+..++.+|+..+ -      .+-+-|.+.++-+..|+.++++|+.....+.+++.+|..+++++..++..+..+..
T Consensus       331 ~~~~~~~~i~el~~~i-~------~~~~~i~~~~~~~~~l~~ei~~l~~~~~~~~~~l~~l~~~l~~~~~~~~~~~ke~~  403 (562)
T PHA02562        331 EFNEQSKKLLELKNKI-S------TNKQSLITLVDKAKKVKAAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKY  403 (562)
T ss_pred             HHHHHHHHHHHHHHHH-H------HHHHHHHHHHHHHHHHHHHHHHHHhhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555666666666666 1      11222677888888899999999888888888888888888888888877776665


Q ss_pred             HH
Q 028999          137 KL  138 (200)
Q Consensus       137 ~L  138 (200)
                      ..
T Consensus       404 ~~  405 (562)
T PHA02562        404 HR  405 (562)
T ss_pred             HH
Confidence            54

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

Probab=92.51  E-value=1.2  Score=34.90  Aligned_cols=55  Identities=22%  Similarity=0.292  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +++=+|+|+-..++   .|...+..|+++++.+..+..+++.+...++.++..|..++
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            56677888877665   34455566666666666666666666666666666665554

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

Probab=92.47  E-value=0.68  Score=42.11  Aligned_cols=16  Identities=31%  Similarity=0.133  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q 028999          129 LILKADKEKLEQQLKV  144 (200)
Q Consensus       129 ~~Lk~e~e~L~~qlk~  144 (200)
                      ..++.+++...++|..
T Consensus       116 ~sl~~q~~~~~~~L~~  131 (314)
T PF04111_consen  116 DSLKNQYEYASNQLDR  131 (314)
T ss_dssp             HHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3344444444444444

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.

>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=92.28  E-value=2.1  Score=34.15  Aligned_cols=65  Identities=29%  Similarity=0.336  Sum_probs=40.0

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH
Q 028999           80 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL---KADKEKLEQQLKV  144 (200)
Q Consensus        80 ~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L---k~e~e~L~~qlk~  144 (200)
                      ..-.+++..=-.-|+++..++..|+.++..|..+-+.+..|+-.|..++..+   ..++..|+.+++.
T Consensus        12 ~~~~~~ve~L~s~lr~~E~E~~~l~~el~~l~~~r~~l~~Eiv~l~~~~e~~~~~~~~~~~L~~el~~   79 (120)
T PF12325_consen   12 GPSVQLVERLQSQLRRLEGELASLQEELARLEAERDELREEIVKLMEENEELRALKKEVEELEQELEE   79 (120)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566666667777777777777777777766666666666665555333   3444444444444

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 [].

>PF13870 DUF4201: Domain of unknown function (DUF4201)

Probab=92.15  E-value=2.2  Score=35.06  Aligned_cols=63  Identities=27%  Similarity=0.441  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  148 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  148 (200)
                      .+.++.-+..+++....+..++..+..++.........++++...++.+.+++..+...+...
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            456677788888888888888899999999999999999999999999999999988887555

>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=92.14  E-value=1.8  Score=35.56  Aligned_cols=44  Identities=34%  Similarity=0.463  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       102 ~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .-+.++..|++++..|+.+++.|..|...+..+++.|.++++.+
T Consensus        49 n~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~   92 (140)
T PF10473_consen   49 NSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKK   92 (140)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445556677777777777777777777777777776666554

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

>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=92.14  E-value=0.64  Score=31.19  Aligned_cols=37  Identities=38%  Similarity=0.487  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      |+..-+.|+...+.|..+-+.|..|+..|+.|...|+
T Consensus         3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~   39 (45)
T PF02183_consen    3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELK   39 (45)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444444444444443

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

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family

Probab=92.09  E-value=1.2  Score=37.58  Aligned_cols=54  Identities=26%  Similarity=0.328  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      +.-...|+.+.+.|+.++..|+.+++.|..+++.|..+...++.+.+-|-+-+.
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            344567777888888888888888888888888888888888777777665443

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.

>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=92.05  E-value=1.1  Score=39.00  Aligned_cols=6  Identities=67%  Similarity=1.769  Sum_probs=3.8

Q ss_pred             ccccCC
Q 028999          179 WQYLPP  184 (200)
Q Consensus       179 wq~~pp  184 (200)
                      |+|+|.
T Consensus       214 W~~l~~  219 (251)
T PF11932_consen  214 WQWLPD  219 (251)
T ss_pred             CeECCH
Confidence            666665

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.

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

Probab=91.93  E-value=1.8  Score=30.58  Aligned_cols=46  Identities=20%  Similarity=0.402  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      |.+|-.+|+.|.....+|..++..|+.+....++|-.+...-++.+
T Consensus         5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN~   50 (56)
T PF04728_consen    5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDNI   50 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            5566667777777666666666666666666666665555444443

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.

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

Probab=91.87  E-value=0.83  Score=40.50  Aligned_cols=52  Identities=23%  Similarity=0.420  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      -=+..+-+..+..|.+|++|++.+..++..|+.|...|+++..+|...++-+
T Consensus        82 pIVtsQRDRFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRyl  133 (248)
T PF08172_consen   82 PIVTSQRDRFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYL  133 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3355667777777778888888888888888888888888888888777766

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

>smart00338 BRLZ basic region leucin zipper

Probab=91.68  E-value=2.3  Score=29.53  Aligned_cols=33  Identities=30%  Similarity=0.517  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          109 KLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus       109 ~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      .|+.++..|..+..+|+.+...|..++..|.++
T Consensus        30 ~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~   62 (65)
T smart00338       30 ELERKVEQLEAENERLKKEIERLRRELEKLKSE   62 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444443

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

Probab=91.49  E-value=2.5  Score=35.08  Aligned_cols=22  Identities=45%  Similarity=0.599  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028999          122 NELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus       122 nELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      ++++.+...|+.|+++|+++|+
T Consensus        76 ~~lr~~~e~L~~eie~l~~~L~   97 (177)
T PF07798_consen   76 AELRSENEKLQREIEKLRQELR   97 (177)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444443

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

Probab=91.43  E-value=1.3  Score=35.25  Aligned_cols=49  Identities=29%  Similarity=0.353  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +=.++..|+.....|..++..|++.+.+|-+|+..|+-|.++|..-|-.
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            4456677777788888899999999999999999999999999886654

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=91.42  E-value=2  Score=31.12  Aligned_cols=52  Identities=29%  Similarity=0.380  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEK-------NELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~ek-------nELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      |..|+.....+...++..+.+.+.|..|.       .....++..|+.|++.|.++++.
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            34455555555555544444444444443       45566777788888888777765

>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89

Probab=91.37  E-value=2.6  Score=30.58  Aligned_cols=51  Identities=22%  Similarity=0.329  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           89 AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        89 AI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      +.+-+...+.....|..+++.....+...-.+.++|++|+..|+.|.+.+.
T Consensus        17 ~~rk~~~~~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r   67 (69)
T PF14197_consen   17 LTRKNSVHEIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELEELR   67 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            444444444555556666666666677777778888888888887766654

>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=91.33  E-value=1.9  Score=34.20  Aligned_cols=59  Identities=36%  Similarity=0.463  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHh
Q 028999           87 DDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN----ELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        87 ~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~ekn----ELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .++|.-|..|+.+.+.++.....|+.+....+..+.    .+..++..|..+++.++..+..+
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            356777777887777777777666666544444333    23344455555555555444443

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

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=91.26  E-value=3.7  Score=29.47  Aligned_cols=46  Identities=28%  Similarity=0.364  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      .+.....+..+...++.++++++.+.++|+.|...|.. .++++.--
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            33445555556666666666666666666666665543 44454433

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.

>TIGR02231 conserved hypothetical protein

Probab=91.23  E-value=1.8  Score=41.37  Aligned_cols=86  Identities=20%  Similarity=0.237  Sum_probs=58.5

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHH
Q 028999           57 RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTE---------------SQELKETNEKLQEEIKSLKAEK  121 (200)
Q Consensus        57 RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~---------------v~~L~~~~~~L~~ei~~L~~ek  121 (200)
                      +-..|.+.+.+|...+ -   .-.++.+.+..-+.||..+...               +.++.+......+++.++..++
T Consensus        72 ~~~~l~~~l~~l~~~~-~---~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (525)
T TIGR02231        72 RLAELRKQIRELEAEL-R---DLEDRGDALKALAKFLEDIREGLTEPIKDSAKRNEPDLKEWFQAFDFNGSEIERLLTED  147 (525)
T ss_pred             HHHHHHHHHHHHHHHH-H---HHHHHHHHHHHHHHHHHHHhhhhccccccccccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555666777777666 2   1256777777778888877642               3445555566667777777777


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999          122 NELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus       122 nELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      .++..+...++.++++|+++|..++
T Consensus       148 ~~~~~~~~~~~~~l~~l~~~l~~l~  172 (525)
T TIGR02231       148 REAERRIRELEKQLSELQNELNALL  172 (525)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            7777777777777788877776654

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.

>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=91.22  E-value=2  Score=34.22  Aligned_cols=62  Identities=27%  Similarity=0.357  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAM  147 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~  147 (200)
                      +.+....+..|..++..|.+.|-.++.++.+++.++.++.++...|+.+...++++++.++.
T Consensus        29 ~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~k~~~~~~l~~   90 (150)
T PF07200_consen   29 VQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQEKEQQQDELSS   90 (150)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            34455566667777777778787778888888888888888889999999999888887743

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.

>COG5570 Uncharacterized small protein [Function unknown]

Probab=91.17  E-value=0.74  Score=32.43  Aligned_cols=46  Identities=33%  Similarity=0.451  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           97 RTESQELKETNEKLQEEIKSLK-------AEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        97 ~~~v~~L~~~~~~L~~ei~~L~-------~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      ...+..|++....|+++|.+-.       -.+.+|...+..||.+||+|..|+
T Consensus         4 eshl~eL~kkHg~le~ei~ea~n~Ps~dd~~i~eLKRrKL~lKeeIEkLka~~   56 (57)
T COG5570           4 ESHLAELEKKHGNLEREIQEAMNSPSSDDLAIRELKRRKLRLKEEIEKLKAQM   56 (57)
T ss_pred             HHHHHHHHHhhchHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHHHHhccC
Confidence            3445556666666666654433       257788889999999999998753

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

Probab=90.86  E-value=2.3  Score=37.98  Aligned_cols=54  Identities=17%  Similarity=0.326  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +|....+.....+++..++-+....++...+.+|..|+..|+.+++.|++++..
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            444444444444444444444444444444444444444444444444444444

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

Probab=90.85  E-value=3.6  Score=36.13  Aligned_cols=59  Identities=27%  Similarity=0.325  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ......=+..|+.++++.+.+.+.++.+...|+.+..++.+|-.+|..|-.+|+.|+..
T Consensus       153 ~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~  211 (216)
T KOG1962|consen  153 NDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIES  211 (216)
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhc
Confidence            34444556667777777777777777777777777777777777777777778777753

>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=90.81  E-value=0.76  Score=31.17  Aligned_cols=32  Identities=28%  Similarity=0.413  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          109 KLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       109 ~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      .-...+.+|..++.+|..++..|+.++..|++
T Consensus        22 rkk~~~~~le~~~~~L~~en~~L~~~i~~L~~   53 (54)
T PF07716_consen   22 RKKQREEELEQEVQELEEENEQLRQEIAQLER   53 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            33445555566666666666666666666554

; 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 ....

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

Probab=90.72  E-value=4.5  Score=38.02  Aligned_cols=87  Identities=28%  Similarity=0.387  Sum_probs=53.4

Q ss_pred             HHHHHhHHHHhhhc-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HH-HHHHHHHHHHH
Q 028999           59 ERLNDRFLDLSCIL-EPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA----EK-NELREEKLILK  132 (200)
Q Consensus        59 ekiNe~F~~Lr~lL-pP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~----ek-nELr~Ek~~Lk  132 (200)
                      +.|-++|.+|..+| .|...+..++..-|++-..+|..+-....+++...+.|..--.-|..    |. ....+|...++
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            45778999999988 22222344565566666555555555555554444443332222221    22 22577889999


Q ss_pred             HHHHHHHHHHHHh
Q 028999          133 ADKEKLEQQLKVM  145 (200)
Q Consensus       133 ~e~e~L~~qlk~~  145 (200)
                      .+++.|+.+|+.+
T Consensus        90 ~~~~~le~~L~~l  102 (363)
T COG0216          90 AKIEELEEELKIL  102 (363)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999988

>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=90.65  E-value=1.2  Score=36.49  Aligned_cols=53  Identities=36%  Similarity=0.518  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHh
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK--LILKADKEKLEQQLKVM  145 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek--~~Lk~e~e~L~~qlk~~  145 (200)
                      +..|..++.+|+.+...|..+++.|+.++..|..+.  ..|..+++.|++++..+
T Consensus        74 l~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l  128 (169)
T PF07106_consen   74 LAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEEL  128 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444443332  34444444454444443

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 [].

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

Probab=90.61  E-value=1.5  Score=41.12  Aligned_cols=42  Identities=48%  Similarity=0.493  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          104 KETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       104 ~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +++.+.++.+...|++-.+||+.-++.|+.++++|+||+..+
T Consensus       224 eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L  265 (365)
T KOG2391|consen  224 EEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSL  265 (365)
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence            344445555555555555555555666666666666665554

>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=90.60  E-value=1.3  Score=39.98  Aligned_cols=57  Identities=14%  Similarity=0.336  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCCCCC
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM-AMPTGGYM  153 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~-~~~p~g~~  153 (200)
                      |+..++.+..+.++++..+..|..+...|.....+-++|.||.+..|+++ ++-|+ ||
T Consensus       167 l~~ai~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPA-fm  224 (267)
T PF10234_consen  167 LKEAIKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPA-FM  224 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChH-HH
Confidence            33444444555555555555555555556555666667777777777776 34444 54

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=90.48  E-value=1  Score=31.28  Aligned_cols=47  Identities=23%  Similarity=0.319  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      |..|++-..+|+.+.+.-..+....+.++.+|+.||..|+.++++++
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            44555556667766654444556777888889999999988888765

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 [, ].

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

Probab=90.46  E-value=1.5  Score=39.15  Aligned_cols=33  Identities=30%  Similarity=0.511  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELRE  126 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~  126 (200)
                      .+++.++..|+++|+.|+.++.+|+.|+..|++
T Consensus       218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~~~  250 (269)
T KOG3119|consen  218 DEMAHRVAELEKENEALRTQVEQLKKELATLRR  250 (269)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            556666777777777777777777766666655

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

Probab=90.41  E-value=0.26  Score=43.73  Aligned_cols=53  Identities=26%  Similarity=0.318  Sum_probs=44.9

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRT   98 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~-~~~K~dKasIL~dAI~YIk~L~~   98 (200)
                      ++..=|.+||.|=-.||+.|..||.+||.. ...|..|...|.-|-.||-.|..
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            567778999999999999999999999632 34689999999989999887754

>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=90.38  E-value=2.9  Score=36.29  Aligned_cols=30  Identities=20%  Similarity=0.285  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          115 KSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       115 ~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +.|+.....+......++.+++.|++|+..
T Consensus        66 e~L~~~~~~l~~~v~~q~~el~~L~~qi~~   95 (251)
T PF11932_consen   66 ENLEVYNEQLERQVASQEQELASLEQQIEQ   95 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333444444445444444

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.

>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=90.34  E-value=2.4  Score=29.69  Aligned_cols=42  Identities=38%  Similarity=0.518  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus       102 ~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      .++.+...|+.++.+++.+..+|+.+...|+.+.+.++...+
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            444444455555555555555555555555545555555444

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

>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=90.22  E-value=6.7  Score=31.37  Aligned_cols=12  Identities=17%  Similarity=0.246  Sum_probs=6.0

Q ss_pred             HHHHhHHHHhhh
Q 028999           60 RLNDRFLDLSCI   71 (200)
Q Consensus        60 kiNe~F~~Lr~l   71 (200)
                      -||..+..++-+
T Consensus         6 yiN~~L~s~G~~   17 (151)
T PF11559_consen    6 YINQQLLSRGYP   17 (151)
T ss_pred             HHHHHHHHCCCC
Confidence            355555554433

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.

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=90.22  E-value=2  Score=42.94  Aligned_cols=44  Identities=25%  Similarity=0.335  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      .-..-|+.|..+++.|+.+|..|+.++.+|+.++.+|+.+...+
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            33455666677777777777777777777777776666655433

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

Probab=90.11  E-value=0.13  Score=51.84  Aligned_cols=81  Identities=21%  Similarity=0.299  Sum_probs=64.3

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCCC----CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPGR----PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE  120 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~----~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~e  120 (200)
                      .+.++|..+|.+||..+.-+|..|-++. .+.    .-|+.++.-+...+.||..+..+...+.++-..|..++.+|++-
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            5789999999999999999999999887 432    23677777899999999998888777777777777777777666


Q ss_pred             HHHHHH
Q 028999          121 KNELRE  126 (200)
Q Consensus       121 knELr~  126 (200)
                      ++-++.
T Consensus       729 ~~~~~q  734 (856)
T KOG3582|consen  729 ISACQQ  734 (856)
T ss_pred             HHHhhc
Confidence            665443

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

Probab=90.06  E-value=2.5  Score=37.52  Aligned_cols=61  Identities=26%  Similarity=0.324  Sum_probs=54.0

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           80 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        80 ~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      .+-.+||.=.+.-=...+.++.+|++++..+..++..|+.|++.|+.+|.+|.-.+--|+.
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            4667788877777788999999999999999999999999999999999999888877765

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

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=89.88  E-value=2.8  Score=36.32  Aligned_cols=40  Identities=35%  Similarity=0.433  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999          107 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus       107 ~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      +..+..+...|..++..|++|+..|..+.+.|+.+.+.++
T Consensus        90 ~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~lk~~~~eL~  129 (193)
T PF14662_consen   90 ARQLEKEQQSLVAEIETLQEENGKLLAERDGLKKRSKELA  129 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHH
Confidence            3444455556666667777777777777777776666653

>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=89.76  E-value=3.5  Score=36.25  Aligned_cols=25  Identities=28%  Similarity=0.360  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEI  114 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei  114 (200)
                      -.+|.+++++.+.|..+.....+++
T Consensus        31 e~~L~e~~kE~~~L~~Er~~h~eeL   55 (230)
T PF10146_consen   31 EKCLEEYRKEMEELLQERMAHVEEL   55 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3566666666666655544443333

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.

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

Probab=89.63  E-value=3.5  Score=37.56  Aligned_cols=37  Identities=38%  Similarity=0.475  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  128 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek  128 (200)
                      -+..|+.+...|..+...|+.+..+|.+|+.+|..|.
T Consensus        51 el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~   87 (314)
T PF04111_consen   51 ELEKLEQEEEELLQELEELEKEREELDQELEELEEEL   87 (314)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444333333333333333333333333

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.

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

Probab=89.48  E-value=2.4  Score=32.80  Aligned_cols=45  Identities=29%  Similarity=0.344  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           97 RTESQELKETNEKL--QEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus        97 ~~~v~~L~~~~~~L--~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      ..+++.++.+.+.|  ..++..|+.++.+++-+...+..+++-+.++
T Consensus        48 ~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~~~l~~~l~~v~~~   94 (106)
T PF10805_consen   48 DRRLQALETKLEHLPTRDDVHDLQLELAELRGELKELSARLQGVSHQ   94 (106)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            34444444444443  3344444444444444444444444444333

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

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

Probab=89.44  E-value=3.4  Score=34.33  Aligned_cols=28  Identities=25%  Similarity=0.239  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          117 LKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       117 L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +..|+.+|++|....+.|++.|+.|.+.
T Consensus       159 ~~~ei~~lk~el~~~~~~~~~LkkQ~~~  186 (192)
T PF05529_consen  159 LSEEIEKLKKELEKKEKEIEALKKQSEG  186 (192)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444443

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

>TIGR00219 mreC rod shape-determining protein MreC

Probab=89.42  E-value=2.6  Score=37.72  Aligned_cols=42  Identities=24%  Similarity=0.264  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          101 QELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       101 ~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .+|.+||++|++++.+|+++.+.+   ...|+.|.++|++.|...
T Consensus        69 ~~l~~EN~~Lr~e~~~l~~~~~~~---~~~l~~EN~rLr~LL~~~  110 (283)
T TIGR00219        69 NNLEYENYKLRQELLKKNQQLEIL---TQNLKQENVRLRELLNSP  110 (283)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCc
Confidence            345566667766666554444432   223677777777755543

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.

>PRK09039 hypothetical protein; Validated

Probab=89.27  E-value=3  Score=38.33  Aligned_cols=54  Identities=11%  Similarity=0.109  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      +.+++-.-|..|+.+++.|+.+...|+.++..++.+..+.+.....|+.+++.+
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            455666667778888888888777777777777776666666666666555554

>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=89.19  E-value=2.7  Score=31.50  Aligned_cols=42  Identities=26%  Similarity=0.366  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          103 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       103 L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      |..+...||..+..|...+.+.++|+..|+.|.+-|++=+..
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            333334444444444444444455555555555555544444

The exact function is unknown.

>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=88.98  E-value=1.3  Score=31.13  Aligned_cols=31  Identities=39%  Similarity=0.456  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNEL  124 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknEL  124 (200)
                      .+++.++++|+.+++.++.+.++|+.++..|
T Consensus        20 ~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l   50 (80)
T PF04977_consen   20 YQLNQEIAELQKEIEELKKENEELKEEIERL   50 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3455555555555555555555555555555

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

>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=88.89  E-value=11  Score=30.23  Aligned_cols=21  Identities=29%  Similarity=0.385  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHhHHHHhhhc
Q 028999           52 CREKLRRERLNDRFLDLSCIL   72 (200)
Q Consensus        52 ~~ER~RRekiNe~F~~Lr~lL   72 (200)
                      .++...|+.+++.+..|.+-+
T Consensus        48 ~r~~~~~e~l~~~~~~l~~d~   68 (151)
T PF11559_consen   48 DRDMEQREDLSDKLRRLRSDI   68 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHhHH
Confidence            455666777777777766655

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.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=88.78  E-value=1.2  Score=34.50  Aligned_cols=43  Identities=26%  Similarity=0.343  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +|+.+++.++.+++.|+       ++..+|+.|...|+...+-++...+.
T Consensus        31 ~l~~q~~~~~~e~~~l~-------~~n~~L~~eI~~L~~~~dyiEe~AR~   73 (105)
T PRK00888         31 RVNDQVAAQQQTNAKLK-------ARNDQLFAEIDDLKGGQEAIEERARN   73 (105)
T ss_pred             HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhhCcHHHHHHHHHH
Confidence            34444444444444444       44444444444444444555555544

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

Probab=88.75  E-value=4.1  Score=29.98  Aligned_cols=21  Identities=24%  Similarity=0.300  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEI  114 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei  114 (200)
                      ++...+++.|+.+|-.|.=.|
T Consensus         3 rEqe~~i~~L~KENF~LKLrI   23 (75)
T PF07989_consen    3 REQEEQIDKLKKENFNLKLRI   23 (75)
T ss_pred             HHHHHHHHHHHHhhhhHHHHH
Confidence            444555555555554444333

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=88.69  E-value=3.8  Score=35.77  Aligned_cols=39  Identities=33%  Similarity=0.563  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       102 ~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ++.++|+.|++|+.+|+.+..++    ..++.|.++|...|..
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    2456777777776654

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

Probab=88.67  E-value=2.7  Score=44.37  Aligned_cols=55  Identities=27%  Similarity=0.434  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      =+++|+.+|++++..+..|.++..+++.+.-+-++|+...+.++..|...+...+
T Consensus       402 k~~~L~~evek~e~~~~~L~~e~~~~~~~~~~~~ee~~~i~~~i~~l~k~i~~~~  456 (1074)
T KOG0250|consen  402 KLEQLKKEVEKLEEQINSLREELNEVKEKAKEEEEEKEHIEGEILQLRKKIENIS  456 (1074)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444444444444445555555555554443

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

Probab=88.63  E-value=2.2  Score=42.28  Aligned_cols=59  Identities=34%  Similarity=0.464  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           87 DDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        87 ~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ...-.-+.+|+.+++.|..+.+.+..+++.|+.++.++.+|....+.+.++|+++++-.
T Consensus       324 ~~~~~el~~l~~~l~~l~~~i~~~~~~~~~l~~~~~q~~~e~~~~~~~~~~le~~~~l~  382 (594)
T PF05667_consen  324 EEQEQELEELQEQLDELESQIEELEAEIKMLKSSLKQLEEELEEKEAENEELEEELKLK  382 (594)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35567788889999999999999999999999999999999999999999999888753

>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=88.33  E-value=7.7  Score=35.92  Aligned_cols=65  Identities=20%  Similarity=0.361  Sum_probs=39.9

Q ss_pred             HHHHHHHhHHHHhhh--------cCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           57 RRERLNDRFLDLSCI--------LEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN  122 (200)
Q Consensus        57 RRekiNe~F~~Lr~l--------LpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~ekn  122 (200)
                      |...++....+|--.        ++|.. .+.+=+.+|.++-+-.+.|+.++..|+.....++-+++-|+..++
T Consensus        38 r~q~LKkk~~el~~~~~~~~d~~~~~~~-~~~~La~lL~~sre~Nk~L~~Ev~~Lrqkl~E~qGD~KlLR~~la  110 (319)
T PF09789_consen   38 RYQALKKKYRELIQEAAGFGDPSIPPEK-ENKNLAQLLSESREQNKKLKEEVEELRQKLNEAQGDIKLLREKLA  110 (319)
T ss_pred             HHHHHHHHHHHhhhhhcccCCccCCccc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHH
Confidence            446666666665521        12221 233445688899888888888888888766666655555555444

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

Probab=88.33  E-value=11  Score=32.30  Aligned_cols=15  Identities=27%  Similarity=0.414  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHHHH
Q 028999          128 KLILKADKEKLEQQL  142 (200)
Q Consensus       128 k~~Lk~e~e~L~~ql  142 (200)
                      ..+|+++.+.+.+++
T Consensus       161 i~~lks~~~~l~~~~  175 (190)
T PF05266_consen  161 ISRLKSEAEALKEEI  175 (190)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            344444444444433

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=88.29  E-value=2.8  Score=37.08  Aligned_cols=49  Identities=16%  Similarity=0.228  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      +-+|+.+++.|+.+...|+-+++++.-+++++.++...+..+++++-.+
T Consensus        56 ~~~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~y~dld~r~~~  104 (263)
T PRK10803         56 LTQLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSSG  104 (263)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4466777777777777777777777777777777777777777776543

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

Probab=88.25  E-value=4  Score=30.74  Aligned_cols=50  Identities=38%  Similarity=0.533  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKA---EKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~---eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      .|+.+++.|+.+...+..++..++.   +..+|..+...++.++..++.+++.
T Consensus        40 ~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~   92 (108)
T PF02403_consen   40 ELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKE   92 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555565555555555544444   2344444444555555444444443

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 ....

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

Probab=88.11  E-value=3.7  Score=40.55  Aligned_cols=50  Identities=32%  Similarity=0.456  Sum_probs=20.9

Q ss_pred             CChhhHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           80 TDKPAILDDAIRVLN----QLRTESQELKETNEKLQEEIKSLKAEKNELREEKL  129 (200)
Q Consensus        80 ~dKasIL~dAI~YIk----~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~  129 (200)
                      +.|+.+|..-++.+.    +|......|+.++..|+.++..|..+++..+++..
T Consensus       135 ~~ka~~lQ~qlE~~qkE~eeL~~~~~~Le~e~~~l~~~v~~l~~eL~~~~ee~e  188 (546)
T PF07888_consen  135 TTKAQLLQNQLEECQKEKEELLKENEQLEEEVEQLREEVERLEAELEQEEEEME  188 (546)
T ss_pred             ehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666655544432    22223333444444444444444444433333333

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

>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=87.87  E-value=5.7  Score=35.90  Aligned_cols=60  Identities=22%  Similarity=0.314  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHh
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK-------ADKEKLEQQLKVM  145 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk-------~e~e~L~~qlk~~  145 (200)
                      +..+..-|.+++..+..+..+...|..+|+.-+.|+.-.+.+...|+       .|-|+|+.+|+.+
T Consensus       171 i~~~~~~~~~~~~~l~~l~~de~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmdEyEklE~EL~~l  237 (267)
T PF10234_consen  171 IKAVQQQLQQTQQQLNNLASDEANLEAKIEKKKQELERNQKRLQSLQSVRPAFMDEYEKLEEELQKL  237 (267)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHH
Confidence            34444556666666777777777788888888888887777777776       6888888888764

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 [].

>PRK09039 hypothetical protein; Validated

Probab=87.75  E-value=4.5  Score=37.23  Aligned_cols=46  Identities=17%  Similarity=0.236  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           99 ESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        99 ~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +|..|+.+.+.|+.++..|..++..+..+....+.+++.|++.|..
T Consensus       138 ~V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~  183 (343)
T PRK09039        138 QVELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNV  183 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444455555555555555555555555555555555544

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

Probab=87.64  E-value=6.3  Score=35.06  Aligned_cols=43  Identities=33%  Similarity=0.303  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  136 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e  136 (200)
                      ..|..+++.+++...+|..++.+|..++.+|.++...|+.++.
T Consensus        92 ~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~  134 (239)
T COG1579          92 RALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLE  134 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444444444444444444444444444444333333333

>PRK13922 rod shape-determining protein MreC; Provisional

Probab=87.64  E-value=3.4  Score=36.09  Aligned_cols=25  Identities=32%  Similarity=0.457  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEI  114 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei  114 (200)
                      +..+.+|+++.++|++++..|+.+.
T Consensus        68 ~~~~~~l~~en~~L~~e~~~l~~~~   92 (276)
T PRK13922         68 LASLFDLREENEELKKELLELESRL   92 (276)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555544443

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

Probab=87.61  E-value=7.1  Score=33.82  Aligned_cols=56  Identities=16%  Similarity=0.297  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  148 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  148 (200)
                      ...|+..++-....-......-+..+.|...|+.|+..++.++..|+.|+..+..+
T Consensus       128 a~~LqaDl~~~~~Q~~~va~~Q~q~r~ea~aL~~e~~aaqaQL~~lQ~qv~~Lq~q  183 (192)
T PF11180_consen  128 ANRLQADLQIARQQQQQVAARQQQARQEAQALEAERRAAQAQLRQLQRQVRQLQRQ  183 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333333333333333333345555666666667777777777777777776544

>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion

Probab=87.59  E-value=5.9  Score=33.61  Aligned_cols=60  Identities=27%  Similarity=0.414  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           84 AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        84 sIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      .=|.+++..+.+=+...+.|..-|..|.++.+..+.....|.++..+|..+.+++..+|.
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            446666666666666777788888888888888888888888888888888888765554

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

Probab=87.48  E-value=9.2  Score=37.91  Aligned_cols=90  Identities=26%  Similarity=0.436  Sum_probs=63.7

Q ss_pred             HHHHHHHHhHHHHhhhcCCCCCCCCChhhH-HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           56 LRRERLNDRFLDLSCILEPGRPARTDKPAI-LDDAIRVLNQLRTESQELKE---TNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        56 ~RRekiNe~F~~Lr~lLpP~~~~K~dKasI-L~dAI~YIk~L~~~v~~L~~---~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      .|=+.+.+|+..|..+-        .|-.. +.+.++|..+++.+.+.|..   ..+.|+.++..+..+..+.-...+..
T Consensus       297 ~~L~~ve~Rl~~L~~l~--------RKY~~~~~~l~~~~~~~~~el~~L~~~~~~~~~Le~~~~~l~~~~~~~A~~Ls~~  368 (557)
T COG0497         297 NRLEEVEERLFALKSLA--------RKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKKLKAELLEAAEALSAI  368 (557)
T ss_pred             HHHHHHHHHHHHHHHHH--------HHhCCCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45566777777777775        24444 78999999999999999885   45678888888888888777766655


Q ss_pred             HHHH-----HHHHHHHHHhcCCCCCCC
Q 028999          132 KADK-----EKLEQQLKVMAMPTGGYM  153 (200)
Q Consensus       132 k~e~-----e~L~~qlk~~~~~p~g~~  153 (200)
                      +...     ..+.++|+.+....+-|.
T Consensus       369 R~~~A~~L~~~v~~eL~~L~Me~a~F~  395 (557)
T COG0497         369 RKKAAKELEKEVTAELKALAMEKARFT  395 (557)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCceEE
Confidence            4333     235677777766555453

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

Probab=87.41  E-value=6.3  Score=37.80  Aligned_cols=20  Identities=35%  Similarity=0.532  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q 028999          106 TNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus       106 ~~~~L~~ei~~L~~eknELr  125 (200)
                      +..+|+.++++++.+++.+.
T Consensus        60 ~~~kL~~~lk~~e~~i~~~~   79 (420)
T COG4942          60 QRAKLEKQLKSLETEIASLE   79 (420)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            33344444444444444333

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

Probab=87.35  E-value=6.1  Score=32.42  Aligned_cols=50  Identities=26%  Similarity=0.436  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLK-------AEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~-------~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ..+.+++.++.....+.+++.++.       .+..+++.+...++.+.+++.+.++.
T Consensus       127 ~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  183 (191)
T PF04156_consen  127 SVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRSQLERLQENLQQLEEKIQE  183 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444       44444555555555555555544443

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 [].

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

Probab=87.14  E-value=4.5  Score=28.76  Aligned_cols=58  Identities=16%  Similarity=0.310  Sum_probs=34.6

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           80 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        80 ~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      .+|-+.|.++-.+|.+....+.+|+-+...+..      .+++.+.......+.++.+|+.+|+
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      4555666666666666666666664

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=87.04  E-value=7.2  Score=30.92  Aligned_cols=30  Identities=33%  Similarity=0.447  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr  125 (200)
                      |+..++.|+.++..+...+.+|.+++++++
T Consensus        42 L~~~l~~L~~q~~s~~qr~~eLqaki~ea~   71 (107)
T PF09304_consen   42 LRNALQSLQAQNASRNQRIAELQAKIDEAR   71 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444444444444444444444443

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.

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

Probab=87.04  E-value=4.8  Score=35.42  Aligned_cols=13  Identities=38%  Similarity=0.598  Sum_probs=4.9

Q ss_pred             HHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKE  105 (200)
Q Consensus        93 Ik~L~~~v~~L~~  105 (200)
                      +..++..++.|..
T Consensus       218 ~~~~r~~~~~l~~  230 (312)
T PF00038_consen  218 LKELRRQIQSLQA  230 (312)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHhhhhHhhh
Confidence            3333333333333

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

>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=86.98  E-value=4.2  Score=33.85  Aligned_cols=35  Identities=37%  Similarity=0.459  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +.+.+|+++|+.|+.+...|...||.|.+.|+.++
T Consensus       157 ~~~~~ei~~lk~el~~~~~~~~~LkkQ~~~l~~ey  191 (192)
T PF05529_consen  157 KKLSEEIEKLKKELEKKEKEIEALKKQSEGLQKEY  191 (192)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            44567777777777777777777777777776543

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

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

Probab=86.94  E-value=4.5  Score=40.36  Aligned_cols=55  Identities=31%  Similarity=0.430  Sum_probs=30.9

Q ss_pred             HHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           91 RVLNQLRTE----SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        91 ~YIk~L~~~----v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ++|++|+.+    ++.|+.+...|++.+..|..+.+.|+.|+......+..|+.+|..+
T Consensus         4 e~l~qlq~Erd~ya~~lk~e~a~~qqr~~qmseev~~L~eEk~~~~~~V~eLE~sL~eL   62 (617)
T PF15070_consen    4 ESLKQLQAERDQYAQQLKEESAQWQQRMQQMSEEVRTLKEEKEHDISRVQELERSLSEL   62 (617)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344445443    3334455555666666666666666666666666666666555554

>COG2433 Uncharacterized conserved protein [Function unknown]

Probab=86.94  E-value=2.9  Score=41.81  Aligned_cols=35  Identities=34%  Similarity=0.545  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr  125 (200)
                      ..++.|+.+++.|+..++.|+.++..|+.++.+++
T Consensus       429 ~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~  463 (652)
T COG2433         429 ETVERLEEENSELKRELEELKREIEKLESELERFR  463 (652)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44555555555555555555555555555554443

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

Probab=86.84  E-value=7.3  Score=31.98  Aligned_cols=43  Identities=26%  Similarity=0.320  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           98 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        98 ~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      +..+..++....+.+..+.+..+..+++.+...++.+.+.+..
T Consensus       123 ~~~~~~~~~l~~l~~~~~~~~~e~~~l~~~~~~~~~~~~~~~~  165 (191)
T PF04156_consen  123 ELLKSVEERLDSLDESIKELEKEIRELQKELQDSREEVQELRS  165 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444445555555555555555555333333333333333

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 [].

>TIGR02492 flgK_ends flagellar hook-associated protein FlgK

Probab=86.78  E-value=8  Score=34.91  Aligned_cols=76  Identities=26%  Similarity=0.358  Sum_probs=52.4

Q ss_pred             HHHHhHHHHhhhc-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           60 RLNDRFLDLSCIL-EPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        60 kiNe~F~~Lr~lL-pP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      .||+-|..|.++- .|.  ....+.++|..|-.....++.--..|.........+++..-.++|.|-++...|..+|..
T Consensus       108 ~l~~ff~a~~~ls~~P~--~~~~r~~vl~~a~~l~~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~~Ia~lN~~I~~  184 (322)
T TIGR02492       108 YLNNFFNALQELAKNPD--SEALRQAVLESAQALANSFNQTSNELQDLRKGINAEIKSAVTEINSLLKQIASLNKEIQQ  184 (322)
T ss_pred             HHHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3555555555554 121  235678888888888888888777777777777777777777777777777777666654

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.

>PF15458 NTR2: Nineteen complex-related protein 2

Probab=86.76  E-value=8.3  Score=34.12  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=15.7

Q ss_pred             CCchhHHHHHHHHHHHHhHHH
Q 028999           47 PGSKACREKLRRERLNDRFLD   67 (200)
Q Consensus        47 ~~sH~~~ER~RRekiNe~F~~   67 (200)
                      +.......++||..|-+.|.+
T Consensus       140 ~ka~~~~~~~rR~~i~e~I~~  160 (254)
T PF15458_consen  140 KKAEREQKRRRREEIEEAIND  160 (254)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            344566777888889888887

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

Probab=86.72  E-value=1.1  Score=40.47  Aligned_cols=54  Identities=24%  Similarity=0.232  Sum_probs=44.8

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRT   98 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~-~~~K~dKasIL~dAI~YIk~L~~   98 (200)
                      .|+..-+.+||+|=..||..|..|+..+|-. ...|.+|-..|.-|-.||.-|-.
T Consensus       173 ~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~  227 (285)
T KOG4395|consen  173 HRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGC  227 (285)
T ss_pred             hhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHH
Confidence            3567778999999999999999999999543 23578899999999999987644

>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]

Probab=86.70  E-value=0.92  Score=44.82  Aligned_cols=39  Identities=31%  Similarity=0.348  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKL  129 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~  129 (200)
                      +|+..|+..+++|..+|+.|+.|...|++++.+|-.|+.
T Consensus       302 Ey~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~  340 (655)
T KOG4343|consen  302 EYMLGLEARLQALLSENEQLKKENATLKRQLDELVSENQ  340 (655)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCc
Confidence            344444444444444444444444444444444444333

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

Probab=86.65  E-value=12  Score=40.24  Aligned_cols=10  Identities=30%  Similarity=0.856  Sum_probs=7.8

Q ss_pred             CCCccccccc
Q 028999            1 MPLIEFNFCV   10 (200)
Q Consensus         1 ~~~~~~~~~~   10 (200)
                      +|.|||.|..
T Consensus       395 LPFIGfTy~~  404 (1317)
T KOG0612|consen  395 LPFIGFTYTH  404 (1317)
T ss_pred             CCeeeeeecc
Confidence            6888998874

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

Probab=86.47  E-value=7.4  Score=27.50  Aligned_cols=48  Identities=19%  Similarity=0.345  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           98 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        98 ~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..+++|.....+|..++..|..+.+-++.+....|.|-.|-.+-|...
T Consensus         3 akid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN~   50 (56)
T PF04728_consen    3 AKIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDNI   50 (56)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            467888888999999999999999999999988888888777766543

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.

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

Probab=86.46  E-value=3.5  Score=38.63  Aligned_cols=51  Identities=18%  Similarity=0.230  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPT  149 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p  149 (200)
                      -.+.|.....+++.++..|+.+.+.+..+.+.++.       |+++++.+++.+..+|
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~   66 (398)
T PTZ00454         16 TERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKR-------ELIRAKEEVKRIQSVP   66 (398)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCC
Confidence            34445455555555555555555555444444444       4444555555554443

>PF14662 CCDC155: Coiled-coil region of CCDC155

Probab=86.43  E-value=6.7  Score=34.01  Aligned_cols=60  Identities=30%  Similarity=0.377  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ++..|...=+.|.++++.|+.....|+++.+.|-++-.++..|+..|-++++.|+.+-..
T Consensus        54 s~Qqal~~aK~l~eEledLk~~~~~lEE~~~~L~aq~rqlEkE~q~L~~~i~~Lqeen~k  113 (193)
T PF14662_consen   54 SLQQALQKAKALEEELEDLKTLAKSLEEENRSLLAQARQLEKEQQSLVAEIETLQEENGK  113 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            445666666666666666666666666666666666666666666666666666655443

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

Probab=86.40  E-value=6.5  Score=38.72  Aligned_cols=80  Identities=23%  Similarity=0.296  Sum_probs=54.2

Q ss_pred             HHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           58 RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        58 RekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      +..||+-|..|..+. -.-..-.-|.+||++|=....++...-..|+........+|...-.++|.|-.+...|..+|-+
T Consensus       110 ~~~L~~ff~s~q~la-~~P~~~a~r~~vl~~a~~l~~~in~~~~~L~~l~~~i~~~I~~~V~~vNsLl~qIa~lN~qI~~  188 (552)
T COG1256         110 STLLNDFFNSLQELA-SNPSDTAARQAVLSKAQTLVNQINNTYEQLTDLRKDINAEIAATVDEVNSLLKQIADLNKQIRK  188 (552)
T ss_pred             HHHHHHHHHHHHHHH-hCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456777777777776 2111236677888888888888887777777777777777777777777776666655555544


Q ss_pred             H
Q 028999          138 L  138 (200)
Q Consensus       138 L  138 (200)
                      .
T Consensus       189 ~  189 (552)
T COG1256         189 V  189 (552)
T ss_pred             h
Confidence            3

>PF14282 FlxA: FlxA-like protein

Probab=86.38  E-value=5  Score=30.97  Aligned_cols=55  Identities=18%  Similarity=0.238  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEE----IKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~e----i~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      -..|..|+.++..|..+...|...    .++-......|..+...|.++|..|+.+...
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            567788888888887777776652    2333344445566666666666666555443

>PHA03011 hypothetical protein; Provisional

Probab=86.33  E-value=8.6  Score=30.60  Aligned_cols=59  Identities=24%  Similarity=0.400  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ...-++-+..|+.+-.+|-.+..-+..+++.+..=+.+-.+|.--|.+|+++|..++..
T Consensus        59 ~Nai~e~ldeL~~qYN~L~dEYn~i~Ne~k~~~~iIQdn~d~I~~LraeIDkLK~niaN  117 (120)
T PHA03011         59 INAIIEILDELIAQYNELLDEYNLIENEIKDLEIIIQDNDDEIHFLRAEIDKLKENIAN  117 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHhc
Confidence            34456677777777778888887888888888888888888888899999999887654

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

Probab=86.29  E-value=13  Score=35.78  Aligned_cols=18  Identities=28%  Similarity=0.434  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHhHHHHhhh
Q 028999           54 EKLRRERLNDRFLDLSCI   71 (200)
Q Consensus        54 ER~RRekiNe~F~~Lr~l   71 (200)
                      ||.||+.|-+.+..+.-.
T Consensus       110 ~r~qr~~La~~L~A~~r~  127 (420)
T COG4942         110 EREQRRRLAEQLAALQRS  127 (420)
T ss_pred             HHHHHHHHHHHHHHHHhc
Confidence            367888888888887763

>PF15397 DUF4618: Domain of unknown function (DUF4618)

Probab=86.20  E-value=4.2  Score=36.58  Aligned_cols=83  Identities=25%  Similarity=0.290  Sum_probs=58.5

Q ss_pred             HHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           59 ERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ-LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        59 ekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~-L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      +.+++.+...+.-+ -.. -...|-.||+.++.-+.. .+..+-..-.+|..++.++..-+.++++|.++...|++|++.
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 DELNEMRQMELASL-SRK-IQEKKEEILSSAAEKTQSPMQPALLQRTLENQVMQKEIVQFREEIDELEEEIPQLRAEVEQ  218 (258)
T ss_pred             HHHHHHHHHHHHHH-HHH-HHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555555555 211 135566788877655444 555565566788888888888889999999999999999998


Q ss_pred             HHHHHH
Q 028999          138 LEQQLK  143 (200)
Q Consensus       138 L~~qlk  143 (200)
                      |..+..
T Consensus       219 L~~~~~  224 (258)
T PF15397_consen  219 LQAQAQ  224 (258)
T ss_pred             HHHhhc
Confidence            888766

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

Probab=86.14  E-value=10  Score=27.07  Aligned_cols=54  Identities=24%  Similarity=0.377  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      |..=|+-=..|+.++.+.+..+-.+...+++-.....+|..+...|+.+++.++
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            444455555666666666666666666666666666666666666666555543

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

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

Probab=86.12  E-value=0.53  Score=47.52  Aligned_cols=51  Identities=25%  Similarity=0.358  Sum_probs=40.6

Q ss_pred             CCchhHHHHHHHHHHHHhHHHHhhhcCC--CCCCCCChhhHHHHHHHHHHHHHH
Q 028999           47 PGSKACREKLRRERLNDRFLDLSCILEP--GRPARTDKPAILDDAIRVLNQLRT   98 (200)
Q Consensus        47 ~~sH~~~ER~RRekiNe~F~~Lr~lLpP--~~~~K~dKasIL~dAI~YIk~L~~   98 (200)
                      |.+-.-+-|-||.|=|+-|.+|..+||-  +..+..|||||+-=||-|++ |++
T Consensus        47 kEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR-lrk   99 (768)
T KOG3558|consen   47 KEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR-LRK   99 (768)
T ss_pred             hhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH-HHH
Confidence            4444456688999999999999999952  12367999999999999998 554

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

Probab=86.00  E-value=5.5  Score=28.50  Aligned_cols=49  Identities=16%  Similarity=0.270  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      +.|.+|+.++.-++...+.|...+-+...++..|+.+...|...+..+.
T Consensus         4 ~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~   52 (69)
T PF04102_consen    4 ERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE   52 (69)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3455666666666666666666666666666666666666666666555

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.

>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=85.95  E-value=6.8  Score=29.39  Aligned_cols=48  Identities=25%  Similarity=0.329  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      =..|..++..|+.....|-..+..++.|-..|+.||..|+.=|..|-.
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            346777888888888889999999999999999999999999998855

The exact function is unknown.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=85.93  E-value=3.7  Score=31.79  Aligned_cols=34  Identities=12%  Similarity=0.219  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          107 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       107 ~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      ...++.++.+++.++.+|++++..|+.|+++|+.
T Consensus        29 ~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~   62 (105)
T PRK00888         29 YWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG   62 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            4456666777777777777777777777777765

>PHA02562 46 endonuclease subunit; Provisional

Probab=85.90  E-value=5.6  Score=37.59  Aligned_cols=16  Identities=13%  Similarity=0.266  Sum_probs=7.2

Q ss_pred             HHHHHHHhHHHHhhhc
Q 028999           57 RRERLNDRFLDLSCIL   72 (200)
Q Consensus        57 RRekiNe~F~~Lr~lL   72 (200)
                      .+..|...+..|...+
T Consensus       307 ~i~~l~~~l~~l~~~i  322 (562)
T PHA02562        307 KLKELQHSLEKLDTAI  322 (562)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3444444444444444

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

Probab=85.88  E-value=9.6  Score=40.43  Aligned_cols=88  Identities=24%  Similarity=0.339  Sum_probs=52.7

Q ss_pred             HHHHHHHHHhHHHHhhhcCCCC----CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           55 KLRRERLNDRFLDLSCILEPGR----PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI  130 (200)
Q Consensus        55 R~RRekiNe~F~~Lr~lLpP~~----~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~  130 (200)
                      |.+.+.++..+..+..-+--..    ..--+|..-|...|+   .|+.++..|..+...+.+++.....++...+.+...
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            4455566666666665551100    011355555555544   455577778877777777777777777777777777


Q ss_pred             HHHHHHHHHHHHHHh
Q 028999          131 LKADKEKLEQQLKVM  145 (200)
Q Consensus       131 Lk~e~e~L~~qlk~~  145 (200)
                      |+..++....+|+.+
T Consensus       448 l~k~i~~~~~~l~~l  462 (1074)
T KOG0250|consen  448 LRKKIENISEELKDL  462 (1074)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            766666666555553

>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=85.75  E-value=7.1  Score=36.32  Aligned_cols=45  Identities=22%  Similarity=0.374  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKL  129 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~  129 (200)
                      +|.-+++-+..|+.+++.|..+++.|+.+...+..++.++-.+|.
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            455666667778888888888887777777777776666555444

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.

>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=85.64  E-value=0.75  Score=35.42  Aligned_cols=48  Identities=35%  Similarity=0.484  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  135 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~  135 (200)
                      +.=+||..|..++..|..++..|..++.+|..++.+++.+...|+..+
T Consensus        22 eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~~~l   69 (131)
T PF05103_consen   22 EVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREEEESLQRAL   69 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT---------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHhh
Confidence            455889999998888888888888888888888888777666665444

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.

>PRK04406 hypothetical protein; Provisional

Probab=85.52  E-value=6.7  Score=28.83  Aligned_cols=48  Identities=10%  Similarity=0.181  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      +.|.+|+.++.-++...+.|...+-+...++..|+.+...|...+..+
T Consensus        11 ~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~   58 (75)
T PRK04406         11 ERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNM   58 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            467777777777777777777777777777777776666665444433

>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]

Probab=85.49  E-value=5.4  Score=40.21  Aligned_cols=64  Identities=20%  Similarity=0.292  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  148 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  148 (200)
                      ||.+-.+.......++.+|+...++|+.+|.++...++||+.+...-+.|.+.|+..+.....+
T Consensus        80 ~~~e~~RI~~sVs~EL~ele~krqel~seI~~~n~kiEelk~~i~~~q~eL~~Lk~~ieqaq~~  143 (907)
T KOG2264|consen   80 ILREQKRILASVSLELTELEVKRQELNSEIEEINTKIEELKRLIPQKQLELSALKGEIEQAQRQ  143 (907)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHhHHHHHHHH
Confidence            3444444444444555566666666666666666666666666666666666666655554433

>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=85.42  E-value=5.5  Score=37.03  Aligned_cols=37  Identities=22%  Similarity=0.347  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  128 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek  128 (200)
                      -+.+|..+.+.|+.+...+..+++++-.+|+++..+.
T Consensus       145 ~~~~L~~enerL~~e~~~~~~qlE~~v~~K~~~E~~L  181 (342)
T PF06632_consen  145 ENEHLQKENERLESEANKLLKQLEKFVNAKEEHEEDL  181 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445666777777777777777777777777765554

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.

>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family

Probab=85.39  E-value=4.8  Score=39.09  Aligned_cols=36  Identities=36%  Similarity=0.460  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  126 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~  126 (200)
                      +-|+.|-.++.+++.+..+|..+.+.|+.|.+.|+.
T Consensus        59 DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~   94 (472)
T TIGR03752        59 DTLRTLVAEVKELRKRLAKLISENEALKAENERLQK   94 (472)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            667777777777777777777777777777777765

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.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=85.36  E-value=3.9  Score=36.18  Aligned_cols=44  Identities=16%  Similarity=0.212  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       102 ~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +|....+.|+.|+.+|+-+++++..+...++..-..+.++|...
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            55666677777777777777777777777766666666677664

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

Probab=85.30  E-value=13  Score=30.12  Aligned_cols=66  Identities=18%  Similarity=0.087  Sum_probs=44.8

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           80 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        80 ~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .+...-...+++....|+.++.......+.|+++++.....+..-.+....|+..+..++.+++..
T Consensus        16 ~~~~~~~e~ll~~~~~LE~qL~~~~~~l~lLq~e~~~~e~~le~d~~~L~~Le~~~~~~~~e~~~~   81 (160)
T PF13094_consen   16 REDSFDYEQLLDRKRALERQLAANLHQLELLQEEIEKEEAALERDYEYLQELEKNAKALEREREEE   81 (160)
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344556677888888888888877777777777777666666555555566666666666555553

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

Probab=85.29  E-value=2.8  Score=39.22  Aligned_cols=43  Identities=30%  Similarity=0.302  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      .++++.|+.+++.|+.++..|..+.+.++.+++.+++|...|+
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (398)
T PTZ00454         21 YEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQ   63 (398)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4567778888999999999999999999999998888776664

>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=85.26  E-value=22  Score=30.12  Aligned_cols=67  Identities=19%  Similarity=0.316  Sum_probs=34.3

Q ss_pred             CCchhHHHH-----HHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           47 PGSKACREK-----LRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRV---LNQLRTESQELKETNEKLQEEIKSLK  118 (200)
Q Consensus        47 ~~sH~~~ER-----~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~Y---Ik~L~~~v~~L~~~~~~L~~ei~~L~  118 (200)
                      -++=.|.||     +=|+.+...|.+...+.      +.+.+-.+..+++.   ..+|+.++..|+.++..|..++.+|+
T Consensus        74 QVTi~C~ERGlLL~rvrde~~~~l~~y~~l~------~s~~~f~~rk~l~~e~~~~~l~~~i~~L~~e~~~L~~~~~~l~  147 (189)
T PF10211_consen   74 QVTIDCPERGLLLLRVRDEYRMTLDAYQTLY------ESSIAFGMRKALQAEQGKQELEEEIEELEEEKEELEKQVQELK  147 (189)
T ss_pred             HHHhCcHHHhHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345567776     33667777777766666      22333333333333   33444455555555554444444443


Q ss_pred             H
Q 028999          119 A  119 (200)
Q Consensus       119 ~  119 (200)
                      .
T Consensus       148 ~  148 (189)
T PF10211_consen  148 N  148 (189)
T ss_pred             H
Confidence            3

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 [].

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

Probab=85.24  E-value=7.6  Score=34.96  Aligned_cols=40  Identities=25%  Similarity=0.311  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          105 ETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       105 ~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      .+.+.+++.++.|..|+..|.+....|-.+..+|+..+..
T Consensus       163 ~e~ee~~erlk~le~E~s~LeE~~~~l~~ev~~L~~r~~E  202 (290)
T COG4026         163 AEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKKRWDE  202 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHHHHHH
Confidence            3333333334444444443333333333444445444433

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

Probab=85.07  E-value=7.2  Score=30.56  Aligned_cols=32  Identities=25%  Similarity=0.343  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREE  127 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~E  127 (200)
                      |..+++.++.+++.|..+...|+++++.|+++
T Consensus        55 l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg   86 (117)
T COG2919          55 LQRQIAAQQAELEKLSARNTALEAEIKDLKDG   86 (117)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            44444445555555554444444444444443

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

Probab=85.05  E-value=14  Score=30.91  Aligned_cols=50  Identities=28%  Similarity=0.415  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      -|++|..++.+....++.|+.|+..|..+.|-+.+....|+.|...|-+.
T Consensus       131 ~~~~l~~~l~ek~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~R  180 (194)
T PF08614_consen  131 KIKDLEEELKEKNKANEILQDELQALQLQLNMLEEKLRKLEEENRELVER  180 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555556666667777777777777777777777777777776543

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.

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

Probab=85.03  E-value=6.6  Score=31.24  Aligned_cols=53  Identities=32%  Similarity=0.400  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      -++.++..++.+..+|..|-+..-.+..+++++|.+...+..+...|+.++..
T Consensus        28 ~~~~~~~~~~~l~~~n~~lAe~nL~~~~~l~~~r~~l~~~~~~~~~L~~~~~~   80 (150)
T PF07200_consen   28 QVQELQQEREELLAENEELAEQNLSLEPELEELRSQLQELYEELKELESEYQE   80 (150)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555555555555555555555555555555555555555555555555543

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.

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

Probab=85.02  E-value=14  Score=27.49  Aligned_cols=52  Identities=21%  Similarity=0.129  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..|+.++.+|+.....-..-|.+|...+.|.+-...+++.+...|-..++.+
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            3567777777777766566678888888888888888888888888888876

>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=84.96  E-value=9.6  Score=25.71  Aligned_cols=29  Identities=41%  Similarity=0.569  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKA  119 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~  119 (200)
                      .|+.+|+.++..|+.+|..|..++..|+.
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            45555666666666666655555555543

; 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 ....

>COG3937 Uncharacterized conserved protein [Function unknown]

Probab=84.87  E-value=7.3  Score=30.92  Aligned_cols=58  Identities=26%  Similarity=0.381  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNE-KLQEEIKSLKAEKN--------ELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~-~L~~ei~~L~~ekn--------ELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      ..+|-+|+.+|-.+.+.-+.+.+ +.+..++++....+        +|+.+...|+.++.+|+++++
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            46788888888887775444332 34555555555444        566666666666666666554

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

Probab=84.82  E-value=11  Score=30.63  Aligned_cols=28  Identities=29%  Similarity=0.476  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLK  118 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~  118 (200)
                      +-+..|+.++..|+..+..+..+|..|.
T Consensus        14 ~r~e~~e~~~K~le~~~~~~E~EI~sL~   41 (143)
T PF12718_consen   14 DRAEELEAKVKQLEQENEQKEQEITSLQ   41 (143)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444333333333

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 [].

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

Probab=84.75  E-value=8.9  Score=35.20  Aligned_cols=53  Identities=25%  Similarity=0.497  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      .-++.|+.+++.+....+.+.+++.+|+.+.+++....+.|..+...+.....
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            45666666777777777777777777777777776666666666666555444

>KOG4360 consensus Uncharacterized coiled coil protein [Function unknown]

Probab=84.73  E-value=9.6  Score=37.72  Aligned_cols=50  Identities=26%  Similarity=0.282  Sum_probs=31.2

Q ss_pred             CChhhHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           80 TDKPAILD----DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKL  129 (200)
Q Consensus        80 ~dKasIL~----dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~  129 (200)
                      ++++.+++    .-++-+..++++..+|..+...++.+++++..|++|+.+-..
T Consensus       211 N~q~~s~~eel~~kt~el~~q~Ee~skLlsql~d~qkk~k~~~~Ekeel~~~Lq  264 (596)
T KOG4360|consen  211 NTQARSGQEELQSKTKELSRQQEENSKLLSQLVDLQKKIKYLRHEKEELDEHLQ  264 (596)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence            45666552    223334445566666777777777888888888887655443

>TIGR00606 rad50 rad50

Probab=84.65  E-value=8.4  Score=41.12  Aligned_cols=82  Identities=17%  Similarity=0.164  Sum_probs=53.3

Q ss_pred             HHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           55 KLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  134 (200)
Q Consensus        55 R~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e  134 (200)
                      ...++++++.+..|...+ ...  +..|.. |..++.-..+|+.++++|..++..+..++.+++.++..|..+...++.+
T Consensus       849 ~~e~e~~~~eI~~Lq~ki-~el--~~~klk-l~~~l~~r~~le~~L~el~~el~~l~~~~~~~~~~~~~~~~~~~~~~~~  924 (1311)
T TIGR00606       849 RKLIQDQQEQIQHLKSKT-NEL--KSEKLQ-IGTNLQRRQQFEEQLVELSTEVQSLIREIKDAKEQDSPLETFLEKDQQE  924 (1311)
T ss_pred             HHHHHHHHHHHHHHHHHH-HHH--HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            455566677777776656 211  233333 3336777778888888888888888777777777777777776666666


Q ss_pred             HHHHHH
Q 028999          135 KEKLEQ  140 (200)
Q Consensus       135 ~e~L~~  140 (200)
                      .+++.+
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).

>smart00787 Spc7 Spc7 kinetochore protein

Probab=84.57  E-value=7.2  Score=35.68  Aligned_cols=15  Identities=27%  Similarity=0.255  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELK  104 (200)
Q Consensus        90 I~YIk~L~~~v~~L~  104 (200)
                      .++...|+.++..|+
T Consensus       178 ~~~~~~L~~e~~~L~  192 (312)
T smart00787      178 RDRKDALEEELRQLK  192 (312)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            344444444444433

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

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

Probab=84.40  E-value=19  Score=36.57  Aligned_cols=18  Identities=28%  Similarity=0.399  Sum_probs=13.5

Q ss_pred             HHHHHHHHHhHHHHhhhc
Q 028999           55 KLRRERLNDRFLDLSCIL   72 (200)
Q Consensus        55 R~RRekiNe~F~~Lr~lL   72 (200)
                      |.||..|..-+..|+.-|
T Consensus       544 r~r~~~lE~E~~~lr~el  561 (697)
T PF09726_consen  544 RQRRRQLESELKKLRREL  561 (697)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            667777777777777777

; GO: 0016021 integral to membrane

>PRK15396 murein lipoprotein; Provisional

Probab=84.32  E-value=8.5  Score=28.74  Aligned_cols=45  Identities=11%  Similarity=0.362  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      |.+|..+|+.|..+.++|..++..++...+.-.+|-.+-...++.
T Consensus        27 vd~LssqV~~L~~kvdql~~dv~~~~~~~~~a~~eA~raN~RlDn   71 (78)
T PRK15396         27 IDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDN   71 (78)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            446666666666666666666666666666555555554444433

>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length

Probab=84.22  E-value=6.2  Score=32.56  Aligned_cols=35  Identities=23%  Similarity=0.407  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQE---EIKSLKAEKNELREEK  128 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~---ei~~L~~eknELr~Ek  128 (200)
                      ..|+.++.....+...|+.   .+.+|+.++.+|+.++
T Consensus        30 ~~~k~ql~~~d~~i~~Lk~~~~d~eeLk~~i~~lq~~~   67 (155)
T PF06810_consen   30 DNLKTQLKEADKQIKDLKKSAKDNEELKKQIEELQAKN   67 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHH
Confidence            3344444433333333333   3344444444444433

The function of this family is unknown.; GO: 0005198 structural molecule activity

>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=84.17  E-value=19  Score=30.12  Aligned_cols=40  Identities=25%  Similarity=0.322  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      -+..++.+++.|+.+...|...++.+-.++.+.+.+...+
T Consensus        23 ~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~   62 (188)
T PF10018_consen   23 EHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTL   62 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3355666777777777777777777777777777766444

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

>PRK02224 chromosome segregation protein; Provisional

Probab=84.12  E-value=13  Score=37.40  Aligned_cols=52  Identities=23%  Similarity=0.392  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +.+..|...+..++.....+..++..+...++.++.+...++.+++.+..++
T Consensus       349 ~~~~~le~~~~~l~~~~~~l~~~~~~~~~~l~~~~~~l~~l~~el~el~~~l  400 (880)
T PRK02224        349 EDADDLEERAEELREEAAELESELEEAREAVEDRREEIEELEEEIEELRERF  400 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333444444444444444444444444444444444444444444444444

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

Probab=84.11  E-value=10  Score=32.36  Aligned_cols=26  Identities=27%  Similarity=0.362  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          120 EKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       120 eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ++..|..+...++.+++..+.++++.
T Consensus       160 ei~~lks~~~~l~~~~~~~e~~F~~~  185 (190)
T PF05266_consen  160 EISRLKSEAEALKEEIENAELEFQSV  185 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444555555555544444

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

Probab=83.86  E-value=6.7  Score=36.99  Aligned_cols=53  Identities=23%  Similarity=0.284  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      |+.++=..+.+|++-+..++++|..|+-+.+++.+|.+|-.+|.+.|..|...
T Consensus       121 vf~k~k~~~q~LE~li~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE  173 (401)
T PF06785_consen  121 VFMKTKGDIQHLEGLIRHLREENQCLQLQLDALQQECGEKEEESQTLNRELAE  173 (401)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            55566667788888899999999999999999999999999998888666554

>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=83.74  E-value=15  Score=30.24  Aligned_cols=72  Identities=26%  Similarity=0.362  Sum_probs=33.3

Q ss_pred             HHHHHHhHHHHhhhcCCCCCCCCChhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           58 RERLNDRFLDLSCILEPGRPARTDKPAILDDA---IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        58 RekiNe~F~~Lr~lLpP~~~~K~dKasIL~dA---I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      .+-|.+++..|-.=|.-   ...++..+.-+|   =..|..|+.++..+..+...|..+...|+.++..|..+....+
T Consensus        19 ~dsle~~v~~LEreLe~---~q~~~e~~~~daEn~k~eie~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q   93 (140)
T PF10473_consen   19 KDSLEDHVESLERELEM---SQENKECLILDAENSKAEIETLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQ   93 (140)
T ss_pred             HhhHHHHHHHHHHHHHH---HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34566677777666622   234444444333   2334444444444444444444444444444444433333333

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

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

Probab=83.70  E-value=5.8  Score=31.46  Aligned_cols=39  Identities=33%  Similarity=0.435  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          100 SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus       100 v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      |-+|+...+.|-+.++.++.|.=.||.|++.|-+=||.|
T Consensus        65 VLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL  103 (120)
T KOG3650|consen   65 VLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL  103 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence            334444444444444444444444455555544444433

>PRK07739 flgK flagellar hook-associated protein FlgK; Validated

Probab=83.55  E-value=12  Score=35.94  Aligned_cols=75  Identities=20%  Similarity=0.209  Sum_probs=53.0

Q ss_pred             HHHhHHHHhhhcC-CCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           61 LNDRFLDLSCILE-PGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        61 iNe~F~~Lr~lLp-P~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      |++-|..|..+-- |.  ...-+..+|..|-.....++.....|+.....+..++...-.++|.|-.+...|..+|..
T Consensus       121 l~~ff~a~~~la~~P~--~~~~r~~vl~~a~~La~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~~Ia~LN~~I~~  196 (507)
T PRK07739        121 LDQFWNSLQELSKNPE--NLGARSVVRQRAQALAETFNYLSQSLTDIQNDLKSEIDVTVKEINSLASQISDLNKQIAK  196 (507)
T ss_pred             HHHHHHHHHHHHhCcC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555541 21  245678889988888888877777777777777777877778888888877777776654

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

Probab=83.55  E-value=12  Score=28.85  Aligned_cols=54  Identities=17%  Similarity=0.324  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSL--KAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L--~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      |..|...+.........++.+++.|  +.+.+.|+-+...++.++..+..+++.++
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            4445555555666777777777777  77777777777777777777777777664

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

>TIGR02209 ftsL_broad cell division protein FtsL

Probab=83.49  E-value=4.5  Score=29.03  Aligned_cols=30  Identities=43%  Similarity=0.501  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNEL  124 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknEL  124 (200)
                      ++..+++.++.+.+.++.+..+|+.|.+.|
T Consensus        28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l   57 (85)
T TIGR02209        28 QLNNELQKLQLEIDKLQKEWRDLQLEVAEL   57 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444

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.

>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type

Probab=83.49  E-value=15  Score=37.30  Aligned_cols=6  Identities=0%  Similarity=-0.246  Sum_probs=2.7

Q ss_pred             eeeccC
Q 028999           18 ADNDIS   23 (200)
Q Consensus        18 ~~~~~~   23 (200)
                      |.+|+.
T Consensus       642 vTldG~  647 (1164)
T TIGR02169       642 VTLEGE  647 (1164)
T ss_pred             EEeCce
Confidence            444443

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.

>KOG4797 consensus Transcriptional regulator [Transcription]

Probab=83.48  E-value=7.3  Score=31.27  Aligned_cols=30  Identities=33%  Similarity=0.541  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          104 KETNEKLQEEIKSLKAEKNELREEKLILKA  133 (200)
Q Consensus       104 ~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~  133 (200)
                      .++.+.|+++|++|....+.|+.|+..||.
T Consensus        66 REEVe~Lk~qI~eL~er~~~Le~EN~lLk~   95 (123)
T KOG4797|consen   66 REEVEVLKEQIRELEERNSALERENSLLKT   95 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            455667777888888888888888888874

>PRK02224 chromosome segregation protein; Provisional

Probab=83.46  E-value=14  Score=37.06  Aligned_cols=16  Identities=25%  Similarity=0.329  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHHHHH
Q 028999           89 AIRVLNQLRTESQELK  104 (200)
Q Consensus        89 AI~YIk~L~~~v~~L~  104 (200)
                      +.+-+..|+.+++.|+
T Consensus       535 ~~~~~~~l~~e~~~l~  550 (880)
T PRK02224        535 KRERAEELRERAAELE  550 (880)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3333334444444443

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

Probab=83.42  E-value=15  Score=28.17  Aligned_cols=26  Identities=23%  Similarity=0.377  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          110 LQEEIKSLKAEKNELREEKLILKADK  135 (200)
Q Consensus       110 L~~ei~~L~~eknELr~Ek~~Lk~e~  135 (200)
                      .+..+++|..+++.|.+|+..|+.++
T Consensus        47 wek~v~~L~~e~~~l~~E~e~L~~~l   72 (87)
T PF12709_consen   47 WEKKVDELENENKALKRENEQLKKKL   72 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444433

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

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

Probab=83.41  E-value=7.5  Score=39.96  Aligned_cols=42  Identities=31%  Similarity=0.512  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          104 KETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       104 ~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .+..+.|.++.+.++..+.+++.++.+|..++|+|.++++.+
T Consensus       215 le~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL  256 (916)
T KOG0249|consen  215 LEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQL  256 (916)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            345567888888899999999999999999999998888776

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=83.40  E-value=1.3  Score=42.81  Aligned_cols=46  Identities=26%  Similarity=0.395  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHhHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHH
Q 028999           52 CREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRT   98 (200)
Q Consensus        52 ~~ER~RRekiNe~F~~Lr~lLpP~~--~~K~dKasIL~dAI~YIk~L~~   98 (200)
                      -.-|.||++=|--|.+|..+||-..  .+..||++|+.=|+.||| |+.
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            3458999999999999999996432  245999999999999998 443

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

Probab=83.27  E-value=8.6  Score=32.57  Aligned_cols=17  Identities=29%  Similarity=0.382  Sum_probs=7.2

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 028999          127 EKLILKADKEKLEQQLK  143 (200)
Q Consensus       127 Ek~~Lk~e~e~L~~qlk  143 (200)
                      +...|+.+++.|+.+|.
T Consensus       111 ~l~~l~~~~~~l~~el~  127 (188)
T PF03962_consen  111 ELEELKKELKELKKELE  127 (188)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            33344444444444444

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

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

Probab=83.20  E-value=1.4  Score=37.13  Aligned_cols=40  Identities=35%  Similarity=0.473  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  128 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek  128 (200)
                      -|..||+.---|+.+++    +.+.|+.+++.|+.|.-+|+.|.
T Consensus         8 klN~AIERnalLE~ELd----EKE~L~~~~QRLkDE~RDLKqEl   47 (166)
T PF04880_consen    8 KLNQAIERNALLESELD----EKENLREEVQRLKDELRDLKQEL   47 (166)
T ss_dssp             HHHHHHHHHHHHHHHHH----HHHHHHHCH--------------
T ss_pred             HHHHHHHHhHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHH
Confidence            36778888888888773    34455555555555555554444

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.

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

Probab=83.12  E-value=9.2  Score=31.08  Aligned_cols=42  Identities=29%  Similarity=0.404  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          103 LKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       103 L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ++..+..|..+...+..++..|...+..|..+++.++.+|+.
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            333333333333444444444444444444444444444443

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 [].

>PRK07191 flgK flagellar hook-associated protein FlgK; Validated

Probab=82.87  E-value=13  Score=35.38  Aligned_cols=77  Identities=12%  Similarity=0.081  Sum_probs=55.4

Q ss_pred             HHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           61 LNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        61 iNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      |++-|..|.++- -.-....-+..+|..|-..+..++.-...|......+..++...-.++|.|-++...|..+|...
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 LNNFFSALSAAT-QLPDSPPMRQQVIESANAMALRFNNVNNFIVQQKKSIGQQRDATVKQINSLTRSIADYNQKILKN  185 (456)
T ss_pred             HHHHHHHHHHHH-hCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            666677776665 11112466888999998888888887777877777777777777778888877777777766543

>PRK04325 hypothetical protein; Provisional

Probab=82.80  E-value=8.4  Score=28.11  Aligned_cols=49  Identities=8%  Similarity=0.093  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      +.|.+|+.++.-++...+.|...+-+-..++..|+.+...|...+..++
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            4577788777777777777777777777777777777666655554443

>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=82.74  E-value=12  Score=31.18  Aligned_cols=46  Identities=26%  Similarity=0.462  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      .++|..+++.|+.++..|....+.+......|.+....|+.+...+
T Consensus        91 ~k~L~~~v~~Le~e~r~L~~~~~~~~~q~~rlee~e~~l~~e~~~l  136 (158)
T PF09744_consen   91 RKDLQSQVEQLEEENRQLELKLKNLSDQSSRLEEREAELKKEYNRL  136 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhccccchhHHHHHHHHHHH
Confidence            3455555555555555555444444444444444444444444444

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

>PRK07521 flgK flagellar hook-associated protein FlgK; Validated

Probab=82.39  E-value=12  Score=35.70  Aligned_cols=75  Identities=20%  Similarity=0.139  Sum_probs=53.2

Q ss_pred             HHHhHHHHhhhc-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           61 LNDRFLDLSCIL-EPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        61 iNe~F~~Lr~lL-pP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      |++-|..|.++- .|.  ...-+..+|+.|-..+..++.-..+|+.....+..++...-.++|.+-++...|..+|-.
T Consensus       104 l~~ff~a~~~la~~P~--~~~~R~~vl~~a~~L~~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~l~~~Ia~LN~~I~~  179 (483)
T PRK07521        104 LSDFQAALQTAASSPD--NTTLAQAAVDAAQDLANSLNDASDAVQSARADADAEIADSVDTLNDLLAQFEDANNAVVS  179 (483)
T ss_pred             HHHHHHHHHHHHhCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            555555555554 121  235577899999888888888888888777777778877778888887777777766654

>KOG4196 consensus bZIP transcription factor MafK [Transcription]

Probab=82.38  E-value=14  Score=30.39  Aligned_cols=38  Identities=18%  Similarity=0.382  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..|+.+-.+|.++++.|++|++.+..|.+-+...++.+
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            34444445555555555555555555555555544443

>PF14988 DUF4515: Domain of unknown function (DUF4515)

Probab=82.37  E-value=13  Score=32.08  Aligned_cols=58  Identities=28%  Similarity=0.381  Sum_probs=33.1

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           82 KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus        82 KasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      |+-.|.-|+  ++.|-.-...+..+|..|..++..|..+...|+..+..|..++..|.++
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  3334444555566666666666666666666666666666666665543

>TIGR01069 mutS2 MutS2 family protein

Probab=82.34  E-value=9.7  Score=38.79  Aligned_cols=15  Identities=33%  Similarity=0.430  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHHH
Q 028999          130 ILKADKEKLEQQLKV  144 (200)
Q Consensus       130 ~Lk~e~e~L~~qlk~  144 (200)
                      .++.+.+.+-.+++.
T Consensus       576 ~a~~~~~~~i~~lk~  590 (771)
T TIGR01069       576 ALKKEVESIIRELKE  590 (771)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            344455555555554

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.

>KOG3156 consensus Uncharacterized membrane protein [Function unknown]

Probab=82.34  E-value=11  Score=33.29  Aligned_cols=38  Identities=37%  Similarity=0.473  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          107 NEKLQEEIKSL-KAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       107 ~~~L~~ei~~L-~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ..+++.++..+ +.|-.-||.|+.+|+.|+|++.++|..
T Consensus       103 f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~  141 (220)
T KOG3156|consen  103 FAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRH  141 (220)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444443222 234445899999999999999998865

>PF14282 FlxA: FlxA-like protein

Probab=82.27  E-value=6.8  Score=30.24  Aligned_cols=59  Identities=24%  Similarity=0.375  Sum_probs=41.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           83 PAILDDAIRVLNQLRTESQELKE----TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus        83 asIL~dAI~YIk~L~~~v~~L~~----~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      .+.+..--.-|+.|+.++.+|..    ..+.-+..+..|..++..|..+...|+.+...-..+
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            55566666777888888888877    224566777777788888887777777666555443

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

Probab=82.20  E-value=11  Score=37.25  Aligned_cols=35  Identities=29%  Similarity=0.427  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          110 LQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       110 L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +......|+.|++.|..++..+...+..|+..++.
T Consensus       197 l~~~~e~l~~E~~~L~~q~~e~~~ri~~LEedi~~  231 (546)
T PF07888_consen  197 LTESSEELKEERESLKEQLAEARQRIRELEEDIKT  231 (546)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333344444444444444444444444444443

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

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

Probab=82.01  E-value=9  Score=39.83  Aligned_cols=61  Identities=25%  Similarity=0.340  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           85 ILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        85 IL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      |.++=-+.|+.|..+++.|+.....|+-+.++|..++.++-.+.+.|+.+.+.|+.||...
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            3333344455555555555555566666666666666666666777788888888888743

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

Probab=81.96  E-value=19  Score=30.81  Aligned_cols=40  Identities=30%  Similarity=0.444  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr  125 (200)
                      |..+=.-++.++.++..|+-+++.|......|..|.++|.
T Consensus        88 L~~~k~rl~~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~  127 (201)
T PF13851_consen   88 LQNLKARLKELEKELKDLKWEHEVLEQRFEKLEQERDELY  127 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344444455555555555555555555555554443

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

Probab=81.94  E-value=6.4  Score=34.64  Aligned_cols=54  Identities=19%  Similarity=0.263  Sum_probs=30.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           83 PAILDDAIRVLNQLRTESQE---LKETNEKLQEEIKSLKAEKNELREEKLILKADKE  136 (200)
Q Consensus        83 asIL~dAI~YIk~L~~~v~~---L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e  136 (200)
                      .+...+.-....+|++...+   ++.....|+.+++++..|.+.|-+|.+.|+.+++
T Consensus       154 ~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~  210 (216)
T KOG1962|consen  154 DKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIE  210 (216)
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHh
Confidence            34444444444444443333   3345566666667777777777777666666654

>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=81.93  E-value=12  Score=39.07  Aligned_cols=50  Identities=34%  Similarity=0.450  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           97 RTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        97 ~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      +.+++.+....+....++.+|.+++.|+++-+..|-.|+..|.+|+|.+.
T Consensus       471 kt~ie~~~~q~e~~isei~qlqarikE~q~kl~~l~~Ekq~l~~qlkq~q  520 (1118)
T KOG1029|consen  471 KTEIEEVTKQRELMISEIDQLQARIKELQEKLQKLAPEKQELNHQLKQKQ  520 (1118)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhh
Confidence            33444445555666677888888888888888888899999999998774

>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=81.79  E-value=19  Score=26.68  Aligned_cols=33  Identities=33%  Similarity=0.417  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           99 ESQELKETNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        99 ~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      +...+..+...++.+...|..|.+.|+-|.+.|
T Consensus        36 ~~~~~~~~l~~l~~~~~~l~~e~~~L~lE~~~l   68 (97)
T PF04999_consen   36 QSRQLFYELQQLEKEIDQLQEENERLRLEIATL   68 (97)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            344444444444444444444444444444444

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

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

Probab=81.78  E-value=30  Score=29.09  Aligned_cols=56  Identities=20%  Similarity=0.368  Sum_probs=30.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           84 AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        84 sIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      .+-..|+.-+.+++.++..|+...+.+...+..|+..+.+|......++.+.+-|.
T Consensus        84 dLAr~al~~k~~~e~~~~~l~~~~~~~~~~~~~l~~~l~~l~~kl~e~k~k~~~l~  139 (221)
T PF04012_consen   84 DLAREALQRKADLEEQAERLEQQLDQAEAQVEKLKEQLEELEAKLEELKSKREELK  139 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445566666666666666666555555555555555555555555544444443

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 [].

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

Probab=81.74  E-value=16  Score=25.89  Aligned_cols=40  Identities=25%  Similarity=0.483  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELK-ETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~-~~~~~L~~ei~~L~~eknELr  125 (200)
                      |.+|-+.|++|.-++..+- .....+...++..+.+++.|+
T Consensus        34 l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk   74 (79)
T PF05008_consen   34 LDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLK   74 (79)
T ss_dssp             HHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455556666666655554 233444444444444444443

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.

>KOG4005 consensus Transcription factor XBP-1 [Transcription]

Probab=81.69  E-value=7.7  Score=35.09  Aligned_cols=89  Identities=27%  Similarity=0.339  Sum_probs=60.6

Q ss_pred             CccCCCCCCCC------C-CCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           35 TRKRARSDSCS------R-PGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETN  107 (200)
Q Consensus        35 ~~kR~r~~~~~------r-~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~  107 (200)
                      .+||.|..--+      | |...-.+-.--||+=+.+..++-..|   +           |-++--..|+.+.+.|...|
T Consensus        55 ~rKr~RL~HLS~EEK~~RrKLKNRVAAQtaRDrKKaRm~eme~~i---~-----------dL~een~~L~~en~~Lr~~n  120 (292)
T KOG4005|consen   55 KRKRRRLDHLSWEEKVQRRKLKNRVAAQTARDRKKARMEEMEYEI---K-----------DLTEENEILQNENDSLRAIN  120 (292)
T ss_pred             HHHHHhhcccCHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH---H-----------HHHHHHHHHHHHHHHHHHHH
Confidence            36666654332      2 33333444455666677777776665   1           22345566888888899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      +.|-.+..+|..++.++++|...|+.+...
T Consensus       121 ~~L~~~n~el~~~le~~~~~l~~~~~~~~~  150 (292)
T KOG4005|consen  121 ESLLAKNHELDSELELLRQELAELKQQQQH  150 (292)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHhhHHHHHH
Confidence            999989999999999999998888766543

>PRK05771 V-type ATP synthase subunit I; Validated

Probab=81.68  E-value=5.6  Score=39.14  Aligned_cols=80  Identities=25%  Similarity=0.306  Sum_probs=39.0

Q ss_pred             HHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           55 KLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  134 (200)
Q Consensus        55 R~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e  134 (200)
                      .++.+++++.+..|+...+-..   ..+..  ...+++. .+.+-.+..+...+.+.+++.++..++++|++|...++.+
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            4566778888888888763211   10000  0011111 0111112333444555555666666666666666666666


Q ss_pred             HHHHHH
Q 028999          135 KEKLEQ  140 (200)
Q Consensus       135 ~e~L~~  140 (200)
                      ++.|+.
T Consensus       123 ~~~l~~  128 (646)
T PRK05771        123 IERLEP  128 (646)
T ss_pred             HHHhhh
Confidence            665553

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

Probab=81.68  E-value=9.7  Score=34.88  Aligned_cols=61  Identities=26%  Similarity=0.366  Sum_probs=39.3

Q ss_pred             CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           80 TDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        80 ~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ++|.+.+-    -|.-|+..+..|++.+..|+.+.++...+.+.++.....|+.+...|+.+|+.
T Consensus       105 Nek~~l~y----qvd~Lkd~lee~eE~~~~~~re~~eK~~elEr~K~~~d~L~~e~~~Lre~L~~  165 (302)
T PF09738_consen  105 NEKSALMY----QVDLLKDKLEELEETLAQLQREYREKIRELERQKRAHDSLREELDELREQLKQ  165 (302)
T ss_pred             hHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56666543    24556667777777777777776666666666666666666666666666654

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

>PRK06665 flgK flagellar hook-associated protein FlgK; Validated

Probab=81.51  E-value=15  Score=36.48  Aligned_cols=60  Identities=15%  Similarity=0.188  Sum_probs=45.5

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           79 RTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        79 K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      -.-+.++|..|-.....++.-...|+.....+..++...-.++|.|-++.+.|..+|-..
T Consensus       138 ~a~R~~vl~~A~~La~~~n~~~~~L~~~~~~~~~~i~~~V~~iN~ll~qIa~LN~qI~~~  197 (627)
T PRK06665        138 LAERQVVLERAQSLGERIHDRYRSLERIRDMANDEIEITVEEINNILRNIADLNEQIVKS  197 (627)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            356778899888888888887777777777777777777777888777777777666553

>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=81.41  E-value=2.5  Score=30.19  Aligned_cols=29  Identities=34%  Similarity=0.475  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          112 EEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       112 ~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      +|++.|+..+.+|.+++..|+.|...|.+
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            34444555555555555555555555555

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.

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

Probab=81.41  E-value=20  Score=35.81  Aligned_cols=31  Identities=16%  Similarity=0.394  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          114 IKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       114 i~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ++.+..|+|+|..+...++.++++|.+.+..
T Consensus       334 ve~mn~Er~~l~r~l~~i~~~~d~l~k~vw~  364 (581)
T KOG0995|consen  334 VERMNLERNKLKRELNKIQSELDRLSKEVWE  364 (581)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4555667777777777777777777654443

>KOG4571 consensus Activating transcription factor 4 [Transcription]

Probab=81.36  E-value=20  Score=32.93  Aligned_cols=50  Identities=24%  Similarity=0.321  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      .|++|=+.=|.+-+       .|..+...|..+..+|+++...|..||..|.|-+-+
T Consensus       238 AAtRYRqKkRae~E-------~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e  287 (294)
T KOG4571|consen  238 AATRYRQKKRAEKE-------ALLGELEGLEKRNEELKDQASELEREIRYLKQLILE  287 (294)
T ss_pred             HHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56777655444443       344444555556666666666666666666665544

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

Probab=81.34  E-value=9.5  Score=38.10  Aligned_cols=55  Identities=24%  Similarity=0.316  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .|...|+.+...++..+..|.+++..|+.++.........|...+.+|+.|+...
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

>TIGR01554 major_cap_HK97 phage major capsid protein, HK97 family

Probab=81.29  E-value=7.8  Score=35.33  Aligned_cols=58  Identities=21%  Similarity=0.295  Sum_probs=27.8

Q ss_pred             HHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           58 RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA  119 (200)
Q Consensus        58 RekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~  119 (200)
                      |+++++.=.+.++++. .   +..+..=+.+.-+-+++|+...++++.+.+.+..+++++..
T Consensus         5 ~~~~~~~~~~~r~l~~-~---~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   62 (378)
T TIGR01554         5 KEQREEIVAEIRSLLD-K---AEKLEKELTAAALEKEELETDVEKLKEEIKLLEDAIADLEK   62 (378)
T ss_pred             HHHHHHHHHHHHHHHh-h---hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6777777777777773 1   11111111222222334555555555555555544444433

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.

>PRK05683 flgK flagellar hook-associated protein FlgK; Validated

Probab=81.17  E-value=14  Score=37.30  Aligned_cols=77  Identities=13%  Similarity=0.218  Sum_probs=53.7

Q ss_pred             HHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           61 LNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        61 iNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      |++-|..|.++- -.-..-.-+..+|+.|-....+++.--..|......+..+++..-.++|.|-++.+.|..+|.+.
T Consensus       109 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        109 LQRFFTALQTAA-ANPTDTAARQLLLTQAQGLSKRFNSLSSQLNQQNSNINSQLSAMTDQVNNLTTSIASYNKQIAQA  185 (676)
T ss_pred             HHHHHHHHHHHH-HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444444444444 11112356788999998888888888888888777778888888888888888777777777543

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=81.17  E-value=6.9  Score=36.18  Aligned_cols=47  Identities=26%  Similarity=0.445  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMP  148 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~  148 (200)
                      .|...+.+++.++++|+...++|.       .+...++.++++++.+++.+..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~   51 (389)
T PRK03992          5 ALEERNSELEEQIRQLELKLRDLE-------AENEKLERELERLKSELEKLKSP   51 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHhhCC
Confidence            344444444444444444444444       44444444555555555554443

>PRK10869 recombination and repair protein; Provisional

Probab=80.99  E-value=21  Score=34.85  Aligned_cols=88  Identities=17%  Similarity=0.234  Sum_probs=61.3

Q ss_pred             HHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           56 LRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKE---TNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        56 ~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~---~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      .|=+.|++++..|..+-   +  |=.  .-+.+.+.|..+++.+.+.|..   ..+.|+.++..++.+..++..+.+..+
T Consensus       296 ~~l~~ie~Rl~~l~~L~---r--Kyg--~~~~~~~~~~~~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~A~~LS~~R  368 (553)
T PRK10869        296 NRLAELEQRLSKQISLA---R--KHH--VSPEELPQHHQQLLEEQQQLDDQEDDLETLALAVEKHHQQALETAQKLHQSR  368 (553)
T ss_pred             HHHHHHHHHHHHHHHHH---H--HhC--CCHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567777777777776   2  222  2478899999999999888764   567788888888888888777776554


Q ss_pred             HH-H----HHHHHHHHHhcCCCC
Q 028999          133 AD-K----EKLEQQLKVMAMPTG  150 (200)
Q Consensus       133 ~e-~----e~L~~qlk~~~~~p~  150 (200)
                      .+ -    +.+..+|+.++.+..
T Consensus       369 ~~aA~~l~~~v~~~L~~L~m~~a  391 (553)
T PRK10869        369 QRYAKELAQLITESMHELSMPHG  391 (553)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCc
Confidence            33 2    334566777766655

>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=80.95  E-value=18  Score=30.99  Aligned_cols=51  Identities=29%  Similarity=0.401  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      ...+.+++.++.+++..+..|+..+..++.++.+.+++...++.+++....
T Consensus        55 ~~~~~~~~~~~~~~~~r~~~l~~~i~~~~~~i~~~r~~l~~~~~~l~~~~~  105 (302)
T PF10186_consen   55 LLEIQQLKREIEELRERLERLRERIERLRKRIEQKRERLEELRESLEQRRS  105 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455555666666666666666666666665555555555544444433

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

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

Probab=80.94  E-value=12  Score=28.13  Aligned_cols=56  Identities=36%  Similarity=0.490  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           90 IRVLNQLRTESQELKETNEKLQE---EIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~---ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +.-+..|+.+...+.++...+..   +..+|..+..++.++...+..+...++.++...
T Consensus        42 ~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e~~l~~~  100 (108)
T PF02403_consen   42 QQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKELEEELNEL  100 (108)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34466666666666666655543   466777777777777777777777777777664

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 ....

>PF00769 ERM: Ezrin/radixin/moesin family; InterPro: IPR011259 The ERM family consists of three closely-related proteins, ezrin, radixin and moesin []

Probab=80.86  E-value=9.7  Score=33.50  Aligned_cols=56  Identities=27%  Similarity=0.369  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           89 AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        89 AI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      |-.-+..|+.+......+...|..++.++..++..|.++...-..+.+.|+.++..
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            34444444444444555566677777777777777777777777777777776655

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.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=80.86  E-value=7.1  Score=36.08  Aligned_cols=44  Identities=23%  Similarity=0.230  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKA  133 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~  133 (200)
                      .++++.|+.++++|+..+..|..+.+.++.++.++++++..|+.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   50 (389)
T PRK03992          7 EERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKS   50 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            45677788899999999999999999999999998888876654

>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6

Probab=80.77  E-value=15  Score=25.86  Aligned_cols=49  Identities=33%  Similarity=0.435  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHh
Q 028999           97 RTESQELKETNEKLQEEIKSLKAEKN--------------ELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        97 ~~~v~~L~~~~~~L~~ei~~L~~ekn--------------ELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..++..|+.+.+.++.++..+..-++              .-++....++.++++|+..|..+
T Consensus         3 ~~E~~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~~~l~~~l~~L   65 (66)
T PF10458_consen    3 EAEIERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEELEKLEEALEQL   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34444455555555544444443322              23445566777778887777654

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.

>PF06120 Phage_HK97_TLTM: Tail length tape measure protein; InterPro: IPR009302 This entry consists of the tail length tape measure protein from Bacteriophage HK97 and related sequences from Escherichia coli (strain K12)

Probab=80.70  E-value=12  Score=34.39  Aligned_cols=56  Identities=21%  Similarity=0.305  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKE-TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~-~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      +||+|=..|-+-.++|++ ...+|...+..+...+.++.+....|+.+++.|+.+++
T Consensus        49 ~A~~fA~~ld~~~~kl~~Ms~~ql~~~~~k~~~si~~q~~~i~~l~~~i~~l~~~i~  105 (301)
T PF06120_consen   49 EAIEFADSLDELKEKLKEMSSTQLRANIAKAEESIAAQKRAIEDLQKKIDSLKDQIK  105 (301)
T ss_pred             HHHHHHHhhHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456665555555555554 23344444444444444444444444555555544443

>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=80.64  E-value=24  Score=27.88  Aligned_cols=30  Identities=27%  Similarity=0.310  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          115 KSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       115 ~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ..|..++.++......|..+..-|.+||..
T Consensus       101 ~~le~e~~~~~~r~~dL~~QN~lLh~QlE~  130 (132)
T PF07926_consen  101 EQLEKELSELEQRIEDLNEQNKLLHDQLES  130 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            344444444444444444444444455443

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

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

Probab=80.56  E-value=20  Score=26.22  Aligned_cols=39  Identities=28%  Similarity=0.426  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      ++.|+..++++....+.+++++..+..|.+++-++...+
T Consensus        21 l~~l~~~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l   59 (90)
T PF06103_consen   21 LKKLKKTLDEVNKTIDTLQEQVDPITKEINDLLHNTNEL   59 (90)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444444444333

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

Probab=80.54  E-value=9.1  Score=31.62  Aligned_cols=45  Identities=31%  Similarity=0.454  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKA  133 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~  133 (200)
                      ..+||+|   |++++++|++..+.|+..+.+|.....+++.+...+.+
T Consensus        92 ~~eAie~---l~k~~~~l~~~~~~l~~~l~~l~~~~~~l~~~~q~~~q  136 (145)
T COG1730          92 ADEAIEF---LKKRIEELEKAIEKLQQALAELAQRIEQLEQEAQQLQQ  136 (145)
T ss_pred             HHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455555   56778888888889999999999998888887776643

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=80.28  E-value=9.9  Score=38.77  Aligned_cols=7  Identities=43%  Similarity=0.591  Sum_probs=3.8

Q ss_pred             CCCCccc
Q 028999          174 GLMPMWQ  180 (200)
Q Consensus       174 ~~~~mwq  180 (200)
                      |||-||-
T Consensus       668 g~~k~~v  674 (782)
T PRK00409        668 GIMKMKV  674 (782)
T ss_pred             CCEEEEE
Confidence            4566653

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

Probab=80.25  E-value=13  Score=29.98  Aligned_cols=49  Identities=20%  Similarity=0.294  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      |..+++.|....++..+-++..+.+..++++.....+.+++.+++-+..
T Consensus        66 LsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~  114 (126)
T PF07889_consen   66 LSQRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVEG  114 (126)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            4455555555555555555666666666666666666666665554443

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

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

Probab=80.23  E-value=14  Score=36.69  Aligned_cols=9  Identities=11%  Similarity=0.172  Sum_probs=3.4

Q ss_pred             HhHHHHhhh
Q 028999           63 DRFLDLSCI   71 (200)
Q Consensus        63 e~F~~Lr~l   71 (200)
                      +-+.+|+..
T Consensus       120 ~e~~elr~~  128 (546)
T KOG0977|consen  120 EELKELRKK  128 (546)
T ss_pred             HHHHHHHHH
Confidence            333333333

>PRK03918 chromosome segregation protein; Provisional

Probab=80.22  E-value=30  Score=34.68  Aligned_cols=30  Identities=23%  Similarity=0.403  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           98 TESQELKETNEKLQEEIKSLKAEKNELREE  127 (200)
Q Consensus        98 ~~v~~L~~~~~~L~~ei~~L~~eknELr~E  127 (200)
                      .+.+.++.....+..++..++.+++++..+
T Consensus       666 ~~~~~l~~~l~~l~~~~~~l~~~i~~l~~~  695 (880)
T PRK03918        666 EEYLELSRELAGLRAELEELEKRREEIKKT  695 (880)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333333333333333333333333

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

Probab=80.16  E-value=9.2  Score=25.49  Aligned_cols=21  Identities=38%  Similarity=0.466  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 028999          120 EKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       120 eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      ++..|+.++..||-++.++..
T Consensus        28 ~l~~LKk~kL~LKDei~~ll~   48 (49)
T PF04325_consen   28 ELERLKKEKLRLKDEIYRLLR   48 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHc
Confidence            445555666666666666554

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

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

Probab=80.15  E-value=10  Score=33.28  Aligned_cols=17  Identities=24%  Similarity=0.524  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEK  109 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~  109 (200)
                      |.+|+..+..+..++..
T Consensus        56 l~~lr~~id~~~~eka~   72 (312)
T PF00038_consen   56 LRELRRQIDDLSKEKAR   72 (312)
T ss_dssp             HHCHHHHHHHHHHHHHH
T ss_pred             HHHhHHhhhhHHHHhhH
Confidence            33444444444433333

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 ....

---

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	200
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	2e-10
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	5e-10
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	3e-09
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	3e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	3e-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,	1e-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	1e-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 = 54.3 bits (131), Expect = 2e-10
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 54  EKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 112
           E+ RR  L   F  L   I E     +  K  IL  A   +  ++ E Q+L    + L++
Sbjct: 14  ERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRK 73

Query: 113 EIKSLKAEKNELR 125
             + 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 = 53.2 bits (128), Expect = 5e-10
 Identities = 14/72 (19%), Positives = 32/72 (44%)

Query: 54  EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE 113
           E+ RR+ + D F  L   +   +  +  +  ILD A   +  +R ++   ++  + L+ +
Sbjct: 10  ERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ 69

Query: 114 IKSLKAEKNELR 125
              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 = 50.8 bits (122), Expect = 3e-09
 Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 54  EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE 113
           EK  R  +ND+ ++L  ++  G  A+ +K A+L  AI  +  L+  +Q+LK+ N  L+  
Sbjct: 14  EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72

Query: 114 IKSLKAEK 121
           +   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 = 45.8 bits (109), Expect = 3e-07
 Identities = 12/60 (20%), Positives = 28/60 (46%)

Query: 54  EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE 113
           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 = 42.5 bits (100), Expect = 3e-06
 Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 1/72 (1%)

Query: 54  EKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 112
           EK RR  L      L   +      +R    ++L  A   + +L    ++     ++LQ 
Sbjct: 9   EKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQR 68

Query: 113 EIKSLKAEKNEL 124
           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 = 42.9 bits (101), Expect = 3e-05
 Identities = 18/108 (16%), Positives = 45/108 (41%)

Query: 36  RKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ 95
             +A+ +   R   +  + +   + L  +   L       +     +  +  +A  +  +
Sbjct: 858 EMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVR 917

Query: 96  LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
           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 = 41.4 bits (97), Expect = 1e-04
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 86   LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 142
            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 = 41.4 bits (97), Expect = 1e-04
 Identities = 19/96 (19%), Positives = 45/96 (46%), Gaps = 7/96 (7%)

Query: 50  KACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEK 109
                +  R RL  +  +L  IL        +  A +++      QL+ E +++++    
Sbjct: 907 LYAEAEEMRVRLAAKKQELEEILH-------EMEARIEEEEERSQQLQAEKKKMQQQMLD 959

Query: 110 LQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM 145
           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 = 41.0 bits (96), Expect = 1e-04
 Identities = 10/54 (18%), Positives = 26/54 (48%)

Query: 93   LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA 146
            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 = 40.2 bits (94), Expect = 2e-04
 Identities = 16/62 (25%), Positives = 30/62 (48%)

Query: 84   AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
            +++ +    L +     QEL++   KL+ E   L  +  EL+ +   LKA   K E++L+
Sbjct: 1039 SMISELEVRLKKEEKSRQELEKIKRKLEGESSDLHEQIAELQAQIAELKAQLAKKEEELQ 1098

Query: 144  VM 145
              
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 = 39.0 bits (91), Expect = 6e-04
 Identities = 12/58 (20%), Positives = 24/58 (41%)

Query: 86   LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
              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: 86   LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
            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: 86   LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
            +    + 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 = 41.2 bits (97), Expect = 1e-04
 Identities = 13/58 (22%), Positives = 26/58 (44%)

Query: 86   LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
            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 = 38.9 bits (91), Expect = 7e-04
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 89  AIRVLNQLRTES---QELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK 143
           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 = 40.1 bits (93), Expect = 1e-04
 Identities = 9/51 (17%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 90  IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ 140
           I   ++L  E + +++  E+ ++ ++      +++ E++   KA K+  E 
Sbjct: 74  IAQADRLTQEPESIRKWREEQRKRLQE-LDAASKVMEQEWREKAKKDLEEW 123

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	200
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.78
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.77
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	99.7
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.69
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.62
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.61
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.56
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.52
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.49
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.35
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.24
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.15
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.11
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.89
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.77
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.06
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	97.64
2jee_A	81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	96.77
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	96.64
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	96.55
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	96.36
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	95.71
3hnw_A	138	Uncharacterized protein; coiled-coil, structural g	95.52
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	95.49
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	95.4
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	95.26
3qh9_A	81	Liprin-beta-2; coiled-coil, dimerization, structur	95.24
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	95.14
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	94.68
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	94.51
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	94.25
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	94.15
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	94.1
2oqq_A	42	Transcription factor HY5; homodimer leucine zipper	93.87
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	93.47
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	93.45
1t2k_D	61	Cyclic-AMP-dependent transcription factor ATF-2; p	93.44
3cve_A	72	Homer protein homolog 1; coiled coil, alternative	93.4
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	92.88
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	92.68
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	92.54
1ci6_A	63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.47
2wt7_A	63	Proto-oncogene protein C-FOS; transcription, trans	92.13
3i00_A	120	HIP-I, huntingtin-interacting protein 1; transcrip	91.83
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	91.71
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	91.69
3q8t_A	96	Beclin-1; autophagy, ATG14L uvrag, apoptosis; 1.90	91.67
2wt7_B	90	Transcription factor MAFB; transcription, transcri	91.64
1jnm_A	62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	91.61
3cvf_A	79	Homer-3, homer protein homolog 3; coiled coil, alt	91.52
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	91.41
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	91.1
3htk_A	60	Structural maintenance of chromosomes protein 5; S	90.93
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	90.86
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	90.84
3m91_A	51	Proteasome-associated ATPase; coil COIL alpha heli	90.82
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	90.79
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	90.77
3he5_A	49	Synzip1; heterodimeric coiled-coil, de novo protei	90.67
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	90.53
1gd2_E	70	Transcription factor PAP1; basic leucine zipper, p	90.51
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	90.48
3m9b_A	251	Proteasome-associated ATPase; coil COIL with 5 bet	90.38
3he5_B	52	Synzip2; heterodimeric coiled-coil, de novo protei	90.36
3s9g_A	104	Protein hexim1; cyclin T-binding domain (TBD), cyc	90.21
1hjb_A	87	Ccaat/enhancer binding protein beta; transcription	89.92
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	89.9
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	89.74
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	89.64
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	89.63
3swy_A	46	Cyclic nucleotide-gated cation channel alpha-3; co	89.51
3swf_A	74	CGMP-gated cation channel alpha-1; coiled-coil, as	89.48
2eqb_B	97	RAB guanine nucleotide exchange factor SEC2; coile	89.4
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	89.35
2yy0_A	53	C-MYC-binding protein; conserved hypothetical prot	89.2
3htk_A	60	Structural maintenance of chromosomes protein 5; S	89.13
3u06_A	412	Protein claret segregational; motor domain, stalk	89.11
1deb_A	54	APC protein, adenomatous polyposis coli protein; c	88.92
2dfs_A	1080	Myosin-5A; myosin-V, inhibited state, cryoelectron	88.61
1m1j_C	409	Fibrinogen gamma chain; coiled coils, disulfide ri	87.77
1gu4_A	78	CAAT/enhancer binding protein beta; transcription/	87.73
2wt7_B	90	Transcription factor MAFB; transcription, transcri	87.58
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	87.25
3ol1_A	119	Vimentin; structural genomics, PSI-2, protein stru	87.16
2fxo_A	129	Myosin heavy chain, cardiac muscle beta isoform; c	87.04
1dh3_A	55	Transcription factor CREB; protein-DNA complex, tr	87.0
3v86_A	27	De novo design helix; computational design of A pr	86.98
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	86.81
1kd8_A	36	GABH AIV, GCN4 acid base heterodimer acid-D12IA16V	86.8
2dgc_A	63	Protein (GCN4); basic domain, leucine zipper, DNA	86.73
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	86.62
2w6a_A	63	ARF GTPase-activating protein GIT1; PIX, zinc, sig	86.58
3a7p_A	152	Autophagy protein 16; coiled-coil, coiled coil, cy	86.55
1go4_E	100	MAD1 (mitotic arrest deficient)-like 1; mitotic sp	86.31
3mq7_A	121	Bone marrow stromal antigen 2; HIV, antiviral prot	86.21
1kd8_B	36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	86.12
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	86.07
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	85.91
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	85.7
3u1c_A	101	Tropomyosin alpha-1 chain; anti-parallel coiled co	85.48
2v66_B	111	Nuclear distribution protein NUDE-like 1; structur	85.42
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	85.39
3m48_A	33	General control protein GCN4; leucine zipper, synt	85.18
2xdj_A	83	Uncharacterized protein YBGF; unknown function; 1.	85.18
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	85.06
3u59_A	101	Tropomyosin beta chain; muscle contraction, actin,	84.7
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	84.62
3gpv_A	148	Transcriptional regulator, MERR family; protein st	84.37
1zbt_A	371	RF-1, peptide chain release factor 1; peptide chai	84.31
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	84.18
2ocy_A	154	RAB guanine nucleotide exchange factor SEC2; RAB,	84.12
3efg_A	78	Protein SLYX homolog; xanthomonas campestris PV. c	83.97
3s4r_A	93	Vimentin; alpha-helix, cytoskeleton, intermediate	83.63
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	83.24
3iv1_A	78	Tumor susceptibility gene 101 protein; coiled_COIL	83.21
1wt6_A	81	Myotonin-protein kinase; coiled-coil, kinase activ	83.2
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	83.18
3m48_A	33	General control protein GCN4; leucine zipper, synt	82.92
3tnu_A	131	Keratin, type I cytoskeletal 14; coiled-coil, stru	82.89
2d4y_A	463	HAP1, flagellar HOOK-associated protein 1; multi-d	82.74
1gk6_A	59	Vimentin; intermediate filament, dimer, parallel c	82.72
2oxj_A	34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	82.61
3nmd_A	72	CGMP dependent protein kinase; leucine zipper, coi	82.51
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	82.48
4dzn_A	33	Coiled-coil peptide CC-PIL; de novo protein; HET:	82.41
1ic2_A	81	Tropomyosin alpha chain, skeletal muscle; alpha-he	82.32
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	82.22
3trt_A	77	Vimentin; cytoskeleton, intermediate filament, alp	81.99
1jcd_A	52	Major outer membrane lipoprotein; protein folding,	81.81
3c3g_A	33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	81.61
3c3g_A	33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	81.43
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	81.36
4h22_A	103	Leucine-rich repeat flightless-interacting protei;	80.94
3ni0_A	99	Bone marrow stromal antigen 2; coiled-coil, antivi	80.53
2ve7_C	250	Kinetochore protein NUF2, kinetochore protein SPC;	80.44
2wq1_A	33	General control protein GCN4; TAA, nucleus, coiled	80.28
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	80.26
3tnu_B	129	Keratin, type II cytoskeletal 5; coiled-coil, stru	80.12
3c3f_A	34	Alpha/beta peptide with the GCN4-PLI SIDE chain S	80.07
2w83_C	77	C-JUN-amino-terminal kinase-interacting protein 4;	80.05

>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=99.78  E-value=2.6e-19  Score=131.12  Aligned_cols=76  Identities=17%  Similarity=0.306  Sum_probs=62.6

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEK  121 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~ek  121 (200)
                      ++.+|+.+||+||+.||++|.+|+++||.....|.||++||..||+||+.|+.+++.|+.+.+.|..+...|.+++
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~~L~~~l   77 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQV   77 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999997655579999999999999999999988887766555555444444443

>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=99.77  E-value=5.8e-19  Score=129.79  Aligned_cols=71  Identities=25%  Similarity=0.384  Sum_probs=63.8

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSL  117 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L  117 (200)
                      ++.+|+.+||+||++||++|.+|+++||+ ...|.||++||.+||+||++|+.+++.|+.+++.|+..+++.
T Consensus         6 rr~~H~~~ErrRR~~in~~f~~L~~lvP~-~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~~~~   76 (82)
T 1am9_A            6 KRTAHNAIEKRYRSSINDKIIELKDLVVG-TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS   76 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTC-SSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHhccC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            46789999999999999999999999955 447999999999999999999999999999888888766544

>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=1.7e-18  Score=129.07  Aligned_cols=79  Identities=22%  Similarity=0.301  Sum_probs=67.1

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL  124 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~-~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknEL  124 (200)
                      ++.+|+.+||+||+.||++|..|+++||... ..|.||++||.+||+||+.|+.+.+.+..+.+.|+.+...|+.++.+|
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            4678999999999999999999999995431 369999999999999999999999988887777776666666666655

>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=124.49  Aligned_cols=77  Identities=21%  Similarity=0.261  Sum_probs=67.4

Q ss_pred             CCchhHHHHHHHHHHHHhHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           47 PGSKACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNE  123 (200)
Q Consensus        47 ~~sH~~~ER~RRekiNe~F~~Lr~lLpP~-~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknE  123 (200)
                      +.+|+..||+||+.||++|..|+++||.. ...|.+|++||.+||+||++|+.+.++|..+++.|+.+...|++++++
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            46899999999999999999999999643 346899999999999999999999999998888888877777776654

>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=99.70  E-value=1.8e-17  Score=120.83  Aligned_cols=69  Identities=17%  Similarity=0.341  Sum_probs=61.4

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE  113 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~e  113 (200)
                      .++.+|+.+||+||+.||++|.+|+++||.....|.+|++||..||+||+.|+.+++.|+.+++.|+.+
T Consensus        11 ~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~~   79 (80)
T 1hlo_A           11 DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   79 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            357899999999999999999999999976555699999999999999999999999888888777653

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=99.69  E-value=4.6e-17  Score=127.17  Aligned_cols=61  Identities=25%  Similarity=0.392  Sum_probs=51.7

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTESQELKET  106 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~--~~K~dKasIL~dAI~YIk~L~~~v~~L~~~  106 (200)
                      ++.+|+..||+||++||++|.+|+++||++.  ..|.||++||.+||+||+.|+.+++.|+.+
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            5889999999999999999999999997664  248899999999999999999999998864

>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=99.62  E-value=1.4e-16  Score=111.64  Aligned_cols=56  Identities=25%  Similarity=0.373  Sum_probs=50.4

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCCCC----CCCChhhHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPGRP----ARTDKPAILDDAIRVLNQLRTES  100 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~----~K~dKasIL~dAI~YIk~L~~~v  100 (200)
                      .++.+|+..||+||++||++|.+|+++||++..    .|.||++||.+||+||++|+.++
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            468999999999999999999999999977653    37899999999999999998764

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.61  E-value=2.9e-16  Score=113.58  Aligned_cols=58  Identities=26%  Similarity=0.393  Sum_probs=51.8

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELK  104 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~  104 (200)
                      ++.+|+..||+||++||++|.+|+++|| +...|.||++||..||+||++|+.++.=|+
T Consensus         8 kR~~Hn~iErrRRd~IN~~i~eL~~LvP-~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            8 KRVSRNKSEKKRRDQFNVLIKELGSMLP-GNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSS-SCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HhhhhhHHHhhHHHHHHHHHHHHHHhCC-CCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            4679999999999999999999999995 445799999999999999999999876543

>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=99.56  E-value=7.2e-16  Score=108.65  Aligned_cols=55  Identities=22%  Similarity=0.354  Sum_probs=48.9

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC-----CCCCChhhHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR-----PARTDKPAILDDAIRVLNQLRTES  100 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~-----~~K~dKasIL~dAI~YIk~L~~~v  100 (200)
                      ++.+|+.+||+||++||++|.+|+++||++.     ..|.+||+||..||+||++|+.++
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            5789999999999999999999999996431     357899999999999999998765

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=99.52  E-value=4.1e-15  Score=108.44  Aligned_cols=60  Identities=22%  Similarity=0.367  Sum_probs=48.6

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCC-CCCCC-ChhhHHHHHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPG-RPART-DKPAILDDAIRVLNQLRTESQELK  104 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~-~~~K~-dKasIL~dAI~YIk~L~~~v~~L~  104 (200)
                      .++..|+.+||+||+.||++|.+|+.+||++ ...|. +|++||..||+||+.|+.++++++
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            5788999999999999999999999999632 33465 799999999999999999988764

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.49  E-value=3.8e-15  Score=107.97  Aligned_cols=54  Identities=22%  Similarity=0.334  Sum_probs=48.0

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTE   99 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~--~~K~dKasIL~dAI~YIk~L~~~   99 (200)
                      ++.+|+..||+||++||++|.+|+++||.+.  ..|.||++||..||+||+.|+.-
T Consensus         9 rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~~   64 (73)
T 4h10_A            9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   64 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhcC
Confidence            4688999999999999999999999996542  36999999999999999999753

>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=99.35  E-value=2.1e-13  Score=97.60  Aligned_cols=57  Identities=26%  Similarity=0.328  Sum_probs=50.2

Q ss_pred             CCCCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHH
Q 028999           44 CSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTES  100 (200)
Q Consensus        44 ~~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v  100 (200)
                      ..++..|+.+||+|+..||+.|..|+.+||.....|.+|+.||..||+||..|+..+
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            346788999999999999999999999996543468999999999999999998754

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=99.24  E-value=5.7e-12  Score=87.97  Aligned_cols=55  Identities=20%  Similarity=0.091  Sum_probs=48.2

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTES  100 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~-~~K~dKasIL~dAI~YIk~L~~~v  100 (200)
                      ++..|+.+||+|+..||+.|..|+.+||... ..|.+|+.||..||+||..|+..+
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            4567999999999999999999999995422 358999999999999999998765

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=99.15  E-value=4.6e-10  Score=83.35  Aligned_cols=51  Identities=25%  Similarity=0.426  Sum_probs=44.7

Q ss_pred             HHHHHHhHHHHhhhcCCCC--CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           58 RERLNDRFLDLSCILEPGR--PARTDKPAILDDAIRVLNQLRTESQELKETNE  108 (200)
Q Consensus        58 RekiNe~F~~Lr~lLpP~~--~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~  108 (200)
                      |..||++|.+|+.+||++.  ..|.+|++||..||+||+.|+.+++.+.++..
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            8899999999999997653  36899999999999999999999888776544

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=99.11  E-value=5e-11  Score=105.12  Aligned_cols=53  Identities=26%  Similarity=0.433  Sum_probs=42.5

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTE   99 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~   99 (200)
                      ++.+|+..||+||++||+.|.+|+++|| +...|.||++||..||.||+.|+..
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            4788999999999999999999999995 4557999999999999999999764

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.89  E-value=5.6e-10  Score=99.74  Aligned_cols=54  Identities=22%  Similarity=0.321  Sum_probs=47.7

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCC--CCCCCChhhHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPG--RPARTDKPAILDDAIRVLNQLRTE   99 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~--~~~K~dKasIL~dAI~YIk~L~~~   99 (200)
                      ++.+|+..||+||++||+.|.+|+.+||.+  ...|.||++||..||+||+.|+..
T Consensus        13 ~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             hcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            378999999999999999999999999632  236999999999999999999853

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.77  E-value=1.5e-09  Score=77.86  Aligned_cols=49  Identities=16%  Similarity=0.150  Sum_probs=42.1

Q ss_pred             hhHHHHHHHHHHHHhHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHH
Q 028999           50 KACREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRT   98 (200)
Q Consensus        50 H~~~ER~RRekiNe~F~~Lr~lLpP~-~~~K~dKasIL~dAI~YIk~L~~   98 (200)
                      =+.+||+|+..||+.|..||.+||.. ...|.+|..||.-||+||..|+.
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            34789999999999999999999532 12589999999999999999974

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=98.06  E-value=5e-06  Score=63.22  Aligned_cols=51  Identities=16%  Similarity=0.134  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHhHHHHhhhcCCC-CCCCCChhhHHHHHHHHHHHHHHHHHH
Q 028999           52 CREKLRRERLNDRFLDLSCILEPG-RPARTDKPAILDDAIRVLNQLRTESQE  102 (200)
Q Consensus        52 ~~ER~RRekiNe~F~~Lr~lLpP~-~~~K~dKasIL~dAI~YIk~L~~~v~~  102 (200)
                      ..||.|=..||+.|..||..||.. ...|.+|..||.-||+||..|+..++.
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            345778889999999999999532 235899999999999999999886653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=97.64  E-value=0.00053  Score=50.52  Aligned_cols=60  Identities=28%  Similarity=0.493  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +..||+-|.-|+-++++|+.+|..|.++..+++.....|+.|+..|+.|....+..|.++
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            467899999999999999999999999999988888888888888888888777766653

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}

Probab=96.77  E-value=0.011  Score=43.48  Aligned_cols=56  Identities=29%  Similarity=0.367  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHh
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLI-------LKADKEKLEQQLKVM  145 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~-------Lk~e~e~L~~qlk~~  145 (200)
                      .+.+.+|..+|+.+-.+..-|+.++++|+.+.+.|.+++..       |..++++|+++...+
T Consensus         5 ~ElleqLE~KIq~avdtI~lLqmEieELKekN~~L~~e~~e~~~~~~~L~~en~qLk~E~~~w   67 (81)
T 2jee_A            5 LEVFEKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQNGW   67 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence            36788899999998888888888888888888887777776       666777777776654

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

Probab=96.64  E-value=0.021  Score=45.23  Aligned_cols=65  Identities=12%  Similarity=0.038  Sum_probs=36.8

Q ss_pred             HHHHHhHHHHhhh--cCCCCCCCCChhhHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           59 ERLNDRFLDLSCI--LEPGRPARTDKPAILDD--AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  126 (200)
Q Consensus        59 ekiNe~F~~Lr~l--LpP~~~~K~dKasIL~d--AI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~  126 (200)
                      ..+|+++.+++..  - |..  -.++.+||.-  .++=+-+++.+.+.|+.+.+.+..++..|+.++.+++.
T Consensus        35 ~~vd~km~ei~~~~~~-~~l--~~~r~aVLaALNiadEl~k~~~~~~~L~~~l~~~~kE~~~lK~el~~~~~  103 (138)
T 3hnw_A           35 SYINNKITEFNKEESY-RRM--SAELRTDMMYLNIADDYFKAKKMADSLSLDIENKDKEIYDLKHELIAAQI  103 (138)
T ss_dssp             HHHHHHHHHHTTCHHH-HTS--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCC-CCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5689999999966  6 422  4788888872  33333335555555555555444444444444433333

>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=96.55  E-value=0.017  Score=39.89  Aligned_cols=58  Identities=28%  Similarity=0.387  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           54 EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  126 (200)
Q Consensus        54 ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~  126 (200)
                      ||++|....++..+.+.--               .-.+|+.+|+.+++.|+.+|..|..++..|+.++..|+.
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            4556666666666666543               234788889999988888888888877777777666654

>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=96.36  E-value=0.0065  Score=43.38  Aligned_cols=42  Identities=31%  Similarity=0.298  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      -.||++|+.++..|+..+..|..+...|+.++..|+.|+..|
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            478888888888888877777666666666666666555443

>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=95.71  E-value=0.019  Score=38.84  Aligned_cols=37  Identities=19%  Similarity=0.283  Sum_probs=10.9

Q ss_pred             HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRT-------ESQELKETNEKLQEEIKSLKAEKNEL  124 (200)
Q Consensus        88 dAI~YIk~L~~-------~v~~L~~~~~~L~~ei~~L~~eknEL  124 (200)
                      +|++||++--.       .++.|+.+++.|+.++.+|+.+..||
T Consensus         2 ~AlefIk~~LG~~~p~~~d~eaLk~E~~eLk~k~~~L~~~~~el   45 (53)
T 2yy0_A            2 SALDFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKL   45 (53)
T ss_dssp             --------------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68899987643       34444444444444444444443333

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

Probab=95.52  E-value=0.074  Score=42.09  Aligned_cols=52  Identities=25%  Similarity=0.187  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      |.++..++..|+.+...++.++++++.++.+|++++..|+.++-+|+..++.
T Consensus        84 l~~~~kE~~~lK~el~~~~~k~e~~~~e~~~l~~~~~~l~~~~~~le~~~~~  135 (138)
T 3hnw_A           84 IENKDKEIYDLKHELIAAQIKAESSAKEIKELKSEINKYQKNIVKLETELND  135 (138)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444555556666666667777777777777777777777777777776653

>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=95.49  E-value=0.045  Score=37.28  Aligned_cols=35  Identities=26%  Similarity=0.428  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr  125 (200)
                      .|+.+|+.++..|+.+|..|..++..|+.|+..|+
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            56666666666666666666655555555554443

>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=95.40  E-value=0.081  Score=40.19  Aligned_cols=56  Identities=32%  Similarity=0.472  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------------HHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKN----------------------------ELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~ekn----------------------------ELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +-+..|+.+++.|+.+++.|.+++..|..++.                            +...+...|++|+++|...+
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            34556777777777777777777777666554                            35566678888888888888


Q ss_pred             HHhc
Q 028999          143 KVMA  146 (200)
Q Consensus       143 k~~~  146 (200)
                      +.|-
T Consensus        92 ~~lE   95 (100)
T 1go4_E           92 RAME   95 (100)
T ss_dssp             TTCC
T ss_pred             HHHh
Confidence            7663

>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=95.26  E-value=0.17  Score=38.58  Aligned_cols=63  Identities=24%  Similarity=0.317  Sum_probs=39.6

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           79 RTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        79 K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .++|..++.+   ||. |...++.|++++..|+......-..+.+|..|...|+.|..+|.++-+.+
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            3778877764   554 88888888888888877555555555555555555555555555444433

>3qh9_A Liprin-beta-2; coiled-coil, dimerization, structural protein; 2.01A {Homo sapiens}

Probab=95.24  E-value=0.19  Score=36.91  Aligned_cols=56  Identities=27%  Similarity=0.407  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           89 AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        89 AI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      -|.-|++|+-.|.+|+.+.-+-+..++..+.|+..|+.....=.+++++|+.||.+
T Consensus        24 L~qEi~~Lr~kv~elEnErlQyEkKLKsTK~El~~Lq~qLe~kd~ei~rL~~~l~~   79 (81)
T 3qh9_A           24 LLQELRHLKIKVEELENERNQYEWKLKATKAEVAQLQEQVALKDAEIERLHSQLSR   79 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhHHHHHHHHHHHhh
Confidence            45789999999999999888888888888888888988888888999999988753

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=95.14  E-value=0.18  Score=40.91  Aligned_cols=86  Identities=16%  Similarity=0.131  Sum_probs=39.0

Q ss_pred             HHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           57 RRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  136 (200)
Q Consensus        57 RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e  136 (200)
                      =|+.+-.+|.+|-.-+ .+.+. ..=+|=+..-+.-|..|+.+...|+..+..|.+++++-......+++|...|+.+..
T Consensus        36 ~Rd~~E~~~~~l~~e~-~~~~~-~~~vs~~~~~~~~I~~L~~El~~l~~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n  113 (152)
T 3a7p_A           36 DRNDKEAHLNELFQDN-SGAIG-GNIVSHDDALLNTLAILQKELKSKEQEIRRLKEVIALKNKNTERLNAALISGTIENN  113 (152)
T ss_dssp             -----------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHhh-ccCCC-cccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3666666666665554 21111 112223334455677777777777776666666666666666666777776666666


Q ss_pred             HHHHHHHH
Q 028999          137 KLEQQLKV  144 (200)
Q Consensus       137 ~L~~qlk~  144 (200)
                      -++..++.
T Consensus       114 ~lE~kl~k  121 (152)
T 3a7p_A          114 VLQQKLSD  121 (152)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66555543

>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=94.68  E-value=0.037  Score=37.88  Aligned_cols=34  Identities=21%  Similarity=0.348  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL  124 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknEL  124 (200)
                      +||.+|+.++..|+.+|..|..++..|+.|+..|
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            5666666666666666666555554444444433

>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=94.51  E-value=0.14  Score=36.86  Aligned_cols=49  Identities=22%  Similarity=0.204  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      -|.+|+..+++-.++....++.|++|..++.|..++...|+.++++++.
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            3888888888888888888888999999999999999999988888743

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

Probab=94.25  E-value=0.13  Score=35.51  Aligned_cols=19  Identities=42%  Similarity=0.611  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQE  112 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~  112 (200)
                      ..|..+++.|+.+|..|..
T Consensus        26 ~~le~~~~~L~~~N~~L~~   44 (63)
T 1ci6_A           26 EALTGECKELEKKNEALKE   44 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3333333333333333333

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=94.15  E-value=0.44  Score=35.20  Aligned_cols=54  Identities=19%  Similarity=0.375  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKL------------QEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L------------~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +-|+.|+.+...|+.+...+            +.+|.+|+.++.++..++..|..|++.|+..+..
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            44555555555555443333            4557777777777878888888888877766654

>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=94.10  E-value=0.46  Score=34.33  Aligned_cols=55  Identities=15%  Similarity=0.166  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +|...-+......+.+.+.-.....++.....+|..||..|+.+++.|+.++..+
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            5666555555555556666566666677777777777777777777777777665

>2oqq_A Transcription factor HY5; homodimer leucine zipper; 2.00A {Arabidopsis thaliana}

Probab=93.87  E-value=0.2  Score=32.60  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  126 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~  126 (200)
                      .|+.+|+.++..|+..+..|++.+..|..|..=||+
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            489999999999988888888777666666555543

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=93.47  E-value=0.67  Score=34.15  Aligned_cols=54  Identities=15%  Similarity=0.151  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +|...-+.....-+...+.-.....++..+..+|..||..|+.+++.|+.++..
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            355544444444444444444445555555666666666666666666555544

>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=93.45  E-value=0.44  Score=43.51  Aligned_cols=37  Identities=19%  Similarity=0.297  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          109 KLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       109 ~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .++.++.+++....+.++....+++|.+.+.++++.+
T Consensus       541 ~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l  577 (597)
T 3oja_B          541 DLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQL  577 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444445555666666666666554

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1

Probab=93.44  E-value=0.28  Score=33.26  Aligned_cols=36  Identities=22%  Similarity=0.392  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          107 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus       107 ~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      ...|+.++..|..+..+|+.+...|+.|+..|.++|
T Consensus        24 ~~~Le~~~~~L~~~n~~L~~~i~~L~~e~~~Lk~~l   59 (61)
T 1t2k_D           24 VQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLL   59 (61)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            445666666666666666666666666666666554

>3cve_A Homer protein homolog 1; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, postsynaptic cell membrane, synapse; 1.75A {Rattus norvegicus}

Probab=93.40  E-value=0.45  Score=34.12  Aligned_cols=49  Identities=14%  Similarity=0.247  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      .+..+++.++..|..|+..+..|...+++-+.+...++.|+.++-++|.
T Consensus         4 ~~~~kLq~~E~~N~~Le~~v~~le~~Le~s~~~q~~~~~Elk~~~e~Ld   52 (72)
T 3cve_A            4 NSHMKLQEVEIRNKDLEGQLSEMEQRLEKSQSEQDAFRSNLKTLLEILD   52 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4566777888888888888888888888888888888888877776654

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=92.88  E-value=0.071  Score=36.01  Aligned_cols=28  Identities=32%  Similarity=0.466  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLK  118 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~  118 (200)
                      .||.+|+.+|..|+.+|..|..++..|+
T Consensus        22 ~~~~~LE~~v~~L~~eN~~L~~~~~~L~   49 (55)
T 1dh3_A           22 EYVKSLENRVAVLENQNKTLIEELKALK   49 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5666666666666666655555554444

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=92.68  E-value=1.6  Score=33.81  Aligned_cols=67  Identities=18%  Similarity=0.294  Sum_probs=34.9

Q ss_pred             CCChhhHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           79 RTDKPAILDDAIRVLNQLRTESQELKET----NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        79 K~dKasIL~dAI~YIk~L~~~v~~L~~~----~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +.+|-.++..=-.-|..|+.+++.+..+    ..+|+..+..|..++.+-+.+++....|.+.|..++..+
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            3444433333333333444444444322    234555566666666666666666666777777766654

>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=92.54  E-value=0.16  Score=35.16  Aligned_cols=32  Identities=19%  Similarity=0.341  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          111 QEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus       111 ~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +..+.+|..+..+|..++..|+.+++.|.+++
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            34455555555555555555555665555544

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

Probab=92.47  E-value=0.98  Score=30.97  Aligned_cols=44  Identities=27%  Similarity=0.351  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           89 AIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        89 AI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      |.+|=..=+...+.|+.+.+.|..+..+|+.+++.|+.|+..|+
T Consensus        14 A~R~R~KKk~~~~~le~~~~~L~~~N~~L~~~i~~L~~E~~~Lk   57 (63)
T 1ci6_A           14 ATRYRQKKRAEQEALTGECKELEKKNEALKERADSLAKEIQYLK   57 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444555555555555544444444444444444443

>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=92.13  E-value=0.6  Score=31.90  Aligned_cols=36  Identities=42%  Similarity=0.469  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          107 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus       107 ~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      ...|+.++..|..+..+|+.+...|+.++..|...|
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            345555555555555555555555555555555544

>3i00_A HIP-I, huntingtin-interacting protein 1; transcription; 2.30A {Homo sapiens} PDB: 2qa7_A

Probab=91.83  E-value=0.84  Score=35.37  Aligned_cols=50  Identities=22%  Similarity=0.147  Sum_probs=36.2

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           82 KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        82 KasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      --.|..++=.||.+|+.++..|+.+++.-+........+.+.|+.|+..|
T Consensus        31 le~l~~E~q~~v~ql~~~i~~Le~eL~e~r~~~q~a~~e~e~Lr~e~~~l   80 (120)
T 3i00_A           31 LENMKTESQRVVLQLKGHVSELEADLAEQQHLRQQAADDCEFLRAELDEL   80 (120)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34578899999999999999999988776655555555555555555444

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=91.71  E-value=0.53  Score=42.69  Aligned_cols=53  Identities=25%  Similarity=0.322  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      |..|+.++..|+++...|++++++++.++.++.++.........+|..+++.+
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            56788888888888889999999999999888888777777777888888775

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

Probab=91.69  E-value=1.2  Score=34.25  Aligned_cols=32  Identities=16%  Similarity=0.410  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNEL  124 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknEL  124 (200)
                      |..|+.++..|...++.|+..+++|.+....|
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            33333333333333333333333333333333

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

Probab=91.67  E-value=1.1  Score=33.26  Aligned_cols=45  Identities=27%  Similarity=0.426  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      ..|+.++..|+.+-..|..++..|..+...+..+...++.+.++|
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            344444444444444444444444444444444444444444444

>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=91.64  E-value=1.5  Score=32.59  Aligned_cols=40  Identities=15%  Similarity=0.272  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          106 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       106 ~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +...|+.+...|..+++.|+.|+..+..|++.+.+.+..+
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            3456777777777788888888888888888887777655

>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=91.61  E-value=0.23  Score=33.82  Aligned_cols=32  Identities=34%  Similarity=0.579  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          109 KLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       109 ~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      .|+.++..|..+..+|..+...|+.|+..|.+
T Consensus        26 ~Le~~v~~L~~~n~~L~~~v~~L~~e~~~Lk~   57 (62)
T 1jnm_A           26 RLEEKVKTLKAQNSELASTANMLREQVAQLKQ   57 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444444444444444433

>3cvf_A Homer-3, homer protein homolog 3; coiled coil, alternative splicing, cell junction, cytoplasm, membrane, phosphoprotein, polymorphism; 2.90A {Homo sapiens}

Probab=91.52  E-value=0.79  Score=33.32  Aligned_cols=48  Identities=21%  Similarity=0.362  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      +..+++.++..|..|+..++.|...+++-+.+...++.|+.++-++|.
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            344566777777777777888877777777777777777777766554

>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=91.41  E-value=1  Score=30.21  Aligned_cols=40  Identities=30%  Similarity=0.443  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      -+.+|+.++..|...|..|.+       .+.+.|++...|+.++++|
T Consensus        10 r~~~l~~~l~~L~~rN~rL~~-------~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           10 DIHQLEARIDSLAARNSKLME-------TLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHh
Confidence            344566666666666666554       4555555555556666655

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=91.10  E-value=0.79  Score=32.93  Aligned_cols=52  Identities=13%  Similarity=0.058  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      +|..++.+|+....-+..-|.+|...+.+.+.+...|+.++..|..+++.+.
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            4556666666666666666666666666666666677777777766666653

>3htk_A Structural maintenance of chromosomes protein 5; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=90.93  E-value=2.4  Score=28.05  Aligned_cols=51  Identities=22%  Similarity=0.208  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      +..|+..+..++.....+..+...++..++++..+......+|..++.|+.
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            445555555555555555555555555555555555555556666655554

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=90.86  E-value=1.6  Score=33.32  Aligned_cols=53  Identities=17%  Similarity=0.197  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      |.-|+..++++++...+++.+.++...+.+.++.....|+.++..|+.||+..
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            55666777777777778888888888888888888888888888888888763

>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=90.84  E-value=5.5  Score=36.20  Aligned_cols=46  Identities=24%  Similarity=0.459  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           98 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        98 ~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      ++.++++.+...++..+++.+....|+++|++.+++|+..|++.+.
T Consensus       537 ~~~~~~~~~~~~le~~~~~~~~~~~~l~~e~~~~~~~~~~l~~~~~  582 (597)
T 3oja_B          537 KETEDLEQENIALEKQLDNKRAKQAELRQETSLKRQKVKQLEAKKN  582 (597)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             cchhhHHhhhHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3444455667777777777777777777777777777777666554

>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=90.82  E-value=1.1  Score=29.91  Aligned_cols=38  Identities=21%  Similarity=0.271  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..|+.++..|......|-+-....+.++.+|..+|..+
T Consensus        12 ~~l~~~l~~L~~rN~rL~~~L~~AR~el~~Lkeele~L   49 (51)
T 3m91_A           12 HQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRL   49 (51)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34555555566666666666666777777777776654

>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=90.79  E-value=2.8  Score=32.18  Aligned_cols=62  Identities=18%  Similarity=0.248  Sum_probs=40.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           84 AILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        84 sIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..+.+|-+....|...-..|+.....+.+.+.+.....++|..++-.|..++..|+.++...
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            34566666666666666666666666666666666666666666666666777776666554

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

Probab=90.77  E-value=2  Score=35.70  Aligned_cols=16  Identities=31%  Similarity=0.351  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNE  108 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~  108 (200)
                      +++|+..+..|..+.+
T Consensus        58 ~~~L~~~~~~L~~E~e   73 (189)
T 2v71_A           58 NRDLQADNQRLKYEVE   73 (189)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3334444444443333

>3he5_A Synzip1; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=90.67  E-value=1.4  Score=28.74  Aligned_cols=44  Identities=25%  Similarity=0.251  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKAD  134 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e  134 (200)
                      ..+.+|+.++..|+.+|++|....-.-+.-+..|..|.+.|+..
T Consensus         3 nlvaqlenevaslenenetlkkknlhkkdliaylekeianlrkk   46 (49)
T 3he5_A            3 NLVAQLENEVASLENENETLKKKNLHKKDLIAYLEKEIANLRKK   46 (49)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhhcccHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence            35778999999999999988765433333333344444444433

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

Probab=90.53  E-value=0.85  Score=46.33  Aligned_cols=15  Identities=20%  Similarity=0.182  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHHHH
Q 028999          130 ILKADKEKLEQQLKV  144 (200)
Q Consensus       130 ~Lk~e~e~L~~qlk~  144 (200)
                      .|+.|+.+|++|+..
T Consensus      1027 ~L~~e~~~L~qq~~~ 1041 (1080)
T 2dfs_A         1027 ELKEQNTLLKTEKEE 1041 (1080)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            344444444444433

>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=0.65  Score=32.92  Aligned_cols=39  Identities=21%  Similarity=0.309  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          106 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       106 ~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ....|+.++.+|......|..|+..|+.+++.|..+++.
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            344555566666666666667777777777777766654

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=90.48  E-value=0.32  Score=42.28  Aligned_cols=36  Identities=22%  Similarity=0.309  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          105 ETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       105 ~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      .++..|..+.+.|+.++++++.|...||.|+++|.+
T Consensus        61 ~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~s   96 (251)
T 3m9b_A           61 ARIDSLAARNSKLMETLKEARQQLLALREEVDRLGQ   96 (251)
T ss_dssp             HHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            333333333334444555555555555555555443

>3m9b_A Proteasome-associated ATPase; coil COIL with 5 beta-strand barrel inter domain, chaperone; 3.94A {Mycobacterium tuberculosis} PDB: 3m9d_A

Probab=90.38  E-value=0.33  Score=42.18  Aligned_cols=46  Identities=24%  Similarity=0.363  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 028999          107 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTGGY  152 (200)
Q Consensus       107 ~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p~g~  152 (200)
                      ...|+.++..|......|.++...++.|+++|+.|++.+..||..|
T Consensus        56 l~eL~~ql~~L~arNe~L~~~Lk~ar~El~~LkeElerL~sPPL~i  101 (251)
T 3m9b_A           56 IHQLEARIDSLAARNSKLMETLKEARQQLLALREEVDRLGQPPSGY  101 (251)
T ss_dssp             HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHSCCEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCceE
Confidence            4467777777766666678888888888888888888887776643

>3he5_B Synzip2; heterodimeric coiled-coil, de novo protein; 1.75A {Artificial gene}

Probab=90.36  E-value=1.1  Score=29.61  Aligned_cols=41  Identities=27%  Similarity=0.342  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADK  135 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~  135 (200)
                      .|+..+..|++.|-+|+..-..|..-+..||+|.++|..|.
T Consensus         7 ylrkkiarlkkdnlqlerdeqnlekiianlrdeiarlenev   47 (52)
T 3he5_B            7 YLRKKIARLKKDNLQLERDEQNLEKIIANLRDEIARLENEV   47 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhhhhhhHhhHHHHHHHHHHHHHHHHHHH
Confidence            47778888888888877766667666777777766665544

>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=90.21  E-value=1.5  Score=33.36  Aligned_cols=50  Identities=28%  Similarity=0.460  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      -+.+|+.+...|+......-..+++|..++..|+.||+.|..|.+-..++
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            34456666666666666667888888888888999998888888877665

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1

Probab=89.92  E-value=0.65  Score=34.20  Aligned_cols=31  Identities=32%  Similarity=0.496  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr  125 (200)
                      +++.++..|+.+|..|+.+|..|+.|+..|+
T Consensus        40 e~~~r~~~Le~EN~~Lr~~v~~L~~E~~~Lr   70 (87)
T 1hjb_A           40 ETQHKVLELTAENERLQKKVEQLSRELSTLR   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455555555555555555554444444443

>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=89.90  E-value=0.97  Score=35.29  Aligned_cols=34  Identities=24%  Similarity=0.304  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          107 NEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       107 ~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      .+.|+.||..|++++.+...|...|+.+++.|..
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            4444445555555554444444445444444443

>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=89.74  E-value=2.2  Score=35.77  Aligned_cols=41  Identities=12%  Similarity=0.276  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELRE  126 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~  126 (200)
                      +.=+++-+..|+.++..|..+++.|+.++..|..++.++-.
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            55555555555555565655555555555555555444433

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=89.64  E-value=2.2  Score=30.96  Aligned_cols=31  Identities=16%  Similarity=0.256  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELRE  126 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~  126 (200)
                      |..+++.|+.+...|+-.++++.-+++++..
T Consensus        25 Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~   55 (83)
T 2xdj_A           25 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVE   55 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            3333443433333333333333333333333

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.63  E-value=2  Score=32.30  Aligned_cols=48  Identities=23%  Similarity=0.299  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      -|.+|+.++...+.+...|..++.+-+...-+...++..+..|+|.|-
T Consensus        13 ~l~~le~~~~~~~~e~~~L~~~l~eE~~~R~~aE~~~~~ie~ElEeLT   60 (97)
T 2eqb_B           13 DYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLT   60 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333344333333333333333333333333333333344444444443

>3swy_A Cyclic nucleotide-gated cation channel alpha-3; coiled-coil, assembly domain, transport protein; 1.90A {Homo sapiens}

Probab=89.51  E-value=1.7  Score=28.52  Aligned_cols=44  Identities=27%  Similarity=0.356  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQ  141 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~q  141 (200)
                      +|++.|+.|+...+.|+.....|-+|.+   .-..+||+-+.+|+.+
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            5788899999999999988888866554   4456888888888875

>3swf_A CGMP-gated cation channel alpha-1; coiled-coil, assembly domain, transport protein; 2.14A {Bos taurus}

Probab=89.48  E-value=1.5  Score=31.65  Aligned_cols=49  Identities=22%  Similarity=0.239  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ++|++.|+.|+...+.|+.....|-+|.+   .-..+||+-+.+|+.+++..
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            35888999999999999998888866555   45678999999999999874

>2eqb_B RAB guanine nucleotide exchange factor SEC2; coiled coil, endocytosis/exocytosis complex; 2.70A {Saccharomyces cerevisiae} SCOP: h.1.33.1

Probab=89.40  E-value=4  Score=30.70  Aligned_cols=15  Identities=20%  Similarity=0.403  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHH
Q 028999          129 LILKADKEKLEQQLK  143 (200)
Q Consensus       129 ~~Lk~e~e~L~~qlk  143 (200)
                      ..++...+.|+.||+
T Consensus        79 ~~~e~kn~~L~~qL~   93 (97)
T 2eqb_B           79 YAIEILNKRLTEQLR   93 (97)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh
Confidence            344444445555544

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens}

Probab=89.35  E-value=3.1  Score=34.07  Aligned_cols=52  Identities=17%  Similarity=0.326  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      .+-+.|.+|+.++..|..+.+.+......+..++..|.+....|..++..++
T Consensus        87 q~se~~~elq~ri~~L~~El~~~k~~~~k~~~e~r~L~Ekl~~lEKe~a~~e  138 (168)
T 3o0z_A           87 HDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEAQDMLNHSEKEKNNLE  138 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3445666666666666666666666666666666666666666666655555

>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=89.20  E-value=0.75  Score=30.83  Aligned_cols=29  Identities=28%  Similarity=0.432  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          114 IKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus       114 i~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +..|+.|+.+|+.+...|+.+++.|..+|
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            33444444444444444444444444443

>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=89.13  E-value=2.8  Score=27.64  Aligned_cols=51  Identities=18%  Similarity=0.190  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      ..-+++..+...+..++.....+...+..+...++..+++...++.+++.+
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            344667777778888888888888899999999999999999998888653

>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=89.11  E-value=1.6  Score=39.81  Aligned_cols=52  Identities=19%  Similarity=0.243  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..|+.++.+|++..++|++++++++.++.++.++......+..+|..++..+
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            5688899999999999999999999999998888877777778888888876

>1deb_A APC protein, adenomatous polyposis coli protein; coiled coil, tumor suppressor, structural protein; 2.40A {Homo sapiens} SCOP: h.1.18.1

Probab=88.92  E-value=2.8  Score=28.28  Aligned_cols=45  Identities=24%  Similarity=0.309  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      .+|-.+|+.|+.+|..|+.|.+.=...++.|..|...+|.=...|
T Consensus         6 dQL~~QVe~Lk~ENshLrrEL~dNS~~lskLE~ets~mKevlk~l   50 (54)
T 1deb_A            6 DQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQL   50 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHhhhhhHHHHHHHH
Confidence            467778889999998888888777777777777777666544433

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

Probab=88.61  E-value=2.1  Score=43.57  Aligned_cols=24  Identities=33%  Similarity=0.602  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          119 AEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus       119 ~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      ..++.|..|++.|+++++.|+.++
T Consensus      1023 ~kv~~L~~e~~~L~qq~~~l~~~~ 1046 (1080)
T 2dfs_A         1023 QLVSELKEQNTLLKTEKEELNRRI 1046 (1080)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444456677777777777776443

>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=87.77  E-value=4.1  Score=37.33  Aligned_cols=59  Identities=15%  Similarity=0.112  Sum_probs=41.0

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           82 KPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        82 KasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      +......++++++.+..++.+|+.......++++.|+..++.++.....|+..+..|+.
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            44445666899999999999988877777777777777776665555555555555543

>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=87.73  E-value=1.6  Score=31.44  Aligned_cols=33  Identities=30%  Similarity=0.405  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELR  125 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr  125 (200)
                      ..+++.++..|+.+|..|+.+|..|+.|+..|+
T Consensus        38 ~~e~~~r~~~L~~eN~~L~~~v~~L~~E~~~Lr   70 (78)
T 1gu4_A           38 NLETQHKVLELTAENERLQKKVEQLSRELSTLR   70 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345566666677777766666666655555543

>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=87.58  E-value=1.3  Score=32.89  Aligned_cols=37  Identities=27%  Similarity=0.416  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          101 QELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus       101 ~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      ..|+.++..|..++..|+.|+.++..|...+|...+.
T Consensus        51 ~~LE~e~~~L~~e~~~L~~e~~~~~~e~d~~k~k~~~   87 (90)
T 2wt7_B           51 HHLENEKTQLIQQVEQLKQEVSRLARERDAYKVKSEK   87 (90)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444455555555555555544444443

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G*

Probab=87.25  E-value=2.9  Score=39.95  Aligned_cols=43  Identities=19%  Similarity=0.177  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKE  136 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e  136 (200)
                      .+|+.+++-|+++...-...|+.|+.-+.+++.+.++|..+|+
T Consensus       113 ~ELRRrIqyLKekVdnQlsnIrvLQsnLedq~~kIQRLEvDId  155 (562)
T 3ghg_A          113 EDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDID  155 (562)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3788888888877765557788888888888888888875553

>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=87.04  E-value=6.8  Score=29.95  Aligned_cols=48  Identities=21%  Similarity=0.293  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           97 RTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus        97 ~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      ......|......|...+.++...+.+..+.+..|..++.+|++++..
T Consensus        68 EE~~~~L~~~k~eLe~~l~el~~rleeeee~~~~L~~~kkkle~e~~~  115 (129)
T 2fxo_A           68 EERCDQLIKNKIQLEAKVKEMNKRLEDEEEMNAELTAKKRKLEDECSE  115 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333444444555566666666666666666666666666666665544

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1

Probab=87.00  E-value=2.7  Score=28.08  Aligned_cols=33  Identities=21%  Similarity=0.235  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          110 LQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus       110 L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      -+..+.+|..+..+|..|+..|+.+++.|++++
T Consensus        20 Kk~~~~~LE~~v~~L~~eN~~L~~~~~~L~~~~   52 (55)
T 1dh3_A           20 KKEYVKSLENRVAVLENQNKTLIEELKALKDLY   52 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345577777777888888888888888777643

>3v86_A De novo design helix; computational design of A protein crystal, helical coil, DE designed helix, de novo protein; 2.91A {Synthetic}

Probab=86.98  E-value=0.64  Score=27.04  Aligned_cols=26  Identities=38%  Similarity=0.521  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSL  117 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L  117 (200)
                      |+-+|+.++-+|+-+...|..++++|
T Consensus         1 yvyqlkdevgelkgevralkdevkdl   26 (27)
T 3v86_A            1 YVYQLKDEVGELKGEVRALKDEVKDL   26 (27)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchhhHHHHHHHhHHHHHHHHHhcc
Confidence            44556666665555555555554443

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=86.81  E-value=7.1  Score=29.71  Aligned_cols=58  Identities=24%  Similarity=0.356  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKA-----------EKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~-----------eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      +.+.-.-|..|+.+++.++..+..|+..+.++..           .+..|..+...++.+.++.-++++
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            3344445566666666666666666655544433           233444444555555554444333

>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=86.80  E-value=1.2  Score=27.91  Aligned_cols=26  Identities=27%  Similarity=0.413  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKA  119 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~  119 (200)
                      +||+.+|++|-.++..|+.++..|+.
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            45555555555555555544444443

>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=86.73  E-value=2  Score=29.45  Aligned_cols=32  Identities=28%  Similarity=0.391  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEK  121 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~ek  121 (200)
                      .+|+.+|+.++..|+.+|..|..++..|+.++
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            36788888888888877777777666665544

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=86.62  E-value=16  Score=32.55  Aligned_cols=39  Identities=15%  Similarity=0.165  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          106 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       106 ~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +.+....+.+....+.+.|++|+.+++.+++.+..++..
T Consensus       429 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  467 (487)
T 3oja_A          429 VQNNAIRDWDMYQHKETQLAEENARLKKLNGEADLALAS  467 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcchhhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHh
Confidence            333344444555555555666666666665555554443

>2w6a_A ARF GTPase-activating protein GIT1; PIX, zinc, signaling protein, CAT-1, cytoplasm, ANK repeat, coiled-coil, zinc-finger, metal-binding; 1.40A {Rattus norvegicus}

Probab=86.58  E-value=2.1  Score=29.77  Aligned_cols=36  Identities=31%  Similarity=0.529  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           97 RTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        97 ~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      +.++++|-+-|..|.+|++-|..+++.|+.|+..|+
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            445677777777777777777777888877777765

>3a7p_A Autophagy protein 16; coiled-coil, coiled coil, cytoplasmic vesicle, protein transport, transport, vacuole; 2.80A {Saccharomyces cerevisiae}

Probab=86.55  E-value=5.9  Score=31.97  Aligned_cols=50  Identities=20%  Similarity=0.230  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      .-|++|..++..-...++.|+.|+..|..+.|.+.+....|+.|...|-+
T Consensus        82 ~ki~dLeeel~eK~K~~e~l~DEl~aLqlq~n~lE~kl~kLq~EN~~LV~  131 (152)
T 3a7p_A           82 QEIRRLKEVIALKNKNTERLNAALISGTIENNVLQQKLSDLKKEHSQLVA  131 (152)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444667788899999999999998888999888877643

>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=86.31  E-value=1.5  Score=33.15  Aligned_cols=34  Identities=35%  Similarity=0.431  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028999          113 EIKSLKAEKNELREEKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus       113 ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      ++..|+.++.+|+.|+..|+.+++.|+-+|-...
T Consensus        13 ~~~~lr~ei~~Le~E~~rLr~~~~~LE~~Le~~~   46 (100)
T 1go4_E           13 EADTLRLKVEELEGERSRLEEEKRMLEAQLERRA   46 (100)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4555666666666666666667777776665543

>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=86.21  E-value=6  Score=30.81  Aligned_cols=34  Identities=24%  Similarity=0.332  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          111 QEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       111 ~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +..+++|.-|+..|.++......++|+|..+...
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            3345555555555555555555555655554443

>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=86.12  E-value=2.1  Score=26.88  Aligned_cols=26  Identities=31%  Similarity=0.465  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLK  118 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~  118 (200)
                      ++||+..|++|-.++..|+.++..|+
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            34555555555444444444444443

>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=86.07  E-value=7.9  Score=28.00  Aligned_cols=46  Identities=30%  Similarity=0.480  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      ..|+..-++|..-..+|+.-+..|..|.+++......|+...+.|+
T Consensus        28 ~sLrrT~~EL~~G~~KL~~mi~~l~~E~~~l~~ni~~lk~K~~EL~   73 (78)
T 3iv1_A           28 NALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELS   73 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455556666666666666666666666666666666655555444

>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=85.91  E-value=1.7  Score=30.76  Aligned_cols=32  Identities=22%  Similarity=0.338  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          114 IKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       114 i~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      |+.|..+..+|..|+..|+.+++.|+++|..+
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            44555555556666666666666666666654

>1jcd_A Major outer membrane lipoprotein; protein folding, coiled coil, helix capping, alanine-zipper, membrane protein; 1.30A {Escherichia coli} SCOP: h.1.16.1 PDB: 1eq7_A 1t8z_A* 2guv_A 2gus_A 1jcc_A 1kfn_A 1kfm_A

Probab=85.70  E-value=4.1  Score=27.32  Aligned_cols=36  Identities=6%  Similarity=0.276  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEK  128 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek  128 (200)
                      |.+|-.+|+.|......|..++..|+.+...-.+|-
T Consensus         6 i~~Lss~V~~L~~kVdqLssdV~al~~~v~~ak~eA   41 (52)
T 1jcd_A            6 ADQASSDAQTANAKADQASNDANAARSDAQAAKDDA   41 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555555555555555555555544444433333

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

Probab=85.48  E-value=9.1  Score=28.22  Aligned_cols=44  Identities=14%  Similarity=0.271  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      .|++-..+++..+..++..+.++..++..|...+..+.++...+
T Consensus        20 ~a~drae~~e~~~k~~e~~~~~~E~Ei~sL~kk~~~lE~eld~~   63 (101)
T 3u1c_A           20 NALDRAEQAEADKKAAEERSKQLEDDIVQLEKQLRVTEDSRDQV   63 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            45555555666555555555555555555555555444444333

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

Probab=85.42  E-value=9.2  Score=29.27  Aligned_cols=19  Identities=37%  Similarity=0.501  Sum_probs=8.6

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQE  112 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~  112 (200)
                      ++|+..+..|..+++.++.
T Consensus         6 rdL~~~~~~L~~E~e~~k~   24 (111)
T 2v66_B            6 RDLQADNQRLKYEVEALKE   24 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            4444444444444444433

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

Probab=85.39  E-value=4.4  Score=33.70  Aligned_cols=22  Identities=27%  Similarity=0.342  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028999           99 ESQELKETNEKLQEEIKSLKAE  120 (200)
Q Consensus        99 ~v~~L~~~~~~L~~ei~~L~~e  120 (200)
                      ++..++..+..|+..+..|+.+
T Consensus        50 eL~~~Ek~~~~L~~~~~~L~~E   71 (189)
T 2v71_A           50 QLVQAEQRNRDLQADNQRLKYE   71 (189)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3333333333344333333333

>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=85.18  E-value=1.1  Score=27.66  Aligned_cols=10  Identities=30%  Similarity=0.421  Sum_probs=3.6

Q ss_pred             HHHHHHHHHH
Q 028999           96 LRTESQELKE  105 (200)
Q Consensus        96 L~~~v~~L~~  105 (200)
                      |+.+|++|-.
T Consensus         5 LE~kVEeLl~   14 (33)
T 3m48_A            5 LEAKVEELLS   14 (33)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            3333333333

>2xdj_A Uncharacterized protein YBGF; unknown function; 1.82A {Escherichia coli} PDB: 2wz7_A

Probab=85.18  E-value=6.4  Score=28.51  Aligned_cols=43  Identities=16%  Similarity=0.195  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       102 ~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +|....+.|+.++..|+-.++++..+...++..-..+.+.|..
T Consensus        24 ~Lq~Ql~~Lq~Ev~~LRGqiE~~~~~l~ql~~rQrd~Y~dLD~   66 (83)
T 2xdj_A           24 QLQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQILLQIDS   66 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555555555555555555555555555544444444543

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.06  E-value=1.7  Score=39.73  Aligned_cols=44  Identities=18%  Similarity=0.318  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 028999          106 TNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPT  149 (200)
Q Consensus       106 ~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p  149 (200)
                      ....|+.+++.|..+.+.+++|...++.++.+++.+++.+..+|
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            33445555566666666777777777778888888887765543

>3u59_A Tropomyosin beta chain; muscle contraction, actin, contractIle protein; 2.50A {Gallus gallus}

Probab=84.70  E-value=9.8  Score=27.88  Aligned_cols=45  Identities=18%  Similarity=0.253  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILK  132 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk  132 (200)
                      .|++-..+++.++..++..+.++..++..|+..+..+.++...+.
T Consensus        20 ~a~d~ae~~e~~~k~~e~~~~~~E~ei~sL~kKiq~lE~eld~~~   64 (101)
T 3u59_A           20 NAIDRAEQAEADKKQAEDRCKQLEEEQQGLQKKLKGTEDEVEKYS   64 (101)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666555555555444333

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

Probab=84.62  E-value=5.3  Score=33.50  Aligned_cols=51  Identities=14%  Similarity=0.167  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      |..|+.++..++.....++.++.++..++..+..+...++..+++.+.++.
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            333444444444444444444444444444444444444444444444443

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=84.37  E-value=2.3  Score=33.05  Aligned_cols=43  Identities=7%  Similarity=0.088  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVMAMPTG  150 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~~~~p~  150 (200)
                      +.|.+...+|..++.+|+.-...|...++.+++.++.......
T Consensus        98 ~~l~~~~~~l~~~i~~L~~~~~~L~~~i~~~~~~~~~~~~~~~  140 (148)
T 3gpv_A           98 KLMKQQEANVLQLIQDTEKNLKKIQQKIAKYEDEISSANATTK  140 (148)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence            3455555556666666666566666666666665554433333

>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=84.31  E-value=4.6  Score=36.75  Aligned_cols=87  Identities=20%  Similarity=0.340  Sum_probs=48.1

Q ss_pred             HHHHHHHhHHHHhhhc-CCCCCCC-------CChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHH
Q 028999           57 RRERLNDRFLDLSCIL-EPGRPAR-------TDKPAILDDAIRVLNQLRTESQELKETNEKLQE-E-IKSLKAEKNELRE  126 (200)
Q Consensus        57 RRekiNe~F~~Lr~lL-pP~~~~K-------~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~-e-i~~L~~eknELr~  126 (200)
                      +-+.+.++|.+|...+ .|+....       +...+-|...++.+..|+...+.++...+-+.+ + -.+|   +.++.+
T Consensus        18 ~l~~~~~r~~el~~~l~~p~~~~d~~~~~~~~ke~~~l~~~v~~~~~~~~~~~d~~~~~el~~~~e~D~e~---~~~a~~   94 (371)
T 1zbt_A           18 QLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAVYREYKQVVQNIADAQEMIKDASGDPEL---EEMAKE   94 (371)
T ss_dssp             HHHHHHHHHHHC--------------------CCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CHH---HHHHHH
T ss_pred             hHHHHHHHHHHHHHHhcCCcchhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHH---HHHHHH
Confidence            4456888999998876 2321111       233456666677777776666666654444332 1 1111   345677


Q ss_pred             HHHHHHHHHHHHHHHHHHhc
Q 028999          127 EKLILKADKEKLEQQLKVMA  146 (200)
Q Consensus       127 Ek~~Lk~e~e~L~~qlk~~~  146 (200)
                      |...|+.+++.|+.+|+.+-
T Consensus        95 e~~~l~~~l~~le~~l~~lL  114 (371)
T 1zbt_A           95 ELKNSKVAKEEYEEKLRFLL  114 (371)
T ss_dssp             HHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHhc
Confidence            88899999999999998763

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=84.18  E-value=6.4  Score=35.17  Aligned_cols=54  Identities=9%  Similarity=0.050  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           92 VLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        92 YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..++++.+.+.++...+..+++++.|+.+++.++.+...+..+++...+.++.+
T Consensus       422 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  475 (487)
T 3oja_A          422 MYVEQQSVQNNAIRDWDMYQHKETQLAEENARLKKLNGEADLALASANATLQEL  475 (487)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcchhhhhhhhhHHHHHHHHhhhhhhhhhhhhhhhHhcccHHHHH
Confidence            444555555556667777788888888888888888888888888877777764

>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=84.12  E-value=7.2  Score=31.43  Aligned_cols=23  Identities=13%  Similarity=0.120  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 028999           86 LDDAIRVLNQLRTESQELKETNE  108 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~  108 (200)
                      |-.||++...|..++..+..+++
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            44566666666665555554444

>3efg_A Protein SLYX homolog; xanthomonas campestris PV. campestris, coiled-coil, structur genomics, PSI-2, protein structure initiative; 2.00A {Xanthomonas campestris PV}

Probab=83.97  E-value=4.1  Score=29.11  Aligned_cols=44  Identities=14%  Similarity=0.139  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          102 ELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       102 ~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .|+.....|+..+.....-+++|-+.......+|++|+.+++.+
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            34444444444444444445555554455555555555555444

>3s4r_A Vimentin; alpha-helix, cytoskeleton, intermediate filament, structural; 2.45A {Homo sapiens} PDB: 3ssu_A

Probab=83.63  E-value=3.1  Score=30.53  Aligned_cols=33  Identities=21%  Similarity=0.322  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          107 NEKLQEEIKSLKAEKNELREEKLILKADKEKLE  139 (200)
Q Consensus       107 ~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~  139 (200)
                      ...|+.++..+..++..|.-|...|..+++++.
T Consensus        58 i~~Lr~~i~~~~~ek~~l~~e~dnl~~~~~~~k   90 (93)
T 3s4r_A           58 MRELRRQVDQLTNDKARVEVERDNLAEDIMRLR   90 (93)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444444444444444444444444444443

>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=83.24  E-value=3.2  Score=36.96  Aligned_cols=53  Identities=11%  Similarity=0.084  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           90 IRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        90 I~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +.=++.|..++.+|+.......+++..|+..+..++.....|+.++..|+..+
T Consensus         4 ~~~~~~~~~~~~~~e~~i~~~~~~i~~L~~~l~~~~~~i~~l~~~i~~l~~~~   56 (323)
T 1lwu_C            4 QKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVNQQFVTRLQQQLVDIRQTC   56 (323)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33455566666666666666666666666666666666666666666665544

>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=83.21  E-value=11  Score=27.25  Aligned_cols=51  Identities=22%  Similarity=0.267  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      +-+.+++.|+...+.|..-...|..=+++|..|...|...++.|+...+.+
T Consensus        22 q~qaEl~sLrrT~~EL~~G~~KL~~mi~~l~~E~~~l~~ni~~lk~K~~EL   72 (78)
T 3iv1_A           22 RAQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEEL   72 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334445555555555555555555556667777777777777777666555

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

Probab=83.20  E-value=11  Score=27.43  Aligned_cols=42  Identities=17%  Similarity=0.315  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           96 LRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        96 L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      +.+++.+.+..|-.++.+.++......+|..|...|+.+.+.
T Consensus        29 i~EELs~vr~~ni~~eskL~eae~rn~eL~~e~~~l~~~~ee   70 (81)
T 1wt6_A           29 LSREMEAIRTDNQNFASQLREAEARNRDLEAHVRQLQERMEL   70 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444444444444444444444444443

>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=83.18  E-value=2.4  Score=26.25  Aligned_cols=19  Identities=21%  Similarity=0.356  Sum_probs=7.3

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 028999          110 LQEEIKSLKAEKNELREEK  128 (200)
Q Consensus       110 L~~ei~~L~~eknELr~Ek  128 (200)
                      |+..+.+|-.++.+|.+|.
T Consensus         6 LE~kVEeLl~~n~~Le~eV   24 (34)
T 2oxj_A            6 LEXKVXELLXKNXHLEXEV   24 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHH
Confidence            3333333333344433333

>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=82.92  E-value=2.1  Score=26.41  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 028999          120 EKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       120 eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      ...||..+|..|+.|++||..
T Consensus         8 kVEeLl~~n~~Le~EV~RLk~   28 (33)
T 3m48_A            8 KVEELLSKNWNLENEVARLKK   28 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHH
Confidence            344444455555555555544

>3tnu_A Keratin, type I cytoskeletal 14; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=82.89  E-value=9.3  Score=29.17  Aligned_cols=56  Identities=20%  Similarity=0.274  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKA-----------EKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~-----------eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      +.-.-|..|+.+++.++..+..|+..+.++..           .+.+|..+...++.++++.-++++
T Consensus        42 elrr~iq~L~~el~~l~~~~~sLE~~l~e~e~~~~~~l~~~q~~i~~lE~eL~~~r~em~~ql~EYq  108 (131)
T 3tnu_A           42 ELRRTMQNLEIELQSQLSMKASLENSLEETKGRYCMQLAQIQEMIGSVEEQLAQLRCEMEQQNQEYK  108 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444555666666666556555555444433           233444444455555444443333

>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=82.74  E-value=6.2  Score=35.75  Aligned_cols=77  Identities=19%  Similarity=0.292  Sum_probs=57.3

Q ss_pred             HHHHHhHHHHhhhc-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           59 ERLNDRFLDLSCIL-EPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus        59 ekiNe~F~~Lr~lL-pP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      ..|++-|..|.++- -|.  .-.-+..+|+.|-.....++.--..|+.....+..+|+..-.++|.|-.+.+.|..+|-+
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            46788888888887 232  235678899999888888888888888777777777777777777777776666666644

>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=82.72  E-value=3.7  Score=27.70  Aligned_cols=49  Identities=27%  Similarity=0.342  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      ++++..+..|+.+...++.++.....|..+|.+=|..|..||..-..-|
T Consensus         3 ~~~q~~i~~le~el~~~r~e~~~q~~eYq~LlniK~~Le~EIatYRkLL   51 (59)
T 1gk6_A            3 KQLEDKVEELLSKNYHLENEVARLKKLVGDLLNVKMALDIEIATYRKLL   51 (59)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            4677778888888888888888888899999999999988886654433

>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=82.61  E-value=2.6  Score=26.13  Aligned_cols=26  Identities=35%  Similarity=0.468  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLK  118 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~  118 (200)
                      +.||+..|++|-.++..|+.++..|+
T Consensus         3 MnQLE~kVEeLl~~n~~Le~eV~rLk   28 (34)
T 2oxj_A            3 MXQLEXKVXELLXKNXHLEXEVXRLK   28 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            45666666666666666666665554

>3nmd_A CGMP dependent protein kinase; leucine zipper, coiled-coil, structural genomics, berkeley S genomics center, BSGC, dimerization; HET: MSE; 2.27A {Homo sapiens}

Probab=82.51  E-value=3.5  Score=29.46  Aligned_cols=45  Identities=20%  Similarity=0.125  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          100 SQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKV  144 (200)
Q Consensus       100 v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~  144 (200)
                      +.+|+.......++++.....+.+|..+......++..|+.+|..
T Consensus        21 i~eLq~~L~~K~eELr~kd~~I~eLEk~L~ekd~eI~~LqseLDK   65 (72)
T 3nmd_A           21 LRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDK   65 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444444444445555555555555555555555543

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

Probab=82.48  E-value=8.2  Score=32.36  Aligned_cols=11  Identities=18%  Similarity=0.287  Sum_probs=4.0

Q ss_pred             HHHHHHHHHHH
Q 028999          130 ILKADKEKLEQ  140 (200)
Q Consensus       130 ~Lk~e~e~L~~  140 (200)
                      .++.++..|+.
T Consensus       101 ~~~~~i~~lE~  111 (256)
T 3na7_A          101 IAKERSNQANR  111 (256)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            33333333333

>4dzn_A Coiled-coil peptide CC-PIL; de novo protein; HET: PHI; 1.59A {Synthetic} PDB: 4dzm_A* 4dzl_A* 4dzk_A 1u0i_A 1u0i_B

Probab=82.41  E-value=3  Score=25.18  Aligned_cols=27  Identities=37%  Similarity=0.412  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          114 IKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus       114 i~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      +..|++|+.-|..|...||-|+.-|.|
T Consensus         4 iaalkqeiaalkkeiaalkfeiaalkq   30 (33)
T 4dzn_A            4 IAALKQEIAALKKEIAALKFEIAALKQ   30 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            344444444455555555555554444

>1ic2_A Tropomyosin alpha chain, skeletal muscle; alpha-helical coiled coil, alanine, symmetry, axial stagger, BEND, contractIle protein; 2.00A {Gallus gallus} SCOP: h.1.5.1

Probab=82.32  E-value=11  Score=26.59  Aligned_cols=56  Identities=14%  Similarity=0.259  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           88 DAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        88 dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      .|.+-+.++...+...+.....+..++..|...+..|.++...+.......+..|.
T Consensus        17 ~a~~~~~~~e~~l~~~e~~~~~~E~ev~~L~kKiq~lE~eld~~ee~l~~a~~kLe   72 (81)
T 1ic2_A           17 NALDRAEQAEADKKAAEERSKQLEDELVALQKKLKGTEDELDKYSESLKDAQEKLE   72 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555555555555566666666666666666666666555555555554443

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

Probab=82.22  E-value=9.4  Score=27.60  Aligned_cols=38  Identities=29%  Similarity=0.372  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      ..|-..+++|+-|+.-|+.|...++.-+.+++..++.+
T Consensus        33 ~DLI~rvdELt~E~e~l~~El~s~~~~~~r~~~ri~el   70 (77)
T 2w83_C           33 NDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNREL   70 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445556666666666666666666666665555443

>3trt_A Vimentin; cytoskeleton, intermediate filament, alpha-helix, structural protein; 2.30A {Homo sapiens} PDB: 3klt_A*

Probab=81.99  E-value=6.7  Score=27.05  Aligned_cols=24  Identities=21%  Similarity=0.331  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          114 IKSLKAEKNELREEKLILKADKEK  137 (200)
Q Consensus       114 i~~L~~eknELr~Ek~~Lk~e~e~  137 (200)
                      +...+.|+.||+...+.|..|++.
T Consensus        51 l~~~k~Ei~elrr~iq~L~~el~s   74 (77)
T 3trt_A           51 LRQAKQESTEYRRQVQSLTMEVDA   74 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            333444455555555555554443

>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=81.81  E-value=9.3  Score=25.53  Aligned_cols=46  Identities=11%  Similarity=0.197  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           98 TESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLK  143 (200)
Q Consensus        98 ~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk  143 (200)
                      .++++|.....+|-.++..|..+.+.|+.+....|.|-.|-.+.|.
T Consensus         4 aki~~Lss~V~~L~~kVdqLssdV~al~~~v~~ak~eA~RAN~RlD   49 (52)
T 1jcd_A            4 AKADQASSDAQTANAKADQASNDANAARSDAQAAKDDAARANQRAD   49 (52)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            4577888888888888888888888888888888877777666554

>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=81.61  E-value=3  Score=25.68  Aligned_cols=22  Identities=0%  Similarity=0.149  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028999          110 LQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus       110 L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      |+..+++|-.++.+|.+|..+|
T Consensus         5 LEdKvEeLl~~~~~Le~EV~RL   26 (33)
T 3c3g_A            5 IEXKLXEIXSKXYHXENXLARI   26 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHH
Confidence            3333333434444444433333

>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=81.43  E-value=3.2  Score=25.59  Aligned_cols=27  Identities=7%  Similarity=0.202  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           93 LNQLRTESQELKETNEKLQEEIKSLKA  119 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei~~L~~  119 (200)
                      ++||+..|++|-.++..|+.++..|+.
T Consensus         2 MnQLEdKvEeLl~~~~~Le~EV~RLk~   28 (33)
T 3c3g_A            2 MKXIEXKLXEIXSKXYHXENXLARIKX   28 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            356666677666666666666665543

>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=81.36  E-value=3.9  Score=29.62  Aligned_cols=31  Identities=32%  Similarity=0.364  Sum_probs=15.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999          108 EKLQEEIKSLKAEKNELREEKLILKADKEKL  138 (200)
Q Consensus       108 ~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L  138 (200)
                      ..|+.+...+..++++|+.++..|+.+++.|
T Consensus        55 ~~L~~~~~~l~~~~~~L~~~n~~L~~rl~~L   85 (88)
T 1nkp_A           55 LSVQAEEQKLISEEDLLRKRREQLKHKLEQL   85 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3444444444455555555555555555444

>4h22_A Leucine-rich repeat flightless-interacting protei; nucleic acid sensor, transcription; 2.89A {Homo sapiens}

Probab=80.94  E-value=11  Score=28.51  Aligned_cols=51  Identities=18%  Similarity=0.150  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           95 QLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        95 ~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .|.-+|+-|+...+.+++...+++.+..|...+...+|-.+..|+.++..+
T Consensus        27 al~YqVdlLKD~LEe~eE~~aql~Re~~eK~re~e~~Kr~~~~L~~~~~~l   77 (103)
T 4h22_A           27 NFMYQVDTLKDMLLELEEQLAESRRQYEEKNKEFEREKHAHSILQFQFAEV   77 (103)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            355567777777777777777777777777777778888888888777664

>3ni0_A Bone marrow stromal antigen 2; coiled-coil, antiviral defense, immune system, GPI anchor; 1.60A {Mus musculus}

Probab=80.53  E-value=16  Score=27.46  Aligned_cols=60  Identities=23%  Similarity=0.205  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           86 LDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        86 L~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      |+.|-+.+.+-+.++.--......|..-.+.-+..-.+.+.+...|+.||..|.++|+..
T Consensus        27 LT~Aq~~l~~~eaQAaTCNqTV~tL~~SL~kekaq~q~qq~~v~elqgEI~~Lnq~Lqda   86 (99)
T 3ni0_A           27 LTRTQDSLLQAETQANSCNLTVVTLQESLEKKVSQALEQQARIKELENEVTKLNQELENL   86 (99)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344444444444433333334444444333333333333445566777777777777664

>2ve7_C Kinetochore protein NUF2, kinetochore protein SPC; mitosis, centromere, cell cycle, microtubule, C division, calponin homology; 2.88A {Homo sapiens} PDB: 3iz0_D*

Probab=80.44  E-value=1.8  Score=36.91  Aligned_cols=59  Identities=14%  Similarity=0.105  Sum_probs=34.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           83 PAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        83 asIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .-||+--|.|++.-+......    +.+..+.+++..+.+.|+.|+..+++++++|++++...
T Consensus       123 ~~iLSalINF~~FRE~~~~~~----~e~~~~~e~~~~~i~ql~~En~~le~~Ie~Lk~e~~e~  181 (250)
T 2ve7_C          123 SRFLSGIINFIHFREACRETY----MEFLWQYKSSADKMQQLNAAHQEALMKLERLEKEVDED  181 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH----HHHHHHTTHHHHHHHHHHHHHHHHHHSCC---------
T ss_pred             HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            448888889988655554433    34455566667777777777777777777777766654

>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=80.28  E-value=3.5  Score=25.35  Aligned_cols=23  Identities=13%  Similarity=0.081  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 028999          109 KLQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus       109 ~L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      +|+..+++|..++.+|.+|..+|
T Consensus         4 QLEdKVEell~~~~~le~EV~Rl   26 (33)
T 2wq1_A            4 QLEDKIEENTSKIYHNTNEIARN   26 (33)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHH
Confidence            34444444444444444444333

>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=80.26  E-value=9.1  Score=31.99  Aligned_cols=52  Identities=25%  Similarity=0.232  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +++..+-..+..++.++..|.++...|..+.++|..+...+-.+++.++.+|
T Consensus       125 elfd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~~qlE~~v~~K~~~E~~L  176 (213)
T 1ik9_A          125 ELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDL  176 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666666677777777777777777777777666666666665555444

>3tnu_B Keratin, type II cytoskeletal 5; coiled-coil, structural support, cytosolic protein; 3.00A {Homo sapiens}

Probab=80.12  E-value=2.7  Score=32.08  Aligned_cols=76  Identities=12%  Similarity=0.184  Sum_probs=41.2

Q ss_pred             HHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHH
Q 028999           62 NDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNELREE----KLILKADKEK  137 (200)
Q Consensus        62 Ne~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~E----k~~Lk~e~e~  137 (200)
                      +.+|.+|...+ .    +.  ..-|..+-.-|.+|+..++.|+.+.+.|+.....|...+.++...    ...++..+..
T Consensus        14 ~~K~eel~~~~-~----~~--~~~l~~~k~Ei~elrr~iq~L~~el~~l~~~~~~LE~~l~e~e~~~~~~l~~~q~~i~~   86 (129)
T 3tnu_B           14 QTKYEELQQTA-G----RH--GDDLRNTKHEISEMNRMIQRLRAEIDNVKKQCANLQNAIADAEQRGELALKDARNKLAE   86 (129)
T ss_dssp             ---------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-H----hh--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44556666655 1    11  123455667788899999999999988888888888888776543    3345556666


Q ss_pred             HHHHHHH
Q 028999          138 LEQQLKV  144 (200)
Q Consensus       138 L~~qlk~  144 (200)
                      |+.+|..
T Consensus        87 lE~eL~~   93 (129)
T 3tnu_B           87 LEEALQK   93 (129)
T ss_dssp             HHHHHHH
T ss_pred             HHHhHHH
Confidence            6665544

>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=80.07  E-value=3.6  Score=25.47  Aligned_cols=22  Identities=5%  Similarity=0.199  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 028999          110 LQEEIKSLKAEKNELREEKLIL  131 (200)
Q Consensus       110 L~~ei~~L~~eknELr~Ek~~L  131 (200)
                      |+..+++|-.++.+|.+|..+|
T Consensus         6 LEdKVEeLl~~~~~Le~EV~RL   27 (34)
T 3c3f_A            6 IEXKLEXILSXLYHXENEXARI   27 (34)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhHHHHHHHHH
Confidence            3333344444444444433333

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

Probab=80.05  E-value=14  Score=26.61  Aligned_cols=47  Identities=32%  Similarity=0.345  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           94 NQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQ  140 (200)
Q Consensus        94 k~L~~~v~~L~~~~~~L~~ei~~L~~eknELr~Ek~~Lk~e~e~L~~  140 (200)
                      ..|-.+..+|......|.---++|-+...||--|+..|+.|++.+++
T Consensus        12 EnLi~EN~eLl~TKNaLnvvk~DLI~rvdELt~E~e~l~~El~s~~~   58 (77)
T 2w83_C           12 ENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQ   58 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            33444444444444444444555666666666666666666666654

---

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	200
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	5e-15
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	8e-13
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-11
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	6e-11
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-10
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	2e-07
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-05
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	6e-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 = 65.3 bits (159), Expect = 5e-15
 Identities = 14/73 (19%), Positives = 32/73 (43%)

Query: 53  REKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 112
            E+ RR+ + D F  L   +   +  +  +  ILD A   +  +R ++   ++  + L+ 
Sbjct: 9   LERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR 68

Query: 113 EIKSLKAEKNELR 125
           +   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 = 59.5 bits (144), Expect = 8e-13
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 53  REKLRRERLNDRFLDL-SCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQ 111
            E+ RR  L   F  L   I E     +  K  IL  A   +  ++ E Q+L    + L+
Sbjct: 13  LERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR 72

Query: 112 EEIKSLKAEKNELR 125
           +  + 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 = 56.1 bits (135), Expect = 1e-11
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 53  REKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQE 112
            EK  R  +ND+ ++L   L  G  A+ +K A+L  AI  +  L+  +Q+LK+ N  L+ 
Sbjct: 13  IEKRYRSSINDKIIELKD-LVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT 71

Query: 113 EIKSLKAEK 121
            +   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 = 54.1 bits (130), Expect = 6e-11
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 53  REKLRRERLNDRFLDLSCILEPGRPA-RTDKPAILDDAIRVLNQLRTESQELKETNEKLQ 111
            EK RR  L      L  ++  G  + R    ++L  A   + +L    ++     ++LQ
Sbjct: 8   MEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ 67

Query: 112 EEIKSLKAEKNE 123
            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 = 53.2 bits (128), Expect = 1e-10
 Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 58  RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSL 117
           R  +ND+ ++L  ++  G  A+  K  +L  AI  +  L+  + +L++ N  L+   +  
Sbjct: 1   RSSINDKIIELKDLV-MGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKN 59

Query: 118 K 118
           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 = 44.9 bits (106), Expect = 2e-07
 Identities = 15/67 (22%), Positives = 29/67 (43%)

Query: 36  RKRARSDSCSRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQ 95
             + ++ +  R  +   RE+ R  ++N+ F  L          R  K  IL +AIR +  
Sbjct: 2   ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEG 61

Query: 96  LRTESQE 102
           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 = 39.4 bits (92), Expect = 1e-05
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 53  REKLRRERLNDRFLDLSCIL----EPGRPARTDKPAILDDAIRVLNQLRTESQ 101
            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 = 34.8 bits (80), Expect = 6e-04
 Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 5/50 (10%)

Query: 53 REKLRRERLNDRFLDL-----SCILEPGRPARTDKPAILDDAIRVLNQLR 97
           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	200
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.77
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.76
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.76
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.6
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.59
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.56
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.51
d1lrza1	65	Methicillin resistance protein FemA probable tRNA-	85.3
d1seta1	110	Seryl-tRNA synthetase (SerRS) {Thermus thermophilu	84.48

>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=99.77  E-value=1.8e-19  Score=130.01  Aligned_cols=78  Identities=17%  Similarity=0.300  Sum_probs=65.6

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNE  123 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknE  123 (200)
                      ++..|+.+||+||++||+.|.+|+++||+....|.||++||..||+||++|+.+++.|..+.+.|..+...|..++++
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~~~~L~~~l~~   79 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNALLEQQVRA   79 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999765557899999999999999999999888887776666665555555544

>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=99.76  E-value=1e-18  Score=125.02  Aligned_cols=76  Identities=21%  Similarity=0.257  Sum_probs=66.5

Q ss_pred             CCchhHHHHHHHHHHHHhHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           47 PGSKACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKN  122 (200)
Q Consensus        47 ~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~-~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~ekn  122 (200)
                      +.+|+..||+||++||++|.+|+++||++. ..|.+|++||..||+||++|+.+++.|..+.+.|..+...|+..++
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            468999999999999999999999997653 4589999999999999999999999888888888877777766554

>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=99.76  E-value=7.5e-19  Score=128.03  Aligned_cols=79  Identities=22%  Similarity=0.301  Sum_probs=67.9

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCC-CCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGR-PARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAEKNEL  124 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~-~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L~~eknEL  124 (200)
                      ++..|+.+||+||++||+.|..|+++||+.. ..|.+|++||..||+||+.|+.+++.|..+.+.|..+...|..++++|
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            4678999999999999999999999997543 357999999999999999999999988888777777777776666655

>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=99.75  E-value=1.6e-18  Score=124.68  Aligned_cols=71  Identities=25%  Similarity=0.384  Sum_probs=62.2

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSL  117 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei~~L  117 (200)
                      ++.+|+..||+||++||++|.+|+++||+ ...|+||++||..||+||++|+.+++.|..++..|+.++..+
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~llP~-~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~~~~~~   76 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLVVG-TEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTAVHKS   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTC-SSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999955 457999999999999999999999998888887776665544

>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=99.60  E-value=2.4e-16  Score=108.71  Aligned_cols=55  Identities=22%  Similarity=0.358  Sum_probs=49.4

Q ss_pred             CCCchhHHHHHHHHHHHHhHHHHhhhcCC-----CCCCCCChhhHHHHHHHHHHHHHHHH
Q 028999           46 RPGSKACREKLRRERLNDRFLDLSCILEP-----GRPARTDKPAILDDAIRVLNQLRTES  100 (200)
Q Consensus        46 r~~sH~~~ER~RRekiNe~F~~Lr~lLpP-----~~~~K~dKasIL~dAI~YIk~L~~~v  100 (200)
                      ++.+|+.+||+||++||++|.+|+++||+     +...|.||++||..||+||++|++++
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            57899999999999999999999999964     23469999999999999999998764

>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=99.59  E-value=9.9e-17  Score=112.51  Aligned_cols=57  Identities=26%  Similarity=0.334  Sum_probs=51.3

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQ  101 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~  101 (200)
                      .++..|+.+||+||++||++|..|+++||++...|.||++||..||+||++|+..++
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            467889999999999999999999999977655689999999999999999987653

>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=99.56  E-value=1.6e-15  Score=104.17  Aligned_cols=56  Identities=23%  Similarity=0.380  Sum_probs=49.7

Q ss_pred             HHHHHHhHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           58 RERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEI  114 (200)
Q Consensus        58 RekiNe~F~~Lr~lLpP~~~~K~dKasIL~dAI~YIk~L~~~v~~L~~~~~~L~~ei  114 (200)
                      |++||++|.+|+++||.+ ..|+|||+||.+||+||+.|+.+++.|+.++..|+.+.
T Consensus         1 R~~in~~f~~L~~lvP~~-~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~~   56 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGT-DAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLAN   56 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCS-SCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999543 46999999999999999999999999998888877654

>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=99.51  E-value=3.3e-15  Score=103.49  Aligned_cols=56  Identities=25%  Similarity=0.383  Sum_probs=49.4

Q ss_pred             CCCCchhHHHHHHHHHHHHhHHHHhhhcCCCC----CCCCChhhHHHHHHHHHHHHHHHH
Q 028999           45 SRPGSKACREKLRRERLNDRFLDLSCILEPGR----PARTDKPAILDDAIRVLNQLRTES  100 (200)
Q Consensus        45 ~r~~sH~~~ER~RRekiNe~F~~Lr~lLpP~~----~~K~dKasIL~dAI~YIk~L~~~v  100 (200)
                      .++.+|+.+||+||++||++|.+|+++||.+.    ..|.||++||..||+||++|+++.
T Consensus         4 ~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            35789999999999999999999999997542    358999999999999999998753

>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=85.30  E-value=3.5  Score=27.04  Aligned_cols=52  Identities=15%  Similarity=0.196  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028999           91 RVLNQLRTESQELKETNEKLQEEI------KSLKAEKNELREEKLILKADKEKLEQQL  142 (200)
Q Consensus        91 ~YIk~L~~~v~~L~~~~~~L~~ei------~~L~~eknELr~Ek~~Lk~e~e~L~~ql  142 (200)
                      +||..|+.+...|......+...+      +--...+.+|..+..+...-|+..++.+
T Consensus         3 eYl~~L~~~~~~L~~~i~k~~~~leknP~skK~~nk~~el~~Q~~s~~~ki~Ea~~li   60 (65)
T d1lrza1           3 EYIKELNEERDILNKDLNKALKDIEKRPENKKAHNKRDNLQQQLDANEQKIEEGKRLQ   60 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999888777654      3344556667666666666666555443

>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=84.48  E-value=3.6  Score=28.44  Aligned_cols=53  Identities=21%  Similarity=0.347  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028999           93 LNQLRTESQELKETNEKLQEEI--------KSLKAEKNELREEKLILKADKEKLEQQLKVM  145 (200)
Q Consensus        93 Ik~L~~~v~~L~~~~~~L~~ei--------~~L~~eknELr~Ek~~Lk~e~e~L~~qlk~~  145 (200)
                      .+.|+.+++.|+.+...+-.++        .+|..+..+|.++...|..+...++.++..+
T Consensus        37 rr~l~~~~e~l~~~rN~~sk~i~k~~~~~~~~l~~~~k~lk~~i~~le~~~~~~~~~l~~~   97 (110)
T d1seta1          37 VQELKKRLQEVQTERNQVAKRVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEAL   97 (110)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555544444333        3444455555555555555555555555553